'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'acceldata2.RData'
Problems with news in 'NEWS.md':
No news entries found.
Found the following significant warnings:
  getLL.c:133:22: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  getLL.c:257:22: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ACDm.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning message:
  In load(p, envir = env) :
    strings not representable in native encoding will be translated to UTF-8
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'Example.jpeg'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown packages 'HI', 'MHadaptive' in Rd xrefs
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'table_AeRobiology'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BerryMielke.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) BlairLacy.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) Kvalseth.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) consensus.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) dsquared.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) l.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) lsquared.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) lsquared.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) var.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) adapt.Rd:41: Escaped LaTeX specials: \$
Package suggested but not available for checking: 'RandomFields'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'ans_19-2.jpg' 'display2d_19-2.jpg' 'dist(3)_19-2.jpg'
  'dist(4)_19-2.jpg' 'dist(mirror)_19-2.jpg' 'dist(mirror2)_19-2.jpg'
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'stuve.pdf'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following significant warnings:
  fun_sublr.cpp:18:22: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ALassoSurvIC.Rcheck/00install.out' for details.
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Zelig'
Found the following significant warnings:
  em.cpp:89:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  em.cpp:89:53: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Amelia.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) deshrink.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) deshrink.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) plot.mat.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) plot.wa.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) predict.prcurve.Rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'BH-0.05-ListOfGenes.txt' 'BH-0.05-VM-ListOfGenes.txt'
  'CompleteListOfGenes.txt' 'GenesOutOfAnalysis.txt'
  'GenesOutOfAnalysis_NotEnoughObs.txt'
  'GenesOutOfAnalysis_NullVar.txt' 'VM-CompleteListOfGenes.txt'
  'bonferroni-0.05-ListOfGenes.txt'
  'bonferroni-0.05-VM-ListOfGenes.txt'
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Problems with news in 'NEWS.md':
No news entries found.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SportsAnalytics'
Found the following significant warnings:
  init.c:11:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Anthropometry.Rcheck/00install.out' for details.
Found the following significant warnings:
  ./header.h:50:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  bicriterion_iterated_local_search_call.c:510:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/anticlust.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  get_subplot_boundary_pixels.cpp:37:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  polygonize_class.cpp:52:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  polygonize_class.cpp:78:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  polygonize_class.cpp:99:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  polygonize_class.cpp:102:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/APAtree.Rcheck/00install.out' for details.
Found the following significant warnings:
  ./me.h:122:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  me.c:234:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ape.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ViterbiC.cpp:217:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ViterbiC.cpp:528:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ViterbiC.cpp:814:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ViterbiC.cpp:1104:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ViterbiC.cpp:1242:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:45:40: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:59:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:60:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:61:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:62:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:63:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:64:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:65:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:66:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:67:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/aphid.Rcheck/00install.out' for details.
Found the following significant warnings:
  ../inst/include/tree_meat.hpp:375:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/aphylo.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File 'apollo/R/apollo_attach.R':
  attach(as.list(apollo_beta), warn.conflicts = FALSE)
  attach(database, warn.conflicts = FALSE)
  attach(draws, warn.conflicts = FALSE)
  attach(randcoeff, warn.conflicts = FALSE)
  attach(lcpars, warn.conflicts = FALSE)
See section 'Good practice' in '?attach'.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BayesianTools'
Problems with news in 'NEWS.md':
No news entries found.
Unknown package 'BayesianTools' in Rd xrefs
Found the following files/directories:
  'APBinary_PPV.csv' 'APBinary_TPF.csv'
  'APBinary_ap_summary(method=perturbation,B=1500).csv'
  'APBinary_auc_summary(method=perturbation,B=1500).csv'
  'APSurv_PPV.csv' 'APSurv_TPF.csv'
  'APSurv_ap_summary(method=bootstrap,B=500).csv'
  'APSurv_auc_summary(method=bootstrap,B=500).csv'
  'CompareAP_Binary_dap_summary(method=none).csv'
  'CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv'
checkRd: (-1) AQuadtree-package.Rd:11: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'ARTP'
Found the following significant warnings:
  ARTP2_init.c:17:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ARTP2.Rcheck/00install.out' for details.
Found the following significant warnings:
  ptree.c:32:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ptree.c:192:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ptree.c:200:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ptree.c:768:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/arulesSequences.Rcheck/00install.out' for details.
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'MSToutput.txt'
Package which this enhances but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'asteRiskData'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Scaled_loops.cpp:203:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Unscaled_loops.cpp:147:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Unscaled_nuts_loops.cpp:206:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ATNr.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
Unknown package 'snpar' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  driver.c:114:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  driver.c:161:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  driver.c:199:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/audio.Rcheck/00install.out' for details.
File 'audio/libs/audio.so':
  Found non-API call to R: 'R_checkActivity'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lixoftConnectors'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following files/directories:
  'exemplary_input1.txt' 'exemplary_input2.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./utilities.h:67:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./utilities.h:68:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./utilities.h:83:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./Ball_omp.h:6:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./Ball_omp.h:7:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./Ball_omp.h:8:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  bd_gwas.c:260:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  utilities.c:1438:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  utilities.c:1446:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  utilities.c:1455:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Ball.Rcheck/00install.out' for details.
Found the following significant warnings:
  bamlss_functions.c:117:10: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bamlss.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:16:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BART.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Earlier versions
Package which this enhances but not available for checking: 'rPython'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
Found the following significant warnings:
  bayesDccGarch.c:48:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  bayesDccGarch.c:110:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  bayesDccGarch.c:172:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bayesDccGarch.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
Found the following significant warnings:
  clusterMix_rcpp_loop.cpp:39:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bayesm.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
checkRd: (-1) bart.Rd:271: Escaped LaTeX specials: \_
Found the following significant warnings:
  priorprob.c:45:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  priorprob.c:93:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  priorprob.c:141:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BayesVarSel.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
checkRd: (-1) create_ThetaMatrix.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) create_ThetaMatrix.Rd:41: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  '.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData'
  '.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData'
  '.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData'
  '.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData'
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'fabiabreast.txt'
Package suggested but not available for checking: 'INLA'
checkRd: (-1) tlsce.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:93: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kBET', 'lisi', 'harmony', 'dlfUtils'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'dump.txt'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'beast_plot_toy.pdf'
GNU make is a SystemRequirements.
Found the following files/directories:
  'alist.txt' 'rpkg'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  chol_down.cpp:21:20: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  chol_down.cpp:22:5: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  chol_down.cpp:23:32: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  chol_down.cpp:49:49: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  chol_down.cpp:51:17: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  chol_down.cpp:51:57: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  chol_down.cpp:101:7: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  chol_down.cpp:101:25: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  chol_down.cpp:205:5: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  outlier.cpp:59:30: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Benchmarking.Rcheck/00install.out' for details.
Found the following significant warnings:
  load.c:11:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./nanotime.h:6:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./nanotime.h:7:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  mark.c:75:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  mark.c:118:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  mark.c:119:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  nanotime.c:61:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  nanotime.c:71:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  process_memory.c:79:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bench.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Found the following significant warnings:
  BHSBVAR.cpp:236:71: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:236:23: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:246:72: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:246:23: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:256:97: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:256:122: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:256:23: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:256:47: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:284:68: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:284:20: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:289:69: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:289:20: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:294:94: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:294:119: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:294:20: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:294:44: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BHSBVAR.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Found the following significant warnings:
  rbimax.c:326:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/biclust.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'ffbase'
Package suggested but not available for checking: 'INLA'
Found the following significant warnings:
  ./lib.h:6:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lib.c:3:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bigGP.Rcheck/00install.out' for details.
Found the following calls to data() loading into the global environment:
File 'biglm/R/bigglm.R':
  data(reset = TRUE)
  data(reset = FALSE)
See section 'Good practice' in '?data'.
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
Checking should be performed on sources prepared by 'R CMD build'.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  pcg_basic.c:73:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  util.c:699:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BigQuic.Rcheck/00install.out' for details.
Found the following files/directories:
  'outputs'
Found the following significant warnings:
  ./binarizeBASCA.h:37:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  TASC.c:258:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  TASC_min.c:256:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  binarizeBASCA.c:358:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Binarize.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) BinaryEPPM.Rd:159: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'ccf_ccf_ID31_ID32_res.jpg' 'ccf_ccf_ID31_ID32_res.pdf'
  'output_ENSO_NHSST.tmp' 'plot_plot_ts_RAW_BIN_enso_sst.pdf'
  'plot_plot_ts_RAW_BIN_enso_sst01.png'
  'plot_plot_ts_RAW_BIN_enso_sst02.png'
  'plot_plot_ts_RAW_BIN_enso_sst03.png'
  'plot_plot_ts_RAW_BIN_enso_sst04.png' 'plot_ts_ACER_ABRUPT.pdf'
  'plot_ts_ACER_ABRUPT01.png' 'plot_ts_ACER_ABRUPT02.png'
  'plot_ts_ACER_ABRUPT03.png' 'plot_ts_ACER_ABRUPT04.png'
  'salida_ACER_ABRUPT.tmp' 'scaterplot_scatterplot_ENSO_SST.jpg'
  'scaterplot_scatterplot_ENSO_SST.pdf'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Found the following files/directories:
  'Plots.pdf'
Found the following files/directories:
  'pointshape.dbf' 'pointshape.shp' 'pointshape.shx'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: replacing previous import 'dbscan::as.dendrogram' by 'stats::as.dendrogram' when loading 'Biopeak'
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Biopeak.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  bit.c:57:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  bit.c:68:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  chunkutil.c:3:24: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  init.c:24:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bit.Rcheck/00install.out' for details.
Found the following significant warnings:
  ./binarizeBASCA.h:37:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  TASC.c:258:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  TASC_min.c:256:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  binarizeBASCA.c:358:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BiTrinA.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
GNU make is a SystemRequirements.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  blockmodelingC.c:3303:24: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  blockmodelingC.c:3303:57: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  blockmodelingC.c:3303:61: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  blockmodelingC.c:3303:71: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  blockmodelingC.c:3303:99: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  blockmodelingC.c:3303:104: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  blockmodelingC.c:3303:119: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  blockmodelingC.c:3304:39: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  blockmodelingC.c:3304:56: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  blockmodelingC.c:3304:69: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  blockmodelingC.c:3307:19: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  blockmodelingC.c:3307:63: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  blockmodelingC.c:3309:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/blockmodeling.Rcheck/00install.out' for details.
Found the following significant warnings:
  cppFunctions.cpp:171:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BLPestimatoR.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Found the following significant warnings:
  node_pos_all.cpp:670:55: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  node_pos_contribution.cpp:348:55: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  node_pos_motifweights.cpp:352:55: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  node_pos_nodeweights.cpp:329:55: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  node_pos_stouffer.cpp:421:55: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  sd.cpp:283:55: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bmotif.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'INLA'
GNU make is a SystemRequirements.
Found the following significant warnings:
  basic-misc.cpp:29:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bnclassify.Rcheck/00install.out' for details.
Found the following significant warnings:
  ./include/register.h:46:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./include/register.h:75:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./include/register.h:76:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./include/register.h:82:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  globals.c:15:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  globals.c:33:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  test.counter.c:26:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  test.counter.c:35:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bnlearn.Rcheck/00install.out' for details.
Found the following significant warnings:
  get_latents.cpp:216:17: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BNPMIXcluster.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following significant warnings:
  common.c:15:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:9:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./random.h:12:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sat_search.c:106:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  symbolic_simulator.c:344:53: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BoolNet.Rcheck/00install.out' for details.
Found the following significant warnings:
  math/cephes/planck.cpp:84:54: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Boom.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    modules 0.x
'LazyData' is specified without a 'data' directory
checkRd: (-1) bpca.Rd:85: Escaped LaTeX specials: \&
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) R2txtJG.Rd:90: Escaped LaTeX specials: \#
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package suggested but not available for checking: 'glmmADMB'
checkRd: (-1) brr-package.Rd:33: Escaped LaTeX specials: \&
Found the following significant warnings:
  BugsHelper.c:76:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  BugsHelper.c:87:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  BugsHelper.c:88:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BRugs.Rcheck/00install.out' for details.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running 'testthat.R' [3s/4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(bsplus)
  > 
  > test_check("bsplus")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 103 ]
  
  == Failed tests ================================================================
  -- Error ('test-shiny.R:10'): iconlink works -----------------------------------
  Error in `.tag_validate(iconlink$children[[1]], name = "i", class = "fa fa-info-circle")`: class is: fasfa-circle-info, needs to include: fafa-info-circle
  Backtrace:
      x
   1. +-testthat::expect_identical(...) at test-shiny.R:10:2
   2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
   3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
   4. \-bsplus:::.tag_validate(iconlink$children[[1]], name = "i", class = "fa fa-info-circle")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 103 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gvcm.cat'
Unknown package 'gvcm.cat' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
Found the following significant warnings:
  cairobem.c:50:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./Rapi.h:9:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./Rapi.h:11:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cairotalk.c:661:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cairotalk.c:1552:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cairotalk.c:1588:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  xlib-backend.c:156:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Cairo.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ReGenesees'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RxODE'
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'tmp.txt'
Found the following files/directories:
  'MDA231_tree.pdf'
checkRd: (-1) caic-class.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) caic-class.Rd:15: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot-methods.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) plot-methods.Rd:96: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'GAMBoost'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'catmapdata.fixed.effects.plot.pdf' 'catmapdata.funnel.plot.pdf'
  'catmapdata.output.txt' 'catmapdata.random.effects.plot.pdf'
Found the following significant warnings:
  ./catnet_rexport.h:63:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/catnet.Rcheck/00install.out' for details.
checkRd: (-1) belt.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) bipf.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) crime.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) da.cat.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) dabipf.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) ecm.cat.Rd:77: Escaped LaTeX specials: \&
checkRd: (-1) em.cat.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) ipf.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) logpost.cat.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) mda.cat.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) mi.inference.Rd:140: Escaped LaTeX specials: \&
checkRd: (-1) older.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) prelim.cat.Rd:67: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Cat.cpp:230:39: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Estimator.cpp:548:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Estimator.cpp:609:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Estimator.cpp:863:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Estimator.cpp:879:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Estimator.cpp:903:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Estimator.cpp:918:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Estimator.cpp:987:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Estimator.cpp:1135:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  QuestionSet.cpp:163:25: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  QuestionSet.cpp:167:29: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  WLEEstimator.cpp:261:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  WLEEstimator.cpp:277:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/catSurv.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  proximus.c:6:12: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/cba.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    News about the ccdf R package
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'hotcold.csv'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'out.png' 'out1.txt' 'out2.txt'
Found the following files/directories:
  'figure01ceg.pdf' 'figure02ceg.pdf' 'staged.tree.graph.pdf'
  'stratified-event-tree-plot.pdf'
'LazyData' is specified without a 'data' directory
Unexported objects imported by ':::' calls:
  'copula:::dCdu' 'copula:::fitCopStart'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'alr3'
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major refactoring of the code
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BSGW'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./graph.h:85:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./session.h:40:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./graph.h:85:6: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype]
  session.c:29:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/cgraph.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ChannelAttribution.cpp:694:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ChannelAttribution.cpp:696:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ChannelAttribution.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'darts'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  treeshap.cpp:148:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/cheem.Rcheck/00install.out' for details.
checkRd: (-1) hyptis.Rd:31: Escaped LaTeX specials: \&
Found the following files/directories:
  'stepres00.txt'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'GenomicInteractions', 'Gviz', 'countreg'
Found the following significant warnings:
  RandIndex.cpp:28:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  RandIndex.cpp:30:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  RandIndex.cpp:33:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/chickn.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'entab'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  newplt.cc:186:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  newplt.cc:188:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CIFsmry.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ChIPseeker', 'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'userfriendlyscience'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
'LazyData' is specified without a 'data' directory
checkRd: (-1) diagwl.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) diagwl.Rd:5: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    clinfun (development version)
checkRd: (-1) coxphCPE.Rd:2: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./criteria.h:45:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./criteria.h:48:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/clusterCrit.Rcheck/00install.out' for details.
checkRd: (-1) genRandomClust.Rd:228: Escaped LaTeX specials: \_
checkRd: (-1) genRandomClust.Rd:259: Escaped LaTeX specials: \_
checkRd: (-1) genRandomClust.Rd:327: Escaped LaTeX specials: \_
checkRd: (-1) plot1DProjection.Rd:95: Escaped LaTeX specials: \_ \_
checkRd: (-1) plot2DProjection.Rd:117: Escaped LaTeX specials: \_ \_
checkRd: (-1) simClustDesign.Rd:235: Escaped LaTeX specials: \_
checkRd: (-1) simClustDesign.Rd:268: Escaped LaTeX specials: \_
checkRd: (-1) simClustDesign.Rd:331: Escaped LaTeX specials: \_
Found the following files/directories:
  'clusterhap_reports'
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [86s/157s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(clustermole)
  > 
  > test_check("clustermole")
  [1] "Calculating ranks..."
  [1] "Calculating absolute values from ranks..."
  [1] "Normalizing..."
  [1] "Calculating ranks..."
  [1] "Calculating absolute values from ranks..."
  [1] "Normalizing..."
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 42 ]
  
  == Failed tests ================================================================
  -- Error ('test-utils.R:3'): read_gmt() output ---------------------------------
  Error in `file(con, "r")`: cannot open the connection to 'http://software.broadinstitute.org/gsea/msigdb/supplemental/scsig.all.v1.0.symbols.gmt'
  Backtrace:
      x
   1. \-clustermole::read_gmt(file = "http://software.broadinstitute.org/gsea/msigdb/supplemental/scsig.all.v1.0.symbols.gmt") at test-utils.R:3:2
   2.   +-base::strsplit(readLines(file), "\t")
   3.   \-base::readLines(file)
   4.     \-base::file(con, "r")
  
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 42 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) HINoV.Mod.rd:3: Escaped LaTeX specials: \&
checkRd: (-1) HINoV.Symbolic.rd:3: Escaped LaTeX specials: \&
checkRd: (-1) cluster.Gen.rd:14: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:18: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:29: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) cluster.Gen.rd:33: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:34: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:36: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:38: Escaped LaTeX specials: \_ \_
checkRd: (-1) cluster.Gen.rd:51: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:52: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:54: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:55: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:62: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) comparing.Partitions.rd:12: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.BC.rd:10: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.GDM.rd:33: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.SM.rd:10: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.C.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.G2.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.G3.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.H.rd:16: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.S.rd:12: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  optimal_assignment.c:47:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/clv.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:22: Escaped LaTeX specials: \#
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tobit1'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package required but not available: 'GenomicInteractions'

Package suggested but not available for checking: 'GenomicFeatures'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) drqssbc.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) qbsks.Rd:81: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'rkward'
Package which this enhances but not available for checking: 'rkward'
Package suggested but not available for checking: 'userfriendlyscience'
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'foo.R' 'foo.html'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'cometExactTest_plot.pdf'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'CAM'
checkRd: (-1) compareGroups-package.Rd:52: Escaped LaTeX specials: \~
checkRd: (-1) HouseholdExp.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) HouseholdExp.Rd:27: Escaped LaTeX specials: \$
checkRd: (-1) mix2compositions.Rd:28: Escaped LaTeX specials: \$
checkRd: (-1) mixRead.Rd:30: Escaped LaTeX specials: \$ \$
checkRd: (-1) mixRead.Rd:31: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Deprecation
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'design_names.csv' 'design_numbers.csv'
  'encoded_orthogonal_factorial_design.csv'
  'orthogonal_factorial_design.csv'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
checkRd: (-1) plotMCC.Rd:19: Escaped LaTeX specials: \_
GNU make is a SystemRequirements.
Found the following significant warnings:
  brentmin.c:237:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ContaminatedMixt.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./options.h:85:57: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CORElearn.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) poss_local.Rd:21: Escaped LaTeX specials: \~
'gs+qpdf' made some significant size reductions:
     compacted 'corncob-intro.pdf' from 430Kb to 179Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
'LazyData' is specified without a 'data' directory
checkRd: (-1) BrownBigrams.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BrownLOBPassives.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BrownPassives.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BrownStats.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) KrennPPV.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) KrennPPV.Rd:74: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) sgt.Rd:16: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) egde.Rd:26: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  bb.c:719:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ibb.c:78:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/countdata.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'covfefe_inauguration.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  CPGLIB.cpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./ProxGrad.hpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  CPGLIB_Main.cpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./CV_ProxGrad.hpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./CV_CPGLIB.hpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  CV_CPGLIB_Main.cpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  CV_ProxGrad.cpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  CV_ProxGrad_Main.cpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ProxGrad.cpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ProxGrad_Main.cpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CPGLIB.Rcheck/00install.out' for details.
Found the following significant warnings:
  bcplm.c:84:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/cplm.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Non-visible changes:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'crop.eps' 'crop.pdf' 'crop.png' 'crop.ps'
Packages required but not available: 'ensembldb', 'EnsDb.Hsapiens.v79'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major features
    Minor features
checkRd: (-1) handmovement.Rd:9: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./structs.h:44:46: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  vector.c:125:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ctl.Rcheck/00install.out' for details.
Found the following significant warnings:
  init.c:11:47: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ctmcd.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'Hello.csv'
Found the following significant warnings:
  ../inst/include/cuba.h:75:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../inst/include/cuba.h:76:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/cubature.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'curl/libs/curl.so':
  Found non-API call to R: 'R_new_custom_connection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'Adjusted_p_values.pdf' 'Effect_Size_Curves.pdf'
  'Mean_Difference_Curves.pdf'
Found the following significant warnings:
  inpolygon.c:109:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/curvHDR.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Package which this enhances but not available for checking: 'RGtk2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'lattice' 'robustbase'
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'gurobi', 'rcbc'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dspg.Rd:29: Escaped LaTeX specials: \^ \^
checkRd: (-1) dspgd2015.Rd:31: Escaped LaTeX specials: \^ \^
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dash'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dash'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dash'
Package suggested but not available for checking: 'dash'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'my new data set.rds'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'stubthat'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Datastream DWE - now decommissioned by Refinitiv
    CRAN
Found the following significant warnings:
  init.c:29:43: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:30:45: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:31:46: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:33:51: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:34:52: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:36:43: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:37:43: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/datastructures.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'SASxport'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ../include/external/random.h:53:52: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../include/external/random.h:54:62: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  randomBase.c:363:52: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  randomBase.c:381:62: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../include/misc/adaptiveRadixTree.h:54:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  adaptiveRadixTree.c:195:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  simd.c:53:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dbarts.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dblog'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  DCLEAR.cpp:54:5: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  DCLEAR.cpp:58:5: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  DCLEAR.cpp:71:5: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  DCLEAR.cpp:75:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DCLEAR.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  ./difeq.h:65:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  difeq.c:123:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./dopri.h:208:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dopri.c:245:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dde.Rcheck/00install.out' for details.
Found the following significant warnings:
  DDHFm.c:101:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  DDHFm.c:101:6: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype]
  DDHFm.c:122:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  DDHFm.c:122:6: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype]
  DDHFm.c:199:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  DDHFm.c:231:26: warning: passing arguments to 'minvC' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  DDHFm.c:199:8: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DDHFm.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  matrix.c:13:48: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./matrix.h:13:48: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  postc0.c:13:48: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/deal.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./globals.h:139:49: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/deBif.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'VariantAnnotation'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following files/directories:
  'res.pdf' 'res1.jpg'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'smd_table.docx'
checkRd: (-1) lifetable.Rd:15: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Running examples in 'dendRoAnalyst-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: daily.data
> ### Title: Calculation of daily statistics for dendrometer data
> ### Aliases: daily.data
> 
> ### ** Examples
> 
> library(dendRoAnalyst)
> data(nepa17)
> daily_stats<-daily.data(df=nepa17, TreeNum=1)
Error in daily.data(df = nepa17, TreeNum = 1) : 
  Date not in the right format
Execution halted
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rdonlp2'
checkRd: (-1) discrimination.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) fitdmm.Rd:59: Escaped LaTeX specials: \$
Package suggested but not available for checking: 'Rdonlp2'
Found the following significant warnings:
  ./deque.h:73:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  constructor.c:43:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  deque.c:31:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dequer_native.c:9:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dequer.Rcheck/00install.out' for details.
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
checkRd: (-1) geom_axis.Rd:10: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RDCOMClient'
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  DetSel_init.c:12:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  GetData.c:33:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  SimulDiv.c:216:68: warning: while loop has empty body [-Wempty-body]
  SimulDiv.c:220:68: warning: while loop has empty body [-Wempty-body]
  SimulDiv.c:233:68: warning: while loop has empty body [-Wempty-body]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DetSel.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  void_dev.c:103:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  void_dev.c:182:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  void_dev.c:197:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/devoid.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./arms.h:50:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dfcomb.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) phihat.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) anova.dglm.Rd:41: Escaped LaTeX specials: \&
Package which this enhances but not available for checking: 'BayesianTools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'INLA'
GNU make is a SystemRequirements.
checkRd: (-1) sammy.Rd:51: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'discreteMTP'
Unknown package 'discreteMTP' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) booter.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) ci.booted.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) pbooter.Rd:57: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'csim' 'xyz' 'xyz.sav' 'xyz.sav.comment'
Found the following files/directories:
  'csim.mean' 'csim.mean.comment'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./rfftw.h:34:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rfftw.c:149:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  util.c:231:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./zzz.h:10:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./zzz.h:44:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/diversitree.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'BOLTSSIRR'
Packages suggested but not available for checking: 'sendplot', 'HWxtest'
checkRd: (-1) fastDivPart.Rd:13: Escaped LaTeX specials: \_
checkRd: (-1) inCalc.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) inCalc.Rd:13: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:20: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:26: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) block.catlg.Rd:61: Escaped LaTeX specials: \^ \^
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following calls to attach():
File 'doParallel/R/doParallel.R':
  attach(exportEnv)
See section 'Good practice' in '?attach'.
Found the following significant warnings:
  alive.c:200:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  alive.c:277:7: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/doRedis.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New features
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File 'doSNOW/R/doSNOW.R':
  attach(exportEnv)
See section 'Good practice' in '?attach'.
Package suggested but not available for checking: 'OpenMPController'
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'myfile.ps' 'myfile.svg'
Unknown package 'broomExtra' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'drawBox.pdf' 'drawCircle.pdf' 'drawCurve.pdf' 'drawLine.pdf'
  'drawPoint.pdf' 'drawSettingsExample.pdf' 'drawText.pdf' 'export.pdf'
'LazyData' is specified without a 'data' directory
checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gompertz.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) hatvalues.drc.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) llogistic.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) modelFit.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) weibull1.Rd:67: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Packages required but not available:
  'GenomicFeatures', 'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Hsapiens.UCSC.hg38.knownGene'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Found the following significant warnings:
  dscore.cpp:135:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dscore.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'dsBaseClient'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lle'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  arms.c:105:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  arms.c:902:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dynsurv.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  trait_model_rc.cpp:214:39: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/EasyABC.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    20181118
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'example_table1.csv' 'example_table1.txt' 'example_table2.csv'
  'example_table2.txt' 'example_table3.csv' 'example_table3.txt'
  'table1.csv' 'table2.csv' 'table2.txt' 'table3.txt' 'table4.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'gurobi'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    breaking changes
    major changes
    minor changes
    Internal
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'gs+qpdf' made some significant size reductions:
     compacted 'ecolMod.pdf' from 800Kb to 544Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  include/ecos_bb.h:161:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ecos_bb/ecos_bb_preproc.c:298:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ecos/include/ecos_bb.h:161:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ECOSolveR.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
Package required and available but unsuitable version: 'biomod2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'eval_test_LG_ROC.pdf' 'test.pdf'
Package suggested but not available for checking: 'eggCountsExtra'
GNU make is a SystemRequirements.
Found the following significant warnings:
  GB_zeroin.c:4:42: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  GB_zeroin.c:4:53: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  eha_zeroin.c:4:42: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  eha_zeroin.c:4:53: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  expreg.c:1:30: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  expreg.c:1:41: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  phexpreg.c:122:6: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  phreg.c:124:6: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/eha.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./eicm.h:70:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/eicm.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AuditErrors.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) compute.audit.errors.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) compute.stark.t.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) find.q.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) find.q.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) stark.test.Rd:50: Escaped LaTeX specials: \$
checkRd: (-1) stark.test.Rd:101: Escaped LaTeX specials: \$ \$
checkRd: (-1) tri.audit.sim.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) tri.calc.sample.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) tri.sample.Rd:34: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) weight.function.Rd:16: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  zeroin.c:54:8: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/EL.Rcheck/00install.out' for details.
Packages required but not available:
  'minfi', 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19',
  'IlluminaHumanMethylation450kanno.ilmn12.hg19'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  emd-rubner.c:143:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  emd-rubner.c:153:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  emd-rubner.c:640:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/emdist.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) freudenstein_roth_func.Rd:29: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'osmar'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./utilities.h:7:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  utilities.c:14:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/emoa.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  conj_EMVS.cpp:68:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  conj_EMVS.cpp:77:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  conj_EMVS.cpp:135:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ind_EMVS.cpp:67:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ind_EMVS.cpp:77:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ind_EMVS.cpp:124:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/EMVS.Rcheck/00install.out' for details.
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'file.path(temp_dir, gp2.csv)'
Package suggested but not available for checking: 'ecospat'
Package suggested but not available for checking: 'ecospat'
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'Environmental variables.csv' 'Inf.txt' 'List of species.csv' 'Mean
  overlap among taxa.csv' 'Overlap among taxa.csv' 'Pointsize.dat'
  'Polar coordinates.csv'
'LazyData' is specified without a 'data' directory
checkRd: (-1) calibrate.Rd:151: Escaped LaTeX specials: \&
checkRd: (-1) cdfCompareCensored.Rd:299: Escaped LaTeX specials: \&
checkRd: (-1) detectionLimitCalibrate.Rd:149: Escaped LaTeX specials: \&
checkRd: (-1) ecdfPlotCensored.Rd:169: Escaped LaTeX specials: \&
checkRd: (-1) egammaAltCensored.Rd:344: Escaped LaTeX specials: \&
checkRd: (-1) egammaCensored.Rd:340: Escaped LaTeX specials: \&
checkRd: (-1) elnormAltCensored.Rd:694: Escaped LaTeX specials: \&
checkRd: (-1) elnormCensored.Rd:270: Escaped LaTeX specials: \&
checkRd: (-1) enormCensored.Rd:852: Escaped LaTeX specials: \&
checkRd: (-1) enparCensored.Rd:343: Escaped LaTeX specials: \&
checkRd: (-1) enparCensored.Rd:358: Escaped LaTeX specials: \&
checkRd: (-1) epoisCensored.Rd:354: Escaped LaTeX specials: \&
checkRd: (-1) ppointsCensored.Rd:406: Escaped LaTeX specials: \&
checkRd: (-1) predIntGammaSimultaneous.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) predIntGammaSimultaneous.Rd:171: Escaped LaTeX specials: \&
checkRd: (-1) predIntLnormSimultaneous.Rd:136: Escaped LaTeX specials: \&
checkRd: (-1) predIntLnormSimultaneous.Rd:137: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneous.Rd:204: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneous.Rd:205: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneousK.Rd:277: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneousK.Rd:278: Escaped LaTeX specials: \&
checkRd: (-1) qqPlotCensored.Rd:261: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTest.Rd:276: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTestCensored.Rd:324: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTestCensored.Rd:331: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'Net1-fromR.inp'
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Package suggested but not available for checking: 'epidict'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_state.h:33:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:380:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:381:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:382:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_wtstate.h:32:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:585:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:586:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:587:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/EpiModel.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'episcan_1geno_cc.txt' 'episcan_1geno_quant.txt'
  'episcan_2geno_cc.txt' 'episcan_2geno_quant.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'taskscheduleR'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'spelling.R' [0s/1s]
  Running 'testthat.R' [19s/25s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(era)
  > 
  > test_check("era")
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 117 ]
  
  == Skipped tests ===============================================================
  * On CRAN (6)
  
  == Failed tests ================================================================
  -- Failure ('test-examples.R:17'): this_year() is vectorised -------------------
  this_year(c("CE", "BP", "AM")) (`actual`) not equal to list(year_now, year_now_bp, year_now_am) (`expected`).
  
  `actual[[3]]`:   "5783"
  `expected[[3]]`: "5782"
  
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 117 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  directed.cpp:65:30: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:66:30: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:67:30: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:96:28: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:97:28: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:121:28: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:256:28: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:257:28: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:258:28: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:269:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:291:24: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:292:24: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:307:24: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:367:24: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:368:24: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:369:24: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  undirected.cpp:141:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ergmclust.Rcheck/00install.out' for details.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_state.h:33:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:380:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:381:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:382:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_wtstate.h:32:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:585:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:586:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:587:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ergm.count.Rcheck/00install.out' for details.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_state.h:33:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:380:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:381:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:382:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_wtstate.h:32:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:585:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:586:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:587:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ergm.ego.Rcheck/00install.out' for details.
Found the following significant warnings:
  induced_submat.cpp:25:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  induced_submat.cpp:27:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ergmito.Rcheck/00install.out' for details.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_state.h:33:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:380:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:381:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:382:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_wtstate.h:32:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:585:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:586:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:587:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ergm.rank.Rcheck/00install.out' for details.
Found the following significant warnings:
  ../inst/include/ergm_state.h:33:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  MPLE.c:28:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ergm_omp.c:36:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ergm_state.c:107:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../inst/include/ergm_wtstate.h:32:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ergm_wtstate.c:107:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:34:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:35:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:36:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:40:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ergm.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) aic.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:64: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
Found the following files/directories:
  'sample .nwk'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ExactData'
checkRd: (-1) exams2sakai.Rd:152: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cec2013'
checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) outlierPlot.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) outlierPlot.Rd:32: Escaped LaTeX specials: \$
Package suggested but not available for checking: 'exuberdata'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'Bogota.tex' 'DogBreeds1.tex'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    minor changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  chli.c:5:48: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/fame.Rcheck/00install.out' for details.
File 'fame/R/windows/zzz.R':
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section 'Good practice' in '?.onAttach'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./lu.h:44:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lu.c:828:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/fastclime.Rcheck/00install.out' for details.
Found the following files/directories:
  'default5.eps'
Package suggested but not available for checking: 'crrp'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  pixelfn.cpp:15:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  pixelfn.cpp:34:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  pixelfn.cpp:41:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/fasterize.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'coxKM'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:8:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/fastmap.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'fastmatch/libs/fastmatch.so':
  Found non-API call to R: 'match5'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Scent.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) Traffic.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
.run: no visible binding for global variable 'init'
.run: no visible global function definition for 'init'
.run: no visible binding for global variable 'run'
Undefined global functions or variables:
  init run
Note: information on .o files is not available
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'NNLM'
GNU make is a SystemRequirements.
Found the following significant warnings:
  fbati_init.c:35:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  fbati_init.c:36:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  fbati_init.c:37:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  fbati_init.c:39:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  fbati_init.c:50:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  fbati_init.c:51:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  fbati_init.c:52:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  fbati_init.c:53:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/fbati.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  func.cpp:124:17: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/fclust.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'test2delete.txt' 'test2delete2_values.txt' 'test2delete_values.txt'
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  '.Rprofile'
Unexported objects imported by ':::' calls:
  'fdapace:::GCVLwls1D1' 'fdapace:::GetSmoothedMeanCurve'
  'fdapace:::HandleNumericsAndNAN' 'fdapace:::interp2lin'
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'vert.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'treesAll.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New Stuff
'LazyData' is specified without a 'data' directory
checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  combNWrapper.c:49:27: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  combNWrapper.c:81:27: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/FFD.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./ff.h:34:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./r_ff.h:62:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./r_ff.h:63:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./r_ff.h:64:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  r_ff.c:289:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  r_ff.c:298:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  r_ff.c:309:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ff.Rcheck/00install.out' for details.
checkRd: (-1) dimnames.ff.rd:18: Escaped LaTeX specials: \_
checkRd: (-1) ff.rd:120: Escaped LaTeX specials: \_
checkRd: (-1) names.ff.rd:22: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./f2c.h:185:49: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:186:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:187:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:188:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:189:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:189:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:190:35: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:191:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:192:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:193:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:194:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:195:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/FGSG.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'MicrobeDS'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'AH_genepop.txt' 'AH_popname.txt' 'JSM_MS_freq.txt'
  'JSM_MS_genepop.txt' 'JSM_genepop_clipped_both.txt'
  'JSM_genepop_clipped_maf.txt' 'JSM_genepop_clipped_name.txt'
  'JSM_mtDNA_freq.txt' 'JSM_popname.txt' 'result_DJ.csv'
  'result_EBDJ.csv' 'result_EBFST.csv' 'result_EBFST_mtDNA.csv'
  'result_EBGstH.csv' 'result_GstH.csv' 'result_GstN.csv'
  'result_GstNC.csv' 'result_thetaWCpair.csv'
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'benchden', 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'fivethirtyeightdata'
Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fk_regression.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) cclust.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) randIndex.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:28: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  intGL_NC.c:330:24: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/flexrsurv.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  float_native.c:40:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  float_native.c:41:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  float_native.c:53:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  machine.c:7:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  NA.c:20:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  NA.c:76:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  NA.c:88:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/float.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
GNU make is a SystemRequirements.
Found the following files/directories:
  'flux.CH4.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) pseudoOptim.Rd:27: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) write.AFNI.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) write.AFNI.Rd:17: Escaped LaTeX specials: \_
checkRd: (-1) write.AFNI.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) write.AFNI.Rd:22: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
checkRd: (-1) forecTheta-package.Rd:11: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  simulations_1.5.cpp:322:18: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  simulations_1.5.cpp:418:18: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  simulations_1.5.cpp:526:18: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/FORTLS.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
Package suggested but not available for checking: 'RandomFields'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CatalogueAccessors.Rd:249: Escaped LaTeX specials: \^ \^
checkRd: (-1) FrF2.Rd:574: Escaped LaTeX specials: \^
checkRd: (-1) FrF2.Rd:629: Escaped LaTeX specials: \^ \^
checkRd: (-1) IAPlot.Rd:87: Escaped LaTeX specials: \$
checkRd: (-1) block.Rd:121: Escaped LaTeX specials: \^
checkRd: (-1) block.Rd:150: Escaped LaTeX specials: \^ \^
checkRd: (-1) blockpick.Rd:114: Escaped LaTeX specials: \^ \^
Packages suggested but not available for checking: 'dggrids', 'INLA'
Unknown package 'frm' in Rd xrefs
Unknown package 'frm' in Rd xrefs
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
Package suggested but not available for checking: 'RTCGA.rnaseq'
Found the following significant warnings:
  init.c:20:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/FSelectorRcpp.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mean.fts.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) median.fts.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) plot.fm.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) residuals.fm.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) sd.fts.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) var.fts.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'completeTrial_byArm_eventPriorRateC3=0.001_eventPriorRateT1=0_eventPriorRateT2=0_eventPriorWt=0.5.RData'
  'completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.2.RData'
  'completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.4.RData'
  'completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.6.RData'
  'completeTrial_pooled_eventPriorRate=0.001_eventPriorWt=0.5.RData'
  'completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.2.RData'
  'completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.4.RData'
  'completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.6.RData'
  'rcdf_byArm_arm=T1_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03.pdf'
  'rcdf_pooled_eventPriorRate=0.06.pdf'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'cBioPortalData'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  gamlr.c:87:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:12:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/gamlr.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LGAclaims.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:36: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) meyer.Rd:11: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'checkdata.csv' 'gbmforest.sas'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
Package in Depends field not imported from: 'tools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'tools:::.Rd_get_argument_names' 'tools:::RdTags' 'tools:::fetchRdDB'
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'gputools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File 'g.data/R/g.data.attach.R':
  attach(NULL, pos, basename(dir))
See section 'Good practice' in '?attach'.
Package suggested but not available for checking: 'gdxrrw'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot_summary.Rd:14: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'genderdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'trackViewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Running examples in 'GenEst-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: averageSS
> ### Title: Tabulate an average search schedule from a multi-unit SS data
> ###   table
> ### Aliases: averageSS
> 
> ### ** Examples
> 
>   data(mock)
>   avgSS <- averageSS(mock$SS)
Error in prepSS(data_SS, SSdate = SSdate) : 
  more than 1 date column in data_SS, and SSdate does not specify which to use.
Calls: averageSS -> prepSS
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'GenEstGUI.Rmd' using rmarkdown
--- finished re-building 'GenEstGUI.Rmd'

--- re-building 'command-line-example.Rmd' using rmarkdown
Quitting from lines 381-390 (command-line-example.Rmd) 
Error: processing vignette 'command-line-example.Rmd' failed with diagnostics:
more than 1 date column in data_SS, and SSdate does not specify which to use.
--- failed re-building 'command-line-example.Rmd'

--- re-building 'solar-examples.Rmd' using rmarkdown
Quitting from lines 286-293 (solar-examples.Rmd) 
Error: processing vignette 'solar-examples.Rmd' failed with diagnostics:
more than 1 date column in data_SS, and SSdate does not specify which to use.
--- failed re-building 'solar-examples.Rmd'

--- re-building 'wind-examples.Rmd' using rmarkdown
Quitting from lines 277-283 (wind-examples.Rmd) 
Error: processing vignette 'wind-examples.Rmd' failed with diagnostics:
more than 1 date column in data_SS, and SSdate does not specify which to use.
--- failed re-building 'wind-examples.Rmd'

SUMMARY: processing the following files failed:
  'command-line-example.Rmd' 'solar-examples.Rmd' 'wind-examples.Rmd'

Error: Vignette re-building failed.
Execution halted
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  MatingPrograms.cpp:31:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  MatingPrograms.cpp:36:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  MatingPrograms.cpp:42:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  MatingPrograms.cpp:47:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  MatingPrograms.cpp:52:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  MatingPrograms.cpp:57:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  MatingPrograms.cpp:62:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  MatingPrograms.cpp:67:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  MatingPrograms.cpp:72:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/GenomicMating.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
Found the following significant warnings:
  init.c:14:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/GenSA.Rcheck/00install.out' for details.
Found the following significant warnings:
  arms.c:99:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  arms.c:900:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/genscore.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  gensvm/include/gensvm_rand.h:44:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  gensvm/src/gensvm_rand.c:105:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  gensvm/src/gensvm_rand.c:112:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  gensvm/src/gensvm_rand.c:153:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/gensvm.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:5:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:5:6: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype]
  init.c:6:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:6:6: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype]
  init.c:7:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:7:6: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/geohashTools.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'geomarocdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  dist.c:117:57: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/geosphere.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'ChAMP', 'minfi', 'IlluminaHumanMethylation450kanno.ilmn12.hg19'
Malformed Description field: should contain one or more complete sentences.
Found the following calls to data() loading into the global environment:
File 'geotools/R/zzz.R':
  data(fr_geo_rad)
See section 'Good practice' in '?data'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) getopt.Rd:60: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
checkRd: (-1) gexp.Rd:123: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'RGtk2'
checkRd: (-1) estGF.Rd:106: Escaped LaTeX specials: \&
checkRd: (-1) estGF.Rd:107: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    earlier versions
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'ggbio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following assignments to the global environment:
File 'ggExtra/R/ggMarginalGadget.R':
  assign(plotname, eval(parse(text = origPlot)), envir = .GlobalEnv)
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dlm'
Error(s) in re-building vignettes:
  ...
--- re-building 'basics.Rmd' using knitr
Loading required package: ggplot2
Loading required package: MASS
Loading required package: strucchange
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: urca
Loading required package: lmtest
--- finished re-building 'basics.Rmd'

--- re-building 'plot_dist.Rmd' using knitr
--- finished re-building 'plot_dist.Rmd'

--- re-building 'plot_lm.Rmd' using knitr
--- finished re-building 'plot_lm.Rmd'

--- re-building 'plot_map.Rmd' using knitr
Loading required package: maps
--- finished re-building 'plot_map.Rmd'

--- re-building 'plot_pca.Rmd' using knitr

Attaching package: 'cluster'

The following object is masked from 'package:maps':

    votes.repub

Warning: `gather_()` was deprecated in tidyr 1.2.0.
i Please use `gather()` instead.
i The deprecated feature was likely used in the ggfortify package.
  Please report the issue at <https://github.com/sinhrks/ggfortify/issues>.
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
--- finished re-building 'plot_pca.Rmd'

--- re-building 'plot_surv.Rmd' using knitr
Warning: Using formula(x) is deprecated when x is a character vector of length > 1.
  Consider formula(paste(x, collapse = " ")) instead.
--- finished re-building 'plot_surv.Rmd'

--- re-building 'plot_ts.Rmd' using knitr
Successfully loaded changepoint package version 2.2.3
 See NEWS for details of changes.
Quitting from lines 158-167 (plot_ts.Rmd) 
Error: processing vignette 'plot_ts.Rmd' failed with diagnostics:
there is no package called 'dlm'
--- failed re-building 'plot_ts.Rmd'

SUMMARY: processing the following file failed:
  'plot_ts.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ggOceanMapsData'
'LazyData' is specified without a 'data' directory
checkRd: (-1) diamonds.Rd:10: Escaped LaTeX specials: \$ \$
Found the following HTML validation problems:
ggplot2-package.html:23:4 (ggplot2-package.Rd:9): Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    History
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'nlmixr', 'lixoftConnectors'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Bug fixes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  repel_boxes.cpp:183:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  repel_boxes.cpp:193:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ggrepel.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    * Changes all data options to .data to decrease possibility of column naming overlap
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'Pictures_analyzed' 'cutoff_vals' 'cutoff_vals1' 'gina_cran.JPG'
Unknown package 'IC2' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'mlr3proba'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  phytr.c:419:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  phytr.c:1348:69: warning: for loop has empty body [-Wempty-body]
  phytr.c:1650:46: warning: for loop has empty body [-Wempty-body]
  phytr.c:2327:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  phytr.c:3266:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  phytr.c:3268:35: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  phytr.c:3298:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  phytr.c:3302:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  phytr.c:3307:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  phytr.c:3310:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  phytr.c:3313:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  phytr.c:3316:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  phytr.c:3319:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  phytr.c:3322:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  phytr.c:3325:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/glinvci.Rcheck/00install.out' for details.
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
checkRd: (-1) glmc.control.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) glmc.control.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) basal.Rd:32: Escaped LaTeX specials: \_
checkRd: (-1) basal.Rd:33: Escaped LaTeX specials: \_ \_ \_
Found the following significant warnings:
  pb.c:27:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/glmnet.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) consensus.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) getfit.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'cplexAPI'
Found the following significant warnings:
  rho_rho_excess.c:16:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/globalKinhom.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
Problems with news in 'NEWS.md':
No news entries found.
Error(s) in re-building vignettes:
  ...
--- re-building 'gloss_factory.Rmd' using rmarkdown
--- finished re-building 'gloss_factory.Rmd'

--- re-building 'glossr.Rmd' using rmarkdown
--- finished re-building 'glossr.Rmd'

--- re-building 'glossr_how.Rmd' using rmarkdown
Warning in gsub(paste0("[\n]{2,}(", fence, "|    )"), "\n\n\\1", x) :
  unable to translate '

```r
my_gloss <- as_gloss(
  ".... ................ .... ................",
  "t.... w....=de-yì-sh....ng dà k....-q....lái,",
  "TSG waa.IDEO-LINK-one-sound big cry-inch",
  translation = "Waaaaa, she began to wail.",
  label = "my-label",
  source ...' to a wide string
Quitting from lines 63-72 (glossr_how.Rmd) 
Error: processing vignette 'glossr_how.Rmd' failed with diagnostics:
input string 1 is invalid
--- failed re-building 'glossr_how.Rmd'

--- re-building 'styling.Rmd' using rmarkdown
--- finished re-building 'styling.Rmd'

SUMMARY: processing the following file failed:
  'glossr_how.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) barleyHeights.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) barleyHeights.Rd:22: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) BVDWSTOXX.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:16: Escaped LaTeX specials: \& \&
checkRd: (-1) BVDWSTOXX.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:37: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  R_register_native.c:11:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  R_register_native.c:12:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  gower.c:60:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  gower.c:72:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  gower.c:83:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/gower.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'gvcm.cat'
Unknown package 'gvcm.cat' in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) barplot2.Rd:219: Escaped LaTeX specials: \_
checkRd: (-1) colorpanel.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) qqnorm.aov.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) venn.Rd:59: Escaped LaTeX specials: \_
checkRd: (-1) GPoM.FDLyapu-package.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) Plague.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) lyapFDGrond.Rd:66: Escaped LaTeX specials: \&
checkRd: (-1) lyapFDGrond.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) lyapFDGrond.Rd:69: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) crdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) descApp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) layoutApp.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) rbdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) ttApp.Rd:43: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) gen_graph_indep.Rd:126: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mlGraphicalVAR.Rd:79: Escaped LaTeX specials: \~
Running 'testthat.R' [15s/17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(grates)
  > 
  > test_check("grates")
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  [ FAIL 2 | WARN 27 | SKIP 23 | PASS 408 ]
  
  == Skipped tests ===============================================================
  * On CRAN (23)
  
  == Failed tests ================================================================
  -- Failure ('test-month.R:128'): as_month.POSIXlt works as expected ------------
  `result` (`actual`) not equal to as.POSIXlt("2021-01-01", tz = "NZ") (`expected`).
  
  `attr(actual, 'balanced')`:   <NA>
  `attr(expected, 'balanced')`: TRUE
  -- Failure ('test-quarter.R:64'): as_quarter.POSIXlt works as expected ---------
  `result` (`actual`) not equal to as.POSIXlt("2021-01-01", tz = "NZ") (`expected`).
  
  `attr(actual, 'balanced')`:   <NA>
  `attr(expected, 'balanced')`: TRUE
  
  [ FAIL 2 | WARN 27 | SKIP 23 | PASS 408 ]
  Deleting unused snapshots:
  * plots/month.png
  * plots/month2.png
  * plots/quarter.png
  * plots/twentyeight_days.png
  * plots/two_weeks.png
  * plots/year.png
  * plots/yearweek_monday.png
  * plots/yearweek_thursday.png
  Error: Test failures
  Execution halted
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
Found the following significant warnings:
  Offset.c:3:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:12:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  omp_diagnose.c:5:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  omp_diagnose.c:18:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/grattan.Rcheck/00install.out' for details.
Found the following significant warnings:
  init.c:11:46: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/gRc.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
accrualReport: multiple local function definitions for 'gg' with
  different formal arguments
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'p1_20up-vs-p2_25up_in_str1.txt' 'p1_20up-vs-p2_25up_in_str2.txt'
  'p2_25up-vs-p1_20up_in_str1.txt' 'p2_25up-vs-p1_20up_in_str2.txt'
  's0_20up.txt' 's0_30up.txt' 's0_f2up.txt' 'strs.vec_01mx.txt'
  'strs.vec_02mx.txt' 'strs.vec_03mx.txt' 'strs.vec_04mx.txt'
  'strs.vec_05mx.txt' 'strs.vec_06mx.txt' 'strs.vec_30up.txt'
  'strs.vec_50up.txt' 'strs.vec_f2up.txt' 'uni_p1_20up-p2_25up.txt'
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
Found the following files/directories:
  'FMD mag discontinuities_disc.png' 'FMD mag
  discontinuities_disc1.res' 'FMD mag discontinuities_disc2.res'
  'IDYLLWILD_bvmed.png' 'IDYLLWILD_fig.png' 'Schuster's
  diagram_schu.png' 'hour.res'
Found the following significant warnings:
  cov-em.cpp:169:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  cov-em.cpp:174:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/GSE.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  smolyak.c:58:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  smolyak.c:79:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  smolyak.c:227:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  smolyak.c:477:10: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/gss.Rcheck/00install.out' for details.
checkRd: (-1) gsym.point.Rd:143: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'RRprof.out'
checkRd: (-1) GUTS-package.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) GUTS.Rd:201: Escaped LaTeX specials: \&
checkRd: (-1) GUTS.Rd:209: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) luzdat.Rd:21: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following files/directories:
  'testdata1.txt' 'testdata2.txt' 'testdata3.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [9s/11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hablar)
  > test_check("hablar")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 416 ]
  
  == Failed tests ================================================================
  -- Failure ('test.convert.R:118'): from Date -----------------------------------
  tibble(a = as.Date(c("1970-05-03", NA, "1987-04-20"))) %>% convert(dtm(a)) not equal to tibble(a = as.POSIXct(as.Date(c("1970-05-03", NA, "1987-04-20")))).
  Component "a": 'tzone' attributes are inconsistent ('Europe/London' and 'UTC')
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 416 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  haplo.stats_init.c:22:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  haplo_em_pin.c:30:19: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./haplo_em_pin.h:28:19: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./haplo_em_pin.h:107:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  haplo_em_pin.c:1143:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  seqhap.c:17:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  seqhap.c:19:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  seqhap.c:110:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  seqhap.c:627:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  seqhap.c:807:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/haplo.stats.Rcheck/00install.out' for details.
checkRd: (-1) haplo.design.Rd:33: Escaped LaTeX specials: \$
checkRd: (-1) haplo.design.Rd:42: Escaped LaTeX specials: \$
checkRd: (-1) haplo.glm.Rd:176: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) haplo.glm.Rd:178: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) haplo.glm.Rd:283: Escaped LaTeX specials: \$ \$
checkRd: (-1) haplo.glm.Rd:292: Escaped LaTeX specials: \$ \$
checkRd: (-1) haplo.glm.Rd:324: Escaped LaTeX specials: \$ \$
Error(s) in re-building vignettes:
  ...
--- re-building 'Getting_started.Rmd' using rmarkdown
IGN web service API is available.
Last news from IGN website : "Mises à jour novembre 2022" on  (https://geoservices.ign.fr/actualites/2022-11-01-mises-a-jour)

Linking to GEOS 3.11.0, GDAL 3.5.2, PROJ 9.1.0; sf_use_s2() is TRUE
Quitting from lines 67-70 (Getting_started.Rmd) 
Error: processing vignette 'Getting_started.Rmd' failed with diagnostics:
Failed to parse text
--- failed re-building 'Getting_started.Rmd'

--- re-building 'SCAN_25_SCAN_100_SCAN_OACI.Rmd' using rmarkdown
--- finished re-building 'SCAN_25_SCAN_100_SCAN_OACI.Rmd'

SUMMARY: processing the following file failed:
  'Getting_started.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) HWAlr.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWAlrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWClr.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) HWClrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWIlr.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) HWf.Rd:25: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) hash-accessors.Rd:46: Escaped LaTeX specials: \$
checkRd: (-1) hash-class.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) hash-class.Rd:45: Escaped LaTeX specials: \$
checkRd: (-1) hash-package.Rd:39: Escaped LaTeX specials: \#
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) prm09.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) prm09.Rd:26: Escaped LaTeX specials: \&
Found the following significant warnings:
  Soil_HBV.cpp:226:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Soil_HBV.cpp:312:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/HBV.IANIGLA.Rcheck/00install.out' for details.
checkRd: (-1) schools.Rd:18: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./H5Error.h:25:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  datatype_export.c:64:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  H5Error.c:122:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/hdf5r.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'synbreed'
'LazyData' is specified without a 'data' directory
checkRd: (-1) erode.hexbin.Rd:43: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
':::' call which should be '::': 'ggplot2:::guide_axis'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'ggplot2:::build_guides' 'ggplot2:::scales_list'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'colorfulVennPlot'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Snow.Rd:118: Escaped LaTeX specials: \&
checkRd: (-1) Snow.Rd:142: Escaped LaTeX specials: \&
checkRd: (-1) Yeast.Rd:56: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'trackr'
Package which this enhances but not available for checking: 'HadoopStreaming'
Found the following significant warnings:
  hkevp.cpp:446:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  hkevp.cpp:475:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  hkevp.cpp:506:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  hkevp.cpp:534:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  hkevp.cpp:573:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  hkevp.cpp:633:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  hkevp.cpp:652:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  hkevp.cpp:905:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  hkevp.cpp:934:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  hkevp.cpp:965:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  hkevp.cpp:993:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  hkevp.cpp:1251:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  hkevp.cpp:1311:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  hkevp.cpp:1330:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/hkevp.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following significant warnings:
  ranksort.c:3:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  ranksort.c:49:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  ranksort.c:76:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Hmisc.Rcheck/00install.out' for details.
Found the following significant warnings:
  cda.cpp:29:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/hmlasso.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'ROI.plugin.mosek'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
checkRd: (-1) attributes_speclib.Rd:73: Escaped LaTeX specials: \$
checkRd: (-1) get_reflectance.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./useful.h:6:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/hSDM.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  humanleague_init.c:14:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/humanleague.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Trancura9414001.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) Trancura9414001.Rd:28: Escaped LaTeX specials: \_
checkRd: (-1) hydroPSO.Rd:390: Escaped LaTeX specials: \&
checkRd: (-1) hydroPSO.Rd:408: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:7: Escaped LaTeX specials: \&
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'AIC.txt' 'AICc.txt' 'IAS.pdf' 'IAS2.pdf' 'IAS3.pdf'
  'P.microlepis-AIC.txt' 'P.microlepis-AICc.txt' 'P.microlepis-IAS.pdf'
  'P.microlepis-IAS2.pdf' 'P.microlepis-IAS3.pdf'
Package suggested but not available for checking: 'gutenbergr'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ibdreg_init.c:22:35: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./mcmemory.h:188:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sim.mark.prop.c:85:64: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sim.mark.prop.c:88:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sim.mark.prop.c:90:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sim.mark.prop.c:303:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sim.mark.prop.c:814:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sim.mark.prop.c:877:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sim.mark.prop.c:912:12: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  sim.mark.prop.c:1018:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ibdreg.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SparkR'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  initds.c:10:29: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/icapca.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'icd'
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
Package suggested but not available for checking: 'ICBayes'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) pulmonary.Rd:13: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rggobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'optiRum'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'IFCdata'
Found the following significant warnings:
  ../inst/include/ut_debug.h:188:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ut_debug.c:102:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ifultools.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  cda3.cpp:26:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/iilasso.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  common.c:62:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:12:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  utils.c:9:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ijtiff.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./RNifti_shim.h:19:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RNifti/include/RNiftiAPI.h:268:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  RNifti_shim.c:39:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./print.h:15:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  core.c:717:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  core.c:751:24: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  core.c:774:24: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/imbibe.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'accdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: 'minfi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Found the following significant warnings:
  keyplayer-utils.c:24:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/influenceR.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
BugReports field should be the URL of a single webpage
Package which this enhances but not available for checking: 'gurobi'
Found the following files/directories:
  'c.txt' 'rho.txt' 'sta.txt' 'topo.txt'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Found the following significant warnings:
  DefinePolygons.c:17:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  DefinePolygons.c:18:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  DefinePolygons.c:44:22: warning: passing arguments to 'FindNextSeg' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  DefinePolygons.c:47:24: warning: passing arguments to 'StartNewSeg' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  DefinePolygons.c:17:5: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype]
  DefinePolygons.c:18:5: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/inlmisc.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    TODO for future releases:
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'Error_Estimation_Response_1.tiff' 'Error_Estimation_Response_2.tiff'
  'Error_Estimation_Response_3.tiff'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./ebm_native/EbmStatisticUtils.h:86:122: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/interpret.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Intervals-class.Rd:109: Escaped LaTeX specials: \_
checkRd: (-1) Intervals-class.Rd:110: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:68: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:76: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:77: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:78: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:79: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:81: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:88: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:89: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) sgd.Rd:12: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'iotools/libs/iotools.so':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  item_analysis.cpp:75:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/irt.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) pine.Rd:20: Escaped LaTeX specials: \&
Found the following significant warnings:
  trace_islasso.c:39:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/islasso.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
Found the following files/directories:
  'RMTplot.pdf'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Package suggested but not available for checking: 'locClass'
checkRd: (-1) ivmodel.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) ivmodelFormula.Rd:79: Escaped LaTeX specials: \&
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  jGDtalk.c:116:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  jGDtalk.c:797:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  javaGD.c:153:9: warning: expression which evaluates to zero treated as a null pointer constant of type 'newJavaGDDesc *' [-Wnon-literal-null-conversion]
  javaGD.c:373:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  javaGD.c:382:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/JavaGD.Rcheck/00install.out' for details.
Output from running autoreconf:
  configure.ac:4: warning: The macro `AC_CONFIG_HEADER' is obsolete.
  configure.ac:4: You should run autoupdate.
  ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from...
  configure.ac:4: the top level
  configure.ac:24: warning: The macro `AC_HEADER_STDC' is obsolete.
  configure.ac:24: You should run autoupdate.
  ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
  configure.ac:24: the top level
  configure.ac:30: warning: The macro `AC_HEADER_TIME' is obsolete.
  configure.ac:30: You should run autoupdate.
  ./lib/autoconf/headers.m4:743: AC_HEADER_TIME is expanded from...
  configure.ac:30: the top level
  configure.ac:34: warning: The macro `AC_TYPE_SIGNAL' is obsolete.
  configure.ac:34: You should run autoupdate.
  ./lib/autoconf/types.m4:776: AC_TYPE_SIGNAL is expanded from...
  configure.ac:34: the top level
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    joineR <1.1
Package which this enhances but not available for checking: 'remMap'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./rjcommon.h:75:44: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/jpeg.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) summ.rq.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) summ.rq.Rd:108: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: multiple methods tables found for 'bootstrap'
  Warning: replacing previous import 'arkhe::bootstrap' by 'dimensio::bootstrap' when loading 'kairos'
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/kairos.Rcheck/00install.out' for details.
Warning: multiple methods tables found for 'bootstrap'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Running examples in 'kairos-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fit
> ### Title: Frequency Increment Test
> ### Aliases: fit fit-method fit,data.frame,numeric-method
> ###   fit,matrix,numeric-method
> 
> ### ** Examples
> 
> data("merzbach", package = "folio")
> 
> ## Keep only decoration types that have a maximum frequency of at least 50
> keep <- apply(X = merzbach, MARGIN = 2, FUN = function(x) max(x) >= 50)
> counts <- merzbach[, keep]
> 
> ## Group by phase
> ## We use the row names as time coordinates (roman numerals)
> dates <- as.numeric(utils::as.roman(rownames(counts)))
> 
> ## Frequency Increment Test
> freq <- fit(counts, dates)
> 
> ## Plot time vs abundance and highlight selection
> plot(freq)
Warning: 'as_long()' is deprecated.
Use 'to_long()' instead.
See help("Deprecated")
Error: Must request at least one colour from a hue palette.
Execution halted
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'my.Mobius.set.func.csv' 'my.card.set.func.csv' 'my.set.func.csv'
Found the following files/directories:
  'song.wav' 'song4karaoke.wav'
Found the following HTML validation problems:
math_to_rd.html:81:2153 (math_to_rd.Rd:45): Warning: <svg> attribute "width" has invalid value "400em"
math_to_rd.html:81:2153 (math_to_rd.Rd:45): Warning: <svg> attribute "height" has invalid value "1.08em"
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ionosphere.Rd:22: Escaped LaTeX specials: \&
checkRd: (-1) ionosphere.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor Changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'cld1.Rdata' 'main.tex' 'myCld.Rdata' 'myCld3d.Rdata' 'scene.asy'
Found the following files/directories:
  'cld1.Rdata' 'ld.Rdata' 'myCld.Rdata'
Found the following significant warnings:
  kmlShape.c:5:81: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  kmlShape.c:157:85: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/kmlShape.Rcheck/00install.out' for details.
checkRd: (-1) pathFrechet.Rd:54: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'Killed after '
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'VARSEDIG'
Unknown package 'VARSEDIG' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'KSEA Bar Plot.tiff' 'KSEA Kinase Scores.csv'
  'KSEA.Merged.Heatmap.png' 'Kinase-Substrate Links.csv'
'LazyData' is specified without a 'data' directory
checkRd: (-1) kstIO-package.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) read_kbase.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) read_kdata.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) read_kfamset.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) read_kspace.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) read_kstructure.Rd:45: Escaped LaTeX specials: \&
checkRd: (-1) read_surmiserelation.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) write_kbase.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) write_kdata.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) write_kspace.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) write_kstructure.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) write_surmiserelation.Rd:36: Escaped LaTeX specials: \&
Found the following files/directories:
  'DF7.bas' 'DF7.dat' 'DF7.rel' 'DF7.spc' 'DF7.struct'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) alphaOnly.Rd:25: Escaped LaTeX specials: \^
checkRd: (-1) alphaOnly.Rd:26: Escaped LaTeX specials: \$
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
checkRd: (-1) natlongsurv.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'MYSLID.csv' 'tabelle.csv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  reader.c:110:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/languageserver.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
Found the following significant warnings:
  init.c:19:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/largeList.Rcheck/00install.out' for details.
Found the following files/directories:
  'example.llo'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ergm.userterms'
checkRd: (-1) simulate.ergmm.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) simulate.ergmm.Rd:36: Escaped LaTeX specials: \$
Unknown package 'ergm.userterms' in Rd xrefs
GNU make is a SystemRequirements.
Found the following significant warnings:
  init.c:12:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:18:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:24:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:27:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:51:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/later.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./lrsmp.h:147:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lrslib.c:1466:18: warning: if statement has empty body [-Wempty-body]
  lrsmp.c:40:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/LatticeDesign.Rcheck/00install.out' for details.
checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'gof', 'lava.tobit'
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File 'lazyData/R/requireData.R':
  attach(NULL, pos = pos, name = searchDataName)
See section 'Good practice' in '?attach'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) goodnessfit.Rd:105: Escaped LaTeX specials: \&
checkRd: (-1) lba.Rd:252: Escaped LaTeX specials: \&
checkRd: (-1) pregnancy.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) pregnancy.Rd:46: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    lcars.0.3.1
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'temp.float.csv' 'temp.result.athena.csv'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  lcopula-init.c:15:50: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/lcopula.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'VariantAnnotation'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) leaps.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [59s/73s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > if (requireNamespace("testthat")) {
  +   library(testthat)
  +   library(learnr)
  + 
  +   test_check("learnr")
  + }
  Loading required namespace: testthat
  [ FAIL 1 | WARN 0 | SKIP 18 | PASS 812 ]
  
  == Skipped tests ===============================================================
  * On CRAN (18)
  
  == Failed tests ================================================================
  -- Failure ('test-exercise.R:1223'): evaluate_exercise() does not return a message for parsable non-ASCII code --
  result$feedback is not NULL
  
  `actual` is a list
  `expected` is NULL
  
  [ FAIL 1 | WARN 0 | SKIP 18 | PASS 812 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  rigraph/src/plfit/gss.h:132:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rigraph/src/plfit/gss.c:60:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rigraph/src/plfit/platform.c:36:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rigraph/src/plfit/mt.c:20:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rigraph/src/attributes.c:281:41: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rigraph/src/init.c:51:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rigraph/src/init.c:104:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rigraph/src/rinterface.c:2354:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rigraph/src/rinterface.c:2370:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rigraph/src/rinterface.c:9538:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rigraph/src/random.c:626:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rigraph/src/glpk_support.c:95:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/leidenbase.Rcheck/00install.out' for details.
Found the following significant warnings:
  lemna.c:98:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lemna.c:109:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lemna.c:120:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lemna.c:129:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lemna.c:138:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/lemna.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./lfe.h:121:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./lfe.h:122:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  utils.c:195:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  utils.c:208:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/lfe.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
Found the following significant warnings:
  init.c:14:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/lhs.Rcheck/00install.out' for details.
Found the following significant warnings:
  trainLinear.c:20:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  trainLinear.c:93:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/LiblineaR.ACF.Rcheck/00install.out' for details.
Found the following significant warnings:
  trainLinear.c:19:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  trainLinear.c:20:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  trainLinear.c:100:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  trainLinear.c:130:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/LiblineaR.Rcheck/00install.out' for details.
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:6:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/liGP.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LIMEcoli.Rd:125: Escaped LaTeX specials: \_
checkRd: (-1) Read.Rd:88: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:92: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:98: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:104: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:105: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:106: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:107: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:108: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:109: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:110: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:111: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:112: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:114: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cauchypoly.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) normpoly.Rd:38: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) normpoly.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) hatr.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'tTestTable.rda'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Author
    Maintainer
checkRd: (-1) SPSloess.Rd:71: Escaped LaTeX specials: \^ \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  CPkPlj.c:160:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  CPkPlj.c:160:6: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype]
  CPkPlj.c:324:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  CPkPlj.c:324:6: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype]
  CcovI.c:21:11: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  CcovI.c:39:7: warning: passing arguments to 'CcovI' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  CcovI.c:55:7: warning: passing arguments to 'CcovI' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  CcovI.c:21:6: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/locits.Rcheck/00install.out' for details.
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) ACS.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) EmployedACS.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSale.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleCA.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleCanton.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleNY.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:24: Escaped LaTeX specials: \$
checkRd: (-1) SalaryGender.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) SandP500.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) SandwichAnts.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) SandwichAnts2.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) TrafficFlow.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) KernelChars.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) Kernels.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) PRDenEstC.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) compKernVals.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) denCVBwSelC.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) equivKernel.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) kernelCtes.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) locPolWeights.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) locpol.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) locpol.Rd:82: Escaped LaTeX specials: \&
checkRd: (-1) locpolSmoothers.Rd:54: Escaped LaTeX specials: \&
checkRd: (-1) pluginBw.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) regCVBwSelC.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) thumbBw.Rd:40: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./veclib.h:316:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/logistf.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'main.tex' 'scene.asy'
'LazyData' is specified without a 'data' directory
checkRd: (-1) butstrap.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.nri.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.s.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.s.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) nri.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) roc.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) roc.s.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.s.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'Model_1.cm' 'dambacher.dot' 'levins.dot'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'scio'
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  LowRankQP.c:278:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  LowRankQP_init.c:29:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/LowRankQP.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) lpepa.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:90: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:65: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kerdiest'
checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) spectral.density.Rd:55: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  period.c:116:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/lubridate.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'test'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  proj_conf_test.c:5:9: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  proj_conf_test.c:4:9: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./liblwgeom/liblwgeom.h:305:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  liblwgeom/lwgeom_geos.c:613:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  liblwgeom/lwgeom_api.c:36:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  liblwgeom/lwgeom_api.c:667:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  liblwgeom/lwgeom_api.c:671:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  liblwgeom/lwboundingcircle.c:36:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  liblwgeom/lwboundingcircle.c:217:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lwin_wkt_lex.l:16:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lwin_wkt_lex.l:129:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/lwgeom.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'GenomicFeatures'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) read.magpie.Rd:20: Escaped LaTeX specials: \_ \_
checkRd: (-1) read.magpie.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) read.magpie.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) read.magpie.Rd:36: Escaped LaTeX specials: \_
checkRd: (-1) read.magpie.Rd:65: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:24: Escaped LaTeX specials: \_ \_
checkRd: (-1) write.magpie.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:42: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:43: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:70: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
checkRd: (-1) cilleruelo.Rd:36: Escaped LaTeX specials: \#
Problems with news in 'NEWS.md':
No news entries found.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  libCEigen.c:76:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  libCEigen.c:76:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ManlyMix.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'RGtk2'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Bug Fixes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'scrubr'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    To do
checkRd: (-1) sw_sfac.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) Interpolation-class.Rd:41: Escaped LaTeX specials: \#
checkRd: (-1) MareyMap-class.Rd:85: Escaped LaTeX specials: \_
checkRd: (-1) MareyMap-methods.Rd:11: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) MareyMap-methods.Rd:12: Escaped LaTeX specials: \_
checkRd: (-1) SpeciesMaps-methods.Rd:11: Escaped LaTeX specials: \_
checkRd: (-1) interpolation-methods.Rd:13: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'flashr'
Package suggested but not available for checking: 'wallace'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
checkRd: (-1) size_t-class.Rd:6: Escaped LaTeX specials: \_
Found the following significant warnings:
  libCEigen.c:76:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  libCEigen.c:76:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/MatManlyMix.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  ./t_sparseVector.c:83:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./chm_common.h:72:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./chm_common.h:93:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./chm_common.h:94:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  chm_common.c:8:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  chm_common.c:25:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  chm_common.c:50:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Matrix.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  allocMatrix2.c:10:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  allocMatrix2.c:16:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/matrixStats.Rcheck/00install.out' for details.
Found the following files/directories:
  'utilities.R'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dlm'
checkRd: (-1) maxControl.Rd:83: Escaped LaTeX specials: \&
Unknown package 'dlm' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'map_5.png' 'maze_5.html'
Found the following significant warnings:
  ./include/GenMatrix.h:56:12: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./include/MBAdata.h:50:12: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./include/UCBsplineSurface.h:48:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./include/MBA.h:73:12: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/MBA.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cplexAPI'
checkRd: (-1) salamander.Rd:22: Escaped LaTeX specials: \&
checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  chMatrix.c:162:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  mcmcsae_init.c:16:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mcmcsae.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) eigp.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:41: Escaped LaTeX specials: \&
Checking should be performed on sources prepared by 'R CMD build'.
'LazyData' is specified without a 'data' directory
Running 'spelling.R' [0s/1s]
  Running 'testthat.R' [40s/43s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(checkmate)
  > library(mctq)
  > library(testthat)
  > 
  > test_check("mctq")
  
  
  
  
  
  ! 'qplot_walk()' clears all plots from your system after it runs. If you don't agree with this, press 'esc' to exit.
  
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 609 ]
  
  == Failed tests ================================================================
  -- Failure ('test-round_time.R:27'): round_time() | scalar test ----------------
  round_time(object) (`actual`) not equal to as.POSIXlt(lubridate::as_datetime(12371, tz = "EST")) (`expected`).
  
  `attr(actual, 'balanced')`:   <NA>
  `attr(expected, 'balanced')`: TRUE
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 609 ]
  Error: Test failures
  Execution halted
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial version.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) glass.Rd:23: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) glass.Rd:24: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) glass.Rd:25: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) glass.Rd:26: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./threat-safe-random.h:58:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./threat-safe-random.h:70:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mdgc.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'RGtk2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mriTest.Rd:9: Escaped LaTeX specials: \&
checkRd: (-1) riTest.Rd:9: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'MethylCapSig'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mebootSpear.Rd:88: Escaped LaTeX specials: \_
checkRd: (-1) ullwan.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ullwan.Rd:8: Escaped LaTeX specials: \& \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'TxDb.Hsapiens.UCSC.hg19.knownGene'
Found the following files/directories:
  'Data_Correlation.txt' 'correlation_FDR_table.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  pspp-system-for-R.c:34:39: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  pspp-system-for-R.c:1291:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/memisc.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'genuMet'
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'cycHumanBloodData.csv' 'cycHumanBloodDesign.csv'
  'cycMouseLiverProtein.txt' 'cycMouseLiverRNA.csv' 'cycSimu4h2d.csv'
  'cycYeastCycle.csv' 'example'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) dslp.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) cardiac.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) plvol.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) sbp.Rd:16: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'MetProc_output.pdf' 'sample_removed.csv' 'sample_retained.csv'
Found the following significant warnings:
  init.c:37:47: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mets.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    mev v.1.9x
    mev v.1.8x
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    First release of mfe:
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following significant warnings:
  loglikelihood.c:483:20: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  loglikelihood_GJR.c:442:20: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mgarchBEKK.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  matrix.c:172:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mgcv.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'structSSI'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Package unavailable to check Rd xrefs: 'DAPAR'
checkRd: (-1) IPDNa.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) fdgs.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) mice.impute.cart.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) mice.impute.rf.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) pmm.match.Rd:41: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./do_nothing.h:4:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  do_nothing.c:11:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:7:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  nanotimer.c:88:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/microbenchmark.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'microcontax.data'
Package unavailable to check Rd xrefs: 'microcontax.data'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'ecospat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AKMCS.Rd:215: Escaped LaTeX specials: \&
checkRd: (-1) BMP.Rd:164: Escaped LaTeX specials: \&
checkRd: (-1) IRW.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) IRW.Rd:151: Escaped LaTeX specials: \&
checkRd: (-1) MP.Rd:142: Escaped LaTeX specials: \&
checkRd: (-1) MetropolisHastings.Rd:58: Escaped LaTeX specials: \&
checkRd: (-1) SubsetSimulation.Rd:152: Escaped LaTeX specials: \&
checkRd: (-1) oscillator_d6.Rd:14: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'karyoploteR'
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
Package which this enhances but not available for checking: 'AnalyzeFMRI'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
checkRd: (-1) mixmeta-package.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) mixmeta.ml.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ml.igls.Rd:62: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'mixRasch'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) RTdata2.Rd:3: Escaped LaTeX specials: \#
checkRd: (-1) boot.comp.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) boot.se.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) compCDF.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) hmeEM.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) logisregmixEM.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) multmixEM.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) mvnormalmixEM.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) normalmixEM.Rd:133: Escaped LaTeX specials: \&
checkRd: (-1) normalmixEM2comp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) poisregmixEM.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) regmixEM.Rd:67: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) qboxplot.Rd:127: Escaped LaTeX specials: \&
checkRd: (-1) qboxplot.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) qbxp.stats.Rd:66: Escaped LaTeX specials: \&
checkRd: (-1) mi.t.test.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) qboxplot.Rd:127: Escaped LaTeX specials: \&
checkRd: (-1) qboxplot.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) qbxp.stats.Rd:66: Escaped LaTeX specials: \&
checkRd: (-1) ssize.propCI.Rd:38: Escaped LaTeX specials: \&
Found the following significant warnings:
  waveform.c:31:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  waveform.c:44:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mlbench.Rcheck/00install.out' for details.
checkRd: (-1) BreastCancer.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) Ionosphere.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) Ionosphere.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) PimaIndiansDiabetes.Rd:19: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Texture.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) AutumnLab.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) gp.list.Rd:16: Escaped LaTeX specials: \#
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'minfi', 'IlluminaHumanMethylation450kmanifest'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following files/directories:
  'MM2S_Predictions_Heatmap.pdf' 'MM2S_Predictions_StackedBarplot.pdf'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./mmap.h:104:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./mmap.h:108:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./mmap.h:117:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  mmap.c:74:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  mmap.c:286:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  types.c:4:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mmap.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Flury'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'MoBPSmaps'
'LazyData' is specified without a 'data' directory
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) polypes.Rd:17: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    * efourier with default norm=TRUE now messages about how wrong it may be
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ordsampler.c:59:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:113:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:124:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:386:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:544:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:560:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:710:11: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:1102:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sampler.c:52:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sampler.c:149:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sampler.c:158:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sampler.c:729:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/monoreg.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'corpus.useR.2008.abstracts'
Found the following significant warnings:
  mpboost.cpp:88:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/MPBoost.Rcheck/00install.out' for details.
checkRd: (-1) Context.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) psyfun.boot.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) psyfun.boot.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
checkRd: (-1) genotype_data.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) phenotype_data.Rd:15: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) F.huggins.estim.Rd:199: Escaped LaTeX specials: \$ \$
checkRd: (-1) F.huggins.estim.Rd:205: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:206: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:207: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:208: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:209: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:210: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:212: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:213: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:214: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:215: Escaped LaTeX specials: \$
checkRd: (-1) lines.cjs.Rd:15: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Mapping.cpp:53:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Mapping.cpp:61:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Mapping.cpp:91:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Mapping.cpp:99:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/MSGARCH.Rcheck/00install.out' for details.
Found the following files/directories:
  'test.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'Acceleration.pdf' 'File1.pdf' 'Forecast.pdf' 'Series.pdf'
  'Velocity.pdf'
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ms_sev.Rd:31: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mkjnw.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) mkjnw.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  muhaz.c:1367:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  muhaz.c:1367:13: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a previous declaration [-Wdeprecated-non-prototype]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mudens.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) MultBiplotR-package.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) MultBiplotR-package.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) print.multcompLetters.Rd:20: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  src/core/attributes/Value.hpp:34:12: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  src/core/attributes/Value.hpp:34:17: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  src/core/attributes/Value.hpp:49:64: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  src/core/attributes/Value.hpp:49:69: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/multinet.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
'LazyData' is specified without a 'data' directory
checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'asreml'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    PREVIOUS (Incomplete below)
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 're2r'
Found the following significant warnings:
  namespace.c:4:11: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/namespace.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  pdf_debye.c:1039:162: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/nanop.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spatialClust'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 're2r'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) netCoin-package.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_ \_
checkRd: (-1) makeNetwork.Rd:31: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'fastshp'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  MMModelClass.cpp:801:25: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/NetMix.Rcheck/00install.out' for details.
checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'map.png' 'maze.html'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  RcppUtils.cpp:48:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  RcppNimbleUtils.cpp:298:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  nimDists.cpp:159:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  nimDists.cpp:189:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  nimDists.cpp:206:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  nimDists.cpp:236:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  nimDists.cpp:263:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  nimDists.cpp:315:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  nimDists.cpp:361:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  nimDists.cpp:380:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  nimbleGraph.cpp:183:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/nimble.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'jpndistrict'
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:11:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  nleqslv.c:4:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  nwout.c:49:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/nleqslv.Rcheck/00install.out' for details.
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) nltm.control.Rd:29: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
checkRd: (-1) Frobenius-nmf.Rd:141: Escaped LaTeX specials: \#
checkRd: (-1) KL-nmf.Rd:158: Escaped LaTeX specials: \#
checkRd: (-1) NMFStrategyIterative-class.Rd:69: Escaped LaTeX specials: \#
checkRd: (-1) NMFstd-class.Rd:179: Escaped LaTeX specials: \#
checkRd: (-1) nmf.Rd:755: Escaped LaTeX specials: \#
checkRd: (-1) nmf_update_KL.Rd:87: Escaped LaTeX specials: \#
checkRd: (-1) nmf_update_euclidean.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) offset-nmf.Rd:144: Escaped LaTeX specials: \#
Running examples in 'NMF-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: profplot
> ### Title: Plotting Expression Profiles
> ### Aliases: profplot profplot.default
> ### Keywords: aplot
> 
> ### ** Examples
> 
> ## Don't show: 
> # roxygen generated flag
> options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
> ## End(Don't show)
> 
> # create a random target matrix
> v <- rmatrix(35, 10)
> 
> # fit a single NMF model
> res <- nmf(v, 3)
> profplot(res)
> 
> # fit a multi-run NMF model
> res2 <- nmf(v, 3, nrun=2)
# NOTE - CRAN check detected: limiting maximum number of cores [2/32]
> # ordering according to first profile
> profplot(res2, Colv=1) # increasing
> 
> # draw a profile correlation plot: this show how the basis components are
> # returned in an unpredictable order
> profplot(res, res2)
Error in col["alpha", ] <- as.character(as.hexmode(alpha)) : 
  incorrect number of subscripts on matrix
Calls: profplot ... <Anonymous> -> .set.list.defaults -> expand_list -> alphacol
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./veclib.h:302:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/nncc.Rcheck/00install.out' for details.
Found the following significant warnings:
  geodesic.c:57:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/nngeo.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Other ideas
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulatePop.Rd:43: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:16:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/norm.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) prepareplot.Rd:64: Escaped LaTeX specials: \#
checkRd: (-1) prepareplot.Rd:68: Escaped LaTeX specials: \#
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./vadr.h:55:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./promises.h:5:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dots.c:5:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  promises.c:93:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  vadr.c:22:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/nseval.Rcheck/00install.out' for details.
checkRd: (-1) Ardechedata.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) nsRFA-package.Rd:231: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'originr', 'parallelsugar'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  gutsRedIT.c:34:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  gutsRedIT.c:58:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  gutsRedSD.c:36:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  gutsRedSD.c:64:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  odeGUTS_init.c:5:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  odeGUTS_init.c:6:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/odeGUTS.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
GNU make is a SystemRequirements.
Packages required but not available:
  'GenomicFeatures', 'TxDb.Hsapiens.UCSC.hg19.knownGene'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'openNLPmodels.en'
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'Graph_layout_Doptbd_trtE'
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
checkRd: (-1) quad_3D.Rd:22: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
Found the following files/directories:
  'Graph_layout_Doptrcd_trtE'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Forest.cpp:361:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ordinalForest.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'cluster of fitted mean data.eps' 'cluster of fitted mean data.txt'
  'cluster of raw data.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  osqp_solve_interface.cpp:200:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  osqp_solve_interface.cpp:203:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  osqp_solve_interface.cpp:206:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  osqp_solve_interface.cpp:230:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  osqp_solve_interface.cpp:238:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  osqp_solve_interface.cpp:245:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/osqp.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following files/directories:
  'result.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes
'LazyData' is specified without a 'data' directory
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
Package required but not available: 'genbankr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'CorShrink'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Imap'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
checkRd: (-1) pan.bd.Rd:65: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'co2' 'co2.1' 'co2.2' 'co2s.1' 'co2s.2' 'ctm.1' 'ctm.2' 'm' 'm.1'
  'm.2' 'test' 'test.1' 'test.2' 'testa.1' 'testa.2' 'xfile.1'
  'xfile.2'
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \# \# \#
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \#
Found the following files/directories:
  'Minimal-concordance.tex' 'Minimal.Rnw' 'Minimal.pdf'
  'Minimal.synctex.gz' 'Minimal.tex' 'figure'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) plot-methods.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) plot-methods.Rd:125: Escaped LaTeX specials: \_
checkRd: (-1) glue_search_tables.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_batch_get_item.Rd:32: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_delete_item.Rd:81: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_get_item.Rd:55: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_put_item.Rd:98: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_query.Rd:237: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_scan.Rd:174: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_update_item.Rd:177: Escaped LaTeX specials: \#
checkRd: (-1) elasticache_create_cache_cluster.Rd:291: Escaped LaTeX specials: \#
checkRd: (-1) elasticache_create_replication_group.Rd:329: Escaped LaTeX specials: \#
checkRd: (-1) cloudwatchlogs_create_log_group.Rd:30: Escaped LaTeX specials: \#
checkRd: (-1) licensemanager_create_license_configuration.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) licensemanager_create_license_configuration.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) opsworks_update_layer.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) opsworkscm_create_server.Rd:76: Escaped LaTeX specials: \#
checkRd: (-1) ssm_send_command.Rd:47: Escaped LaTeX specials: \$
checkRd: (-1) ssm_send_command.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) apigatewayv2_create_stage.Rd:34: Escaped LaTeX specials: \#
checkRd: (-1) apigatewayv2_update_stage.Rd:36: Escaped LaTeX specials: \#
checkRd: (-1) iam_update_account_password_policy.Rd:21: Escaped LaTeX specials: \#
Found the following significant warnings:
  pbatR_init.c:11:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  pbatR_init.c:17:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/pbatR.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) l1pcastar.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) pcaL1-package.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Dist.Rd:50: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  kepdf.c:29:32: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/pdfCluster.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'PythonInR'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  PeakSegJoint_interface.c:113:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/PeakSegJoint.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'crrstep'
checkRd: (-1) pec.Rd:250: Escaped LaTeX specials: \&
checkRd: (-1) pec.Rd:251: Escaped LaTeX specials: \&
checkRd: (-1) pec.Rd:256: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'georob'
GNU make is a SystemRequirements.
checkRd: (-1) breslow.Rd:27: Escaped LaTeX specials: \# \#
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) simulate.data.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) simulate.data.Rd:28: Escaped LaTeX specials: \_ \_
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) my.bspline.Rd:21: Escaped LaTeX specials: \$ \$ \$ \$ \$ \$
checkRd: (-1) my.bspline.Rd:27: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) pendensity.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:57: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:82: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:96: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:100: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:105: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:13:51: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Peptides.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) chart.ECDF.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'DMwR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dendextendRcpp'
Found the following files/directories:
  'permus_per_dist_4' 'permus_per_shape_bin_4_0'
  'permus_per_shape_bin_4_1' 'permus_per_shape_bin_4_2'
  'permus_per_shape_bin_4_3'
'LazyData' is specified without a 'data' directory
checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRD.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRDUS.Rd:4: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'animation.gif'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  ml.c:39:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/phangorn.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'test.pdf'
'LazyData' is specified without a 'data' directory
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:29: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:31: Escaped LaTeX specials: \_ \_
checkRd: (-1) maxConnectedSet.Rd:35: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:37: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:39: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:41: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:45: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:47: Escaped LaTeX specials: \_ \_
Found the following significant warnings:
  ../src/correlation.h:49:28: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ../src/correlation.h:94:27: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ../src/correlation.h:137:28: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/philentropy.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  '1khz.wav' 'snd.wav'
checkRd: (-1) phylo4d-methods.Rd:209: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GarlandJanis.IC.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.IC.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'ggsubplot'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sanitize_latex.Rd:49: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Running examples in 'pkgmaker-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alphacol
> ### Title: Colour utilities
> ### Aliases: alphacol
> 
> ### ** Examples
> 
> 
> # Alphas
> alphacol('red') # do nothing
Error in apply(col, 2, function(x) paste("#", paste(x, collapse = ""),  : 
  dim(X) must have a positive length
Calls: alphacol -> apply
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'VariantAnnotation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'VariantAnnotation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'P2Run.csv' 'P2Run.html' 'P2Run.png'
Packages suggested but not available for checking:
  'harmony', 'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) PLS_beta_wvc.Rd:5: Escaped LaTeX specials: \_
checkRd: (-1) plsRbeta.Rd:104: Escaped LaTeX specials: \^
Package suggested but not available for checking: 'plsdepot'
checkRd: (-1) PLS_glm_wvc.Rd:5: Escaped LaTeX specials: \_
checkRd: (-1) PLS_lm_wvc.Rd:5: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [12s/15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(plyr)
  > 
  > test_check("plyr")
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 761 ]
  
  == Skipped tests ===============================================================
  * On CRAN (6)
  * empty test (1)
  
  == Failed tests ================================================================
  -- Failure ('test-rbind.r:21'): variable classes are preserved -----------------
  `x` not equal to `expected`.
  Component "e": Attributes: < Names: 1 string mismatch >
  Component "e": Attributes: < Length mismatch: comparison on first 1 components >
  Component "e": Attributes: < Component 1: Modes: logical, character >
  Component "e": Attributes: < Component 1: Lengths: 1, 2 >
  Component "e": Attributes: < Component 1: target is logical, current is character >
  Backtrace:
      x
   1. \-testthat::expect_that(ab1, equals(ab2)) at test-rbind.r:21:2
   2.   \-testthat (local) condition(object)
   3.     \-testthat::expect_equal(x, expected, ..., expected.label = label)
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 761 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'pollimetrydata'
Found the following files/directories:
  'polyfreqs-mcmc.out'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'VariantAnnotation', 'GenomicFeatures'
Packages unavailable to check Rd xrefs: 'GenomicFeatures', 'VariantAnnotation'
Found the following files/directories:
  'test-data.R' 'test-inits.R' 'test.bug' 'test.cmd'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
Packages suggested but not available for checking:
  'BASIX', 'WhopGenome', 'BlockFeST'
Found the following significant warnings:
  tabix/bedidx.c:20:1: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  tabix/bgzf.c:50:1: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  tabix/bgzf.c:138:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  tabix/bam_endian.h:6:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  tabix/index.c:49:1: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  tabix/index.c:50:1: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  tabix/index.c:808:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/PopGenome.Rcheck/00install.out' for details.
checkRd: (-1) BayeScanR.Rd:7: Escaped LaTeX specials: \&
checkRd: (-1) MKT-methods.Rd:8: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'lfa'
Package suggested but not available for checking: 'RClone'
Found the following significant warnings:
  init.c:24:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  omp_test.c:7:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/poppr.Rcheck/00install.out' for details.
checkRd: (-1) genetic_distance.Rd:106: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tradelist-class.Rd:91: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:146: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:148: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:126: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:219: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:221: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:225: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:229: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:231: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:233: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:235: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:237: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:301: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:303: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:305: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:307: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:309: Escaped LaTeX specials: \&
checkRd: (-1) med_pn.Rd:129: Escaped LaTeX specials: \&
Unknown package 'advclust' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) findRes.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) ppmlasso-package.Rd:42: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  sum.c:358:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  prod.c:27:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:28:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:29:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/PreciseSums.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    CalEquation function can calculate intercept in multiple regression model with interaction
    New arguments summarymode added to fit2newdata(), predict3d() and ggPredict()
    New arguments xlab, ylab and zlab added to predict3d()
    New function gg_color_hue() and theme_bw2() added
    Bug-fixed
    New function restoreData2(), restoreData3()  added
    New function add_lines() added
    New function ggPredict() and predict3d() added
    New function fit2newdata() added
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'ffbase'
Unknown package 'ffbase' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'hista.png' 'plotcd.png' 'test.R' 'test.html' 'testR2html.R'
  'testglm.csv' 'testglm.html' 'testglm.tab'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:17:43: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:22:48: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  zhegv.c:232:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  zhegv.c:3715:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/PRIMME.Rcheck/00install.out' for details.
checkRd: (-1) prim.box.Rd:60: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:10:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  procmap.c:20:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/procmaps.Rcheck/00install.out' for details.
checkRd: (-1) prodlim.Rd:119: Escaped LaTeX specials: \&
checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'BayesianTools'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ProFit'
Found the following significant warnings:
  pause.c:10:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/profvis.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'SDMTools'
Running 'testthat.R' [28s/33s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(propr)
  > 
  > test_check("propr")
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 197 ]
  
  == Failed tests ================================================================
  -- Failure ('test-aldex2propr.R:97'): iqlr matches ALDEx2 implementation -------
  perb(marg.abs[, 1:50] + 0.5, ivar = "iqlr")@matrix not equal to perb(marg.abs[, 1:50] + 0.5, ivar = z)@matrix.
  2450/2500 mismatches (average diff: 0.0509)
  [2]   0.45221 -  0.3838 ==  0.06842
  [3]  -0.65122 - -0.7554 ==  0.10416
  [4]  -0.82028 - -0.8190 == -0.00130
  [5]   0.40911 -  0.3153 ==  0.09377
  [6]  -0.58339 - -0.6845 ==  0.10112
  [7]   0.51454 -  0.5107 ==  0.00379
  [8]  -0.57212 - -0.6929 ==  0.12082
  [9]  -0.00375 -  0.0136 == -0.01739
  [10]  0.59415 -  0.5631 ==  0.03102
  ...
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 197 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'cin'
Found the following significant warnings:
  computeParentIonMass.c:59:9: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/protViz.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'rdt'
Package suggested but not available for checking: 'rdt'
Package suggested but not available for checking: 'rdt'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rdt'
Found the following significant warnings:
  util.c:6:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/pscl.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Logistic_Model.cpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./Logistic_Model.hpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  Main_CV_PSGD.cpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./PSGD.hpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./PS_Model.hpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./Set_Diff.hpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  Main_PSGD.cpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  PSGD.cpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./Stepwise_Split.hpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./Step_Model.hpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./Model_Functions.hpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  PS_Model.cpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  Step_Model.cpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/PSGD.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) esa.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) meta_varcov.Rd:9: Escaped LaTeX specials: \&
checkRd: (-1) meta_varcov.Rd:120: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'fulltext'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'GenomicFeatures'

Package suggested but not available for checking: 'TxDb.Hsapiens.UCSC.hg19.knownGene'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Ch05-detail.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:32: Escaped LaTeX specials: \#
checkRd: (-1) Ch0C-plot.cpd.PwrGSD.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) aid_st2.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'exampleplot_1_blockdist_1.png' 'exampleplot_1_blockdist_2.png'
  'exampleplot_1_blockdist_3.png' 'exampleplot_1_bootdist.png'
  'exampleplot_1_dist.png' 'exampleplot_1_histogramtest_EMD.png'
  'exampleplot_1_roc_dynamic.png' 'exampleplot_1_slidedist_1.png'
  'exampleplot_1_slidedist_2.png' 'exampleplot_1_slidedist_3.png'
  'exampleplot_1_trimmeddist.png' 'exampleplot_blockdist_1.png'
  'exampleplot_blockdist_2.png' 'exampleplot_blockdist_3.png'
  'exampleplot_bootdist.png' 'exampleplot_dist.png'
  'exampleplot_lim_dyn.png' 'exampleplot_lim_sig.png'
  'exampleplot_lim_sta.png' 'exampleplot_noc.png'
  'exampleplot_roc_dyn.png' 'exampleplot_roc_sta.png'
  'exampleplot_slidedist_1.png' 'exampleplot_slidedist_2.png'
  'exampleplot_slidedist_3.png' 'exampleplot_trimmeddist.png'
  'myworkflow_result.xml' 'test_2_roc_dynamic.png' 'test_4_dist.png'
  'test_5_blockdist_1.png' 'test_5_blockdist_2.png'
  'test_5_blockdist_3.png' 'test_6_slidedist_1.png'
  'test_6_slidedist_2.png' 'test_6_slidedist_3.png'
  'test_7_trimmeddist.png' 'test_8_bootdist.png' 'test_emd_1d.png'
  'test_emd_2d.png' 'test_jsd_1d.png' 'test_jsd_2d.png'
  'test_kld_1d.png' 'test_kld_2d.png' 'test_ms_1d.png' 'test_ms_2d.png'
  'test_rms_1d.png' 'test_rms_2d.png'
Found the following significant warnings:
  ./lp_rlp.h:1161:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./lp_rlp.h:1293:49: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./lp_rlp.h:1401:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lp_rlp.c:569:11: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  yacc_read.c:139:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  yacc_read.c:547:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/QCA.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'EWAS_QC_graph_effectsize.png' 'EWAS_QC_graph_precision.png'
  'EWAS_QC_legend.txt' 'sample1.txt.gz' 'sample2.txt.gz'
  'sample_map.txt.gz' 'sample_output.graph_M.png'
  'sample_output.graph_QQ.png' 'sample_output.graph_p.png'
  'sample_output.graph_volcano.png' 'sample_output.histo.png'
  'sample_output.txt' 'sample_output1.graph_M.png'
  'sample_output1.graph_QQ.png' 'sample_output1.graph_p.png'
  'sample_output1.graph_volcano.png' 'sample_output1.histo.png'
  'sample_output2.graph_M.png' 'sample_output2.graph_QQ.png'
  'sample_output2.graph_p.png' 'sample_output2.graph_volcano.png'
  'sample_output2.histo.png' 'translation_table.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CentAndClusfuns.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) EBICglasso.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) pathways.Rd:36: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:9:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:10:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/qoi.Rcheck/00install.out' for details.
Found the following files/directories:
  'lambda.pdf' 'qqplot.pdf'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Quadtree.cpp:298:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/quadtree.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) GRI.Rd:3: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File 'quantmod/R/attachSymbols.R':
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section 'Good practice' in '?attach'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  glmBias.c:84:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/QuasiSeq.Rcheck/00install.out' for details.
Found the following significant warnings:
  loops.cpp:69:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/queuecomputer.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fastshp', 'visualTest'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) qwraps2.Rd:73: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ReGenesees'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File 'R2OpenBUGS/R/attach.all.R':
  attach(x, name = name)
See section 'Good practice' in '?attach'.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ../inst/include/sundials/sundials_nvector.h:163:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_nonlinearsolver.h:131:56: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_matrix.h:105:41: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_linearsolver.h:137:50: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lib/sundials/sundials_nonlinearsolver.c:26:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lib/sundials/sundials_matrix.c:29:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lib/sundials/sundials_nvector.c:28:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lib/sundials/sundials_linearsolver.c:28:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/r2sundials.Rcheck/00install.out' for details.
Found the following calls to attach():
File 'R2WinBUGS/R/attach.all.R':
  attach(x, name = name)
See section 'Good practice' in '?attach'.
Package suggested but not available for checking: 'BayesianTools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'blcs.dot' 'ex1.dot' 'ex1bridge1.dot' 'ex1bridge2.dot'
  'ex1bridge3.dot' 'ex1effect1.dot' 'ex1effect2.dot' 'gcmlinear.dot'
  'latent.dot' 'lcs.dot' 'mimic.dot'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RandomFields'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Bug Fixes
    New Features
    Major Changes
    Minor changes
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ri'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Packages suggested but not available for checking:
  'ecospat', 'googlesheets'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  RankCluster.cpp:601:17: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  test.cpp:34:17: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rankcluster.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  sketch.c:33:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sketch.c:38:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sketch.c:172:9: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sketch.c:206:6: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RaProR.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  geodesic.c:50:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/raster.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
Found the following significant warnings:
  rbm_haplos_thresholds_filling.cpp:14:19: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  rbm_haplos_thresholds_filling.cpp:14:27: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  rbm_haplos_thresholds_filling.cpp:49:34: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Ravages.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./charsets.h:22:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  bib2be.c:29:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  bibtexdirectin.c:93:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  charsets.c:34614:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rbibutils.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File 'rbmi/R/parallel.R':
  attach(getNamespace("rbmi"))
See section 'Good practice' in '?attach'.
GNU make is a SystemRequirements.
checkRd: (-1) mn4joint1condi.Rd:39: Escaped LaTeX specials: \$
checkRd: (-1) mn4joint1condi.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) objets.Rd:66: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'rcanvec.cache'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'temp.RData'
Found the following significant warnings:
  cddmp.c:23:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cddmp.c:63:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cddmp_f.c:24:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cddmp_f.c:64:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  nonred.c:99:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rcdd.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'data.csv'
Found the following significant warnings:
  RClickhouse_init.c:23:54: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  vendor/clickhouse-cpp/contrib/lz4/lz4.c:373:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  vendor/clickhouse-cpp/contrib/lz4/lz4.c:1474:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RClickhouse.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'outcmaesdisp.dat'
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) RcmdrPlugin.MA-package.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ROpenOffice'
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package suggested but not available for checking: 'conics'
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:11:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RcppEigen.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rredis'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rDEA_init.c:11:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rDEA.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  dsdp/include/dsdp5.h:206:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../../include/dsdp5.h:206:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dsdpcops.c:20:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dsdpcops.c:28:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dsdpsetoptions.c:280:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sdpalloc.c:4:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sdpexit.c:4:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dsdperror.c:129:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rdsdp.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) re2_syntax.Rd:539: Escaped LaTeX specials: \_
Package suggested but not available for checking: 'dataui'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'temp.txt' 'temp2.csv' 'temp3.rda'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  libxls/endian.c:38:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  libxls/locale.c:50:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/readxl.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  mygllm.c:11:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  mygllm.c:43:7: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  mygllm.c:52:25: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  mygllm.c:55:24: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  mygllm.c:72:62: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  mygllm.c:101:20: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  mygllm.c:108:30: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  mygllm.c:108:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  mygllm.c:115:28: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  mygllm.c:115:34: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  mygllm.c:161:30: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  mygllm.c:161:36: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RecordLinkage.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  'Filled.RData' 'cleaned.RData' 'days' 'gridded'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  redland.c:771:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  redland.c:817:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  redland.c:1846:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/redland.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'EnvironmentalA.txt' 'EnvironmentalB.txt' 'Example.txt'
  'Example_Predictions.txt' 'Example_RRDist.txt'
  'Example_RRDistCol.TIF' 'Example_RRDistGrey.TIF' 'GeneticA.txt'
  'GeneticB.txt' 'Inds.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:9:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:13:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/reglogit.Rcheck/00install.out' for details.
checkRd: (-1) pima.Rd:24: Escaped LaTeX specials: \^
checkRd: (-1) reglogit.Rd:120: Escaped LaTeX specials: \&
checkRd: (-1) reglogit.Rd:124: Escaped LaTeX specials: \&
checkRd: (-1) reglogit.Rd:136: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'MfUSampler'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) calc.relimp.Rd:41: Escaped LaTeX specials: \~
checkRd: (-1) classesmethods.relaimpo.Rd:27: Escaped LaTeX specials: \$
checkRd: (-1) classesmethods.relaimpo.Rd:104: Escaped LaTeX specials: \$
checkRd: (-1) mianalyze.relimp.Rd:69: Escaped LaTeX specials: \~
checkRd: (-1) mianalyze.relimp.Rd:73: Escaped LaTeX specials: \~
checkRd: (-1) relimplm-class.Rd:63: Escaped LaTeX specials: \$
checkRd: (-1) relimplmbootMI-class.Rd:121: Escaped LaTeX specials: \$
checkRd: (-1) relimplmbooteval-class.Rd:146: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'pbdRPC'
checkRd: (-1) ena.plot.group.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:46: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:38: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:42: Escaped LaTeX specials: \$
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'PackageCites.bib'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [20m/23m]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(reportr)
  > 
  > test_check("reportr")
  Killed
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) KitchenhamEtAl.CorrelationsAmongParticipants.Madeyski10.Rd:7: Escaped LaTeX specials: \&
checkRd: (-1) KitchenhamEtAl.CorrelationsAmongParticipants.Madeyski10.Rd:56: Escaped LaTeX specials: \&
Running 'test-all.R' [73s/105s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("reproducible")
  Loading required package: reproducible
    adding: tmp/RtmpP3tmjx/Require/ZjQzS0/XYnd2hl.tif (stored 0%)
    adding: tmp/RtmpP3tmjx/Require/ZjQzS0/0L9Yq5a.grd (stored 0%)
  Error : TopologyException: Input geom 1 is invalid: Self-intersection at 6.0905735768254896 49.981782482072084
  Error : TopologyException: Input geom 1 is invalid: Self-intersection at 6095858.7074040668 6626138.0681269821
  [ FAIL 1 | WARN 1 | SKIP 67 | PASS 430 ]
  
  == Skipped tests ===============================================================
  * No Drive token (6)
  * On CRAN (52)
  * Temporary pipe for magrittr 2.0 (1)
  * empty test (7)
  * test cloudCache inside Cache -- Not fully written test (1)
  
  == Failed tests ================================================================
  -- Failure ('test-postProcessTerra.R:120'): testing terra ----------------------
  terra::wrap(vv) not identical to terra::wrap(t11).
  Attributes: < Component "crs": 1 string mismatch >
  
  [ FAIL 1 | WARN 1 | SKIP 67 | PASS 430 ]
  Error: Test failures
  Execution halted
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'P.csv' 'correct_alpha.csv' 'correct_beta.csv' 'correct_gamma.csv'
  'correct_lambda.csv' 'correct_perm_list.csv' 'correct_psi.csv'
'LazyData' is specified without a 'data' directory
checkRd: (-1) cast.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) cast.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-df-v7.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-matrix-59.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-df-bu.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-matrix-2y.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) cast-9g.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:46: Escaped LaTeX specials: \_ \_
checkRd: (-1) clean-vars-rc.rd:13: Escaped LaTeX specials: \_
checkRd: (-1) expand-kx.rd:15: Escaped LaTeX specials: \_
checkRd: (-1) reshape-4u.rd:17: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
checkRd: (-1) Burns.Rd:28: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'evdbayes'
Found the following significant warnings:
  init.c:120:52: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/revdbayes.Rcheck/00install.out' for details.
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RevGadgets'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) boot.james.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) boot.student2.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) coljack.means.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) collognorm.mle.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) collognorm.mle.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) fipois.reg.Rd:66: Escaped LaTeX specials: \&
checkRd: (-1) halfcauchy.mle.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) halfcauchy.mle.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) jack.mean.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) lm.parboot.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) multivm.mle.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) ancova1.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) ancovas.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) boot.ttest2.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) colnormal.mle.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) colnormal.mle.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) colnormal.mle.Rd:77: Escaped LaTeX specials: \&
checkRd: (-1) colrint.regbx.Rd:58: Escaped LaTeX specials: \&
checkRd: (-1) colvarcomps.mom.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) colvarcomps.mom.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) ftest.Rd:90: Escaped LaTeX specials: \&
checkRd: (-1) ftests.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) gammamle.Rd:81: Escaped LaTeX specials: \&
checkRd: (-1) gammamle.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) gammamle.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) rint.regbx.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) rint.regs.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) twoway.anovas.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) varcomps.mom.Rd:66: Escaped LaTeX specials: \&
checkRd: (-1) varcomps.mom.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) vm.mle.Rd:60: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) CardioRiskFactors.Rd:35: Escaped LaTeX specials: \&
Found the following significant warnings:
  ./fmrandom.h:56:17: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  lp_matrix.c:2913:59: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  yacc_read.c:147:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  yacc_read.c:555:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rfmtool.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  pcg_basic.c:69:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RGBM.Rcheck/00install.out' for details.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/sp/include/sp.h:95:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./rgdal.h:28:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./rgdal.h:29:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./rgdal.h:130:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./rgdal.h:134:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./rgdal.h:135:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./rgdal.h:136:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./rgdal.h:138:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rgdal.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./IP2Loc_DBInterface.h:51:35: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./IP2Loc_DBInterface.h:55:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./IP2Location.h:186:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  IP2Loc_DBInterface.c:242:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  IP2Location.c:208:49: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  IP2Location.c:275:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  IP2Location.c:841:49: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rgeolocate.Rcheck/00install.out' for details.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/sp/include/sp.h:95:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rgeos.Rcheck/00install.out' for details.
Found the following significant warnings:
  Rglpk_read_file.c:17:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:42:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rglpk.Rcheck/00install.out' for details.
checkRd: (-1) Rglpk_read_file.Rd:6: Escaped LaTeX specials: \_
Found the following significant warnings:
  ./gl2ps.h:254:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  gl2ps.c:6479:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rgl.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) columbus.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) columbus.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) columbus.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) columbus.Rd:30: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./qoma-hli.h:23:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./qoma-hli.h:24:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./qoma-hli.h:25:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./qoma-hli.h:26:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  qoma-hli.c:29:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  qoma-hli.c:39:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  qoma-hli.c:58:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  qoma-hli.c:131:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rhli.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'mydata.rda' 'thedata.rda'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./convert.h:12:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  convert.c:79:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ring.Rcheck/00install.out' for details.
File 'RInside/libs/RInside.so':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/RInside.so':
  Found non-API calls to R: 'R_CStackLimit', 'R_CleanTempDir',
    'R_DefParams', 'R_ReplDLLdo1', 'R_ReplDLLinit',
    'R_RunExitFinalizers', 'R_SetParams', 'R_SignalHandlers',
    'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ipw'
Found the following files/directories:
  'B110711CD4.CSV' 'inputparam2.txt' 'itcout0.pdf' 'itcout1.eps'
  'origin_data.csv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./init.h:19:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./init.h:26:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./init.h:30:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rjags.Rcheck/00install.out' for details.
Non-standard file/directory found at top level:
  'jri'
Found the following possibly unsafe calls:
File 'rJava/R/import.R':
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File 'rJava/R/jinit.R':
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rJava/libs/rJava.so':
  Found '_exit', possibly from '_exit' (C)
  Found 'stderr', possibly from 'stderr' (C)
  Found 'stdout', possibly from 'stdout' (C)
File 'rJava/libs/rJava.so':
  Found non-API calls to R: 'R_CStackLimit', 'R_CStackStart'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rlibjson.c:364:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RJSONIO.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
Found the following significant warnings:
  RemoteSensing.cpp:79:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  RemoteSensing.cpp:82:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rlda.Rcheck/00install.out' for details.
Found the following significant warnings:
  RngWrap.c:12:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  RngWrap.c:23:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  RngWrap.c:304:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  RngWrap.c:328:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  zzz.c:11:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  zzz.c:13:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  zzz.c:17:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rlecuyer.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Previous version rmangal
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'blockcluster'
Package suggested but not available for checking: 'blockcluster'
Found the following calls to attach():
File 'Rmosek/R/builder.R':
  attach(builderenv, pos, name, warn.conflicts)
See section 'Good practice' in '?attach'.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
Package required but not available: 'ensembldb'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rnaturalearthhires'
Malformed Title field: should not end in a period.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
Found the following significant warnings:
  ./RNetCDF.h:149:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  udunits.c:385:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RNetCDF.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) addLR.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) addLRinv.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) adtestWrapper.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) arcticLake.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cenLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) cenLRinv.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) expenditures.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) gemas.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) machineOperators.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) plot.imp.Rd:138: Escaped LaTeX specials: \&
checkRd: (-1) robCompositions-package.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) skyeLavas.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) variation.Rd:45: Escaped LaTeX specials: \&
Unknown package 'StatDA' in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./RMquick.h:32:5: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./RMquick.h:42:29: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./RMquick.h:52:26: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./RMquick.h:53:20: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./RMquick.h:130:61: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./RMquick.h:188:32: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./Line.h:15:51: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./Line.h:15:61: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./Edge.h:105:51: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./segment_tree.h:176:25: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./segment_tree.h:177:54: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./segment_tree.h:179:32: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./segment_tree.h:180:36: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./segment_tree.h:181:36: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/robfilter.Rcheck/00install.out' for details.
checkRd: (-1) hybrid.filter.Rd:159: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'beadarrayExampleData'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  monitor.c:15:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/robustbase.Rcheck/00install.out' for details.
checkRd: (-1) aircraft.Rd:8: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  graph_geodesic.c:9:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rnr/common.h:84:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rnr/common.h:85:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rnr/BitVector.h:57:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rnr/BitVector.h:58:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rnr/BitVector.c:36:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rnr/BitVector.c:46:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rnr/common.c:33:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rnr/common.c:110:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rnr/common.c:133:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rogue.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  /tmp/Rtmp00ntku/R.INSTALLcb1a93cd22f3c/rolog/src/swipl-devel/src/os/pl-os.c:2159:26: warning: the comparison will always evaluate as 'true' for the address of 'S__iob' will never be NULL [-Waddress]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rolog.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  vMF.cpp:35:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rotasym.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RandomFields'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following files/directories:
  'Rpdb.pdb'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    IMPROVEMENTS AND ### BUG FIXES
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'HL_H0.pdf' 'pi0infer.pdf' 'rate.txt' 'summary.txt'
Found the following significant warnings:
  Rrdrand.c:107:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rrdrand.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'test.bpl' 'test.cr' 'test.ct'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gdalUtils'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./Stopwatch.h:13:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  Stopwatch.c:4:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rscimark.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  cli.c:172:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cli.c:211:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cli.c:1152:19: warning: 'RSA_size' is deprecated [-Wdeprecated-declarations]
  cli.c:1152:42: warning: 'RSA_size' is deprecated [-Wdeprecated-declarations]
  cli.c:1153:11: warning: 'RSA_public_encrypt' is deprecated [-Wdeprecated-declarations]
  cli.c:1194:11: warning: 'd2i_RSAPublicKey' is deprecated [-Wdeprecated-declarations]
  dummy.c:5:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dummy.c:6:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dummy.c:8:11: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RSclient.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: information on .o files is not available
File '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rserve/libs/Rserve.so':
  Found 'exit', possibly from 'exit' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'random', possibly from 'random' (C)
  Found 'srandom', possibly from 'srandom' (C)
  Found 'stderr', possibly from 'stderr' (C)
File 'Rserve/libs/Rserve.so':
  Found non-API calls to R: 'R_Consolefile', 'R_InputHandlers',
    'R_Outputfile', 'R_TempDir', 'R_Visible', 'addInputHandler',
    'ptr_R_Busy', 'ptr_R_ClearerrConsole', 'ptr_R_FlushConsole',
    'ptr_R_ReadConsole', 'ptr_R_ResetConsole', 'ptr_R_ShowMessage',
    'ptr_R_WriteConsole', 'ptr_R_WriteConsoleEx'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Vdgraph'
Unknown package 'Vdgraph' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  miniz.c:2200:41: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  miniz.c:2941:45: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RstoxData.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./rsyslog.h:15:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rsyslog.c:50:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rsyslog.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'test_addPageBreak.doc' 'test_addPlot.doc' 'test_addSessionInfo.doc'
  'test_addTable.doc'
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'Gviz'
Found the following significant warnings:
  line_AABB_rcpp.cpp:59:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  line_AABB_rcpp.cpp:60:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  line_AABB_rcpp.cpp:61:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  line_AABB_rcpp.cpp:70:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  line_AABB_rcpp.cpp:71:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  line_AABB_rcpp.cpp:72:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rTLS.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running 'testthat.R' [4s/5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rtry)
  > 
  > test_check("rtry")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 92 ]
  
  == Failed tests ================================================================
  -- Error ('test-geocoding.R:10'): basic test -----------------------------------
  Error in `rtry_geocoding(input_address, "john.doe@example.com")`: object 'geocode' not found
  Backtrace:
      x
   1. \-rtry::rtry_geocoding(input_address, "john.doe@example.com") at test-geocoding.R:10:2
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 92 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'cmdstanr'
Unknown package 'cmdstanr' in Rd xrefs
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
Found the following files/directories:
  'Tsttwalk.dat'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
Found the following files/directories:
  'results'
checkRd: (-1) run.jags.study.Rd:67: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:60:47: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rust.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'glmmADMB'
Package required but not available: 'GSVAdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gpuR'
Problems with news in 'NEWS.md':
No news entries found.
Found the following significant warnings:
  haversine_dbox.cpp:45:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  haversine_dbox.cpp:50:14: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  haversine_dbox.cpp:113:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  haversine_dbox.cpp:118:14: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rvoterdistance.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mapBubbles.Rd:62: Escaped LaTeX specials: \$
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) butterfat.df.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) butterfat.df.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) fire.df.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) fruitfly.df.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) fruitfly.df.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) house.df.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) house.df.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) incomes.df.Rd:8: Escaped LaTeX specials: \$
checkRd: (-1) skulls.df.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) skulls.df.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) technitron.df.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) zoo.df.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./Gen_fun.h:17:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  Gen_fun.c:121:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./IFscratch.h:64:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  load_IFscratch.c:64:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  load_env.c:162:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/samon.Rcheck/00install.out' for details.
Found the following significant warnings:
  ./init.h:28:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./init.h:29:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SamplerCompare.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
Package suggested but not available for checking: 'networkTomography'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'FitARMA'
checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Malformed Title field: should not end in a period.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./error.h:33:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/scclust.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SingleCellSignalR'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ssvd'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  metrics.cpp:105:13: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  metrics.cpp:124:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/scPOP.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'infercnv'
Package unavailable to check Rd xrefs: 'infercnv'
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'untitled_consensus_cluster'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  linsys/cpu/direct/private.c:4:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/scs.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'glmGamPoi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'MC p-value.ps' 'Output.csv' 'Rh.ps' 'Th.ps' 'dataratio .Rdata'
  'featuresRmax.csv' 'featuresT.csv'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'xbioc', 'MuSiC', 'seAMLessData'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'effect-of-climate-dependent-flux.Rmd' using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Don't know how to automatically pick scale for object of type ts. Defaulting to continuous.
Killed
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spgrass6'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ../inst/include/selectRegGen.hpp:4:47: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SelvarMix.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sobol_indices.Rd:119: Escaped LaTeX specials: \&
checkRd: (-1) fahst.rd:39: Escaped LaTeX specials: \^
checkRd: (-1) fahst.rd:36: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:46: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:42: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:43: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:49: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:44: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:45: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:46: Escaped LaTeX specials: \^
checkRd: (-1) hsortplot.rd:24: Escaped LaTeX specials: \^
checkRd: (-1) nappesortplot.Rd:30: Escaped LaTeX specials: \^
checkRd: (-1) nappesortplot.Rd:28: Escaped LaTeX specials: \^
checkRd: (-1) plot.fahst.rd:45: Escaped LaTeX specials: \^
checkRd: (-1) plot.fasnt.Rd:47: Escaped LaTeX specials: \^
checkRd: (-1) plot.fast.Rd:45: Escaped LaTeX specials: \^
checkRd: (-1) print.fahst.rd:22: Escaped LaTeX specials: \^
checkRd: (-1) print.fasnt.Rd:22: Escaped LaTeX specials: \^
checkRd: (-1) print.fast.Rd:22: Escaped LaTeX specials: \^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'assocpointpair_result.csv' 'foundereffectfinder_result.csv'
  'getfreqs_result.csv' 'getfreqs_result.png' 'orPlot.pdf1_1.pdf'
  'orPlot.pdf2_1.pdf' 'orPlot.pdf3_1.pdf' 'orPlot.pdf4_1.pdf'
  'orPlot.pdf5_1.pdf' 'orPlot.pdf6_1.pdf' 'orPlot.pdf7_1.pdf'
  'orPlot.pdf8_1.pdf' 'q-values_result.csv' 'rewritetuple_result.csv'
  'tartan_plot.pdf' 'vispair_plot.pdf' 'vispairfeat_plot.pdf'
  'volcano_plot.pdf'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  util.c:42:20: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  util.c:42:36: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  util.c:42:49: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/seqinr.Rcheck/00install.out' for details.
checkRd: (-1) aaindex.Rd:525: Escaped LaTeX specials: \_
checkRd: (-1) aaindex.Rd:526: Escaped LaTeX specials: \_
checkRd: (-1) acnucopen.Rd:38: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_
checkRd: (-1) acnucopen.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) read.alignment.Rd:47: Escaped LaTeX specials: \_ \_
checkRd: (-1) read.alignment.Rd:48: Escaped LaTeX specials: \_ \_
Found the following significant warnings:
  ./bcf.h:173:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./bam_endian.h:6:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  bcfutils.c:11:1: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  bcfutils.c:38:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  bedidx.c:23:1: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  bgzf.c:107:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  tabix_index.c:19:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  tabix_index.c:48:1: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  tabix_index.c:49:1: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  tabix_index.c:789:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/seqminer.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  proj_conf_test.c:5:9: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/sf.Rcheck/00install.out' for details.
checkRd: (-1) TA.plot.Rd:32: Escaped LaTeX specials: \~
checkRd: (-1) diagDA.Rd:51: Escaped LaTeX specials: \#
checkRd: (-1) hatMat.Rd:35: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) gPLS.Rd:72: Escaped LaTeX specials: \^
checkRd: (-1) gPLS.Rd:74: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:67: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:69: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:75: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:77: Escaped LaTeX specials: \^
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Other ideas
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hydromad'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  '.shiny_run' 'shinyShortcut.desktop'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./cairodev.h:86:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cairodev.c:11:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./outline.h:64:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./util.h:44:39: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./util.h:47:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  outline.c:169:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  register_routines.c:8:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  showtext.c:111:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  util.c:43:39: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  util.c:53:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/showtext.Rcheck/00install.out' for details.
Found the following significant warnings:
  do_shrinkDSM.cpp:361:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  do_shrinkDSM.cpp:366:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  do_shrinkDSM.cpp:371:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  do_shrinkDSM.cpp:376:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  do_shrinkDSM.cpp:702:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  do_shrinkDSM.cpp:706:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  do_shrinkDSM.cpp:710:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  do_shrinkDSM.cpp:714:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/shrinkDSM.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'MM.csv' 'Simul.csv' 'catalytic.csv'
Package suggested but not available for checking: 'biovizBase'
Package unavailable to check Rd xrefs: 'biovizBase'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following files/directories:
  'ExportFigtree1.tre'
checkRd: (-1) chol_s2Dp.Rd:147: Escaped LaTeX specials: \&
checkRd: (-1) chol_s2Dp.Rd:149: Escaped LaTeX specials: \&
checkRd: (-1) precision_builder.Rd:87: Escaped LaTeX specials: \&
checkRd: (-1) sim2D_RandSet_HPPP.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) sim2D_binarymap.Rd:157: Escaped LaTeX specials: \&
checkRd: (-1) sim_MVN_X.Rd:140: Escaped LaTeX specials: \&
checkRd: (-1) sim_Y_Binary_X.Rd:221: Escaped LaTeX specials: \&
checkRd: (-1) sim_Y_Binary_X.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) sim_Y_MVN_X.Rd:213: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'database.csv' 'output.csv' 'output_clst.csv'
GNU make is a SystemRequirements.
Found the following files/directories:
  'res_mutation.tsv' 'res_mutationCounts.txt'
  'res_processContribution.txt' 'res_processes.txt'
Package required but not available: 'qpgraph'

Packages suggested but not available for checking: 'clipper', 'topologyGSA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'simu.pheno' 'usedpars.txt'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'SimRAD-exampleRefSeq-Fasta.fa' 'SimRAD-exampleRefSeq.fa'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'kmndirs'
Unavailable namespace imported from by a ':::' call: 'kmndirs'
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ex0723.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ex0915.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) ex1515.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) roadwear.Rd:26: Escaped LaTeX specials: \&
Found the following significant warnings:
  init.c:69:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:72:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  slider-vctrs-private.c:12:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  slider-vctrs-public.c:3:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./summary-core.h:9:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./summary-core.h:10:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/slider.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rPython'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) hoods2dsmooth.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dmeitsjer.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dsmooth.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) smoothie-package.Rd:42: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following files/directories:
  'my_new_social_media_plot.png'
Unknown package 'andrews' in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  SnowballC_init.c:7:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  stem.c:59:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SnowballC.Rcheck/00install.out' for details.
Packages required but not available:
  'VariantAnnotation', 'TxDb.Hsapiens.UCSC.hg19.knownGene'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'MfUSampler'
Found the following calls to attach():
File 'SOAR/R/SOAR.R':
  attach(NULL, pos, basename(directory))
See section 'Good practice' in '?attach'.
Found the following files/directories:
  '.R_Test'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  SoDA_init.c:5:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  crc32.c:161:23: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  crc32.c:204:21: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  crc32.c:244:21: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  digest_C.c:180:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SoDA.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.som.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) som.Rd:128: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SciencesPo'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'NLMR'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package 'sparsebn' in Rd xrefs
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RandomFields'
checkRd: (-1) grid2latlong.Rd:22: Escaped LaTeX specials: \$
checkRd: (-1) latlong2grid.Rd:22: Escaped LaTeX specials: \$
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Found the following significant warnings:
  ./KWD_Histogram2D.h:2542:47: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./KWD_Histogram2D.h:2652:47: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./KWD_Histogram2D.h:2986:48: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./KWD_Histogram2D.h:3104:48: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SpatialKWD.Rcheck/00install.out' for details.
checkRd: (-1) sarorderedprobit.Rd:84: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RandomFields'
Unknown package 'RandomFields' in Rd xrefs
Running examples in 'spatstat.core-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Emark
> ### Title: Diagnostics for random marking
> ### Aliases: Emark Vmark
> ### Keywords: spatial nonparametric
> 
> ### ** Examples
> 
>     plot(Emark(spruces))
>     E <- Emark(spruces, method="density", kernel="epanechnikov")
>     plot(Vmark(spruces))
> 
>     plot(Emark(finpines))
Loading required namespace: spatstat.explore
Failed with error:  'there is no package called 'spatstat.explore''
Error: Package 'spatstat.explore' is required for plotting objects of class 'fv'
Execution halted
Packages suggested but not available for checking:
  'spatstat.explore', 'spatstat.model'
Package unavailable to check Rd xrefs: 'spatstat.model'
Packages suggested but not available for checking:
  'spatstat.explore', 'spatstat.model'
Package unavailable to check Rd xrefs: 'spatstat.model'
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.core',
  'spatstat.linnet', 'spatstat.data', 'spatstat', 'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  netbase.c:17:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spatstat.Knet.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages suggested but not available for checking:
  'RandomFields', 'spatstat.explore', 'spatstat.model'
Packages unavailable to check Rd xrefs: 'spatstat.model', 'RandomFields'
Error(s) in re-building vignettes:
  ...
--- re-building 'bugfixes.Rnw' using Sweave
Loading required package: spatstat.data
Loading required package: spatstat.geom
spatstat.geom 3.0-3
Loading required package: spatstat.random
spatstat.random 3.0-1
Loading required package: spatstat.core
Loading required package: nlme
Loading required package: rpart
spatstat.core 2.4-4
Loading required package: spatstat.linnet
spatstat.linnet 2.3-2

spatstat 2.3-4       (nickname: 'Watch this space') 
For an introduction to spatstat, type 'beginner' 

--- finished re-building 'bugfixes.Rnw'

--- re-building 'datasets.Rnw' using Sweave
--- finished re-building 'datasets.Rnw'

--- re-building 'getstart.Rnw' using Sweave
--- finished re-building 'getstart.Rnw'

--- re-building 'replicated.Rnw' using Sweave
Loading required namespace: spatstat.explore
Failed with error:  'there is no package called 'spatstat.explore''

Error: processing vignette 'replicated.Rnw' failed with diagnostics:
 chunk 31 
Error : Package 'spatstat.explore' is required for plotting objects of class 'fv'

--- failed re-building 'replicated.Rnw'

--- re-building 'shapefiles.Rnw' using Sweave
--- finished re-building 'shapefiles.Rnw'

--- re-building 'updates.Rnw' using Sweave
--- finished re-building 'updates.Rnw'

SUMMARY: processing the following file failed:
  'replicated.Rnw'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'spatstat.model'
Package unavailable to check Rd xrefs: 'spatstat.model'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spDataLarge'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  '.neig'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following files/directories:
  'AlphaGA_3.txt' 'AlphaML_3.txt' 'BetaGA_3.txt' 'BetaML_3.txt'
  'Performance_GA_ML_ 3 .pdf' 'SPIGA_3Pmon.Pm_St1.pdf'
  'SPIGA_3Pmon.Pm_St2.pdf' 'SPI_AG_3.txt' 'SPI_ML_3.txt'
  'SPI_ML_3Pm_St1.pdf' 'SPI_ML_3Pm_St2.pdf' 'SPI_ML_3Pm_St3.pdf'
  'SPI_ML_3Pm_St4.pdf' 'SPI_PARAM_3.txt' 'SPI_PARAM_3Pm_St1.pdf'
  'SPI_PARAM_3Pm_St2.pdf' 'SPI_PARAM_3Pm_St3.pdf'
  'SPI_PARAM_3Pm_St4.pdf'
checkRd: (-1) PimaIndiansDiabetes_long.Rd:14: Escaped LaTeX specials: \^
checkRd: (-1) PimaIndiansDiabetes_wide.Rd:16: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  CV_Split_WEN.cpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./CV_WEN.hpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./WEN.hpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./CV_Split_WEN.hpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./Split_WEN.hpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  CV_Split_WEN_Main.cpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  CV_WEN.cpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  Split_WEN.cpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  Split_WEN_Main.cpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  WEN.cpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SplitGLM.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Feature Changes
Found the following significant warnings:
  timeObj.c:34:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  timeObj.c:63:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  zoneObj.c:29:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  zoneObj.c:52:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/splusTimeDate.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./spMC.h:44:11: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  spMC.c:303:11: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spMC.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./maqmap.h:62:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  maqmap.c:15:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spp.Rcheck/00install.out' for details.
Found the following significant warnings:
  ./sp.h:95:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/sp.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Found the following significant warnings:
  update_t.cpp:14:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spruce.Rcheck/00install.out' for details.
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  ./mathematics.h:10:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./mathematics.h:11:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./mathematics.h:11:8: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype]
  ./mathematics.h:10:8: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spTDyn.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) B_sraAutoreg.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) C_sraMechanistic.Rd:68: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Snacks.Rd:6: Escaped LaTeX specials: \~
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major changes
    Bug fixes
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) katrina.Rd:36: Escaped LaTeX specials: \&
Found the following significant warnings:
  include/misc/adaptiveRadixTree.h:54:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  misc_adaptiveRadixTree.c:195:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/stan4bart.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    To do
Package suggested but not available for checking: 'starsdata'
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'testmat.sdml' 'testmat2.sdml'
Package suggested but not available for checking: 'asreml'
Package suggested but not available for checking: 'asreml'
Package suggested but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following possibly unsafe calls:
File 'statnet.common/R/control.utilities.R':
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: 'networksis'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'INLA'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  CV_WEN.cpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./WEN.hpp:8:13: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./CV_WEN.hpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  Model.cpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./Model.hpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  WEN.cpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  stepSplitReg_Main.cpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./Model_Functions.hpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./Set_Diff.hpp:8:14: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/stepSplitReg.Rcheck/00install.out' for details.
Running 'testthat.R' [73s/92s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(stevedore)
  > 
  > test_check("stevedore")
  [ FAIL 1 | WARN 0 | SKIP 162 | PASS 3273 ]
  
  == Skipped tests ===============================================================
  * On CRAN (20)
  * df containers output looks broken to me (1)
  * docker using tests not enabled (STEVEDORE_TEST_USE_DOCKER) (125)
  * does not work in covr (1)
  * events this needs some streaming support (1)
  * httppipe cannot be loaded (1)
  * httppipe needs update for new python/reticulate (8)
  * might also work? (1)
  * not yet tested (2)
  * wip (1)
  * work in progress (1)
  
  == Failed tests ================================================================
  -- Failure ('test-util.R:490'): parse_timestamp --------------------------------
  `t` not identical to `cmp`.
  Objects equal but not identical
  
  [ FAIL 1 | WARN 0 | SKIP 162 | PASS 3273 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'corrviz.html'
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial TODO
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'myNewStrat.R'
Package suggested but not available for checking: 'StrathE2E2examples'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'STRaitRazoR'
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./rk_sobol.h:108:11: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./rk_sobol.h:109:51: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  rk_mt.c:118:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rk_sobol.c:486:48: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/subrank.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Found the following significant warnings:
  ../inst/include/sundials/sundials_nvector.h:163:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_nonlinearsolver.h:131:56: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_matrix.h:106:41: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_linearsolver.h:137:50: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sundials/sundials/sundials_linearsolver.c:28:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sundials/sundials/sundials_matrix.c:29:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sundials/sundials/sundials_nonlinearsolver.c:26:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sundials/sundials/sundials_nvector.c:28:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/sundialr.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'extraTrees'
Unknown package 'extraTrees' in Rd xrefs
Package suggested but not available for checking: 'extraTrees'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Found the following significant warnings:
  surveillance.c:5:24: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/surveillance.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) estweights.Rd:42: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'gurobi'
Package suggested but not available for checking: 'INLA'
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'distr6'
Unknown package 'distr6' in Rd xrefs
Found the following significant warnings:
  survivalROC.c:16:7: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/survivalROC.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ChangesInVolatility.cpp:47:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/svars.Rcheck/00install.out' for details.
DNF: multiple local function definitions for 'mu_x' with different
  formal arguments
DNF: multiple local function definitions for 'mu_y' with different
  formal arguments
DNF: multiple local function definitions for 'sigma_x' with different
  formal arguments
DNF: multiple local function definitions for 'sigma_y' with different
  formal arguments
DNFOptim : MLE_f: multiple local function definitions for 'mu_x' with
  different formal arguments
DNFOptim : MLE_f: multiple local function definitions for 'mu_y' with
  different formal arguments
DNFOptim : MLE_f: multiple local function definitions for 'sigma_x'
  with different formal arguments
DNFOptim : MLE_f: multiple local function definitions for 'sigma_y'
  with different formal arguments
modelSim: multiple local function definitions for 'mu_x' with different
  formal arguments
modelSim: multiple local function definitions for 'mu_y' with different
  formal arguments
modelSim: multiple local function definitions for 'sigma_x' with
  different formal arguments
modelSim: multiple local function definitions for 'sigma_y' with
  different formal arguments
'LazyData' is specified without a 'data' directory
checkRd: (-1) diabetes.Rd:18: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'swephRdata'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    CRAN release
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cplexAPI'
Packages suggested but not available for checking: 'cplexAPI', 'clpAPI'
Found the following math rendering problems:
optObj-class.Rd:240: Undefined control sequence: \boldmath in \mbox{\boldmath$Sv$\unboldmath...
robAna.Rd:53-67: Undefined control sequence: \boldmath in ...       & \mbox{\boldmath$c$\unboldmath}...
setRhsZero-methods.Rd:18: Undefined control sequence: \boldmath in \mbox{\boldmath$Sv$\unboldmath...
sysBiolAlg_fba-class.Rd:114-126: Undefined control sequence: \boldmath in ...       & \mbox{\boldmath$c$\unboldmath}...
sysBiolAlg_fba-class.Rd:132-135: Undefined control sequence: \boldmath in 
        \mbox{\boldmath$c$\unboldmath}...
sysBiolAlg_fbaEasyConstraint-class.Rd:93-105: Undefined control sequence: \boldmath in ...       & \mbox{\boldmath$c$\unboldmath}...
sysBiolAlg_fbaEasyConstraint-class.Rd:111-114: Undefined control sequence: \boldmath in 
        \mbox{\boldmath$c$\unboldmath}...
sysBiolAlg_fv-class.Rd:139-152: Undefined control sequence: \boldmath in ...       & \mbox{\boldmath$Sv$\unboldmath...
sysBiolAlg_lmoma-class.Rd:145-165: No such environment: minipage in ...       & \begin{minipage}[b]{5em}
        ...
sysBiolAlg_lmoma-class.Rd:167-169: Undefined control sequence: \boldmath in 
      \mbox{\boldmath$v$\unboldmath}...
sysBiolAlg_lmoma-class.Rd:177-205: No such environment: minipage in ...       & \begin{minipage}[b]{5em}
        ...
sysBiolAlg_moma-class.Rd:131-148: No such environment: minipage in ...       & \begin{minipage}[b]{5em}
        ...
sysBiolAlg_moma-class.Rd:155-157: Undefined control sequence: \boldmath in 
      \mbox{\boldmath$v$\unboldmath}...
sysBiolAlg_mtf-class.Rd:160-179: No such environment: minipage in ...      &  \begin{minipage}[b]{2.5em}
      ...
sysBiolAlg_mtf-class.Rd:181-184: Undefined control sequence: \boldmath in 
        \mbox{\boldmath$c$\unboldmath}...
sysBiolAlg_room-class.Rd:157-177: No such environment: minipage in ...       & \begin{minipage}[b]{5em}
        ...
Found the following significant warnings:
  sylcount_native.c:11:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sylcount_nthreads.c:9:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sylcount_nthreads.c:31:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/sylcount.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
checkRd: (-1) HINoV.SDA.rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  SymTS.c:22:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  SymTS.c:28:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SymTS.Rcheck/00install.out' for details.
Found the following significant warnings:
  syncrng.c:192:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  syncrng.c:231:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  syncrng.c:236:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  syncrng.c:241:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SyncRNG.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'test.csv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  '.xls' 'attenu.xls' 'chick1.xls' 'chick2.xls' 'generic1.xls'
  'hands.xls' 'table1.xls'
'LazyData' is specified without a 'data' directory
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: multiple methods tables found for 'bootstrap'
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tabula.Rcheck/00install.out' for details.
Missing link or links in documentation object 'reexports.Rd':
  '[arkhe:remove]{remove_empty}' '[arkhe:remove]{remove_NA}'
  '[arkhe:remove]{remove_zero}' '[arkhe:replace]{replace_NA}'
  '[arkhe:replace]{replace_zero}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following significant warnings:

  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Error(s) in re-building vignettes:
  ...
--- re-building 'bibliography.Rmd' using rmarkdown
--- finished re-building 'bibliography.Rmd'

--- re-building 'diversity.Rmd' using rmarkdown
Quitting from lines 355-358 (diversity.Rmd) 
Error: processing vignette 'diversity.Rmd' failed with diagnostics:
Continuous value supplied to discrete scale
--- failed re-building 'diversity.Rmd'

SUMMARY: processing the following file failed:
  'diversity.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tashudata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'R2wd'
checkRd: (-1) R2txt.Rd:164: Escaped LaTeX specials: \#
checkRd: (-1) bct.Rd:18: Escaped LaTeX specials: \^
checkRd: (-1) bct.Rd:19: Escaped LaTeX specials: \^
checkRd: (-1) ineq.Rd:10: Escaped LaTeX specials: \&
checkRd: (-1) put.points.demo.Rd:39: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:10: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:31: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_state.h:33:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:380:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:381:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:382:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_wtstate.h:32:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:585:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:586:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ergm/include/ergm_stubs.c:587:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tergm.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  proj_conf_test.c:5:9: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/terra.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'bootstrap'
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tesselle.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Problems with news in 'inst/NEWS.Rd':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Unknown package 'textreadr' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./thor.h:18:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./thor.h:21:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./thor.h:23:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./thor.h:106:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  thor.c:9:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  thor.c:23:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  thor.c:35:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  thor.c:748:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/thor.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3dimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor changes:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  common.c:36:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tiff.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ntr.c:65:8: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  ntr.c:91:8: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  ntr.c:113:8: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
  ntr.c:164:8: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TIMP.Rcheck/00install.out' for details.
checkRd: (-1) dat-class.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) dat-class.Rd:48: Escaped LaTeX specials: \_
checkRd: (-1) dat-class.Rd:49: Escaped LaTeX specials: \_
checkRd: (-1) dat-class.Rd:50: Escaped LaTeX specials: \_
Found the following files/directories:
  '_paramEst.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found an obsolete/platform-specific call in the following function:
  '.my.tkdev'
Found the platform-specific device:
  'X11'
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  external_metis.c:102:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:17:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TMB.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'lasso2', 'corpus.JSS.papers'
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Package required but not available: 'qpgraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'toscaData'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'p3state.msm'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Enhancements
    Other changes
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'taxidata'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:15:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TraMineR.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'TreeDistData'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Bug fixes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) ltriangle.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) triangle.Rd:70: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sepIdGaps.Rd:18: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Updates for the development version (0.1.0.9000) on Github
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  libqhull/geom2.c:1950:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TukeyRegion.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) lindner.Rd:44: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'sl3'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
No news entries found.
Found the following significant warnings:
  simz.cpp:31:14: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ubms.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  interface.c:114:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ucminf.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'VariantAnnotation'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ursa.c:3714:9: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ursa.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'USAboundariesData'
Package suggested but not available for checking: 'USA.state.boundaries.data'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) arctic.oscillations.Rd:19: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) arctic.oscillations.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) babies.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:43: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) exec.pay.Rd:5: Escaped LaTeX specials: \$
checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) sp500.excess.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ensembldb', 'GenomicFeatures'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  rand.c:90:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rand.c:92:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rand.c:103:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rand.c:138:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/uuid.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'PredValidationPlots.pdf' 'RepStructValidationPlots.pdf'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) irf.Rd:111: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glass.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) Glass.Rd:22: Escaped LaTeX specials: \&
checkRd: (-1) Glass.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) Glass.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) Glass.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) Glass.Rd:28: Escaped LaTeX specials: \&
Found the following HTML validation problems:
RequestHandlerCrul.html:50:6 (RequestHandlerCrul.Rd:78): Warning: missing </span> before <p>
RequestHandlerCrul.html:50:92 (RequestHandlerCrul.Rd:78): Warning: inserting implicit <span>
RequestHandlerCrul.html:53:6 (RequestHandlerCrul.Rd:79): Warning: missing </span> before <p>
RequestHandlerCrul.html:53:96 (RequestHandlerCrul.Rd:79): Warning: inserting implicit <span>
RequestHandlerHttr.html:53:6 (RequestHandlerHttr.Rd:55): Warning: missing </span> before <p>
RequestHandlerHttr.html:53:92 (RequestHandlerHttr.Rd:55): Warning: inserting implicit <span>
lightswitch.html:113:79 (lightswitch.Rd:67): Warning: inserting implicit <p>
lightswitch.html:150:58 (lightswitch.Rd:102): Warning: inserting implicit <p>
lightswitch.html:181:33 (lightswitch.Rd:131): Warning: inserting implicit <p>
lightswitch.html:202:42 (lightswitch.Rd:150): Warning: inserting implicit <p>
request-matching.html:83:57 (request-matching.Rd:49): Warning: inserting implicit <p>
Running 'testthat.R' [133s/149s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(vctrs)
  > 
  > test_check("vctrs")
  [ FAIL 2 | WARN 0 | SKIP 256 | PASS 5057 ]
  
  == Skipped tests ===============================================================
  * Can't profile memory on this system. (2)
  * FIXME: dimnames of matrices are not properly concatenated (1)
  * Factors now have a `c()` method (1)
  * Not testing performance (2)
  * On CRAN (246)
  * data.table cannot be loaded (3)
  * sf cannot be loaded (1)
  
  == Failed tests ================================================================
  -- Failure ('test-slice-assign.R:536'): can optionally assign names ------------
  `actual` (vec_assign_params(oo_x, 2, oo_y, assign_names = TRUE)) not identical to `expected` (`oo_out`).
  
  `attr(actual, 'balanced')`:   <NA>
  `attr(expected, 'balanced')`: TRUE
  Backtrace:
      x
   1. \-vctrs:::expect_identical(...) at test-slice-assign.R:536:2
   2.   \-vctrs:::expect_waldo_equal("identical", act, exp, info, ...) at tests/testthat/helper-vctrs.R:43:2
  -- Failure ('test-slice-assign.R:561'): can optionally assign names ------------
  `actual` (vec_assign_params(nested_x, 2, nested_y, assign_names = TRUE)) not identical to `expected` (`nested_out`).
  
  `attr(actual$oo, 'balanced')`:   <NA>
  `attr(expected$oo, 'balanced')`: TRUE
  Backtrace:
      x
   1. \-vctrs:::expect_identical(...) at test-slice-assign.R:561:2
   2.   \-vctrs:::expect_waldo_equal("identical", act, exp, info, ...) at tests/testthat/helper-vctrs.R:43:2
  
  [ FAIL 2 | WARN 0 | SKIP 256 | PASS 5057 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  computeCox.c:15:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/vdra.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  vliC.cpp:539:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/VeryLargeIntegers.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex125.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'gs+qpdf' made some significant size reductions:
     compacted 'How_to_work_with_package_VFP.pdf' from 383Kb to 131Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
checkRd: (-1) huse.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) checkTS.VGAMextra.Rd:176: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    NEW FEATURES
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    NEWS UPDATES:
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
Package required but not available: 'ecospat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'ReconstructedData.txt' 'ReconstructedDataStDev.txt'
  'ResampledReconstructions.txt'
  'ResampledReconstructionsStandardVariation.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:20:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/wdnet.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'prepr'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:11:39: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/WeightedCluster.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'ATE'
Unknown package 'ATE' in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  corFunctions.c:59:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  networkFunctions.c:182:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/WGCNA.Rcheck/00install.out' for details.
checkRd: (-1) rgcolors.func.Rd:27: Escaped LaTeX specials: \#
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  random_wrap.c:9:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/wnominate.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
Found the following files/directories:
  'aphiainfo.csv' 'tax.csv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  assp/freqconv.c:73:19: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  assp/ksv.h:30:19: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  assp/math.c:190:8: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./wrassp.h:197:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  types.c:10:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  types.c:38:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  types.c:65:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  wrassp_init.c:20:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  wrassp_init.c:21:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  wrassp_init.c:22:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/wrassp.Rcheck/00install.out' for details.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'RP2_data_1.txt' 'RP2_data_4.txt' 'RP2_qtl_1.txt' 'RP2_qtl_4.txt'
  'hp1_effect_qtl.txt' 'hp1_freq_mrk.txt' 'hp1_freq_qtl.txt'
  'hp1_genome.txt' 'hp1_last_hp_data.txt' 'hp1_lm_mrk.txt'
  'hp1_lm_qtl.txt' 'hp1_lm_qtl_mrk.txt' 'hp1_mrk.txt' 'hp1_qtl.txt'
  'hp2_effect_qtl.txt' 'hp2_freq_mrk.txt' 'hp2_freq_qtl.txt'
  'hp2_genome.txt' 'hp2_last_hp_data.txt' 'hp2_lm_mrk.txt'
  'hp2_lm_qtl.txt' 'hp2_lm_qtl_mrk.txt' 'hp2_mrk.txt' 'hp2_qtl.txt'
  'my_RP_data_1.txt' 'my_RP_data_4.txt' 'my_RP_mrk_1.txt'
  'my_RP_mrk_4.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'xgb.txt'
Found the following significant warnings:
  init.c:51:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/xgboost.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:24:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:25:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:71:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:72:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/xml2.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) read.npc.vpc.results.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) read.npc.vpc.results.Rd:19: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_
checkRd: (-1) read.npc.vpc.results.Rd:22: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'xtable.html' 'xtable.tex'
Found the following files/directories:
  'OPT.csv' 'testTecan_defaultLiquid.csv' 'testTecan_setLiquid.csv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rcpparma_hello_world.cpp:377:37: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ziphsmm.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'zdat'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    NEW DEPENDENCIES
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:74: Escaped LaTeX specials: \_
checkRd: (-1) zid.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
Package suggested but not available for checking: 'SDMTools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘acceldata2.RData’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown packages ‘HI’, ‘MHadaptive’ in Rd xrefs
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘table_AeRobiology’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BerryMielke.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) BlairLacy.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) Kvalseth.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) consensus.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) dsquared.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) l.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) lsquared.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) lsquared.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) var.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) adapt.Rd:41: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘RandomFields’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘ans_19-2.jpg’ ‘display2d_19-2.jpg’ ‘dist(3)_19-2.jpg’
  ‘dist(4)_19-2.jpg’ ‘dist(mirror)_19-2.jpg’ ‘dist(mirror2)_19-2.jpg’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
mapLevels.html:111:9 (mapLevels.Rd:93): Warning: <code> anchor "codes" already defined
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Zelig’
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) deshrink.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) deshrink.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) plot.mat.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) plot.wa.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) predict.prcurve.Rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘BH-0.05-ListOfGenes.txt’ ‘BH-0.05-VM-ListOfGenes.txt’
  ‘CompleteListOfGenes.txt’ ‘GenesOutOfAnalysis.txt’
  ‘GenesOutOfAnalysis_NotEnoughObs.txt’
  ‘GenesOutOfAnalysis_NullVar.txt’ ‘VM-CompleteListOfGenes.txt’
  ‘bonferroni-0.05-ListOfGenes.txt’
  ‘bonferroni-0.05-VM-ListOfGenes.txt’
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SportsAnalytics’
Found the following significant warnings:
  init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Anthropometry.Rcheck/00install.out’ for details.
Found the following significant warnings:
  header.h:50:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bicriterion_iterated_local_search_call.c:510:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/anticlust.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  me.h:122:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  me.c:234:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ape.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggtree’
Running examples in ‘aplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: insert_left
> ### Title: plot-insertion
> ### Aliases: insert_left insert_right insert_top insert_bottom
> 
> ### ** Examples
> 
> library(ggplot2)
> library(aplot)
> 
> p <- ggplot(mtcars, aes(mpg, disp)) + geom_point()
> p2 <- ggplot(mtcars, aes(mpg)) + 
+     geom_density(fill='steelblue', alpha=.5) + 
+         ggtree::theme_dendrogram()
Error in loadNamespace(x) : there is no package called ‘ggtree’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘apollo/R/apollo_attach.R’:
  attach(as.list(apollo_beta), warn.conflicts = FALSE)
  attach(database, warn.conflicts = FALSE)
  attach(draws, warn.conflicts = FALSE)
  attach(randcoeff, warn.conflicts = FALSE)
  attach(lcpars, warn.conflicts = FALSE)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BayesianTools’
Problems with news in ‘NEWS.md’:
No news entries found.
Unknown package ‘BayesianTools’ in Rd xrefs
Found the following files/directories:
  ‘APBinary_PPV.csv’ ‘APBinary_TPF.csv’
  ‘APBinary_ap_summary(method=perturbation,B=1500).csv’
  ‘APBinary_auc_summary(method=perturbation,B=1500).csv’
  ‘APSurv_PPV.csv’ ‘APSurv_TPF.csv’
  ‘APSurv_ap_summary(method=bootstrap,B=500).csv’
  ‘APSurv_auc_summary(method=bootstrap,B=500).csv’
  ‘CompareAP_Binary_dap_summary(method=none).csv’
  ‘CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv’
checkRd: (-1) AQuadtree-package.Rd:11: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Found the following HTML validation problems:
writeDataFrame.AromaUnitSignalBinaryFile.html:82:9 (writeDataFrame.AromaUnitSignalBinaryFile.Rd:44): Warning: <code> anchor "sep" already defined
writeDataFrame.AromaUnitTabularBinaryFile.html:82:9 (writeDataFrame.AromaUnitTabularBinaryFile.Rd:44): Warning: <code> anchor "sep" already defined
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘ARTP’
Found the following significant warnings:
  ARTP2_init.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ARTP2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ptree.c:32:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ptree.c:192:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ptree.c:200:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ptree.c:768:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arulesSequences.Rcheck/00install.out’ for details.
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MSToutput.txt’
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ASSISTant-internal.html:86:9 (ASSISTant-internal.Rd:40): Warning: <code> anchor "low" already defined
ASSISTant-internal.html:90:9 (ASSISTant-internal.Rd:42): Warning: <code> anchor "high" already defined
ASSISTant-internal.html:94:9 (ASSISTant-internal.Rd:44): Warning: <code> anchor "low" already defined
ASSISTant-internal.html:98:9 (ASSISTant-internal.Rd:46): Warning: <code> anchor "high" already defined
ASSISTant-internal.html:102:9 (ASSISTant-internal.Rd:48): Warning: <code> anchor "low" already defined
ASSISTant-internal.html:106:9 (ASSISTant-internal.Rd:50): Warning: <code> anchor "high" already defined
Package suggested but not available for checking: ‘asteRiskData’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘snpar’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  driver.c:114:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  driver.c:161:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  driver.c:199:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lixoftConnectors’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘exemplary_input1.txt’ ‘exemplary_input2.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  utilities.h:67:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilities.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilities.h:83:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Ball_omp.h:6:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Ball_omp.h:7:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Ball_omp.h:8:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bd_gwas.c:260:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilities.c:1438:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilities.c:1446:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilities.c:1455:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Ball.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bamlss_functions.c:117:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bamlss.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:16:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BART.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Earlier versions
Package which this enhances but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
Found the following significant warnings:
  bayesDccGarch.c:48:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bayesDccGarch.c:110:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bayesDccGarch.c:172:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bayesDccGarch.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ forming offset [112, 115] is out of the bounds [0, 112] of object ‘cbetaAllRow’ with type ‘arma::uvec’ {aka ‘arma::Col<unsigned int>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bayesm.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
Found the following HTML validation problems:
bayesBisurvreg.help.html:130:9 (bayesBisurvreg.help.Rd:64): Warning: <code> anchor "store" already defined
bayessurvreg1.help.html:71:44 (bayessurvreg1.help.Rd:40): Warning: <code> anchor "nrandom" already defined
bayessurvreg1.help.html:71:79 (bayessurvreg1.help.Rd:40): Warning: <code> anchor "ncluster" already defined
bayessurvreg2.help.html:115:9 (bayessurvreg2.help.Rd:59): Warning: <code> anchor "init" already defined
bayessurvreg3.help.html:122:9 (bayessurvreg3.help.Rd:68): Warning: <code> anchor "init" already defined
give.init.html:147:9 (give.init.Rd:89): Warning: <code> anchor "init.y" already defined
checkRd: (-1) bart.Rd:271: Escaped LaTeX specials: \_
Found the following HTML validation problems:
extractSamples.html:59:15 (extractSamples.Rd:25): Error: <function> is not recognized!
extractSamples.html:59:15 (extractSamples.Rd:25): Warning: discarding unexpected <function>
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
checkRd: (-1) create_ThetaMatrix.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) create_ThetaMatrix.Rd:41: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘fabiabreast.txt’
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) tlsce.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:93: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kBET', 'lisi', 'harmony', 'dlfUtils'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘dump.txt’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘beast_plot_toy.pdf’
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘alist.txt’ ‘rpkg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  load.c:11:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nanotime.h:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nanotime.h:7:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mark.c:75:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mark.c:118:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mark.c:119:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nanotime.c:61:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nanotime.c:71:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  process_memory.c:79:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bench.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Found the following significant warnings:
  rbimax.c:326:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/biclust.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ffbase’
Package suggested but not available for checking: ‘INLA’
Found the following significant warnings:
  lib.h:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lib.c:3:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bigGP.Rcheck/00install.out’ for details.
Found the following calls to data() loading into the global environment:
File ‘biglm/R/bigglm.R’:
  data(reset = TRUE)
  data(reset = FALSE)
See section ‘Good practice’ in ‘?data’.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
Checking should be performed on sources prepared by ‘R CMD build’.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rename.h:420:41: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BigQuic.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘outputs’
Found the following significant warnings:
  binarizeBASCA.h:37:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  TASC.c:258:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  TASC_min.c:256:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  binarizeBASCA.c:358:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Binarize.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) BinaryEPPM.Rd:159: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘ccf_ccf_ID31_ID32_res.jpg’ ‘ccf_ccf_ID31_ID32_res.pdf’
  ‘output_ENSO_NHSST.tmp’ ‘plot_plot_ts_RAW_BIN_enso_sst.pdf’
  ‘plot_plot_ts_RAW_BIN_enso_sst01.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst02.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst03.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst04.png’ ‘plot_ts_ACER_ABRUPT.pdf’
  ‘plot_ts_ACER_ABRUPT01.png’ ‘plot_ts_ACER_ABRUPT02.png’
  ‘plot_ts_ACER_ABRUPT03.png’ ‘plot_ts_ACER_ABRUPT04.png’
  ‘salida_ACER_ABRUPT.tmp’ ‘scaterplot_scatterplot_ENSO_SST.jpg’
  ‘scaterplot_scatterplot_ENSO_SST.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Found the following files/directories:
  ‘Plots.pdf’
Found the following files/directories:
  ‘pointshape.dbf’ ‘pointshape.shp’ ‘pointshape.shx’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: replacing previous import ‘dbscan::as.dendrogram’ by ‘stats::as.dendrogram’ when loading ‘Biopeak’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Biopeak.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  bit.c:57:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bit.c:68:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:24:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  binarizeBASCA.h:37:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  TASC.c:258:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  TASC_min.c:256:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  binarizeBASCA.c:358:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BiTrinA.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ forming offset [176, 183] is out of the bounds [0, 176] of object ‘nMaxCritMet’ with type ‘arma::rowvec’ {aka ‘arma::Row<double>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bmabasket.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
Found the following significant warnings:
  include/register.h:46:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  include/register.h:75:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  include/register.h:76:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  include/register.h:82:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  globals.c:15:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  globals.c:33:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  test.counter.c:26:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  test.counter.c:35:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bnlearn.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  common.c:15:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  random.h:12:22: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sat_search.c:106:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  symbolic_simulator.c:344:30: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BoolNet.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    modules 0.x
'LazyData' is specified without a 'data' directory
checkRd: (-1) bpca.Rd:85: Escaped LaTeX specials: \&
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) R2txtJG.Rd:90: Escaped LaTeX specials: \#
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Package suggested but not available for checking: ‘glmmADMB’
checkRd: (-1) brr-package.Rd:33: Escaped LaTeX specials: \&
Found the following significant warnings:
  BugsHelper.c:76:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  BugsHelper.c:87:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  BugsHelper.c:88:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BRugs.Rcheck/00install.out’ for details.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running ‘testthat.R’ [2s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bsplus)
  > 
  > test_check("bsplus")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 103 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-shiny.R:10'): iconlink works ───────────────────────────────────
  Error in `.tag_validate(iconlink$children[[1]], name = "i", class = "fa fa-info-circle")`: class is: fasfa-circle-info, needs to include: fafa-info-circle
  Backtrace:
      ▆
   1. ├─testthat::expect_identical(...) at test-shiny.R:10:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─bsplus:::.tag_validate(iconlink$children[[1]], name = "i", class = "fa fa-info-circle")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 103 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gvcm.cat’
Unknown package ‘gvcm.cat’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  defns.h:671:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  defns.h:761:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redefine.h:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redefine.h:27:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  getdata.c:47:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  hash.h:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  modelfiles.c:197:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  modelfiles.c:521:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  modelfiles.c:592:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  modelfiles.c:778:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rc50.c:42:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redefine.c:46:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redefine.c:191:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rsample.c:59:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  top.c:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utility.c:795:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/C50.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
Found the following significant warnings:
  cairobem.c:50:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Rapi.h:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Rapi.h:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cairotalk.c:661:23: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cairotalk.c:1552:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cairotalk.c:1588:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  xlib-backend.c:156:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Cairo.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘MOEADr’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Adapting_Algorithm_for_CAISEr.Rmd’ using rmarkdown
Quitting from lines 51-73 (Adapting_Algorithm_for_CAISEr.Rmd) 
Error: processing vignette ‘Adapting_Algorithm_for_CAISEr.Rmd’ failed with diagnostics:
there is no package called 'MOEADr'
--- failed re-building ‘Adapting_Algorithm_for_CAISEr.Rmd’

SUMMARY: processing the following file failed:
  ‘Adapting_Algorithm_for_CAISEr.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘simstudy_survival.Rnw’ using Sweave
Loading required package: mice

Attaching package: ‘mice’

The following object is masked from ‘package:stats’:

    filter

The following objects are masked from ‘package:base’:

    cbind, rbind

Warning in parallel::mclapply(1:N, doanalysis) :
  all scheduled cores encountered errors in user code

Error: processing vignette ‘simstudy_survival.Rnw’ failed with diagnostics:
 chunk 9 
Error in x[[method]] : subscript out of bounds

--- failed re-building ‘simstudy_survival.Rnw’

SUMMARY: processing the following file failed:
  ‘simstudy_survival.Rnw’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RxODE’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tmp.txt’
Found the following files/directories:
  ‘MDA231_tree.pdf’
checkRd: (-1) caic-class.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) caic-class.Rd:15: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Running examples in ‘caroline-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: volins
> ### Title: Plot a Series of Vioplot Violins
> ### Aliases: violins
> 
> ### ** Examples
> 
> 
> n <- rnorm(130, 10, 3)
> p <- rpois(110, 4)
> u <- runif(300, 0, 20)
> l <- rlnorm(130, log(2))
> g <- rgamma(140, 3)
> e <- rexp(160)
> 
> violins(list(e=e, p=p,u=u,n=n,l=l,g=g), ylim=c(0,20),
+          col=c('purple','lightblue','lightgreen','red','orange','yellow'),
+          stats=TRUE)
Loading required namespace: sm
Failed with error:  ‘there is no package called ‘sm’’
Loading required namespace: MASS
Error in loadNamespace(x) : there is no package called ‘sm’
Calls: violins ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot-methods.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) plot-methods.Rd:96: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GAMBoost’
Found the following HTML validation problems:
plot.html:46:9 (plot.Rd:19): Warning: <code> anchor "x" already defined
plot.html:50:9 (plot.Rd:21): Warning: <code> anchor "y" already defined
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
Found the following significant warnings:
  catnet_rexport.h:63:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/catnet.Rcheck/00install.out’ for details.
checkRd: (-1) belt.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) bipf.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) crime.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) da.cat.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) dabipf.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) ecm.cat.Rd:77: Escaped LaTeX specials: \&
checkRd: (-1) em.cat.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) ipf.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) logpost.cat.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) mda.cat.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) mi.inference.Rd:140: Escaped LaTeX specials: \&
checkRd: (-1) older.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) prelim.cat.Rd:67: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    News about the ccdf R package
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hotcold.csv’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘out.png’ ‘out1.txt’ ‘out2.txt’
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
'LazyData' is specified without a 'data' directory
Unexported objects imported by ‘:::’ calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘alr3’
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major refactoring of the code
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BSGW’
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  graph.h:85:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  session.h:40:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  session.c:29:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cgraph.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘darts’
'LazyData' is specified without a 'data' directory
checkRd: (-1) hyptis.Rd:31: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘stepres00.txt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘countreg’
Found the following HTML validation problems:
PLS_chill_force.html:215:15 (PLS_chill_force.Rd:92): Error: <chill_model> is not recognized!
PLS_chill_force.html:215:15 (PLS_chill_force.Rd:92): Warning: discarding unexpected <chill_model>
PLS_chill_force.html:215:29 (PLS_chill_force.Rd:92): Error: <heat_model> is not recognized!
PLS_chill_force.html:215:29 (PLS_chill_force.Rd:92): Warning: discarding unexpected <heat_model>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘entab’
Error(s) in re-building vignettes:
  ...
--- re-building ‘ChronochRt.Rmd’ using rmarkdown
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Quitting from lines 67-73 (ChronochRt.Rmd) 
Error: processing vignette ‘ChronochRt.Rmd’ failed with diagnostics:
Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error in `draw_panel()`:
! object ‘new_data_frame’ not found
--- failed re-building ‘ChronochRt.Rmd’

--- re-building ‘Examples.Rmd’ using rmarkdown
Loading required namespace: readxl
Quitting from lines 63-68 (Examples.Rmd) 
Error: processing vignette ‘Examples.Rmd’ failed with diagnostics:
Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error in `draw_panel()`:
! object ‘new_data_frame’ not found
--- failed re-building ‘Examples.Rmd’

SUMMARY: processing the following files failed:
  ‘ChronochRt.Rmd’ ‘Examples.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ChIPseeker’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
'LazyData' is specified without a 'data' directory
checkRd: (-1) diagwl.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) diagwl.Rd:5: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    clinfun (development version)
checkRd: (-1) coxphCPE.Rd:2: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  criteria.h:45:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  criteria.h:48:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/clusterCrit.Rcheck/00install.out’ for details.
checkRd: (-1) genRandomClust.Rd:228: Escaped LaTeX specials: \_
checkRd: (-1) genRandomClust.Rd:259: Escaped LaTeX specials: \_
checkRd: (-1) genRandomClust.Rd:327: Escaped LaTeX specials: \_
checkRd: (-1) plot1DProjection.Rd:95: Escaped LaTeX specials: \_ \_
checkRd: (-1) plot2DProjection.Rd:117: Escaped LaTeX specials: \_ \_
checkRd: (-1) simClustDesign.Rd:235: Escaped LaTeX specials: \_
checkRd: (-1) simClustDesign.Rd:268: Escaped LaTeX specials: \_
checkRd: (-1) simClustDesign.Rd:331: Escaped LaTeX specials: \_
Found the following files/directories:
  ‘clusterhap_reports’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) HINoV.Mod.rd:3: Escaped LaTeX specials: \&
checkRd: (-1) HINoV.Symbolic.rd:3: Escaped LaTeX specials: \&
checkRd: (-1) cluster.Gen.rd:14: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:18: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:29: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) cluster.Gen.rd:33: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:34: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:36: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:38: Escaped LaTeX specials: \_ \_
checkRd: (-1) cluster.Gen.rd:51: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:52: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:54: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:55: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:62: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) comparing.Partitions.rd:12: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.BC.rd:10: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.GDM.rd:33: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.SM.rd:10: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.C.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.G2.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.G3.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.H.rd:16: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.S.rd:12: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  optimal_assignment.c:47:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/clv.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:22: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tobit1’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) drqssbc.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) qbsks.Rd:81: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggtern’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘rkward’
Package which this enhances but not available for checking: ‘rkward’
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘CAM’
checkRd: (-1) compareGroups-package.Rd:52: Escaped LaTeX specials: \~
checkRd: (-1) HouseholdExp.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) HouseholdExp.Rd:27: Escaped LaTeX specials: \$
checkRd: (-1) mix2compositions.Rd:28: Escaped LaTeX specials: \$
checkRd: (-1) mixRead.Rd:30: Escaped LaTeX specials: \$ \$
checkRd: (-1) mixRead.Rd:31: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Deprecation
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
checkRd: (-1) plotMCC.Rd:19: Escaped LaTeX specials: \_
GNU make is a SystemRequirements.
Found the following significant warnings:
  brentmin.c:237:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ContaminatedMixt.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggtree’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/stdio2.h:54:35: warning: ‘int __builtin___snprintf_chk(char*, long unsigned int, int, long unsigned int, const char*, ...)’ specified bound 2048 exceeds destination size 5 [-Wstringop-overflow=]
  /usr/include/x86_64-linux-gnu/bits/stdio2.h:54:35: warning: ‘int __builtin___snprintf_chk(char*, long unsigned int, int, long unsigned int, const char*, ...)’ specified bound 2048 exceeds destination size 20 [-Wstringop-overflow=]
  /usr/include/x86_64-linux-gnu/bits/stdio2.h:54:35: warning: ‘int __builtin___snprintf_chk(char*, long unsigned int, int, long unsigned int, const char*, ...)’ specified bound 2048 exceeds destination size 16 [-Wstringop-overflow=]
  /usr/include/x86_64-linux-gnu/bits/stdio2.h:54:35: warning: ‘int __builtin___snprintf_chk(char*, long unsigned int, int, long unsigned int, const char*, ...)’ specified bound 2048 exceeds destination size 128 [-Wstringop-overflow=]
  trutil.cpp:147:49: warning: ‘%s’ directive output may be truncated writing up to 2047 bytes into a region of size between 2035 and 2044 [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CORElearn.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) poss_local.Rd:21: Escaped LaTeX specials: \~
‘gs+qpdf’ made some significant size reductions:
     compacted ‘corncob-intro.pdf’ from 430Kb to 179Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
'LazyData' is specified without a 'data' directory
checkRd: (-1) BrownBigrams.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BrownLOBPassives.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BrownPassives.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BrownStats.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) KrennPPV.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) KrennPPV.Rd:74: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) sgt.Rd:16: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) egde.Rd:26: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  bb.c:719:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ibb.c:78:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/countdata.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
dWeibullgammaCount.html:151:9 (dWeibullgammaCount.Rd:80): Warning: <code> anchor "shape" already defined
dWeibullgammaCount.html:155:9 (dWeibullgammaCount.Rd:82): Warning: <code> anchor "x" already defined
dWeibullgammaCount.html:159:9 (dWeibullgammaCount.Rd:84): Warning: <code> anchor "time" already defined
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘covfefe_inauguration.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  bcplm.c:84:22: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cplm.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Non-visible changes:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘clusterProfiler’
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major features
    Minor features
checkRd: (-1) handmovement.Rd:9: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
expressions-internal.html:149:287 (expressions-internal.Rd:144): Warning: <code> anchor "selections" already defined
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  structs.h:44:29: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  vector.c:125:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ctl.Rcheck/00install.out’ for details.
Found the following significant warnings:
  init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ctmcd.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Hello.csv’
Found the following significant warnings:
  ../inst/include/cuba.h:75:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/cuba.h:76:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cubature.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  redefine.h:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redefine.h:27:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  getdata.c:44:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  hash.h:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rcubist.c:40:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redefine.c:46:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redefine.c:191:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  top.c:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Cubist.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Package which this enhances but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘xpectr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Creating_a_confusion_matrix.Rmd’ using rmarkdown
--- finished re-building ‘Creating_a_confusion_matrix.Rmd’

--- re-building ‘available_metrics.Rmd’ using rmarkdown
--- finished re-building ‘available_metrics.Rmd’

--- re-building ‘cross_validating_custom_functions.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

--- finished re-building ‘cross_validating_custom_functions.Rmd’

--- re-building ‘evaluate_by_id.Rmd’ using rmarkdown
--- finished re-building ‘evaluate_by_id.Rmd’

--- re-building ‘picking_the_number_of_folds_for_cross-validation.Rmd’ using rmarkdown
Quitting from lines 76-137 (picking_the_number_of_folds_for_cross-validation.Rmd) 
Error: processing vignette ‘picking_the_number_of_folds_for_cross-validation.Rmd’ failed with diagnostics:
there is no package called 'xpectr'
--- failed re-building ‘picking_the_number_of_folds_for_cross-validation.Rmd’

SUMMARY: processing the following file failed:
  ‘picking_the_number_of_folds_for_cross-validation.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'gurobi', 'rcbc'
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dspg.Rd:29: Escaped LaTeX specials: \^ \^
checkRd: (-1) dspgd2015.Rd:31: Escaped LaTeX specials: \^ \^
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggtree’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggtern’
Running examples in ‘dartR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gl.report.hwe
> ### Title: Reports departure from Hardy-Weinberg proportions
> ### Aliases: gl.report.hwe
> 
> ### ** Examples
> 
> gl.report.hwe(x = bandicoot.gl)
Starting gl.report.hwe 
  Processing genlight object with SNP data
Error in gl.report.hwe(x = bandicoot.gl) : 
  Package ggtern  needed for this function to work. Please install it.
Execution halted
Package suggested but not available for checking: ‘dash’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dash’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dash’
Package suggested but not available for checking: ‘dash’
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
getCartesianCoordinates.html:37:60 (getCartesianCoordinates.Rd:7): Warning: <code> anchor "Columns]" already defined
setdiffMatrix.html:33:62 (setdiffMatrix.Rd:6): Warning: <code> anchor "k]" already defined
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘my new data set.rds’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘stubthat’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Datastream DWE - now decommissioned by Refinitiv
    CRAN
Found the following significant warnings:
  init.c:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:30:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:36:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:37:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/datastructures.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ../include/external/random.h:53:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../include/external/random.h:54:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  randomBase.c:363:21: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  randomBase.c:381:26: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../include/misc/adaptiveRadixTree.h:54:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  adaptiveRadixTree.c:195:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  simd.c:53:24: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dbarts.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dblog’
Found the following significant warnings:
  d011ch.c:17:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:41:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:42:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:44:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:45:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:352:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:427:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:520:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:531:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:686:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  d011ch.c:698:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ma.c:7:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  urnew010.c:17:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  urnew010.c:36:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  urnew010.c:37:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wur.c:23:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dblcens.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  difeq.h:65:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  difeq.c:123:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dopri.h:208:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dopri.c:245:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dde.Rcheck/00install.out’ for details.
Found the following significant warnings:
  DDHFm.c:101:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  DDHFm.c:122:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  DDHFm.c:199:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DDHFm.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  globals.h:139:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/deBif.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggtree’
‘::’ or ‘:::’ import not declared from: ‘cli’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘smd_table.docx’
checkRd: (-1) lifetable.Rd:15: Escaped LaTeX specials: \$
Found the following HTML validation problems:
compare.demogdata.html:94:15 (compare.demogdata.Rd:37): Error: <error> is not recognized!
compare.demogdata.html:94:15 (compare.demogdata.Rd:37): Warning: discarding unexpected <error>
compare.demogdata.html:98:15 (compare.demogdata.Rd:38): Error: <logerror> is not recognized!
compare.demogdata.html:98:15 (compare.demogdata.Rd:38): Warning: discarding unexpected <logerror>
fdm.html:108:26 (fdm.Rd:43): Error: <series> is not recognized!
fdm.html:108:26 (fdm.Rd:43): Warning: discarding unexpected <series>
lca.html:141:15 (lca.Rd:64): Error: <series> is not recognized!
lca.html:141:15 (lca.Rd:64): Warning: discarding unexpected <series>
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Running examples in ‘dendRoAnalyst-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: daily.data
> ### Title: Calculation of daily statistics for dendrometer data
> ### Aliases: daily.data
> 
> ### ** Examples
> 
> library(dendRoAnalyst)
> data(nepa17)
> daily_stats<-daily.data(df=nepa17, TreeNum=1)
Error in daily.data(df = nepa17, TreeNum = 1) : 
  Date not in the right format
Execution halted
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rdonlp2’
checkRd: (-1) discrimination.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) fitdmm.Rd:59: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘Rdonlp2’
Found the following significant warnings:
  deque.h:73:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  constructor.c:43:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  deque.c:31:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dequer_native.c:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dequer.Rcheck/00install.out’ for details.
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
checkRd: (-1) geom_axis.Rd:10: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
Found the following HTML validation problems:
BootCI.html:89:15 (BootCI.Rd:44): Error: <fun> is not recognized!
BootCI.html:89:15 (BootCI.Rd:44): Warning: discarding unexpected <fun>
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
internals.html:75:9 (internals.Rd:36): Warning: <code> anchor "terms1" already defined
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  DetSel_init.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  GetData.c:33:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DetSel.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  void_dev.c:103:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  void_dev.c:182:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  void_dev.c:197:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/devoid.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  arms.h:50:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dfcomb.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) phihat.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) anova.dglm.Rd:41: Escaped LaTeX specials: \&
Package which this enhances but not available for checking: ‘BayesianTools’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
checkRd: (-1) sammy.Rd:51: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘discreteMTP’
Unknown package ‘discreteMTP’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘disprose-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_seq_info
> ### Title: Get NCBI sequence record
> ### Aliases: get_seq_info get_seq_info_fix info_listtodata
> 
> ### ** Examples
> 
> info.dataframe <- get_seq_info (org.name = "txid9606", db = "nucleotide", n.start = 1,
+                                n.stop = 10, step = 5, return.dataframe = TRUE,
+                                check.result = TRUE)
Error : HTTP failure: 500
{"error":"error forwarding request","api-key":"137.208.57.142","type":"ip",
"status":"ok"}
Error in get_seq_info(org.name = "txid9606", db = "nucleotide", n.start = 1,  : 
  Could not connect to server. Please try again.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) booter.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) ci.booted.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) pbooter.Rd:57: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
internals.html:275:9 (internals.Rd:205): Warning: <code> anchor "support" already defined
internals.html:341:9 (internals.Rd:226): Warning: <code> anchor "f" already defined
Found the following files/directories:
  ‘csim’ ‘xyz’ ‘xyz.sav’ ‘xyz.sav.comment’
Found the following files/directories:
  ‘csim.mean’ ‘csim.mean.comment’
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
labDive-internal.html:51:9 (labDive-internal.Rd:37): Warning: <code> anchor "g" already defined
labDive-internal.html:51:32 (labDive-internal.Rd:37): Warning: <code> anchor "ordpen" already defined
Found the following significant warnings:
  rfftw.h:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rfftw.c:149:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  util.c:231:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/diversitree.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘BOLTSSIRR’
Packages suggested but not available for checking: 'sendplot', 'HWxtest'
checkRd: (-1) fastDivPart.Rd:13: Escaped LaTeX specials: \_
checkRd: (-1) inCalc.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) inCalc.Rd:13: Escaped LaTeX specials: \_
Found the following HTML validation problems:
corPlotter.html:42:9 (corPlotter.Rd:15): Warning: <code> anchor "x" already defined
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:20: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:26: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [4s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(docxtools)
  > 
  > test_check("docxtools")
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 22 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_put.R:21'): put_axes() attributes match expectations ─────────
  p$layers[[1]]$geom$non_missing_aes not identical to c("linetype", "size", "shape").
  1/3 mismatches
  x[2]: "linewidth"
  y[2]: "size"
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 22 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) block.catlg.Rd:61: Escaped LaTeX specials: \^ \^
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
Found the following significant warnings:
  alive.c:200:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  alive.c:277:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/doRedis.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New features
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘doSNOW/R/doSNOW.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
Package suggested but not available for checking: ‘OpenMPController’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
Unknown package ‘broomExtra’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
'LazyData' is specified without a 'data' directory
checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gompertz.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) hatvalues.drc.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) llogistic.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) modelFit.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) weibull1.Rd:67: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Error(s) in re-building vignettes:
  ...
--- re-building ‘DriveML.Rmd’ using rmarkdown
Quitting from lines 329-331 (DriveML.Rmd) 
Error: processing vignette ‘DriveML.Rmd’ failed with diagnostics:
Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error in `new_data_frame()`:
! `n` must be an integer of size 1.
--- failed re-building ‘DriveML.Rmd’

SUMMARY: processing the following file failed:
  ‘DriveML.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Package suggested but not available for checking: ‘dsBaseClient’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
dynamac-deprecated.html:53:9 (dynamac-deprecated.Rd:21): Warning: <code> anchor "x" already defined
dynamac-deprecated.html:57:9 (dynamac-deprecated.Rd:23): Warning: <code> anchor "response" already defined
dynamac-deprecated.html:62:9 (dynamac-deprecated.Rd:26): Warning: <code> anchor "bw" already defined
Found the following significant warnings:
  nwout.c:49:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DynamicGP.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lle’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  arms.c:105:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  arms.c:902:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dynsurv.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    20181118
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘example_table1.csv’ ‘example_table1.txt’ ‘example_table2.csv’
  ‘example_table2.txt’ ‘example_table3.csv’ ‘example_table3.txt’
  ‘table1.csv’ ‘table2.csv’ ‘table2.txt’ ‘table3.txt’ ‘table4.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    breaking changes
    major changes
    minor changes
    Internal
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
‘gs+qpdf’ made some significant size reductions:
     compacted ‘ecolMod.pdf’ from 800Kb to 544Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  include/ecos_bb.h:161:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ecos_bb/ecos_bb_preproc.c:298:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ecos/include/ecos_bb.h:161:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ECOSolveR.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Package required and available but unsuitable version: ‘biomod2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Package suggested but not available for checking: ‘eggCountsExtra’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  eicm.h:70:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/eicm.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AuditErrors.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) compute.audit.errors.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) compute.stark.t.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) find.q.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) find.q.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) stark.test.Rd:50: Escaped LaTeX specials: \$
checkRd: (-1) stark.test.Rd:101: Escaped LaTeX specials: \$ \$
checkRd: (-1) tri.audit.sim.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) tri.calc.sample.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) tri.sample.Rd:34: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) weight.function.Rd:16: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [6s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(elfgen)
  > 
  > test_check("elfgen")
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 17 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-elfdata.R:37'): Function returns a dataframe ───────────────────
  Error in `data.frame(MAF = watershed.df$MAF, NT.TOTAL.UNIQUE = watershed.df$NT.TOTAL.UNIQUE, 
      watershed.code = watershed.df$watershed.code, COMID_NHDv2 = watershed.df$COMID_NHDv2)`: arguments imply differing number of rows: 0, 4
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-elfdata.R:37:12
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─base::is.data.frame(...)
   5. └─elfgen::elfdata(watershed.code = test.ichthy.dataframe, ichthy.localpath = tempdir())
   6.   └─base::data.frame(...)
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 17 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  zeroin.c:54:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EL.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  emd-rubner.c:143:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  emd-rubner.c:153:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  emd-rubner.c:640:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  emd-rubner.c:810:20: warning: ‘minI’ is used uninitialized [-Wuninitialized]
  emd-rubner.c:810:26: warning: ‘minJ’ is used uninitialized [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/emdist.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) freudenstein_roth_func.Rd:29: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘osmar’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  utilities.h:7:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilities.c:14:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/emoa.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘file.path(temp_dir, gp2.csv)’
Package suggested but not available for checking: ‘ecospat’
Package suggested but not available for checking: ‘ecospat’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Environmental variables.csv’ ‘Inf.txt’ ‘List of species.csv’ ‘Mean
  overlap among taxa.csv’ ‘Overlap among taxa.csv’ ‘Pointsize.dat’
  ‘Polar coordinates.csv’
'LazyData' is specified without a 'data' directory
checkRd: (-1) calibrate.Rd:151: Escaped LaTeX specials: \&
checkRd: (-1) cdfCompareCensored.Rd:299: Escaped LaTeX specials: \&
checkRd: (-1) detectionLimitCalibrate.Rd:149: Escaped LaTeX specials: \&
checkRd: (-1) ecdfPlotCensored.Rd:169: Escaped LaTeX specials: \&
checkRd: (-1) egammaAltCensored.Rd:344: Escaped LaTeX specials: \&
checkRd: (-1) egammaCensored.Rd:340: Escaped LaTeX specials: \&
checkRd: (-1) elnormAltCensored.Rd:694: Escaped LaTeX specials: \&
checkRd: (-1) elnormCensored.Rd:270: Escaped LaTeX specials: \&
checkRd: (-1) enormCensored.Rd:852: Escaped LaTeX specials: \&
checkRd: (-1) enparCensored.Rd:343: Escaped LaTeX specials: \&
checkRd: (-1) enparCensored.Rd:358: Escaped LaTeX specials: \&
checkRd: (-1) epoisCensored.Rd:354: Escaped LaTeX specials: \&
checkRd: (-1) ppointsCensored.Rd:406: Escaped LaTeX specials: \&
checkRd: (-1) predIntGammaSimultaneous.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) predIntGammaSimultaneous.Rd:171: Escaped LaTeX specials: \&
checkRd: (-1) predIntLnormSimultaneous.Rd:136: Escaped LaTeX specials: \&
checkRd: (-1) predIntLnormSimultaneous.Rd:137: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneous.Rd:204: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneous.Rd:205: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneousK.Rd:277: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneousK.Rd:278: Escaped LaTeX specials: \&
checkRd: (-1) qqPlotCensored.Rd:261: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTest.Rd:276: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTestCensored.Rd:324: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTestCensored.Rd:331: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘epidict’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘statnet’
Package suggested but not available for checking: ‘statnet’
Package required but not available: ‘tergm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘episcan_1geno_cc.txt’ ‘episcan_1geno_quant.txt’
  ‘episcan_2geno_cc.txt’ ‘episcan_2geno_quant.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taskscheduleR’
Found the following HTML validation problems:
expand_idf_regex.html:65:9 (expand_idf_regex.Rd:31): Warning: <code> anchor "pattern" already defined
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [14s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(era)
  > 
  > test_check("era")
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 117 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (6)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-examples.R:17'): this_year() is vectorised ───────────────────
  this_year(c("CE", "BP", "AM")) (`actual`) not equal to list(year_now, year_now_bp, year_now_am) (`expected`).
  
  `actual[[3]]`:   "5783"
  `expected[[3]]`: "5782"
  
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 117 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) aic.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:64: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘ETAS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: catalog
> ### Title: Create an Earthquake Catalog
> ### Aliases: catalog
> ### Keywords: spatial math earthquake modeling
> 
> ### ** Examples
> 
>   summary(iran.quakes)
         date               time           long            lat       
 2014-08-18:  44   00:04:50.70:   2   Min.   :40.01   Min.   :22.13  
 2011-10-23:  42   04:46:33.00:   2   1st Qu.:48.34   1st Qu.:28.32  
 2013-04-09:  31   07:02:27.00:   2   Median :51.88   Median :32.13  
 2013-05-11:  27   00:00:19.42:   1   Mean   :52.20   Mean   :32.80  
 2011-10-24:  19   00:00:41.44:   1   3rd Qu.:56.39   3rd Qu.:37.52  
 1990-06-21:  18   00:00:46.52:   1   Max.   :65.00   Max.   :41.98  
 (Other)   :5789   (Other)    :5961                                  
      mag       
 Min.   :4.000  
 1st Qu.:4.200  
 Median :4.400  
 Mean   :4.468  
 3rd Qu.:4.700  
 Max.   :6.200  
                
> 
>   # creating a catalog with rectangular study region
>   iran.cat <- catalog(iran.quakes, time.begin="1973/01/01",
+      study.start="1985/01/01", study.end="2016/01/01",
+      lat.range=c(25, 42), long.range=c(42, 63),
+      mag.threshold=4.5)
Error in catalog(iran.quakes, time.begin = "1973/01/01", study.start = "1985/01/01",  : 
  no more than one event can occur simultaneously! check events 
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘sample .nwk’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ExactData’
checkRd: (-1) exams2sakai.Rd:152: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cec2013’
checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) outlierPlot.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) outlierPlot.Rd:32: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘exuberdata’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Bogota.tex’ ‘DogBreeds1.tex’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    minor changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  chli.c:5:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fame.Rcheck/00install.out’ for details.
File ‘fame/R/windows/zzz.R’:
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section ‘Good practice’ in ‘?.onAttach’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  lu.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lu.c:828:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fastclime.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘default5.eps’
Package suggested but not available for checking: ‘crrp’
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
sampling.ER.html:84:9 (sampling.ER.Rd:40): Warning: <code> anchor "index" already defined
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘coxKM’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fastmap.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Scent.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) Traffic.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
Found the following significant warnings:
  Rconnection.cc:282:52: warning: format ‘%p’ expects argument of type ‘void*’, but argument 3 has type ‘Rexp*’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘NNLM’
GNU make is a SystemRequirements.
Found the following significant warnings:
  fbati_init.c:35:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  fbati_init.c:36:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  fbati_init.c:37:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  fbati_init.c:39:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  fbati_init.c:50:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  fbati_init.c:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  fbati_init.c:52:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  fbati_init.c:53:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fbati.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.Rprofile’
Unexported objects imported by ‘:::’ calls:
  ‘fdapace:::GCVLwls1D1’ ‘fdapace:::GetSmoothedMeanCurve’
  ‘fdapace:::HandleNumericsAndNAN’ ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fdistr)
  > 
  > test_check("fdistr")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 13 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_create_pareto.R:7'): (code run outside of `test_that()`) ───────
  Error in `create_pareto(table)`: object 'g' not found
  Backtrace:
      ▆
   1. └─fdistr::create_pareto(table) at test_create_pareto.R:7:0
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 13 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘vert.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘treesAll.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New Stuff
'LazyData' is specified without a 'data' directory
checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ff.h:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  r_ff.h:62:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  r_ff.h:63:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  r_ff.h:64:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  r_ff.c:289:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  r_ff.c:298:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  r_ff.c:309:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ff.Rcheck/00install.out’ for details.
checkRd: (-1) dimnames.ff.rd:18: Escaped LaTeX specials: \_
checkRd: (-1) ff.rd:120: Escaped LaTeX specials: \_
checkRd: (-1) names.ff.rd:22: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
checkStream.html:55:9 (checkStream.Rd:22): Warning: <code> anchor "functionName" already defined
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  f2c.h:185:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:186:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:187:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:188:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:189:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:190:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:191:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:192:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:193:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:194:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:195:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FGSG.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘MicrobeDS’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘AH_genepop.txt’ ‘AH_popname.txt’ ‘JSM_MS_freq.txt’
  ‘JSM_MS_genepop.txt’ ‘JSM_genepop_clipped_both.txt’
  ‘JSM_genepop_clipped_maf.txt’ ‘JSM_genepop_clipped_name.txt’
  ‘JSM_mtDNA_freq.txt’ ‘JSM_popname.txt’ ‘result_DJ.csv’
  ‘result_EBDJ.csv’ ‘result_EBFST.csv’ ‘result_EBFST_mtDNA.csv’
  ‘result_EBGstH.csv’ ‘result_GstH.csv’ ‘result_GstN.csv’
  ‘result_GstNC.csv’ ‘result_thetaWCpair.csv’
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'benchden', 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fk_regression.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) cclust.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) randIndex.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:28: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  flexiblas_api_standalone.c:64:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  flexiblas_api_standalone.c:86:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  flexiblas_api_standalone.c:452:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:7:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrapper.c:25:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrapper.c:34:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrapper.c:47:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrapper.c:58:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrapper.c:74:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrapper.c:132:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/flexiblas.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  float_native.c:40:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  float_native.c:41:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  float_native.c:53:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  machine.c:7:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  NA.c:20:21: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  NA.c:76:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  NA.c:88:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/float.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘flux.CH4.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) pseudoOptim.Rd:27: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) write.AFNI.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) write.AFNI.Rd:17: Escaped LaTeX specials: \_
checkRd: (-1) write.AFNI.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) write.AFNI.Rd:22: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
checkRd: (-1) forecTheta-package.Rd:11: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
Package suggested but not available for checking: ‘RandomFields’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CatalogueAccessors.Rd:249: Escaped LaTeX specials: \^ \^
checkRd: (-1) FrF2.Rd:574: Escaped LaTeX specials: \^
checkRd: (-1) FrF2.Rd:629: Escaped LaTeX specials: \^ \^
checkRd: (-1) IAPlot.Rd:87: Escaped LaTeX specials: \$
checkRd: (-1) block.Rd:121: Escaped LaTeX specials: \^
checkRd: (-1) block.Rd:150: Escaped LaTeX specials: \^ \^
checkRd: (-1) blockpick.Rd:114: Escaped LaTeX specials: \^ \^
Packages suggested but not available for checking: 'dggrids', 'INLA'
Unknown package ‘frm’ in Rd xrefs
Unknown package ‘frm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
Found the following significant warnings:
  init.c:20:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FSelectorRcpp.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mean.fts.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) median.fts.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) plot.fm.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) residuals.fm.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) sd.fts.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) var.fts.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘completeTrial_byArm_eventPriorRateC3=0.001_eventPriorRateT1=0_eventPriorRateT2=0_eventPriorWt=0.5.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.2.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.4.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.6.RData’
  ‘completeTrial_pooled_eventPriorRate=0.001_eventPriorWt=0.5.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.2.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.4.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.6.RData’
  ‘rcdf_byArm_arm=T1_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03.pdf’
  ‘rcdf_pooled_eventPriorRate=0.06.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  gamlr.c:87:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gamlr.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LGAclaims.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:36: Escaped LaTeX specials: \_
Found the following significant warnings:
  loessc.c:74:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  loessc.c:76:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  loessc.c:78:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  loessc.c:80:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  loessc.c:82:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  loessc.c:84:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  loessc.c:86:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  loessc.c:88:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  loessc.c:90:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gam.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) meyer.Rd:11: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘checkdata.csv’ ‘gbmforest.sas’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ‘:::’ calls:
  ‘tools:::.Rd_get_argument_names’ ‘tools:::RdTags’ ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘gputools’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘g.data/R/g.data.attach.R’:
  attach(NULL, pos, basename(dir))
See section ‘Good practice’ in ‘?attach’.
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot_summary.Rd:14: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘genderdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Found the following HTML validation problems:
setdiffMatrix.html:33:62 (setdiffMatrix.Rd:6): Warning: <code> anchor "k]" already defined
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Running examples in ‘GenEst-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: averageSS
> ### Title: Tabulate an average search schedule from a multi-unit SS data
> ###   table
> ### Aliases: averageSS
> 
> ### ** Examples
> 
>   data(mock)
>   avgSS <- averageSS(mock$SS)
Error in prepSS(data_SS, SSdate = SSdate) : 
  more than 1 date column in data_SS, and SSdate does not specify which to use.
Calls: averageSS -> prepSS
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GenEstGUI.Rmd’ using rmarkdown
--- finished re-building ‘GenEstGUI.Rmd’

--- re-building ‘command-line-example.Rmd’ using rmarkdown
Quitting from lines 381-390 (command-line-example.Rmd) 
Error: processing vignette ‘command-line-example.Rmd’ failed with diagnostics:
more than 1 date column in data_SS, and SSdate does not specify which to use.
--- failed re-building ‘command-line-example.Rmd’

--- re-building ‘solar-examples.Rmd’ using rmarkdown
Quitting from lines 286-293 (solar-examples.Rmd) 
Error: processing vignette ‘solar-examples.Rmd’ failed with diagnostics:
more than 1 date column in data_SS, and SSdate does not specify which to use.
--- failed re-building ‘solar-examples.Rmd’

--- re-building ‘wind-examples.Rmd’ using rmarkdown
Quitting from lines 277-283 (wind-examples.Rmd) 
Error: processing vignette ‘wind-examples.Rmd’ failed with diagnostics:
more than 1 date column in data_SS, and SSdate does not specify which to use.
--- failed re-building ‘wind-examples.Rmd’

SUMMARY: processing the following files failed:
  ‘command-line-example.Rmd’ ‘solar-examples.Rmd’ ‘wind-examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  init.c:14:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GenSA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  arms.c:99:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  arms.c:900:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/genscore.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  gensvm/include/gensvm_rand.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gensvm/src/gensvm_rand.c:105:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gensvm/src/gensvm_rand.c:112:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gensvm/src/gensvm_rand.c:153:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gensvm.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:5:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:7:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geohashTools.Rcheck/00install.out’ for details.
Found the following HTML validation problems:
inputs-webprocess.html:73:9 (inputs-webprocess.Rd:34): Warning: <code> anchor "..." already defined
Package suggested but not available for checking: ‘geomarocdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘clusterProfiler’
Running examples in ‘GeoTcgaData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: countToFpkm_matrix
> ### Title: Convert count to FPKM
> ### Aliases: countToFpkm_matrix
> 
> ### ** Examples
> 
> lung_squ_count2 <- matrix(c(1,2,3,4,5,6,7,8,9),ncol=3)
> rownames(lung_squ_count2) <- c("DISC1","TCOF1","SPPL3")
> colnames(lung_squ_count2) <- c("sample1","sample2","sample3")
> jieguo <- countToFpkm_matrix(lung_squ_count2, keyType = "SYMBOL", 
+     gene_cov = gene_cov)
Error in loadNamespace(x) : there is no package called ‘clusterProfiler’
Calls: countToFpkm_matrix ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GeoTcgaData.Rmd’ using rmarkdown
Quitting from lines 326-330 (GeoTcgaData.Rmd) 
Error: processing vignette ‘GeoTcgaData.Rmd’ failed with diagnostics:
there is no package called 'clusterProfiler'
--- failed re-building ‘GeoTcgaData.Rmd’

SUMMARY: processing the following file failed:
  ‘GeoTcgaData.Rmd’

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Found the following calls to data() loading into the global environment:
File ‘geotools/R/zzz.R’:
  data(fr_geo_rad)
See section ‘Good practice’ in ‘?data’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) getopt.Rd:60: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
checkRd: (-1) gexp.Rd:123: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘RGtk2’
checkRd: (-1) estGF.Rd:106: Escaped LaTeX specials: \&
checkRd: (-1) estGF.Rd:107: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    earlier versions
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘ggbeeswarm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: position_beeswarm
> ### Title: Violin point-style plots to show overlapping points. x must be
> ###   discrete.
> ### Aliases: position_beeswarm
> 
> ### ** Examples
> 
> 
>   ggplot2::qplot(class, hwy, data = ggplot2::mpg, position=position_beeswarm())
Error:
! The `position` argument of `qplot()` was deprecated in ggplot2 2.0.0
  and is now defunct.
Backtrace:
    ▆
 1. └─ggplot2::qplot(class, hwy, data = ggplot2::mpg, position = position_beeswarm())
 2.   └─lifecycle::deprecate_stop("2.0.0", "qplot(position)")
 3.     └─lifecycle:::deprecate_stop0(msg)
 4.       └─rlang::cnd_signal(...)
Execution halted
Running examples in ‘ggblanket-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gg_hex
> ### Title: Hex ggplot.
> ### Aliases: gg_hex
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> diamonds %>% gg_hex(depth, price)
Warning: Computation failed in `stat_binhex()`
Caused by error in `compute_group()`:
! The package `hexbin` is required for `stat_binhex()`
Error in `build_longer_spec()`:
! `cols` must select at least one column.
Backtrace:
    ▆
 1. ├─diamonds %>% gg_hex(depth, price)
 2. ├─ggblanket::gg_hex(., depth, price)
 3. │ └─... %>% dplyr::pull(.data$value)
 4. ├─dplyr::pull(., .data$value)
 5. ├─tidyr::pivot_longer(., cols = tidyselect::everything())
 6. └─tidyr:::pivot_longer.data.frame(., cols = tidyselect::everything())
 7.   └─tidyr::build_longer_spec(...)
 8.     └─rlang::abort(glue::glue("`cols` must select at least one column."))
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘ggconf-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: theme2
> ### Title: an enhanced version of ggplot2::theme()
> ### Aliases: theme2
> 
> ### ** Examples
> 
> 
> if (requireNamespace("ggplot2", quietly = TRUE)) {
+ 
+ library(ggplot2)
+ ggplot(mtcars) + geom_point(aes(wt, hp, color=as.factor(cyl))) +
+   theme2(
+     text(f="bold", z=24, fmly="Times New Roman"),
+     pnl.bg(fill="white"),
+     lgd.box.margin(.2, .2, .2, .2, "cm"),
+     lgd.box.bg(c="black"),
+     lgd.key(fill="white"),
+     lgd.position("bottom"),
+     lgd.txt(z=rel(.8)),
+     lgd.title(fmly="Consolas", c="royalblue"),  
+     axs.title(fmly="Consolas", c="royalblue"),  
+     axs.title.y(angle=0, vjust=.5),             
+     axs.txt(z=rel(1.1)),
+     axs.line(arrow=arrow(type="open", angle=20), z=2),
+     axs.tick(z=1),                              
+     axs.tick.len(.5, "cm"),
+     plt.subttl(f="plain", hjust=1),
+     plt.margin(.3, .3, .3, .1, "inch")          
+   )
+ 
+ 
+ ggplot(mtcars) + geom_point(aes(wt, hp, color=cyl)) +
+    theme2(a.txt(family = c("Consolas", "Times")[1]))
+ 
+ # all of the following three generate the same plot
+ 
+ ggplot(mtcars) + geom_point(aes(wt, hp, color=cyl)) +
+    theme(text = element_text(size=20, face="bold"),
+    axis.line = element_line(size=2),
+    legend.key = element_rect(color="black"))
+ 
+ ggplot(mtcars) + geom_point(aes(wt, hp, color=cyl)) +
+    theme2(text(size=20, face="bold"), axis.line(size=2),
+           legend.key(color="black"))
+ 
+ ggplot(mtcars) + geom_point(aes(wt, hp, color=cyl)) +
+    theme2(txt(sz=20, f="bold"), aline(sz=2), l.key(c="black"))
+ 
+ 
+ 
+ }
Error in ggplot2::element_line(fill = 1) : unused argument (fill = 1)
Calls: theme2 ... exec_ggconf -> eval -> eval -> <Anonymous> -> find_args -> mget
Execution halted
Running ‘testthat.R’ [4s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggconf)
  > 
  > test_check("ggconf")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 33 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-theme2.R:37'): theme2 ──────────────────────────────────────────
  Error in `ggplot2::element_line(fill = 1)`: unused argument (fill = 1)
  Backtrace:
      ▆
   1. └─ggconf::theme2(...) at test-theme2.R:37:4
   2.   └─ggconf:::exec_ggconf(...)
   3.     ├─base::eval(parse(text = ggobj_verbose))
   4.     │ └─base::eval(parse(text = ggobj_verbose))
   5.     └─ggplot2::theme(...)
   6.       └─ggplot2:::find_args(..., complete = NULL, validate = NULL)
   7.         └─base::mget(args, envir = env)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 33 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
‘::’ or ‘:::’ import not declared from: ‘cli’
'LazyData' is specified without a 'data' directory
Found the following assignments to the global environment:
File ‘ggExtra/R/ggMarginalGadget.R’:
  assign(plotname, eval(parse(text = origPlot)), envir = .GlobalEnv)
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dlm’
Error(s) in re-building vignettes:
  ...
--- re-building ‘basics.Rmd’ using knitr
Loading required package: ggplot2
Loading required package: MASS
Loading required package: strucchange
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: urca
Loading required package: lmtest
--- finished re-building ‘basics.Rmd’

--- re-building ‘plot_dist.Rmd’ using knitr
--- finished re-building ‘plot_dist.Rmd’

--- re-building ‘plot_lm.Rmd’ using knitr
--- finished re-building ‘plot_lm.Rmd’

--- re-building ‘plot_map.Rmd’ using knitr
Loading required package: maps
--- finished re-building ‘plot_map.Rmd’

--- re-building ‘plot_pca.Rmd’ using knitr

Attaching package: 'cluster'

The following object is masked from 'package:maps':

    votes.repub

Warning: `gather_()` was deprecated in tidyr 1.2.0.
ℹ Please use `gather()` instead.
ℹ The deprecated feature was likely used in the ggfortify package.
  Please report the issue at <https://github.com/sinhrks/ggfortify/issues>.
Scale for y is already present.
Adding another scale for y, which will replace the existing scale.
--- finished re-building ‘plot_pca.Rmd’

--- re-building ‘plot_surv.Rmd’ using knitr
Warning: Using formula(x) is deprecated when x is a character vector of length > 1.
  Consider formula(paste(x, collapse = " ")) instead.
--- finished re-building ‘plot_surv.Rmd’

--- re-building ‘plot_ts.Rmd’ using knitr
Successfully loaded changepoint package version 2.2.4
 See NEWS for details of changes.
Quitting from lines 158-167 (plot_ts.Rmd) 
Error: processing vignette ‘plot_ts.Rmd’ failed with diagnostics:
there is no package called 'dlm'
--- failed re-building ‘plot_ts.Rmd’

SUMMARY: processing the following file failed:
  ‘plot_ts.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘gghalves.Rmd’ using rmarkdown
Quitting from lines 66-69 (gghalves.Rmd) 
Error: processing vignette ‘gghalves.Rmd’ failed with diagnostics:
Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error in `data.frame()`:
! arguments imply differing number of rows: 1, 0
--- failed re-building ‘gghalves.Rmd’

SUMMARY: processing the following file failed:
  ‘gghalves.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ggtree’
Running ‘testthat.R’ [8s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggip)
  Loading required package: ggplot2
  Loading required package: ipaddress
  > 
  > test_check("ggip")
  [ FAIL 2 | WARN 21 | SKIP 5 | PASS 92 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (5)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-geom-hilbert-outline.R:89'): networks outside 2D grid raise warning ──
  `layer_grob(p + geom_hilbert_outline(na.rm = TRUE))` produced warnings.
  ── Failure ('test-geom-hilbert-outline.R:99'): networks without outline are silently ignored ──
  `layer_grob(p)` produced warnings.
  
  [ FAIL 2 | WARN 21 | SKIP 5 | PASS 92 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggPredict.Rmd’ using rmarkdown
Loading required package: ggplot2
`geom_smooth()` using formula = 'y ~ x'
Loading required package: ggiraph
Loading required package: ggiraphExtra

Attaching package: 'ggiraphExtra'

The following objects are masked from 'package:moonBook':

    addLabelDf, getMapping

Loading required package: plyr
Quitting from lines 45-49 (ggPredict.Rmd) 
Error: processing vignette ‘ggPredict.Rmd’ failed with diagnostics:
Problem while converting geom to grob.
ℹ Error occurred in the 3rd layer.
Caused by error in `[.data.frame`:
! undefined columns selected
--- failed re-building ‘ggPredict.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
Problem while converting geom to grob.
ℹ Error occurred in the 3rd layer.
Caused by error in `[.data.frame`:
! undefined columns selected
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘ggPredict.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
Package required but not available: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggOceanMapsData’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggpie.Rmd’ using rmarkdown
Error: processing vignette ‘ggpie.Rmd’ failed with diagnostics:
there is no package called ‘prettydoc’
--- failed re-building ‘ggpie.Rmd’

SUMMARY: processing the following file failed:
  ‘ggpie.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    History
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'nlmixr', 'lixoftConnectors'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug fixes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    * Changes all data options to .data to decrease possibility of column naming overlap
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggshadow.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘ggspatial-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: load_longlake_data
> ### Title: Load longlake test data
> ### Aliases: load_longlake_data
> 
> ### ** Examples
> 
> load_longlake_data(which = "longlake_waterdf")
Error in CPL_read_ogr(dsn, layer, query, as.character(options), quiet,  : 
  Evaluation error: a valid "POSIXlt" object has names.
Calls: load_longlake_data ... <Anonymous> -> st_read -> st_read.character -> CPL_read_ogr
Execution halted
‘::’ or ‘:::’ import not declared from: ‘cli’
'LazyData' is specified without a 'data' directory
‘::’ or ‘:::’ import not declared from: ‘cli’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggtern.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Unknown package ‘IC2’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mlr3proba’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  phytr.c:419:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:2327:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3266:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3268:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3298:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3302:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3307:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3310:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3313:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3316:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3319:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3322:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  phytr.c:3325:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/glinvci.Rcheck/00install.out’ for details.
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
checkRd: (-1) glmc.control.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) glmc.control.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) basal.Rd:32: Escaped LaTeX specials: \_
checkRd: (-1) basal.Rd:33: Escaped LaTeX specials: \_ \_ \_
Found the following significant warnings:
  pb.c:27:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/glmnet.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) consensus.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) getfit.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘cplexAPI’
Found the following significant warnings:
  rho_rho_excess.c:16:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/globalKinhom.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following HTML validation problems:
walkAST.html:53:9 (walkAST.Rd:23): Warning: <code> anchor "name" already defined
walkAST.html:57:9 (walkAST.Rd:25): Warning: <code> anchor "call" already defined
walkAST.html:61:9 (walkAST.Rd:27): Warning: <code> anchor "pairlist" already defined
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  glpkAPI.h:81:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.h:84:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.h:87:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.h:101:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.h:104:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.h:107:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.h:460:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.h:491:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.c:433:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.c:446:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.c:459:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.c:722:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.c:791:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.c:825:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  glpkAPI.c:3400:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/glpkAPI.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
Found the following significant warnings:
  helpFunctions.cpp:100:20: warning: array subscript 1 is outside array bounds of ‘double [1]’ [-Warray-bounds]
  helpFunctions.cpp:152:20: warning: array subscript 1 is outside array bounds of ‘double [1]’ [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gMWT.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) barleyHeights.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) barleyHeights.Rd:22: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) BVDWSTOXX.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:16: Escaped LaTeX specials: \& \&
checkRd: (-1) BVDWSTOXX.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:37: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
pipe.html:40:9 (pipe.Rd:12): Warning: <code> anchor "lhs" already defined
pipe.html:44:9 (pipe.Rd:14): Warning: <code> anchor "rhs" already defined
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  R_register_native.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  R_register_native.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gower.c:60:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gower.c:72:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gower.c:83:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gower.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘gvcm.cat’
Unknown package ‘gvcm.cat’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) barplot2.Rd:219: Escaped LaTeX specials: \_
checkRd: (-1) colorpanel.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) qqnorm.aov.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) venn.Rd:59: Escaped LaTeX specials: \_
checkRd: (-1) GPoM.FDLyapu-package.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) Plague.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) lyapFDGrond.Rd:66: Escaped LaTeX specials: \&
checkRd: (-1) lyapFDGrond.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) lyapFDGrond.Rd:69: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘clusterProfiler’
Package unavailable to check Rd xrefs: ‘clusterProfiler’
'LazyData' is specified without a 'data' directory
checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) crdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) descApp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) layoutApp.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) rbdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) ttApp.Rd:43: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) gen_graph_indep.Rd:126: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mlGraphicalVAR.Rd:79: Escaped LaTeX specials: \~
Running ‘testthat.R’ [11s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(grates)
  > 
  > test_check("grates")
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  [ FAIL 2 | WARN 27 | SKIP 23 | PASS 408 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (23)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-month.R:128'): as_month.POSIXlt works as expected ────────────
  `result` (`actual`) not equal to as.POSIXlt("2021-01-01", tz = "NZ") (`expected`).
  
  `attr(actual, 'balanced')`:   <NA>
  `attr(expected, 'balanced')`: TRUE
  ── Failure ('test-quarter.R:64'): as_quarter.POSIXlt works as expected ─────────
  `result` (`actual`) not equal to as.POSIXlt("2021-01-01", tz = "NZ") (`expected`).
  
  `attr(actual, 'balanced')`:   <NA>
  `attr(expected, 'balanced')`: TRUE
  
  [ FAIL 2 | WARN 27 | SKIP 23 | PASS 408 ]
  Deleting unused snapshots:
  • plots/month.png
  • plots/month2.png
  • plots/quarter.png
  • plots/twentyeight_days.png
  • plots/two_weeks.png
  • plots/year.png
  • plots/yearweek_monday.png
  • plots/yearweek_thursday.png
  Error: Test failures
  Execution halted
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
Found the following significant warnings:
  Offset.c:3:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  omp_diagnose.c:5:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  omp_diagnose.c:18:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/grattan.Rcheck/00install.out’ for details.
Found the following significant warnings:
  init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gRc.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘xpectr’
Running examples in ‘groupdata2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: collapse_groups
> ### Title: Collapse groups with categorical, numerical, ID, and size
> ###   balancing
> ### Aliases: collapse_groups
> 
> ### ** Examples
> 
> # Attach packages
> library(groupdata2)
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> 
> # Set seed
> xpectr::set_test_seed(42)
Error in loadNamespace(x) : there is no package called ‘xpectr’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘automatic_groups_with_groupdata2.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

--- finished re-building ‘automatic_groups_with_groupdata2.Rmd’

--- re-building ‘cross-validation_with_groupdata2.Rmd’ using rmarkdown
Loading required package: lme4
Loading required package: Matrix

Attaching package: 'lmerTest'

The following object is masked from 'package:lme4':

    lmer

The following object is masked from 'package:stats':

    step

Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Quitting from lines 139-147 (cross-validation_with_groupdata2.Rmd) 
Error: processing vignette ‘cross-validation_with_groupdata2.Rmd’ failed with diagnostics:
there is no package called 'xpectr'
--- failed re-building ‘cross-validation_with_groupdata2.Rmd’

--- re-building ‘description_of_groupdata2.Rmd’ using rmarkdown

Attaching package: 'tidyr'

The following objects are masked from 'package:Matrix':

    expand, pack, unpack

--- finished re-building ‘description_of_groupdata2.Rmd’

--- re-building ‘introduction_to_groupdata2.Rmd’ using rmarkdown
--- finished re-building ‘introduction_to_groupdata2.Rmd’

--- re-building ‘time_series_with_groupdata2.Rmd’ using rmarkdown
Don't know how to automatically pick scale for object of type <ts>. Defaulting
to continuous.
--- finished re-building ‘time_series_with_groupdata2.Rmd’

SUMMARY: processing the following file failed:
  ‘cross-validation_with_groupdata2.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘p1_20up-vs-p2_25up_in_str1.txt’ ‘p1_20up-vs-p2_25up_in_str2.txt’
  ‘p2_25up-vs-p1_20up_in_str1.txt’ ‘p2_25up-vs-p1_20up_in_str2.txt’
  ‘s0_20up.txt’ ‘s0_30up.txt’ ‘s0_f2up.txt’ ‘strs.vec_01mx.txt’
  ‘strs.vec_02mx.txt’ ‘strs.vec_03mx.txt’ ‘strs.vec_04mx.txt’
  ‘strs.vec_05mx.txt’ ‘strs.vec_06mx.txt’ ‘strs.vec_30up.txt’
  ‘strs.vec_50up.txt’ ‘strs.vec_f2up.txt’ ‘uni_p1_20up-p2_25up.txt’
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘FMD mag discontinuities_disc.png’ ‘FMD mag
  discontinuities_disc1.res’ ‘FMD mag discontinuities_disc2.res’
  ‘IDYLLWILD_bvmed.png’ ‘IDYLLWILD_fig.png’ ‘Schuster's
  diagram_schu.png’ ‘hour.res’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  smolyak.c:58:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  smolyak.c:79:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  smolyak.c:227:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  smolyak.c:477:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gss.Rcheck/00install.out’ for details.
checkRd: (-1) gsym.point.Rd:143: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RRprof.out’
checkRd: (-1) GUTS-package.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) GUTS.Rd:201: Escaped LaTeX specials: \&
checkRd: (-1) GUTS.Rd:209: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) luzdat.Rd:21: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [6s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hablar)
  > test_check("hablar")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 416 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test.convert.R:118'): from Date ───────────────────────────────────
  tibble(a = as.Date(c("1970-05-03", NA, "1987-04-20"))) %>% convert(dtm(a)) not equal to tibble(a = as.POSIXct(as.Date(c("1970-05-03", NA, "1987-04-20")))).
  Component "a": 'tzone' attributes are inconsistent ('Europe/London' and 'UTC')
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 416 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  haplo.stats_init.c:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  haplo_em_pin.h:107:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  haplo_em_pin.c:1143:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  seqhap.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  seqhap.c:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  seqhap.c:110:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  seqhap.c:627:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  seqhap.c:807:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/haplo.stats.Rcheck/00install.out’ for details.
checkRd: (-1) haplo.design.Rd:33: Escaped LaTeX specials: \$
checkRd: (-1) haplo.design.Rd:42: Escaped LaTeX specials: \$
checkRd: (-1) haplo.glm.Rd:176: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) haplo.glm.Rd:178: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) haplo.glm.Rd:283: Escaped LaTeX specials: \$ \$
checkRd: (-1) haplo.glm.Rd:292: Escaped LaTeX specials: \$ \$
checkRd: (-1) haplo.glm.Rd:324: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
checkRd: (-1) HWAlr.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWAlrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWClr.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) HWClrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWIlr.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) HWf.Rd:25: Escaped LaTeX specials: \&
Package required but not available: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hash-accessors.Rd:46: Escaped LaTeX specials: \$
checkRd: (-1) hash-class.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) hash-class.Rd:45: Escaped LaTeX specials: \$
checkRd: (-1) hash-package.Rd:39: Escaped LaTeX specials: \#
Found the following significant warnings:
  readstat/readstat_bits.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/readstat_bits.c:11:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/readstat_variable.c:5:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/readstat_variable.c:8:25: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/sas/../readstat_bits.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/sas/ieee.c:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/sas/ieee.c:99:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/sas/readstat_sas.c:123:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/sas/readstat_xport_read.c:48:21: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/spss/readstat_por.h:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/spss/readstat_por.c:67:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/spss/readstat_por_write.c:170:25: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/spss/../readstat_bits.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  readstat/stata/../readstat_bits.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/haven.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) prm09.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) prm09.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) schools.Rd:18: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  H5Error.h:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  datatype_export.c:64:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  H5Error.c:122:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hdf5r.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
hergm.terms.html:71:78 (hergm.terms.Rd:68): Warning: <code> anchor "directed-network)" already defined
Package suggested but not available for checking: ‘synbreed’
'LazyData' is specified without a 'data' directory
checkRd: (-1) erode.hexbin.Rd:43: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
‘:::’ call which should be ‘::’: ‘ggplot2:::guide_axis’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ‘:::’ calls:
  ‘ggplot2:::build_guides’ ‘ggplot2:::scales_list’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘colorfulVennPlot’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  registerDynamicSymbol.c:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:14:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:18:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:20:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:21:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:23:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:24:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  registerDynamicSymbol.c:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hisse.Rcheck/00install.out’ for details.
checkRd: (-1) Snow.Rd:118: Escaped LaTeX specials: \&
checkRd: (-1) Snow.Rd:142: Escaped LaTeX specials: \&
checkRd: (-1) Yeast.Rd:56: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘trackr’
Package which this enhances but not available for checking: ‘HadoopStreaming’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ranksort.c:3:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ranksort.c:49:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ranksort.c:76:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Hmisc.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘ROI.plugin.mosek’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
checkRd: (-1) attributes_speclib.Rd:73: Escaped LaTeX specials: \$
checkRd: (-1) get_reflectance.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  useful.h:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hSDM.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  htree.c:126:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:135:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:324:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:362:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:408:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:517:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:693:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:711:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:813:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1476:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1494:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1528:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1679:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1754:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1839:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1869:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1909:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:2906:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:3696:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/htree.Rcheck/00install.out’ for details.
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  humanleague_init.c:14:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/humanleague.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Trancura9414001.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) Trancura9414001.Rd:28: Escaped LaTeX specials: \_
checkRd: (-1) hydroPSO.Rd:390: Escaped LaTeX specials: \&
checkRd: (-1) hydroPSO.Rd:408: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:7: Escaped LaTeX specials: \&
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘AIC.txt’ ‘AICc.txt’ ‘IAS.pdf’ ‘IAS2.pdf’ ‘IAS3.pdf’
  ‘P.microlepis-AIC.txt’ ‘P.microlepis-AICc.txt’ ‘P.microlepis-IAS.pdf’
  ‘P.microlepis-IAS2.pdf’ ‘P.microlepis-IAS3.pdf’
Package suggested but not available for checking: ‘gutenbergr’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ibdreg_init.c:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mcmemory.h:188:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sim.mark.prop.c:85:29: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sim.mark.prop.c:88:29: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sim.mark.prop.c:90:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sim.mark.prop.c:303:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sim.mark.prop.c:814:22: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sim.mark.prop.c:877:29: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sim.mark.prop.c:1018:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ibdreg.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SparkR’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘icd’
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘ICBayes’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) pulmonary.Rd:13: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rggobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggtree’
Package suggested but not available for checking: ‘optiRum’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘IFCdata’
Found the following significant warnings:
  ../inst/include/ut_debug.h:188:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ut_debug.c:102:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ifultools.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  core/core/error.c:65:29: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  vendor/plfit/gss.h:132:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  vendor/plfit/gss.c:60:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  vendor/plfit/mt.c:20:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  vendor/plfit/platform.c:36:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rrandom.h:26:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:104:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rinterface.c:2506:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rinterface.c:2522:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rinterface.c:9433:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rrandom.c:108:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/igraph.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Running ‘testthat.R’ [4s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(iheiddown)
  iheiddown  for IHEID
   Version  0.9.5  created on  2022-09-22 
  
  > 
  > test_check("iheiddown")
  [ FAIL 1 | WARN 1 | SKIP 2 | PASS 33 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  • On Linux (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-theme.R:28'): theme_iheid() grid is correct ──────────────────
  p[["theme"]][["panel.grid"]][["size"]] not identical to 0.2.
  target is NULL, current is numeric
  
  [ FAIL 1 | WARN 1 | SKIP 2 | PASS 33 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  RNifti_shim.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RNifti_shim.c:39:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  print.h:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  core.c:717:9: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/imbibe.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘accdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Found the following significant warnings:
  keyplayer-utils.c:24:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/influenceR.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
BugReports field should be the URL of a single webpage
Package which this enhances but not available for checking: ‘gurobi’
Found the following files/directories:
  ‘c.txt’ ‘rho.txt’ ‘sta.txt’ ‘topo.txt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Found the following significant warnings:
  DefinePolygons.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  DefinePolygons.c:18:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/inlmisc.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO for future releases:
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Error_Estimation_Response_1.tiff’ ‘Error_Estimation_Response_2.tiff’
  ‘Error_Estimation_Response_3.tiff’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Intervals-class.Rd:109: Escaped LaTeX specials: \_
checkRd: (-1) Intervals-class.Rd:110: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:68: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:76: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:77: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:78: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:79: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:81: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:88: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:89: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) sgd.Rd:12: Escaped LaTeX specials: \_
Running ‘testthat.R’ [51s/78s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(inTextSummaryTable)
  > 
  > test_check("inTextSummaryTable")
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 978 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_subjectProfileSummaryPlot-theme.R:39'): The line size is correctly set ──
  Error in `expect_setequal(ggDataLine$size, sizeLine)`: `object` and `expected` must both be vectors
  Backtrace:
      ▆
   1. └─testthat::expect_setequal(ggDataLine$size, sizeLine) at test_subjectProfileSummaryPlot-theme.R:39:8
   2.   └─rlang::abort("`object` and `expected` must both be vectors")
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 978 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) pine.Rd:20: Escaped LaTeX specials: \&
Found the following HTML validation problems:
analyseISE.html:206:15 (analyseISE.Rd:89): Error: <parametername> is not recognized!
analyseISE.html:206:15 (analyseISE.Rd:89): Warning: discarding unexpected <parametername>
analyseISE.html:210:15 (analyseISE.Rd:90): Error: <parametername> is not recognized!
analyseISE.html:210:15 (analyseISE.Rd:90): Warning: discarding unexpected <parametername>
describeISE.html:211:15 (describeISE.Rd:98): Error: <parametername> is not recognized!
describeISE.html:211:15 (describeISE.Rd:98): Warning: discarding unexpected <parametername>
describeISE.html:215:15 (describeISE.Rd:99): Error: <parametername> is not recognized!
describeISE.html:215:15 (describeISE.Rd:99): Warning: discarding unexpected <parametername>
Found the following significant warnings:
  trace_islasso.c:39:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/islasso.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘RMTplot.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Package suggested but not available for checking: ‘locClass’
checkRd: (-1) ivmodel.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) ivmodelFormula.Rd:79: Escaped LaTeX specials: \&
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  jGDtalk.c:116:16: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  jGDtalk.c:797:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  javaGD.c:373:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  javaGD.c:382:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/JavaGD.Rcheck/00install.out’ for details.
Output from running autoreconf:
  configure.ac:4: warning: The macro `AC_CONFIG_HEADER' is obsolete.
  configure.ac:4: You should run autoupdate.
  ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from...
  configure.ac:4: the top level
  configure.ac:24: warning: The macro `AC_HEADER_STDC' is obsolete.
  configure.ac:24: You should run autoupdate.
  ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
  configure.ac:24: the top level
  configure.ac:30: warning: The macro `AC_HEADER_TIME' is obsolete.
  configure.ac:30: You should run autoupdate.
  ./lib/autoconf/headers.m4:743: AC_HEADER_TIME is expanded from...
  configure.ac:30: the top level
  configure.ac:34: warning: The macro `AC_TYPE_SIGNAL' is obsolete.
  configure.ac:34: You should run autoupdate.
  ./lib/autoconf/types.m4:776: AC_TYPE_SIGNAL is expanded from...
  configure.ac:34: the top level
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    joineR <1.1
Package which this enhances but not available for checking: ‘remMap’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rjcommon.h:75:31: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jpeg.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) summ.rq.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) summ.rq.Rd:108: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: multiple methods tables found for ‘bootstrap’
  Warning: replacing previous import ‘arkhe::bootstrap’ by ‘dimensio::bootstrap’ when loading ‘kairos’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kairos.Rcheck/00install.out’ for details.
Warning: multiple methods tables found for ‘bootstrap’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Running examples in ‘kairos-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fit
> ### Title: Frequency Increment Test
> ### Aliases: fit fit-method fit,data.frame,numeric-method
> ###   fit,matrix,numeric-method
> 
> ### ** Examples
> 
> data("merzbach", package = "folio")
> 
> ## Keep only decoration types that have a maximum frequency of at least 50
> keep <- apply(X = merzbach, MARGIN = 2, FUN = function(x) max(x) >= 50)
> counts <- merzbach[, keep]
> 
> ## Group by phase
> ## We use the row names as time coordinates (roman numerals)
> dates <- as.numeric(utils::as.roman(rownames(counts)))
> 
> ## Frequency Increment Test
> freq <- fit(counts, dates)
> 
> ## Plot time vs abundance and highlight selection
> plot(freq)
Warning: 'as_long()' is deprecated.
Use 'to_long()' instead.
See help("Deprecated")
Error: Must request at least one colour from a hue palette.
Execution halted
Found the following HTML validation problems:
set_names-matrix-method.html:61:9 (set_names-matrix-method.Rd:20): Warning: <code> anchor "x" already defined
set_names-matrix-method.html:65:9 (set_names-matrix-method.Rd:22): Warning: <code> anchor "nodes" already defined
set_names-matrix-method.html:69:9 (set_names-matrix-method.Rd:24): Warning: <code> anchor "my_list" already defined
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘my.Mobius.set.func.csv’ ‘my.card.set.func.csv’ ‘my.set.func.csv’
Found the following files/directories:
  ‘song.wav’ ‘song4karaoke.wav’
Found the following HTML validation problems:
math_to_rd.html:81:2153 (math_to_rd.Rd:45): Warning: <svg> attribute "width" has invalid value "400em"
math_to_rd.html:81:2153 (math_to_rd.Rd:45): Warning: <svg> attribute "height" has invalid value "1.08em"
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ionosphere.Rd:22: Escaped LaTeX specials: \&
checkRd: (-1) ionosphere.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘Kmedians-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Kmeans
> ### Title: Kmeans
> ### Aliases: Kmeans
> ### Keywords: K-means
> 
> ### ** Examples
> 
> n <- 500
> K <- 3
> pcont <- 0.2
> ech <- gen_K(n=n,K=K,pcont=pcont)
> X <-ech$X
> res <- Kmeans(X,par=FALSE)
Error in library(p, character.only = TRUE) : 
  there is no package called ‘dplyr’
Calls: Kmeans -> %do% -> <Anonymous> -> library
Execution halted
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cld1.Rdata’ ‘main.tex’ ‘myCld.Rdata’ ‘myCld3d.Rdata’ ‘scene.asy’
Found the following files/directories:
  ‘cld1.Rdata’ ‘ld.Rdata’ ‘myCld.Rdata’
checkRd: (-1) pathFrechet.Rd:54: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Killed after ’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘VARSEDIG’
Unknown package ‘VARSEDIG’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘KSEA Bar Plot.tiff’ ‘KSEA Kinase Scores.csv’
  ‘KSEA.Merged.Heatmap.png’ ‘Kinase-Substrate Links.csv’
'LazyData' is specified without a 'data' directory
checkRd: (-1) kstIO-package.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) read_kbase.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) read_kdata.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) read_kfamset.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) read_kspace.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) read_kstructure.Rd:45: Escaped LaTeX specials: \&
checkRd: (-1) read_surmiserelation.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) write_kbase.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) write_kdata.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) write_kspace.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) write_kstructure.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) write_surmiserelation.Rd:36: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘DF7.bas’ ‘DF7.dat’ ‘DF7.rel’ ‘DF7.spc’ ‘DF7.struct’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) alphaOnly.Rd:25: Escaped LaTeX specials: \^
checkRd: (-1) alphaOnly.Rd:26: Escaped LaTeX specials: \$
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
checkRd: (-1) natlongsurv.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
Found the following significant warnings:
  init.c:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/largeList.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘example.llo’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ergm.userterms’
checkRd: (-1) simulate.ergmm.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) simulate.ergmm.Rd:36: Escaped LaTeX specials: \$
Unknown package ‘ergm.userterms’ in Rd xrefs
GNU make is a SystemRequirements.
Found the following significant warnings:
  init.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:18:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:24:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:27:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/later.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  lrsmp.h:147:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lrsmp.c:40:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LatticeDesign.Rcheck/00install.out’ for details.
checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'gof', 'lava.tobit'
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘lazyData/R/requireData.R’:
  attach(NULL, pos = pos, name = searchDataName)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) goodnessfit.Rd:105: Escaped LaTeX specials: \&
checkRd: (-1) lba.Rd:252: Escaped LaTeX specials: \&
checkRd: (-1) pregnancy.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) pregnancy.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    lcars.0.3.1
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  lcopula-init.c:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lcopula.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) leaps.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  rigraph/src/plfit/gss.h:132:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/plfit/gss.c:60:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/plfit/platform.c:36:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/plfit/mt.c:20:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/init.c:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/init.c:104:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/rinterface.c:2354:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/rinterface.c:2370:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/rinterface.c:9538:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rigraph/src/glpk_support.c:95:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/leidenbase.Rcheck/00install.out’ for details.
Found the following significant warnings:
  lemna.c:98:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lemna.c:109:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lemna.c:120:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lemna.c:129:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lemna.c:138:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lemna.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Running examples in ‘lemon-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotate_y_axis
> ### Title: Annotations in the axis
> ### Aliases: annotate_y_axis annotate_x_axis
> 
> ### ** Examples
> 
> library(ggplot2)

Attaching package: ‘ggplot2’

The following objects are masked from ‘package:lemon’:

    CoordCartesian, element_render

> 
> p <- ggplot(mtcars, aes(mpg, hp, colour=disp)) + geom_point()
> 
> l <- p + annotate_y_axis('mark at', y=200, tick=TRUE)
> l
Error in if (is.primary) { : argument is of length zero
Calls: <Anonymous> ... <Anonymous> -> draw -> <Anonymous> -> get_annotations
Execution halted
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lemon)
  > 
  > 
  > if (TRUE) {
  +   test_check("lemon")
  + } #else {
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 137 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_lemon_plot.r:12'): ggplot2 does not break lemon_plot by altering class ──
  `l + 1` threw an error with unexpected message.
  Expected match: "Can't add `1` to a ggplot object."
  Actual message: "Can't add `1` to a <ggplot> object."
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_lemon_plot.r:12:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─ggplot2:::`+.gg`(l, 1)
    7.   └─ggplot2:::add_ggplot(e1, e2, e2name)
    8.     ├─ggplot2::ggplot_add(object, p, objectname)
    9.     └─ggplot2:::ggplot_add.default(object, p, objectname)
   10.       └─cli::cli_abort("Can't add {.var {object_name}} to a {.cls ggplot} object.")
   11.         └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 137 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘capped-axes.Rmd’ using rmarkdown
Quitting from lines 61-62 (capped-axes.Rmd) 
Error: processing vignette ‘capped-axes.Rmd’ failed with diagnostics:
argument is of length zero
--- failed re-building ‘capped-axes.Rmd’

--- re-building ‘facet-rep-labels.Rmd’ using rmarkdown
Quitting from lines 38-42 (facet-rep-labels.Rmd) 
Error: processing vignette ‘facet-rep-labels.Rmd’ failed with diagnostics:
argument is of length zero
--- failed re-building ‘facet-rep-labels.Rmd’

--- re-building ‘geoms.Rmd’ using rmarkdown
--- finished re-building ‘geoms.Rmd’

--- re-building ‘gtable_show_lemonade.Rmd’ using rmarkdown
--- finished re-building ‘gtable_show_lemonade.Rmd’

--- re-building ‘legends.Rmd’ using rmarkdown
Quitting from lines 333-338 (legends.Rmd) 
Error: processing vignette ‘legends.Rmd’ failed with diagnostics:
argument is of length zero
--- failed re-building ‘legends.Rmd’

--- re-building ‘lemon_print.Rmd’ using rmarkdown
Warning: code chunks must not depend on the uncached chunk "unnamed-chunk-1"
Warning in sprintf("\n\n    ```{r %s}\n", opts, "\n") :
  one argument not used by format ‘

    ```{r %s}
’
Warning in sprintf("\n\n    ```{r %s}\n", opts, "\n") :
  one argument not used by format ‘

    ```{r %s}
’
Warning: code chunks must not depend on the uncached chunk "unnamed-chunk-4"
Warning in sprintf("\n\n    ```{r %s}\n", opts, "\n") :
  one argument not used by format ‘

    ```{r %s}
’
Warning in sprintf("\n\n    ```{r %s}\n", opts, "\n") :
  one argument not used by format ‘

    ```{r %s}
’
Warning in sprintf("\n\n    ```{r %s}\n", opts, "\n") :
  one argument not used by format ‘

    ```{r %s}
’
--- finished re-building ‘lemon_print.Rmd’

SUMMARY: processing the following files failed:
  ‘capped-axes.Rmd’ ‘facet-rep-labels.Rmd’ ‘legends.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  lfe.h:121:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lfe.h:122:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utils.c:195:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utils.c:208:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lfe.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  init.c:14:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lhs.Rcheck/00install.out’ for details.
Found the following significant warnings:
  trainLinear.c:20:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  trainLinear.c:93:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LiblineaR.ACF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  trainLinear.c:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  trainLinear.c:20:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  trainLinear.c:100:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  trainLinear.c:130:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LiblineaR.Rcheck/00install.out’ for details.
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/liGP.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LIMEcoli.Rd:125: Escaped LaTeX specials: \_
checkRd: (-1) Read.Rd:88: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:92: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:98: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:104: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:105: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:106: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:107: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:108: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:109: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:110: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:111: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:112: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:114: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.r’ [9s/13s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > library(testthat)
  > library(listdown)
  > 
  > test_check("listdown")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 35 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-create-doc.r:27'): Create page bundle works ──────────────────
  `ldb` not equal to read_reference("listdown-page-bundle.rds").
  Component "cc": Component "Sepal.Length": Component "Sepal.Width": Component "layers": Component 1: Names: 10 string mismatches
  Component "cc": Component "Sepal.Length": Component "Sepal.Width": Component "layers": Component 1: Length mismatch: comparison on first 11 components
  Component "cc": Component "Sepal.Length": Component "Sepal.Width": Component "layers": Component 1: Component 2: Modes of target, current: call, list
  Component "cc": Component "Sepal.Length": Component "Sepal.Width": Component "layers": Component 1: Component 2: target, current do not match when deparsed
  Component "cc": Component "Sepal.Length": Component "Sepal.Width": Component "layers": Component 1: Component 3: 'target' is not an environment
  Component "cc": Component "Sepal.Length": Component "Sepal.Width": Component "layers": Component 1: Component 4: 'current' is not an environment
  Component "cc": Component "Sepal.Length": Component "Sepal.Width": Component "layers": Component 1: Component 5: Modes: list, logical
  Component "cc": Component "Sepal.Length": Component "Sepal.Width": Component "layers": Component 1: Component 5: names for target but not for current
  Component "cc": Component "Sepal.Length": Component "Sepal.Width": Component "layers": Component 1: Component 5: Component 1: 1 element mismatch
  ...
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 35 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cauchypoly.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) normpoly.Rd:38: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) normpoly.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) hatr.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tTestTable.rda’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Author
    Maintainer
checkRd: (-1) SPSloess.Rd:71: Escaped LaTeX specials: \^ \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  CPkPlj.c:160:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  CPkPlj.c:324:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  CcovI.c:21:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/locits.Rcheck/00install.out’ for details.
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) ACS.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) EmployedACS.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSale.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleCA.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleCanton.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleNY.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:24: Escaped LaTeX specials: \$
checkRd: (-1) SalaryGender.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) SandP500.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) SandwichAnts.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) SandwichAnts2.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) TrafficFlow.Rd:18: Escaped LaTeX specials: \#
Found the following significant warnings:
  locpol.c:101:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/locpol.Rcheck/00install.out’ for details.
checkRd: (-1) KernelChars.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) Kernels.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) PRDenEstC.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) compKernVals.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) denCVBwSelC.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) equivKernel.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) kernelCtes.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) locPolWeights.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) locpol.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) locpol.Rd:82: Escaped LaTeX specials: \&
checkRd: (-1) locpolSmoothers.Rd:54: Escaped LaTeX specials: \&
checkRd: (-1) pluginBw.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) regCVBwSelC.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) thumbBw.Rd:40: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  veclib.h:316:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/logistf.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘main.tex’ ‘scene.asy’
'LazyData' is specified without a 'data' directory
checkRd: (-1) butstrap.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.nri.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.s.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.s.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) nri.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) roc.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) roc.s.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.s.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
‘::’ or ‘:::’ import not declared from: ‘cli’
Found the following files/directories:
  ‘Model_1.cm’ ‘dambacher.dot’ ‘levins.dot’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scio’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  LowRankQP.c:278:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  LowRankQP_init.c:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LowRankQP.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) lpepa.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:90: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:65: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘kerdiest’
checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) spectral.density.Rd:55: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  proj_conf_test.c:5:5: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  proj_conf_test.c:4:5: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  liblwgeom/liblwgeom.h:305:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  liblwgeom/lwboundingcircle.c:36:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  liblwgeom/lwboundingcircle.c:217:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lwin_wkt_lex.l:16:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lwgeom.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) read.magpie.Rd:20: Escaped LaTeX specials: \_ \_
checkRd: (-1) read.magpie.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) read.magpie.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) read.magpie.Rd:36: Escaped LaTeX specials: \_
checkRd: (-1) read.magpie.Rd:65: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:24: Escaped LaTeX specials: \_ \_
checkRd: (-1) write.magpie.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:42: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:43: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:70: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
checkRd: (-1) cilleruelo.Rd:36: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  libCEigen.c:76:9: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ManlyMix.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fixes
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘terminology.Rmd’ using rmarkdown
--- finished re-building ‘terminology.Rmd’

--- re-building ‘userguide.Rmd’ using rmarkdown
Linking to GEOS 3.11.0, GDAL 3.5.2, PROJ 9.1.0; sf_use_s2() is TRUE

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 346-352 (userguide.Rmd) 
Error: processing vignette ‘userguide.Rmd’ failed with diagnostics:
Not compatible with requested type: [type=character; target=double].
--- failed re-building ‘userguide.Rmd’

SUMMARY: processing the following file failed:
  ‘userguide.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scrubr’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    To do
checkRd: (-1) sw_sfac.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) Interpolation-class.Rd:41: Escaped LaTeX specials: \#
checkRd: (-1) MareyMap-class.Rd:85: Escaped LaTeX specials: \_
checkRd: (-1) MareyMap-methods.Rd:11: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) MareyMap-methods.Rd:12: Escaped LaTeX specials: \_
checkRd: (-1) SpeciesMaps-methods.Rd:11: Escaped LaTeX specials: \_
checkRd: (-1) interpolation-methods.Rd:13: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘clusterProfiler’
Package suggested but not available for checking: ‘flashr’
Package suggested but not available for checking: ‘wallace’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
checkRd: (-1) size_t-class.Rd:6: Escaped LaTeX specials: \_
Found the following significant warnings:
  libCEigen.c:76:9: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MatManlyMix.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  t_sparseVector.c:83:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  chm_common.h:72:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  chm_common.h:93:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  chm_common.h:94:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  chm_common.c:8:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  chm_common.c:25:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  chm_common.c:50:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Matrix.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  allocMatrix2.c:10:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  allocMatrix2.c:16:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/matrixStats.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘utilities.R’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dlm’
checkRd: (-1) maxControl.Rd:83: Escaped LaTeX specials: \&
Unknown package ‘dlm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map_5.png’ ‘maze_5.html’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cplexAPI’
checkRd: (-1) salamander.Rd:22: Escaped LaTeX specials: \&
checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  chMatrix.c:162:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mcmcsae_init.c:16:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mcmcsae.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) eigp.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:41: Escaped LaTeX specials: \&
Checking should be performed on sources prepared by ‘R CMD build’.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial version.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) glass.Rd:23: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) glass.Rd:24: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) glass.Rd:25: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) glass.Rd:26: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  threat-safe-random.h:58:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  threat-safe-random.h:70:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mdgc.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mriTest.Rd:9: Escaped LaTeX specials: \&
checkRd: (-1) riTest.Rd:9: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MethylCapSig’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mebootSpear.Rd:88: Escaped LaTeX specials: \_
checkRd: (-1) ullwan.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ullwan.Rd:8: Escaped LaTeX specials: \& \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Data_Correlation.txt’ ‘correlation_FDR_table.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  pspp-system-for-R.c:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  pspp-system-for-R.c:1291:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/memisc.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘genuMet’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) dslp.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) cardiac.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) plvol.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) sbp.Rd:16: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Found the following significant warnings:
  init.c:37:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mets.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    mev v.1.9x
    mev v.1.8x
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    First release of mfe:
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package unavailable to check Rd xrefs: ‘DAPAR’
checkRd: (-1) IPDNa.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) fdgs.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) mice.impute.cart.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) mice.impute.rf.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) pmm.match.Rd:41: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  do_nothing.h:4:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  do_nothing.c:11:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:7:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nanotimer.c:88:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/microbenchmark.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ecospat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AKMCS.Rd:215: Escaped LaTeX specials: \&
checkRd: (-1) BMP.Rd:164: Escaped LaTeX specials: \&
checkRd: (-1) IRW.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) IRW.Rd:151: Escaped LaTeX specials: \&
checkRd: (-1) MP.Rd:142: Escaped LaTeX specials: \&
checkRd: (-1) MetropolisHastings.Rd:58: Escaped LaTeX specials: \&
checkRd: (-1) SubsetSimulation.Rd:152: Escaped LaTeX specials: \&
checkRd: (-1) oscillator_d6.Rd:14: Escaped LaTeX specials: \&
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ forming offset [176, 183] is out of the bounds [0, 176] of object ‘b’ with type ‘arma::vec’ {aka ‘arma::Col<double>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mixedClust.Rcheck/00install.out’ for details.
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
Package which this enhances but not available for checking: ‘AnalyzeFMRI’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
Found the following HTML validation problems:
MixMAPclass.html:51:9 (MixMAPclass.Rd:23): Warning: <code> anchor "num.genes.detected" already defined
checkRd: (-1) mixmeta-package.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) mixmeta.ml.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ml.igls.Rd:62: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mixRasch’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) RTdata2.Rd:3: Escaped LaTeX specials: \#
checkRd: (-1) boot.comp.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) boot.se.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) compCDF.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) hmeEM.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) logisregmixEM.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) multmixEM.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) mvnormalmixEM.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) normalmixEM.Rd:133: Escaped LaTeX specials: \&
checkRd: (-1) normalmixEM2comp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) poisregmixEM.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) regmixEM.Rd:67: Escaped LaTeX specials: \&
Found the following HTML validation problems:
mixtools-internal.html:95:9 (mixtools-internal.Rd:66): Warning: <code> anchor "h" already defined
'LazyData' is specified without a 'data' directory
checkRd: (-1) mi.t.test.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) qboxplot.Rd:127: Escaped LaTeX specials: \&
checkRd: (-1) qboxplot.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) qbxp.stats.Rd:66: Escaped LaTeX specials: \&
checkRd: (-1) ssize.propCI.Rd:38: Escaped LaTeX specials: \&
Found the following significant warnings:
  waveform.c:31:4: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  waveform.c:44:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mlbench.Rcheck/00install.out’ for details.
checkRd: (-1) BreastCancer.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) Ionosphere.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) Ionosphere.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) PimaIndiansDiabetes.Rd:19: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Texture.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) AutumnLab.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) gp.list.Rd:16: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘mlr3hyperband-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mlr_optimizers_hyperband
> ### Title: Optimizer Using the Hyperband Algorithm
> ### Aliases: mlr_optimizers_hyperband OptimizerHyperband
> 
> ### ** Examples
> 
> library(bbotk)
> library(data.table)
> 
> # set search space
> search_space = domain = ps(
+   x1 = p_dbl(-5, 10),
+   x2 = p_dbl(0, 15),
+   fidelity = p_dbl(1e-2, 1, tags = "budget")
+ )
> 
> # objective with modified branin function, see `bbotk::branin()`
> objective = ObjectiveRFun$new(
+   fun = branin,
+   domain = domain,
+   codomain = ps(y = p_dbl(tags = "minimize"))
+ )
Error in .__ObjectiveRFun__initialize(self = self, private = private,  : 
  Assertion on 'fun' failed: Must have formal arguments: xs.
Calls: <Anonymous> ... .__ObjectiveRFun__initialize -> assert_function -> makeAssertion -> mstop
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mlrCPO.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.pdf’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  mmap.h:104:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mmap.h:108:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mmap.h:117:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mmap.c:74:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mmap.c:286:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  types.c:4:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mmap.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Flury’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘alstructure’

Packages which this enhances but not available for checking:
  'miraculix', 'MoBPSmaps'
'LazyData' is specified without a 'data' directory
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [2s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(modelr)
  > 
  > test_check("modelr")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 120 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-typical.R:41'): typical.integer works as expected ────────────
  typical(c(1L, 2L, 3L, 8L)) not identical to 2L.
  Objects equal but not identical
  ── Failure ('test-typical.R:42'): typical.integer works as expected ────────────
  typical(c(1L, 2L, 3L, 8L, NA_integer_)) not identical to 2L.
  Objects equal but not identical
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 120 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) polypes.Rd:17: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    * efourier with default norm=TRUE now messages about how wrong it may be
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ordsampler.c:59:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:113:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:124:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:386:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:544:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:560:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:710:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:1102:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sampler.c:52:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sampler.c:149:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sampler.c:158:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sampler.c:729:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/monoreg.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘mlrCPO’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
checkRd: (-1) Context.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) psyfun.boot.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) psyfun.boot.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
checkRd: (-1) genotype_data.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) phenotype_data.Rd:15: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) F.huggins.estim.Rd:199: Escaped LaTeX specials: \$ \$
checkRd: (-1) F.huggins.estim.Rd:205: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:206: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:207: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:208: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:209: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:210: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:212: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:213: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:214: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:215: Escaped LaTeX specials: \$
checkRd: (-1) lines.cjs.Rd:15: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ms_sev.Rd:31: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mkjnw.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) mkjnw.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  muhaz.c:1367:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mudens.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) MultBiplotR-package.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) MultBiplotR-package.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) print.multcompLetters.Rd:20: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘statnet’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
'LazyData' is specified without a 'data' directory
checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘asreml’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    PREVIOUS (Incomplete below)
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
Found the following significant warnings:
  namespace.c:4:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/namespace.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(nasapower)
  > 
  > test_check("nasapower")
  [ FAIL 1 | WARN 0 | SKIP 11 | PASS 53 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (11)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-get_power.R:317'): (code run outside of `test_that()`) ─────────
  Error in `vapply(interactions, function(x) {
      sprintf("%s => %s", request_summary(Request$new()$from_hash(x$request)), 
          response_summary(VcrResponse$new()$from_hash(x$response)))
  }, "")`: values must be length 1,
   but FUN(X[[1]]) result is length 0
  Backtrace:
      ▆
   1. └─vcr::use_cassette(...) at test-get_power.R:317:0
   2.   └─vcr::insert_cassette(...)
   3.     └─Cassette$new(...)
   4.       └─vcr (local) initialize(...)
   5.         └─self$http_interactions()
   6.           └─HTTPInteractionList$new(...)
   7.             └─vcr (local) initialize(...)
   8.               └─base::vapply(...)
  
  [ FAIL 1 | WARN 0 | SKIP 11 | PASS 53 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘spatialClust’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘ncdfgeom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read_attribute_data
> ### Title: Read attribute dataframe from NetCDF-DSG file
> ### Aliases: read_attribute_data
> 
> ### ** Examples
> 
> hucPolygons <- sf::read_sf(system.file('extdata','example_huc_eta.json', package = 'ncdfgeom'))
Error in CPL_read_ogr(dsn, layer, query, as.character(options), quiet,  : 
  Evaluation error: a valid "POSIXlt" object has names.
Calls: <Anonymous> -> st_read -> st_read.character -> CPL_read_ogr
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘geometry.Rmd’ using rmarkdown
Quitting from lines 34-45 (geometry.Rmd) 
Error: processing vignette ‘geometry.Rmd’ failed with diagnostics:
Evaluation error: a valid "POSIXlt" object has names.
--- failed re-building ‘geometry.Rmd’

--- re-building ‘ncdfgeom.Rmd’ using rmarkdown
Linking to GEOS 3.11.0, GDAL 3.5.2, PROJ 9.1.0; sf_use_s2() is TRUE

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

****Support Package****
This package is a USGS-R Support package. 
see: https://owi.usgs.gov/R/packages.html#support
--- finished re-building ‘ncdfgeom.Rmd’

--- re-building ‘timeseries.Rmd’ using rmarkdown
--- finished re-building ‘timeseries.Rmd’

SUMMARY: processing the following file failed:
  ‘geometry.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tergm’
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) netCoin-package.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_ \_
checkRd: (-1) makeNetwork.Rd:31: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘fastshp’
Package suggested but not available for checking: ‘statnet’
'LazyData' is specified without a 'data' directory
checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map.png’ ‘maze.html’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘nhdplusTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_plus_network_attributes
> ### Title: Add NHDPlus Network Attributes to a provided network.
> ### Aliases: add_plus_network_attributes
> 
> ### ** Examples
> 
> 
> source(system.file("extdata", "walker_data.R", package = "nhdplusTools"))
Warning in CPL_read_ogr(dsn, layer, query, as.character(options), quiet,  :
  GDAL Message 1: Non-conformant content for record 1 in column FDATE, 1999-07-03T05:00:00Z, successfully parsed
Error in CPL_read_ogr(dsn, layer, query, as.character(options), quiet,  : 
  Evaluation error: a valid "POSIXlt" object has names.
Calls: source ... <Anonymous> -> st_read -> st_read.character -> CPL_read_ogr
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘US_data.Rmd’ using rmarkdown
--- finished re-building ‘US_data.Rmd’

--- re-building ‘advanced_network.Rmd’ using rmarkdown
Warning in CPL_read_ogr(dsn, layer, query, as.character(options), quiet,  :
  GDAL Message 1: Non-conformant content for record 21 in column FDATE, 1999-10-05T00:00:00Z, successfully parsed
Quitting from lines 90-97 (advanced_network.Rmd) 
Error: processing vignette ‘advanced_network.Rmd’ failed with diagnostics:
Evaluation error: a valid "POSIXlt" object has names.
--- failed re-building ‘advanced_network.Rmd’

--- re-building ‘indexing.Rmd’ using rmarkdown
--- finished re-building ‘indexing.Rmd’

--- re-building ‘nhdplusTools.Rmd’ using rmarkdown
--- finished re-building ‘nhdplusTools.Rmd’

--- re-building ‘nhdplushr.Rmd’ using rmarkdown
--- finished re-building ‘nhdplushr.Rmd’

--- re-building ‘plot_nhdplus.Rmd’ using rmarkdown
--- finished re-building ‘plot_nhdplus.Rmd’

SUMMARY: processing the following file failed:
  ‘advanced_network.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nleqslv.c:4:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nwout.c:49:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nleqslv.Rcheck/00install.out’ for details.
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) nltm.control.Rd:29: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) Frobenius-nmf.Rd:141: Escaped LaTeX specials: \#
checkRd: (-1) KL-nmf.Rd:158: Escaped LaTeX specials: \#
checkRd: (-1) NMFStrategyIterative-class.Rd:69: Escaped LaTeX specials: \#
checkRd: (-1) NMFstd-class.Rd:179: Escaped LaTeX specials: \#
checkRd: (-1) nmf.Rd:755: Escaped LaTeX specials: \#
checkRd: (-1) nmf_update_KL.Rd:87: Escaped LaTeX specials: \#
checkRd: (-1) nmf_update_euclidean.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) offset-nmf.Rd:144: Escaped LaTeX specials: \#
Running examples in ‘NMF-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: profplot
> ### Title: Plotting Expression Profiles
> ### Aliases: profplot profplot.default
> ### Keywords: aplot
> 
> ### ** Examples
> 
> ## Don't show: 
> # roxygen generated flag
> options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
> ## End(Don't show)
> 
> # create a random target matrix
> v <- rmatrix(35, 10)
> 
> # fit a single NMF model
> res <- nmf(v, 3)
> profplot(res)
> 
> # fit a multi-run NMF model
> res2 <- nmf(v, 3, nrun=2)
# NOTE - CRAN check detected: limiting maximum number of cores [2/32]
> # ordering according to first profile
> profplot(res2, Colv=1) # increasing
> 
> # draw a profile correlation plot: this show how the basis components are
> # returned in an unpredictable order
> profplot(res, res2)
Error in col["alpha", ] <- as.character(as.hexmode(alpha)) : 
  incorrect number of subscripts on matrix
Calls: profplot ... <Anonymous> -> .set.list.defaults -> expand_list -> alphacol
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  veclib.h:302:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nncc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  geodesic.c:57:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nngeo.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Other ideas
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulatePop.Rd:43: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:16:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/norm.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ggtree’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) prepareplot.Rd:64: Escaped LaTeX specials: \#
checkRd: (-1) prepareplot.Rd:68: Escaped LaTeX specials: \#
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  vadr.h:55:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  promises.h:5:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dots.c:5:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  promises.c:93:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  vadr.c:22:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nseval.Rcheck/00install.out’ for details.
checkRd: (-1) Ardechedata.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) nsRFA-package.Rd:231: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'originr', 'parallelsugar'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  gutsRedIT.c:34:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gutsRedIT.c:58:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gutsRedSD.c:36:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gutsRedSD.c:64:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  odeGUTS_init.c:5:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  odeGUTS_init.c:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/odeGUTS.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘odetector.Rmd’ using rmarkdown
Error: processing vignette ‘odetector.Rmd’ failed with diagnostics:
there is no package called ‘prettydoc’
--- failed re-building ‘odetector.Rmd’

SUMMARY: processing the following file failed:
  ‘odetector.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘clusterProfiler’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘openNLPmodels.en’
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'gurobi', 'ggtree'
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
checkRd: (-1) quad_3D.Rd:22: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ forming offset [176, 183] is out of the bounds [0, 176] of object ‘b’ with type ‘arma::vec’ {aka ‘arma::Col<double>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ordinalClust.Rcheck/00install.out’ for details.
Found the following significant warnings:
  utilityFuns.c:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilityFuns.c:30:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilityFuns.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilityFuns.c:32:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilityFuns.c:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilityFuns.c:37:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilityFuns.c:41:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilityFuns.c:42:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilityFuns.c:43:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ordinal.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘result.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Error(s) in re-building vignettes:
  ...
--- re-building ‘graph_packing.Rmd’ using rmarkdown
--- finished re-building ‘graph_packing.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
--- finished re-building ‘intro.Rmd’

--- re-building ‘progressive_packing.Rmd’ using rmarkdown
Quitting from lines 204-226 (progressive_packing.Rmd) 
Error: processing vignette ‘progressive_packing.Rmd’ failed with diagnostics:
Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error in `check.length()`:
! ‘gpar’ element ‘lwd’ must not be length 0
--- failed re-building ‘progressive_packing.Rmd’

SUMMARY: processing the following file failed:
  ‘progressive_packing.Rmd’

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
'LazyData' is specified without a 'data' directory
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘CorShrink’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Imap’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
checkRd: (-1) pan.bd.Rd:65: Escaped LaTeX specials: \$
Error(s) in re-building vignettes:
  ...
--- re-building ‘PS1_Cat.Rmd’ using rmarkdown
Quitting from lines 30-32 (PS1_Cat.Rmd) 
Error: processing vignette ‘PS1_Cat.Rmd’ failed with diagnostics:
Timeout was reached: [mast.stsci.edu] Failed to connect to mast.stsci.edu port 443 after 7532 ms: Connection timed out
--- failed re-building ‘PS1_Cat.Rmd’

--- re-building ‘PS1_Images.Rmd’ using rmarkdown
Quitting from lines 29-33 (PS1_Images.Rmd) 
Error: processing vignette ‘PS1_Images.Rmd’ failed with diagnostics:
Timeout was reached: [ps1images.stsci.edu] SSL connection timeout
--- failed re-building ‘PS1_Images.Rmd’

SUMMARY: processing the following files failed:
  ‘PS1_Cat.Rmd’ ‘PS1_Images.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  ../inst/include/sundials/sundials_nvector.h:163:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_matrix.h:105:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_linearsolver.h:137:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_linearsolver.c:28:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_matrix.c:29:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_nonlinearsolver.h:131:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_nonlinearsolver.c:26:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_nvector.c:28:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/arkode/arkode_adapt_impl.h:125:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/arkode/arkode_impl.h:825:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/arkode/arkode.c:58:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/arkode/arkode_adapt.c:42:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/paropt.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘co2’ ‘co2.1’ ‘co2.2’ ‘co2s.1’ ‘co2s.2’ ‘ctm.1’ ‘ctm.2’ ‘m’ ‘m.1’
  ‘m.2’ ‘test’ ‘test.1’ ‘test.2’ ‘testa.1’ ‘testa.2’ ‘xfile.1’
  ‘xfile.2’
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \# \# \#
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [39s/59s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pathviewr)
  > #library(vdiffr)
  > 
  > test_check("pathviewr")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 288 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plot_by_subject.R:85'): top views created correctly via purrr::map ──
  environment(top_view[[4]][[3]][["facet"]][["super"]])[["args"]] not equal to NULL.
  Modes: list, NULL
  Lengths: 1, 0
  current is not list-like
  ── Failure ('test-plot_by_subject.R:161'): elev views created correctly via purrr::map ──
  environment(elev_view[[4]][[3]][["facet"]][["super"]])[["args"]] not equal to NULL.
  Modes: list, NULL
  Lengths: 1, 0
  current is not list-like
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 288 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [44s/74s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(patientProfilesVis)
  > 
  > test_check("patientProfilesVis")
  [ FAIL 1 | WARN 2 | SKIP 20 | PASS 360 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════
  • On CRAN (20)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════
  ── Failure ('test_addReferenceLinesProfilePlot.R:135'): Reference lines are correctly set from a specified data set with a custom subject variable ──
  {
      ...
  } not equal to {
      ...
  }.
  Component "layers": Component 2: Component 12: Component 5: Component 21: Component 7: Names: 1 string mismatch
  Component "layers": Component 2: Component 12: Component 5: Component 21: Component 9: Names: 1 string mismatch
  Component "layers": Component 2: Component 12: Component 5: Component 21: Component 18: 1 string mismatch
  Component "layers": Component 3: Component 12: Component 5: Component 21: Component 7: Names: 1 string mismatch
  Component "layers": Component 3: Component 12: Component 5: Component 21: Component 9: Names: 1 string mismatch
  Component "layers": Component 3: Component 12: Component 5: Component 21: Component 18: 1 string mismatch
  
  [ FAIL 1 | WARN 2 | SKIP 20 | PASS 360 ]
  Error: Test failures
  Execution halted
GNU make is a SystemRequirements.
checkRd: (-1) plot-methods.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) plot-methods.Rd:125: Escaped LaTeX specials: \_
checkRd: (-1) glue_search_tables.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_batch_get_item.Rd:32: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_delete_item.Rd:81: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_get_item.Rd:55: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_put_item.Rd:98: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_query.Rd:237: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_scan.Rd:174: Escaped LaTeX specials: \#
checkRd: (-1) dynamodb_update_item.Rd:177: Escaped LaTeX specials: \#
checkRd: (-1) elasticache_create_cache_cluster.Rd:291: Escaped LaTeX specials: \#
checkRd: (-1) elasticache_create_replication_group.Rd:329: Escaped LaTeX specials: \#
checkRd: (-1) cloudwatchlogs_create_log_group.Rd:30: Escaped LaTeX specials: \#
checkRd: (-1) licensemanager_create_license_configuration.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) licensemanager_create_license_configuration.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) opsworks_update_layer.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) opsworkscm_create_server.Rd:76: Escaped LaTeX specials: \#
checkRd: (-1) ssm_send_command.Rd:47: Escaped LaTeX specials: \$
checkRd: (-1) ssm_send_command.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) apigatewayv2_create_stage.Rd:34: Escaped LaTeX specials: \#
checkRd: (-1) apigatewayv2_update_stage.Rd:36: Escaped LaTeX specials: \#
checkRd: (-1) iam_update_account_password_policy.Rd:21: Escaped LaTeX specials: \#
Found the following significant warnings:
  pbatR_init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  pbatR_init.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pbatR.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  PBSddesolve.c:149:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PBSddesolve.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) l1pcastar.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) pcaL1-package.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Dist.Rd:50: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggtree’
Error(s) in re-building vignettes:
  ...
--- re-building ‘PCMBase.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'ggtree''
Quitting from lines 37-53 (PCMBase.Rmd) 
Error: processing vignette ‘PCMBase.Rmd’ failed with diagnostics:
The ggtree installation did not succeed. The vignette cannot be built.
--- failed re-building ‘PCMBase.Rmd’

--- re-building ‘PCMCreateModel.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'ggtree''
Quitting from lines 37-54 (PCMCreateModel.Rmd) 
Error: processing vignette ‘PCMCreateModel.Rmd’ failed with diagnostics:
The ggtree installation did not succeed. The vignette cannot be built.
--- failed re-building ‘PCMCreateModel.Rmd’

--- re-building ‘PCMParam.Rmd’ using rmarkdown
--- finished re-building ‘PCMParam.Rmd’

--- re-building ‘PCMTracePruning.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'ggtree''
Quitting from lines 37-59 (PCMTracePruning.Rmd) 
Error: processing vignette ‘PCMTracePruning.Rmd’ failed with diagnostics:
The ggtree installation did not succeed. The vignette cannot be built.
--- failed re-building ‘PCMTracePruning.Rmd’

SUMMARY: processing the following files failed:
  ‘PCMBase.Rmd’ ‘PCMCreateModel.Rmd’ ‘PCMTracePruning.Rmd’

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘PythonInR’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  PeakSegJoint_interface.c:113:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PeakSegJoint.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘crrstep’
checkRd: (-1) pec.Rd:250: Escaped LaTeX specials: \&
checkRd: (-1) pec.Rd:251: Escaped LaTeX specials: \&
checkRd: (-1) pec.Rd:256: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘georob’
GNU make is a SystemRequirements.
checkRd: (-1) breslow.Rd:27: Escaped LaTeX specials: \# \#
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) simulate.data.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) simulate.data.Rd:28: Escaped LaTeX specials: \_ \_
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) my.bspline.Rd:21: Escaped LaTeX specials: \$ \$ \$ \$ \$ \$
checkRd: (-1) my.bspline.Rd:27: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) pendensity.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:57: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:82: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:96: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:100: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:105: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Peptides.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) chart.ECDF.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘DMwR’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dendextendRcpp’
Found the following files/directories:
  ‘permus_per_dist_4’ ‘permus_per_shape_bin_4_0’
  ‘permus_per_shape_bin_4_1’ ‘permus_per_shape_bin_4_2’
  ‘permus_per_shape_bin_4_3’
'LazyData' is specified without a 'data' directory
checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRD.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRDUS.Rd:4: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘animation.gif’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  ml.c:39:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.pdf’
'LazyData' is specified without a 'data' directory
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:29: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:31: Escaped LaTeX specials: \_ \_
checkRd: (-1) maxConnectedSet.Rd:35: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:37: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:39: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:41: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:45: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:47: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
checkRd: (-1) phylo4d-methods.Rd:209: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GarlandJanis.IC.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.IC.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘ggsubplot’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sanitize_latex.Rd:49: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Running examples in ‘pkgmaker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alphacol
> ### Title: Colour utilities
> ### Aliases: alphacol
> 
> ### ** Examples
> 
> 
> # Alphas
> alphacol('red') # do nothing
Error in apply(col, 2, function(x) paste("#", paste(x, collapse = ""),  : 
  dim(X) must have a positive length
Calls: alphacol -> apply
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
Package required but not available: ‘ggtree’

Packages suggested but not available for checking:
  'harmony', 'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggtern’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘plotmm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_gmm
> ### Title: Plots Mixture Components from Gaussian Mixture Models
> ### Aliases: plot_gmm
> 
> ### ** Examples
> 
> if(require(mixtools)){
+ mixmdl <- mixtools::normalmixEM(faithful$waiting, k = 2)
+ }
Loading required package: mixtools
mixtools package, version 1.2.0, Released 2020-02-05
This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.

number of iterations= 29 
> plot_gmm(mixmdl, 2)
Error in `ggplot2::stat_function()`:
! Problem while setting up geom.
ℹ Error occurred in the 2nd layer.
Caused by error in `compute_geom_1()`:
! `geom_line()` requires the following missing aesthetics: y
Backtrace:
     ▆
  1. ├─base (local) `<fn>`(x)
  2. └─ggplot2:::print.ggplot(x)
  3.   ├─ggplot2::ggplot_build(x)
  4.   └─ggplot2:::ggplot_build.ggplot(x)
  5.     └─ggplot2:::by_layer(...)
  6.       ├─rlang::try_fetch(...)
  7.       │ ├─base::tryCatch(...)
  8.       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9.       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 11.       │ └─base::withCallingHandlers(...)
 12.       └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
 13.         └─l$compute_geom_1(d)
 14.           └─ggplot2 (local) compute_geom_1(..., self = self)
 15.             └─ggplot2:::check_required_aesthetics(...)
 16.               └─cli::cli_abort(message, call = call)
 17.                 └─rlang::abort(...)
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) PLS_beta_wvc.Rd:5: Escaped LaTeX specials: \_
checkRd: (-1) plsRbeta.Rd:104: Escaped LaTeX specials: \^
Package suggested but not available for checking: ‘plsdepot’
checkRd: (-1) PLS_glm_wvc.Rd:5: Escaped LaTeX specials: \_
checkRd: (-1) PLS_lm_wvc.Rd:5: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [10s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(plyr)
  > 
  > test_check("plyr")
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 761 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (6)
  • empty test (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-rbind.r:21'): variable classes are preserved ─────────────────
  `x` not equal to `expected`.
  Component "e": Attributes: < Names: 1 string mismatch >
  Component "e": Attributes: < Length mismatch: comparison on first 1 components >
  Component "e": Attributes: < Component 1: Modes: logical, character >
  Component "e": Attributes: < Component 1: Lengths: 1, 2 >
  Component "e": Attributes: < Component 1: target is logical, current is character >
  Backtrace:
      ▆
   1. └─testthat::expect_that(ab1, equals(ab2)) at test-rbind.r:21:2
   2.   └─testthat (local) condition(object)
   3.     └─testthat::expect_equal(x, expected, ..., expected.label = label)
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 761 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [13s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmparser)
  > 
  > test_check('pmparser')
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 179 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (4)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_modify_pubmed_db_std.R:32'): modifyPubmedDb create matches standard ──
  readme not equal to DBI::dbReadTable(conExp, tableName).
  Component "text": 1 string mismatch
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 179 ]
  Error: Test failures
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘pollimetrydata’
Found the following files/directories:
  ‘polyfreqs-mcmc.out’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
Packages suggested but not available for checking:
  'BASIX', 'WhopGenome', 'BlockFeST'
Found the following significant warnings:
  tabix/khash.h:129:38: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  tabix/bgzf.c:138:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  tabix/bam_endian.h:6:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PopGenome.Rcheck/00install.out’ for details.
checkRd: (-1) BayeScanR.Rd:7: Escaped LaTeX specials: \&
checkRd: (-1) MKT-methods.Rd:8: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘lfa’
Package suggested but not available for checking: ‘RClone’
Found the following significant warnings:
  init.c:24:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  omp_test.c:7:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/poppr.Rcheck/00install.out’ for details.
checkRd: (-1) genetic_distance.Rd:106: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tradelist-class.Rd:91: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:146: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:148: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:126: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:219: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:221: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:225: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:229: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:231: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:233: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:235: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:237: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:301: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:303: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:305: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:307: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:309: Escaped LaTeX specials: \&
checkRd: (-1) med_pn.Rd:129: Escaped LaTeX specials: \&
Unknown package ‘advclust’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) findRes.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) ppmlasso-package.Rd:42: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  sum.c:358:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  prod.c:27:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:28:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PreciseSums.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    CalEquation function can calculate intercept in multiple regression model with interaction
    New arguments summarymode added to fit2newdata(), predict3d() and ggPredict()
    New arguments xlab, ylab and zlab added to predict3d()
    New function gg_color_hue() and theme_bw2() added
    Bug-fixed
    New function restoreData2(), restoreData3()  added
    New function add_lines() added
    New function ggPredict() and predict3d() added
    New function fit2newdata() added
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘ffbase’
Unknown package ‘ffbase’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zhegv.c:232:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zhegv.c:3715:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PRIMME.Rcheck/00install.out’ for details.
checkRd: (-1) prim.box.Rd:60: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  procmap.c:20:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/procmaps.Rcheck/00install.out’ for details.
checkRd: (-1) prodlim.Rd:119: Escaped LaTeX specials: \&
checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘BayesianTools’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProFit’
Found the following significant warnings:
  pause.c:10:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/profvis.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘SDMTools’
Running ‘testthat.R’ [20s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(propr)
  > 
  > test_check("propr")
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 197 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-aldex2propr.R:97'): iqlr matches ALDEx2 implementation ───────
  perb(marg.abs[, 1:50] + 0.5, ivar = "iqlr")@matrix not equal to perb(marg.abs[, 1:50] + 0.5, ivar = z)@matrix.
  2450/2500 mismatches (average diff: 0.0509)
  [2]   0.45221 -  0.3838 ==  0.06842
  [3]  -0.65122 - -0.7554 ==  0.10416
  [4]  -0.82028 - -0.8190 == -0.00130
  [5]   0.40911 -  0.3153 ==  0.09377
  [6]  -0.58339 - -0.6845 ==  0.10112
  [7]   0.51454 -  0.5107 ==  0.00379
  [8]  -0.57212 - -0.6929 ==  0.12082
  [9]  -0.00375 -  0.0136 == -0.01739
  [10]  0.59415 -  0.5631 ==  0.03102
  ...
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 197 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘cin’
Found the following significant warnings:
  computeParentIonMass.c:59:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/protViz.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rdt’
Found the following significant warnings:
  util.c:6:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pscl.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘pspatreg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: impactsnopar
> ### Title: Compute direct, indirect and total impacts functions for
> ###   continous non-parametric covariates in semiparametric spatial
> ###   regression models.
> ### Aliases: impactsnopar
> 
> ### ** Examples
> 
> ################################################
> # Examples using spatial data of Ames Houses.
> ###############################################
> # Getting and preparing the data
> library(pspatreg)
> library(spdep)
Loading required package: sp
Loading required package: spData
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
Loading required package: sf
Linking to GEOS 3.11.0, GDAL 3.5.2, PROJ 9.1.0; sf_use_s2() is TRUE
> library(sf)
> ames <- AmesHousing::make_ames() # Raw Ames Housing Data
> ames_sf <- st_as_sf(ames, coords = c("Longitude", "Latitude"))
> ames_sf$Longitude <- ames$Longitude
> ames_sf$Latitude <- ames$Latitude
> ames_sf$lnSale_Price <- log(ames_sf$Sale_Price)
> ames_sf$lnLot_Area <- log(ames_sf$Lot_Area)
> ames_sf$lnTotal_Bsmt_SF <- log(ames_sf$Total_Bsmt_SF+1)
> ames_sf$lnGr_Liv_Area <- log(ames_sf$Gr_Liv_Area)
> ########### Constructing the spatial weights matrix
> ames_sf1 <- ames_sf[(duplicated(ames_sf$Longitude) == FALSE), ]
> coord_sf1 <- cbind(ames_sf1$Longitude, ames_sf1$Latitude)
> ID <- row.names(as(ames_sf1, "sf"))
> col_tri_nb <- tri2nb(coord_sf1)
> soi_nb <- graph2nb(soi.graph(col_tri_nb, 
+                             coord_sf1), 
+                    row.names = ID)
Error in soi.graph(col_tri_nb, coord_sf1) : dbscan required
Calls: graph2nb -> soi.graph
Execution halted
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) esa.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) meta_varcov.Rd:9: Escaped LaTeX specials: \&
checkRd: (-1) meta_varcov.Rd:120: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘fulltext’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Ch05-detail.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:32: Escaped LaTeX specials: \#
checkRd: (-1) Ch0C-plot.cpd.PwrGSD.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) aid_st2.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘exampleplot_1_blockdist_1.png’ ‘exampleplot_1_blockdist_2.png’
  ‘exampleplot_1_blockdist_3.png’ ‘exampleplot_1_bootdist.png’
  ‘exampleplot_1_dist.png’ ‘exampleplot_1_histogramtest_EMD.png’
  ‘exampleplot_1_roc_dynamic.png’ ‘exampleplot_1_slidedist_1.png’
  ‘exampleplot_1_slidedist_2.png’ ‘exampleplot_1_slidedist_3.png’
  ‘exampleplot_1_trimmeddist.png’ ‘exampleplot_blockdist_1.png’
  ‘exampleplot_blockdist_2.png’ ‘exampleplot_blockdist_3.png’
  ‘exampleplot_bootdist.png’ ‘exampleplot_dist.png’
  ‘exampleplot_lim_dyn.png’ ‘exampleplot_lim_sig.png’
  ‘exampleplot_lim_sta.png’ ‘exampleplot_noc.png’
  ‘exampleplot_roc_dyn.png’ ‘exampleplot_roc_sta.png’
  ‘exampleplot_slidedist_1.png’ ‘exampleplot_slidedist_2.png’
  ‘exampleplot_slidedist_3.png’ ‘exampleplot_trimmeddist.png’
  ‘myworkflow_result.xml’ ‘test_2_roc_dynamic.png’ ‘test_4_dist.png’
  ‘test_5_blockdist_1.png’ ‘test_5_blockdist_2.png’
  ‘test_5_blockdist_3.png’ ‘test_6_slidedist_1.png’
  ‘test_6_slidedist_2.png’ ‘test_6_slidedist_3.png’
  ‘test_7_trimmeddist.png’ ‘test_8_bootdist.png’ ‘test_emd_1d.png’
  ‘test_emd_2d.png’ ‘test_jsd_1d.png’ ‘test_jsd_2d.png’
  ‘test_kld_1d.png’ ‘test_kld_2d.png’ ‘test_ms_1d.png’ ‘test_ms_2d.png’
  ‘test_rms_1d.png’ ‘test_rms_2d.png’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘EWAS_QC_graph_effectsize.png’ ‘EWAS_QC_graph_precision.png’
  ‘EWAS_QC_legend.txt’ ‘sample1.txt.gz’ ‘sample2.txt.gz’
  ‘sample_map.txt.gz’ ‘sample_output.graph_M.png’
  ‘sample_output.graph_QQ.png’ ‘sample_output.graph_p.png’
  ‘sample_output.graph_volcano.png’ ‘sample_output.histo.png’
  ‘sample_output.txt’ ‘sample_output1.graph_M.png’
  ‘sample_output1.graph_QQ.png’ ‘sample_output1.graph_p.png’
  ‘sample_output1.graph_volcano.png’ ‘sample_output1.histo.png’
  ‘sample_output2.graph_M.png’ ‘sample_output2.graph_QQ.png’
  ‘sample_output2.graph_p.png’ ‘sample_output2.graph_volcano.png’
  ‘sample_output2.histo.png’ ‘translation_table.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CentAndClusfuns.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) EBICglasso.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) pathways.Rd:36: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qoi.Rcheck/00install.out’ for details.
Running examples in ‘qqboxplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_qqboxplot
> ### Title: A modification of the boxplot with information about the tails
> ### Aliases: geom_qqboxplot
> 
> ### ** Examples
> 
> p <- ggplot2::ggplot(simulated_data, ggplot2::aes(factor(group,
+ levels=c("normal, mean=2", "t distribution, df=32", "t distribution, df=16",
+ "t distribution, df=8", "t distribution, df=4")), y=y))
> p + geom_qqboxplot()
Error in `geom_qqboxplot()`:
! Problem while computing stat.
ℹ Error occurred in the 1st layer.
Caused by error in `has_groups()`:
! could not find function "has_groups"
Backtrace:
     ▆
  1. ├─base (local) `<fn>`(x)
  2. ├─ggplot2:::print.ggplot(x)
  3. │ ├─ggplot2::ggplot_build(x)
  4. │ └─ggplot2:::ggplot_build.ggplot(x)
  5. │   └─ggplot2:::by_layer(...)
  6. │     ├─rlang::try_fetch(...)
  7. │     │ ├─base::tryCatch(...)
  8. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 11. │     │ └─base::withCallingHandlers(...)
 12. │     └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
 13. │       └─l$compute_statistic(d, layout)
 14. │         └─ggplot2 (local) compute_statistic(..., self = self)
 15. │           └─self$stat$setup_params(data, self$stat_params)
 16. │             └─qqboxplot (local) setup_params(...)
 17. └─base::.handleSimpleError(...)
 18.   └─rlang (local) h(simpleError(msg, call))
 19.     └─handlers[[1L]](cnd)
 20.       └─cli::cli_abort(...)
 21.         └─rlang::abort(...)
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘qqboxplot-basic-usage.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 39-50 (qqboxplot-basic-usage.Rmd) 
Error: processing vignette ‘qqboxplot-basic-usage.Rmd’ failed with diagnostics:
Problem while computing stat.
ℹ Error occurred in the 1st layer.
Caused by error in `has_groups()`:
! could not find function "has_groups"
--- failed re-building ‘qqboxplot-basic-usage.Rmd’

--- re-building ‘qqboxplot-paper-replication.Rmd’ using rmarkdown
Quitting from lines 39-78 (qqboxplot-paper-replication.Rmd) 
Error: processing vignette ‘qqboxplot-paper-replication.Rmd’ failed with diagnostics:
Problem while computing stat.
ℹ Error occurred in the 1st layer.
Caused by error in `has_groups()`:
! could not find function "has_groups"
--- failed re-building ‘qqboxplot-paper-replication.Rmd’

SUMMARY: processing the following files failed:
  ‘qqboxplot-basic-usage.Rmd’ ‘qqboxplot-paper-replication.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘lambda.pdf’ ‘qqplot.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) GRI.Rd:3: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  glmBias.c:84:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/QuasiSeq.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fastshp', 'visualTest'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) qwraps2.Rd:73: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘R2admb.Rnw’ using knitr
Loading required package: stats4

Attaching package: 'bbmle'

The following object is masked from 'package:R2admb':

    stdEr

Warning: Removed 36 rows containing missing values (`geom_line()`).
Warning: Removed 111 rows containing missing values (`geom_point()`).
Loading required package: Matrix
Error: processing vignette ‘R2admb.Rnw’ failed with diagnostics:
Running ‘texi2dvi’ on ‘R2admb.tex’ failed.
LaTeX errors:
! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Emergency stop.
 ...                                              
                                                  
l.224 .....`) was deprecated in ggplot2 3.4.0.\\\#
                                                  \# i Please use `after\_st...
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘R2admb.Rnw’

SUMMARY: processing the following file failed:
  ‘R2admb.Rnw’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ../inst/include/sundials/sundials_nvector.h:163:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_nonlinearsolver.h:131:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_matrix.h:105:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_linearsolver.h:137:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lib/sundials/sundials_nonlinearsolver.c:26:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lib/sundials/sundials_matrix.c:29:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lib/sundials/sundials_nvector.c:28:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lib/sundials/sundials_linearsolver.c:28:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/r2sundials.Rcheck/00install.out’ for details.
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
Package suggested but not available for checking: ‘BayesianTools’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggtree’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘blcs.dot’ ‘ex1.dot’ ‘ex1bridge1.dot’ ‘ex1bridge2.dot’
  ‘ex1bridge3.dot’ ‘ex1effect1.dot’ ‘ex1effect2.dot’ ‘gcmlinear.dot’
  ‘latent.dot’ ‘lcs.dot’ ‘mimic.dot’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RandomFields’
Found the following significant warnings:
  win_linux_aux.h:40:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RandomFieldsUtils.h:46:2: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RandomFieldsUtils.h:47:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RandomFieldsUtils.h:64:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RandomFieldsUtils.h:66:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RandomFieldsUtils.h:67:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RandomFieldsUtils.h:68:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RandomFieldsUtils.h:72:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Utils.h:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  options.h:152:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  options.h:155:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz_RandomFieldsUtils.h:96:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz_RandomFieldsUtils.h:97:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz_RandomFieldsUtils.h:132:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RandomFieldsUtils.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fixes
    New Features
    Major Changes
    Minor changes
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘article.Rnw’ using knitr
Loading required package: ggplot2
Loading required package: plotrix
Loading required package: survival
Warning: The following aesthetics were dropped during statistical
transformation: weight
ℹ This can happen when ggplot fails to infer the correct grouping
  structure in the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a
  numerical variable into a factor?
Warning: Computation failed in `stat_boxplot()`
Caused by error in `loadNamespace()`:
! there is no package called 'quantreg'
Warning: Computation failed in `stat_boxplot()`
Caused by error in `loadNamespace()`:
! there is no package called 'quantreg'
Error: processing vignette ‘article.Rnw’ failed with diagnostics:
Running ‘texi2dvi’ on ‘article.tex’ failed.
LaTeX errors:
! LaTeX Error: Unicode character ℹ (U+2139)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! Emergency stop.
 ...                                              
                                                  
l.1084 ...plot fails to infer the correct grouping
                                                  
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘article.Rnw’

--- re-building ‘comparison-example.Rnw’ using knitr
--- finished re-building ‘comparison-example.Rnw’

--- re-building ‘desirability-example.Rnw’ using knitr
--- finished re-building ‘desirability-example.Rnw’

--- re-building ‘randomizeR-refCard.Rnw’ using knitr
--- finished re-building ‘randomizeR-refCard.Rnw’

SUMMARY: processing the following file failed:
  ‘article.Rnw’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ri’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Running examples in ‘rangeBuilder-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coordError
> ### Title: Coordinate error
> ### Aliases: coordError
> 
> ### ** Examples
> 
> data(crotalus)
> 
> xy <- crotalus[1:100, c('decimallongitude','decimallatitude')]
> 
> coordError(xy)

  |                                                  | 0 % ~calculating  Error in sp::spTransform(pts, CRS("+proj=cea +lon_0=0 +lat_ts=30 +x_0=0 +y_0=0 +ellps=WGS84 +units=m +no_defs")) : 
  package rgdal is required for spTransform methods
Calls: coordError -> <Anonymous> -> FUN -> <Anonymous> -> <Anonymous>
Execution halted
Packages suggested but not available for checking:
  'ecospat', 'googlesheets'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  sketch.c:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sketch.c:38:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sketch.c:172:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sketch.c:206:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RaProR.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following HTML validation problems:
paRaoP.html:71:9 (paRaoP.Rd:22): Warning: <code> anchor "debugging" already defined
paRaoS.html:72:9 (paRaoS.Rd:23): Warning: <code> anchor "debugging" already defined
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  geodesic.c:50:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/raster.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  bedrock_leveldb.h:74:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.h:100:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.h:102:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.h:103:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  support.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.c:545:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.c:785:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.c:797:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.c:802:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:39:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:136:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:137:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:138:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nbt.c:35:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  random.c:44:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  random.c:56:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  random.c:90:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  subchunk.c:9:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  support.c:205:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rbedrock.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  charsets.h:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bib2be.c:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bibtexdirectin.c:93:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  charsets.c:34614:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rbibutils.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Running ‘test-all.R’ [4s/5s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("rbison")
  Loading required package: rbison
  [ FAIL 2 | WARN 0 | SKIP 5 | PASS 15 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (5)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-bison.R:4'): bison returns the correct value ───────────────────
  Error: lexical error: invalid char in json text.
                                         eyJvY2N1cnJlbmNlcyI6eyJsZWdlbmQ
                       (right here) ------^
  
  Backtrace:
      ▆
   1. ├─vcr::use_cassette(...) at test-bison.R:4:2
   2. │ └─cassette$call_block(...)
   3. └─rbison::bison(species = "Bison bison", count = 5) at test-bison.R:5:4
   4.   ├─rbison:::bison_data(...)
   5.   └─rbison:::bison_GET(...)
   6.     └─jsonlite::fromJSON(out, FALSE)
   7.       └─jsonlite:::parse_and_simplify(...)
   8.         └─jsonlite:::parseJSON(txt, bigint_as_char)
   9.           └─jsonlite:::parse_string(txt, bigint_as_char)
  ── Error ('test-bisonmap.R:4'): bisonmap returns the correct class ─────────────
  Error: lexical error: invalid char in json text.
                                         eyJvY2N1cnJlbmNlcyI6eyJsZWdlbmQ
                       (right here) ------^
  
  Backtrace:
      ▆
   1. ├─vcr::use_cassette(...) at test-bisonmap.R:4:2
   2. │ └─cassette$call_block(...)
   3. └─rbison::bison(species = "Aquila chrysaetos", count = 100) at test-bisonmap.R:5:4
   4.   ├─rbison:::bison_data(...)
   5.   └─rbison:::bison_GET(...)
   6.     └─jsonlite::fromJSON(out, FALSE)
   7.       └─jsonlite:::parse_and_simplify(...)
   8.         └─jsonlite:::parseJSON(txt, bigint_as_char)
   9.           └─jsonlite:::parse_string(txt, bigint_as_char)
  
  [ FAIL 2 | WARN 0 | SKIP 5 | PASS 15 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘rbmi/R/parallel.R’:
  attach(getNamespace("rbmi"))
See section ‘Good practice’ in ‘?attach’.
GNU make is a SystemRequirements.
checkRd: (-1) mn4joint1condi.Rd:39: Escaped LaTeX specials: \$
checkRd: (-1) mn4joint1condi.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) objets.Rd:66: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘rcanvec.cache’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.RData’
Found the following significant warnings:
  nonred.c:99:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rcdd.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
compute_metrics.html:76:15 (compute_metrics.Rd:28): Error: <metric> is not recognized!
compute_metrics.html:76:15 (compute_metrics.Rd:28): Warning: discarding unexpected <metric>
compute_metrics.html:80:15 (compute_metrics.Rd:29): Error: <metric> is not recognized!
compute_metrics.html:80:15 (compute_metrics.Rd:29): Warning: discarding unexpected <metric>
get_best.html:86:15 (get_best.Rd:34): Error: <metric> is not recognized!
get_best.html:86:15 (get_best.Rd:34): Warning: discarding unexpected <metric>
get_best.html:90:15 (get_best.Rd:35): Error: <metric> is not recognized!
get_best.html:90:15 (get_best.Rd:35): Warning: discarding unexpected <metric>
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘data.csv’
Running ‘test-all.R’ [11s/61s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(rcites)
  > library(tibble)
  > test_check("rcites")
  i Now processing taxon_id '4521'...................... v
  i Now processing taxon_id '0'......................... x
  i Now processing taxon_id '4521'...................... v
  i Now processing taxon_id '4521'...................... v
  i Skipping '1wrong234'.
  
  i Now processing taxon_id '4521'...................... v
  i Retrieving info from page 1 ........................ v
  i 483 pages available, retrieving info from 1 more
  i 8304 pages available, retrieving info from 1 more
  i Authentication token stored for the session.
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 108 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (6)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-token.R:14'): caught wrong token ───────────────────────────────
  Error in `vapply(interactions, function(x) {
      sprintf("%s => %s", request_summary(Request$new()$from_hash(x$request)), 
          response_summary(VcrResponse$new()$from_hash(x$response)))
  }, "")`: values must be length 1,
   but FUN(X[[1]]) result is length 0
  Backtrace:
      ▆
   1. └─vcr::use_cassette(...) at test-token.R:14:2
   2.   └─vcr::insert_cassette(...)
   3.     └─Cassette$new(...)
   4.       └─vcr (local) initialize(...)
   5.         └─self$http_interactions()
   6.           └─HTTPInteractionList$new(...)
   7.             └─vcr (local) initialize(...)
   8.               └─base::vapply(...)
  
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 108 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  RClickhouse_init.c:23:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RClickhouse.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘outcmaesdisp.dat’
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) RcmdrPlugin.MA-package.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package suggested but not available for checking: ‘conics’
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rredis’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rDEA_init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rDEA.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  dsdp/include/dsdp5.h:206:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../../include/dsdp5.h:206:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dsdpcops.c:20:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dsdpsetoptions.c:280:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sdpalloc.c:4:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rdsdp.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) re2_syntax.Rd:539: Escaped LaTeX specials: \_
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
grepNumeric.html:44:9 (grepNumeric.Rd:15): Warning: <code> anchor "x" already defined
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [44s/66s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(readwritesqlite)
  > 
  > test_check("readwritesqlite")
  Saving files to '/home/hornik/tmp/scratch/Rtmp0i4SCB'
  hi
  [ FAIL 1 | WARN 37 | SKIP 3 | PASS 610 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • 'no age' should not be converted to 0 (2)
  • Getting error Column 'zz' in table 'age' has 'No' meta data for the input data but 'class: logical' for the existing data. (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-export.R:15'): rws_export_gpkg works ───────────────────────────
  <Rcpp::not_compatible/C++Error/error/condition>
  Error in `CPL_write_ogr(obj, dsn, layer, driver, as.character(dataset_options), 
      as.character(layer_options), geom, dim, fids, config_options, 
      quiet, append, delete_dsn, delete_layer, write_geometries, 
      getOption("width"))`: Not compatible with requested type: [type=character; target=double].
  Backtrace:
      ▆
   1. └─readwritesqlite::rws_export_gpkg(conn = conn, dir = dir, overwrite = FALSE) at test-export.R:15:2
   2.   ├─sf::st_write(table, path, delete_dsn = overwrite, quiet = TRUE)
   3.   └─sf:::st_write.sf(table, path, delete_dsn = overwrite, quiet = TRUE)
   4.     └─sf:::CPL_write_ogr(...)
  
  [ FAIL 1 | WARN 37 | SKIP 3 | PASS 610 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘xpectr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
internals.html:129:9 (internals.Rd:93): Warning: <code> anchor "W" already defined
internals.html:129:32 (internals.Rd:93): Warning: <code> anchor "M" already defined
internals.html:129:55 (internals.Rd:93): Warning: <code> anchor "U" already defined
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘Filled.RData’ ‘cleaned.RData’ ‘days’ ‘gridded’
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
partitionNEEGL.html:146:23 (partitionNEEGL.Rd:62): Error: <suffix> is not recognized!
partitionNEEGL.html:146:23 (partitionNEEGL.Rd:62): Warning: discarding unexpected <suffix>
partitionNEEGL.html:150:22 (partitionNEEGL.Rd:63): Error: <suffix> is not recognized!
partitionNEEGL.html:150:22 (partitionNEEGL.Rd:63): Warning: discarding unexpected <suffix>
partitionNEEGL.html:154:15 (partitionNEEGL.Rd:64): Error: <lrc> is not recognized!
partitionNEEGL.html:154:15 (partitionNEEGL.Rd:64): Warning: discarding unexpected <lrc>
Found the following significant warnings:
  redland.c:771:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redland.c:817:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redland.c:1846:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/redland.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘EnvironmentalA.txt’ ‘EnvironmentalB.txt’ ‘Example.txt’
  ‘Example_Predictions.txt’ ‘Example_RRDist.txt’
  ‘Example_RRDistCol.TIF’ ‘Example_RRDistGrey.TIF’ ‘GeneticA.txt’
  ‘GeneticB.txt’ ‘Inds.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/reglogit.Rcheck/00install.out’ for details.
checkRd: (-1) pima.Rd:24: Escaped LaTeX specials: \^
checkRd: (-1) reglogit.Rd:120: Escaped LaTeX specials: \&
checkRd: (-1) reglogit.Rd:124: Escaped LaTeX specials: \&
checkRd: (-1) reglogit.Rd:136: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MfUSampler’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) calc.relimp.Rd:41: Escaped LaTeX specials: \~
checkRd: (-1) classesmethods.relaimpo.Rd:27: Escaped LaTeX specials: \$
checkRd: (-1) classesmethods.relaimpo.Rd:104: Escaped LaTeX specials: \$
checkRd: (-1) mianalyze.relimp.Rd:69: Escaped LaTeX specials: \~
checkRd: (-1) mianalyze.relimp.Rd:73: Escaped LaTeX specials: \~
checkRd: (-1) relimplm-class.Rd:63: Escaped LaTeX specials: \$
checkRd: (-1) relimplmbootMI-class.Rd:121: Escaped LaTeX specials: \$
checkRd: (-1) relimplmbooteval-class.Rd:146: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘ExampleBinary.md’ using md
Error: processing vignette ‘ExampleBinary.md’ failed with diagnostics:
there is no package called ‘markdown’
--- failed re-building ‘ExampleBinary.md’

--- re-building ‘ExampleGauss.md’ using md
Error: processing vignette ‘ExampleGauss.md’ failed with diagnostics:
there is no package called ‘markdown’
--- failed re-building ‘ExampleGauss.md’

--- re-building ‘introremiod.md’ using md
Error: processing vignette ‘introremiod.md’ failed with diagnostics:
there is no package called ‘markdown’
--- failed re-building ‘introremiod.md’

SUMMARY: processing the following files failed:
  ‘ExampleBinary.md’ ‘ExampleGauss.md’ ‘introremiod.md’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘pbdRPC’
Package suggested but not available for checking: ‘statnet’
checkRd: (-1) ena.plot.group.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:46: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:38: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:42: Escaped LaTeX specials: \$
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PackageCites.bib’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) KitchenhamEtAl.CorrelationsAmongParticipants.Madeyski10.Rd:7: Escaped LaTeX specials: \&
checkRd: (-1) KitchenhamEtAl.CorrelationsAmongParticipants.Madeyski10.Rd:56: Escaped LaTeX specials: \&
Running ‘test-all.R’ [55s/145s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("reproducible")
  Loading required package: reproducible
    adding: home/hornik/tmp/scratch/RtmpoClM73/Require/ZjQzS0/XYnd2hl.tif (stored 0%)
    adding: home/hornik/tmp/scratch/RtmpoClM73/Require/ZjQzS0/0L9Yq5a.grd (stored 0%)
  Error : TopologyException: Input geom 1 is invalid: Self-intersection at 6.0905735768254896 49.981782482072084
  Error : TopologyException: Input geom 1 is invalid: Self-intersection at 6095858.7074040668 6626138.0681269821
  [ FAIL 1 | WARN 1 | SKIP 67 | PASS 430 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • No Drive token (6)
  • On CRAN (52)
  • Temporary pipe for magrittr 2.0 (1)
  • empty test (7)
  • test cloudCache inside Cache -- Not fully written test (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-postProcessTerra.R:120'): testing terra ──────────────────────
  terra::wrap(vv) not identical to terra::wrap(t11).
  Attributes: < Component "crs": 1 string mismatch >
  
  [ FAIL 1 | WARN 1 | SKIP 67 | PASS 430 ]
  Error: Test failures
  Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘P.csv’ ‘correct_alpha.csv’ ‘correct_beta.csv’ ‘correct_gamma.csv’
  ‘correct_lambda.csv’ ‘correct_perm_list.csv’ ‘correct_psi.csv’
'LazyData' is specified without a 'data' directory
checkRd: (-1) cast.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) cast.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-df-v7.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-matrix-59.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-df-bu.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-matrix-2y.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) cast-9g.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:46: Escaped LaTeX specials: \_ \_
checkRd: (-1) clean-vars-rc.rd:13: Escaped LaTeX specials: \_
checkRd: (-1) expand-kx.rd:15: Escaped LaTeX specials: \_
checkRd: (-1) reshape-4u.rd:17: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
checkRd: (-1) Burns.Rd:28: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘evdbayes’
Found the following significant warnings:
  init.c:120:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/revdbayes.Rcheck/00install.out’ for details.
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RevGadgets’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) boot.james.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) boot.student2.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) coljack.means.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) collognorm.mle.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) collognorm.mle.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) fipois.reg.Rd:66: Escaped LaTeX specials: \&
checkRd: (-1) halfcauchy.mle.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) halfcauchy.mle.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) jack.mean.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) lm.parboot.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) multivm.mle.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) ancova1.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) ancovas.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) boot.ttest2.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) colnormal.mle.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) colnormal.mle.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) colnormal.mle.Rd:77: Escaped LaTeX specials: \&
checkRd: (-1) colrint.regbx.Rd:58: Escaped LaTeX specials: \&
checkRd: (-1) colvarcomps.mom.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) colvarcomps.mom.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) ftest.Rd:90: Escaped LaTeX specials: \&
checkRd: (-1) ftests.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) gammamle.Rd:81: Escaped LaTeX specials: \&
checkRd: (-1) gammamle.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) gammamle.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) rint.regbx.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) rint.regs.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) twoway.anovas.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) varcomps.mom.Rd:66: Escaped LaTeX specials: \&
checkRd: (-1) varcomps.mom.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) vm.mle.Rd:60: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CardioRiskFactors.Rd:35: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rgdal.h:28:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rgdal.h:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rgdal.h:130:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rgdal.h:134:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rgdal.h:135:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rgdal.h:136:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rgdal.h:138:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rgdal.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  IP2Loc_DBInterface.h:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  IP2Loc_DBInterface.h:55:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  IP2Location.h:186:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  IP2Loc_DBInterface.c:242:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  IP2Location.c:208:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  IP2Location.c:275:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  IP2Location.c:841:27: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rgeolocate.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rglpk_read_file.c:17:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:42:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rglpk.Rcheck/00install.out’ for details.
checkRd: (-1) Rglpk_read_file.Rd:6: Escaped LaTeX specials: \_
Found the following significant warnings:
  gl2ps.h:254:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gl2ps.c:6479:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rgl.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) columbus.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) columbus.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) columbus.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) columbus.Rd:30: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggtree’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 40-46 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'ggtree'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  qoma-hli.h:23:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  qoma-hli.h:24:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  qoma-hli.h:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  qoma-hli.h:26:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  qoma-hli.c:29:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  qoma-hli.c:39:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  qoma-hli.c:58:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  qoma-hli.c:131:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rhli.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘mydata.rda’ ‘thedata.rda’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  convert.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  convert.c:79:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ring.Rcheck/00install.out’ for details.
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/riot.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ipw’
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.h:19:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.h:26:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.h:30:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rjags.Rcheck/00install.out’ for details.
Non-standard file/directory found at top level:
  ‘jri’
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rlibjson.c:364:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RJSONIO.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
Found the following significant warnings:
  RngWrap.c:12:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RngWrap.c:23:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RngWrap.c:304:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.c:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rlecuyer.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Previous version rmangal
Running ‘testthat.R’ [19s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("rmapshaper")
  > 
  > test_check("rmapshaper")
  [ FAIL 1 | WARN 0 | SKIP 32 | PASS 293 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Not old v8 (1)
  • has_sys_mapshaper() is not TRUE (30)
  • possible bug in mapshaper https://github.com/mbloch/mapshaper/issues/487 (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-simplify.R:298'): ms_simplify works with various column types ──
  <Rcpp::eval_error/C++Error/error/condition>
  Error in `CPL_read_ogr(dsn, layer, query, as.character(options), quiet, 
      type, fid_column_name, drivers, wkt_filter, promote_to_multi, 
      int64_as_string, dsn_exists, dsn_isdb, getOption("width"))`: Evaluation error: a valid "POSIXlt" object has names.
  Backtrace:
      ▆
   1. ├─rmapshaper::ms_simplify(xsf) at test-simplify.R:298:4
   2. └─rmapshaper:::ms_simplify.sf(xsf)
   3.   └─rmapshaper:::ms_sf(input, call, sys = sys, sys_mem = sys_mem)
   4.     └─rmapshaper:::GeoJSON_to_sf(ret, proj = attr(geojson, "proj"))
   5.       ├─base::suppressWarnings(...)
   6.       │ └─base::withCallingHandlers(...)
   7.       ├─sf::st_read(unclass(geojson), quiet = TRUE, stringsAsFactors = FALSE)
   8.       └─sf:::st_read.character(unclass(geojson), quiet = TRUE, stringsAsFactors = FALSE)
   9.         └─sf:::CPL_read_ogr(...)
  
  [ FAIL 1 | WARN 0 | SKIP 32 | PASS 293 ]
  Error: Test failures
  Execution halted
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘blockcluster’
Package suggested but not available for checking: ‘blockcluster’
Found the following calls to attach():
File ‘Rmosek/R/builder.R’:
  attach(builderenv, pos, name, warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rnaturalearthhires’
Malformed Title field: should not end in a period.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
Found the following significant warnings:
  RNetCDF.h:149:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  udunits.c:385:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RNetCDF.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
internal_plots.html:174:9 (internal_plots.Rd:98): Warning: <code> anchor "dots" already defined
internal_plots.html:250:9 (internal_plots.Rd:123): Warning: <code> anchor "dots" already defined
internal_plots.html:259:9 (internal_plots.Rd:126): Warning: <code> anchor "xlim" already defined
internal_plots.html:263:9 (internal_plots.Rd:127): Warning: <code> anchor "ylim" already defined
'LazyData' is specified without a 'data' directory
checkRd: (-1) addLR.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) addLRinv.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) adtestWrapper.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) arcticLake.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cenLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) cenLRinv.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) expenditures.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) gemas.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) machineOperators.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) plot.imp.Rd:138: Escaped LaTeX specials: \&
checkRd: (-1) robCompositions-package.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) skyeLavas.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) variation.Rd:45: Escaped LaTeX specials: \&
Unknown package ‘StatDA’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  monitor.c:15:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/robustbase.Rcheck/00install.out’ for details.
checkRd: (-1) aircraft.Rd:8: Escaped LaTeX specials: \$
Found the following significant warnings:
  /usr/lib/gcc/x86_64-linux-gnu/12/include/emmintrin.h:131:24: warning: array subscript ‘__m128d_u[0]’ is partly outside array bounds of ‘Eigen::internal::plain_matrix_type<Eigen::Product<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false>, Eigen::Transpose<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false> >, 0>, Eigen::Dense>::type [1]’ {aka ‘Eigen::Matrix<double, 1, 1, 0, 1, 1> [1]’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RobustGaSP.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  graph_geodesic.c:9:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/common.h:84:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/common.h:85:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/BitVector.h:57:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/BitVector.h:58:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/BitVector.c:36:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/BitVector.c:46:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/common.c:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/common.c:110:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rnr/common.c:133:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rogue.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  /home/hornik/tmp/scratch/RtmpuejweT/R.INSTALL2f631469e0871f/rolog/src/swipl-devel/src/os/pl-os.c:2159:26: warning: the comparison will always evaluate as ‘true’ for the address of ‘S__iob’ will never be NULL [-Waddress]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rolog.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
internal-interpolate.html:216:9 (internal-interpolate.Rd:116): Warning: <code> anchor "..." already defined
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
roxy_block.html:84:36 (roxy_block.Rd:34): Warning: <code> anchor "tags" already defined
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RandomFields’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘Rpdb.pdb’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    IMPROVEMENTS AND ### BUG FIXES
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.bpl’ ‘test.cr’ ‘test.ct’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gdalUtils’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Stopwatch.h:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Stopwatch.c:4:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rscimark.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  cli.c:172:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cli.c:211:18: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cli.c:1152:9: warning: ‘RSA_size’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
  cli.c:1153:9: warning: ‘RSA_public_encrypt’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
  cli.c:1194:5: warning: ‘d2i_RSAPublicKey’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
  dummy.c:5:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dummy.c:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dummy.c:8:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RSclient.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Vdgraph’
Unknown package ‘Vdgraph’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rsyslog.h:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rsyslog.c:50:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rsyslog.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
Unknown package ‘cmdstanr’ in Rd xrefs
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘Tsttwalk.dat’
Running ‘testthat.R’ [12s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Use conditionally testthat
  > tests_are_doable <- requireNamespace("rtweet", quietly = TRUE) && 
  +   requireNamespace("testthat", quietly = TRUE) && 
  +   requireNamespace("vcr", quietly = TRUE)
  > if (tests_are_doable) {
  +   library(testthat)
  +   library(rtweet)
  +   
  +   test_check("rtweet")
  +   
  + }
  [ FAIL 1 | WARN 0 | SKIP 111 | PASS 46 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Auth not available (90)
  • On CRAN (14)
  • Without old data (1)
  • requires manual testing (4)
  • webshot::is_phantomjs_installed() is not TRUE (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-post-tweet.R:28'): can set alt text ────────────────────────────
  Error in `vapply(interactions, function(x) {
      sprintf("%s => %s", request_summary(Request$new()$from_hash(x$request)), 
          response_summary(VcrResponse$new()$from_hash(x$response)))
  }, "")`: values must be length 1,
   but FUN(X[[2]]) result is length 0
  Backtrace:
      ▆
   1. └─vcr::use_cassette(...) at test-post-tweet.R:28:2
   2.   └─vcr::insert_cassette(...)
   3.     └─Cassette$new(...)
   4.       └─vcr (local) initialize(...)
   5.         └─self$http_interactions()
   6.           └─HTTPInteractionList$new(...)
   7.             └─vcr (local) initialize(...)
   8.               └─base::vapply(...)
  
  [ FAIL 1 | WARN 0 | SKIP 111 | PASS 46 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘results’
checkRd: (-1) run.jags.study.Rd:67: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:60:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rust.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
parse.SmartComments.html:59:9 (parse.SmartComments.Rd:32): Warning: <code> anchor "letter" already defined
Package which this enhances but not available for checking: ‘glmmADMB’
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gpuR’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mapBubbles.Rd:62: Escaped LaTeX specials: \$
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) butterfat.df.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) butterfat.df.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) fire.df.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) fruitfly.df.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) fruitfly.df.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) house.df.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) house.df.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) incomes.df.Rd:8: Escaped LaTeX specials: \$
checkRd: (-1) skulls.df.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) skulls.df.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) technitron.df.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) zoo.df.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Gen_fun.h:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Gen_fun.c:121:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  IFscratch.h:64:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  load_IFscratch.c:64:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/samon.Rcheck/00install.out’ for details.
Found the following significant warnings:
  init.h:28:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.h:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SamplerCompare.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘SamplingStrata.Rmd’ using rmarkdown
Loading required package: memoise
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: pbapply
Loading required package: SamplingBigData
Loading required package: glue

Report issues at https://github.com/barcaroli/SamplingStrata/issues
Get a complete documentation on https://barcaroli.github.io/SamplingStrata
--- finished re-building ‘SamplingStrata.Rmd’

--- re-building ‘models.Rmd’ using rmarkdown
--- finished re-building ‘models.Rmd’

--- re-building ‘spatial.Rmd’ using rmarkdown
Error: processing vignette ‘spatial.Rmd’ failed with diagnostics:
there is no package called ‘bookdown’
--- failed re-building ‘spatial.Rmd’

SUMMARY: processing the following file failed:
  ‘spatial.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
Package suggested but not available for checking: ‘networkTomography’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘FitARMA’
checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Malformed Title field: should not end in a period.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  error.h:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/scclust.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SingleCellSignalR’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [4s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(schtools)
  > 
  > test_check("schtools")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 46 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plot.R:7'): theme_sovacool works ─────────────────────────────
  plot_sovacool$theme not equal to structure(...).
  Names: 7 string mismatches
  Length mismatch: comparison on first 93 components
  Component "line": Names: 1 string mismatch
  Component "rect": Names: 1 string mismatch
  Component "axis.ticks": Names: 1 string mismatch
  Component "legend.background": Names: 1 string mismatch
  Component "legend.key": Names: 1 string mismatch
  Component "panel.background": Names: 1 string mismatch
  Component "panel.border": Names: 1 string mismatch
  ...
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 46 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ssvd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘untitled_consensus_cluster’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmGamPoi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MC p-value.ps’ ‘Output.csv’ ‘Rh.ps’ ‘Th.ps’ ‘dataratio .Rdata’
  ‘featuresRmax.csv’ ‘featuresT.csv’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggtern’

Packages suggested but not available for checking:
  'xbioc', 'MuSiC', 'seAMLessData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spgrass6’
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sobol_indices.Rd:119: Escaped LaTeX specials: \&
checkRd: (-1) fahst.rd:39: Escaped LaTeX specials: \^
checkRd: (-1) fahst.rd:36: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:46: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:42: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:43: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:49: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:44: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:45: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:46: Escaped LaTeX specials: \^
checkRd: (-1) hsortplot.rd:24: Escaped LaTeX specials: \^
checkRd: (-1) nappesortplot.Rd:30: Escaped LaTeX specials: \^
checkRd: (-1) nappesortplot.Rd:28: Escaped LaTeX specials: \^
checkRd: (-1) plot.fahst.rd:45: Escaped LaTeX specials: \^
checkRd: (-1) plot.fasnt.Rd:47: Escaped LaTeX specials: \^
checkRd: (-1) plot.fast.Rd:45: Escaped LaTeX specials: \^
checkRd: (-1) print.fahst.rd:22: Escaped LaTeX specials: \^
checkRd: (-1) print.fasnt.Rd:22: Escaped LaTeX specials: \^
checkRd: (-1) print.fast.Rd:22: Escaped LaTeX specials: \^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘assocpointpair_result.csv’ ‘foundereffectfinder_result.csv’
  ‘getfreqs_result.csv’ ‘getfreqs_result.png’ ‘orPlot.pdf1_1.pdf’
  ‘orPlot.pdf2_1.pdf’ ‘orPlot.pdf3_1.pdf’ ‘orPlot.pdf4_1.pdf’
  ‘orPlot.pdf5_1.pdf’ ‘orPlot.pdf6_1.pdf’ ‘orPlot.pdf7_1.pdf’
  ‘orPlot.pdf8_1.pdf’ ‘q-values_result.csv’ ‘rewritetuple_result.csv’
  ‘tartan_plot.pdf’ ‘vispair_plot.pdf’ ‘vispairfeat_plot.pdf’
  ‘volcano_plot.pdf’
'LazyData' is specified without a 'data' directory
checkRd: (-1) aaindex.Rd:525: Escaped LaTeX specials: \_
checkRd: (-1) aaindex.Rd:526: Escaped LaTeX specials: \_
checkRd: (-1) acnucopen.Rd:38: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_
checkRd: (-1) acnucopen.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) read.alignment.Rd:47: Escaped LaTeX specials: \_ \_
checkRd: (-1) read.alignment.Rd:48: Escaped LaTeX specials: \_ \_
Found the following significant warnings:
  BGenFile.cpp:12:55: warning: member ‘BGenFile::N’ is used uninitialized [-Wuninitialized]
  bcf.h:173:9: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bam_endian.h:6:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  khash.h:129:38: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bcfutils.c:38:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bgzf.c:107:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  tabix_index.c:19:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/seqminer.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  proj_conf_test.c:5:5: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sf.Rcheck/00install.out’ for details.
checkRd: (-1) TA.plot.Rd:32: Escaped LaTeX specials: \~
checkRd: (-1) diagDA.Rd:51: Escaped LaTeX specials: \#
checkRd: (-1) hatMat.Rd:35: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) gPLS.Rd:72: Escaped LaTeX specials: \^
checkRd: (-1) gPLS.Rd:74: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:67: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:69: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:75: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:77: Escaped LaTeX specials: \^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Other ideas
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hydromad’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Package required but not available: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  cairodev.h:86:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cairodev.c:11:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  outline.h:64:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  util.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  util.h:47:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  outline.c:169:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  register_routines.c:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  showtext.c:111:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  util.c:43:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  util.c:53:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/showtext.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MM.csv’ ‘Simul.csv’ ‘catalytic.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘ExportFigtree1.tre’
checkRd: (-1) chol_s2Dp.Rd:147: Escaped LaTeX specials: \&
checkRd: (-1) chol_s2Dp.Rd:149: Escaped LaTeX specials: \&
checkRd: (-1) precision_builder.Rd:87: Escaped LaTeX specials: \&
checkRd: (-1) sim2D_RandSet_HPPP.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) sim2D_binarymap.Rd:157: Escaped LaTeX specials: \&
checkRd: (-1) sim_MVN_X.Rd:140: Escaped LaTeX specials: \&
checkRd: (-1) sim_Y_Binary_X.Rd:221: Escaped LaTeX specials: \&
checkRd: (-1) sim_Y_Binary_X.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) sim_Y_MVN_X.Rd:213: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
Found the following files/directories:
  ‘simu.pheno’ ‘usedpars.txt’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘SimRAD-exampleRefSeq-Fasta.fa’ ‘SimRAD-exampleRefSeq.fa’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggtern’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ‘:::’ call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ex0723.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ex0915.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) ex1515.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) roadwear.Rd:26: Escaped LaTeX specials: \&
Found the following significant warnings:
  init.c:69:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:72:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  slider-vctrs-private.c:12:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  slider-vctrs-public.c:3:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  summary-core.h:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  summary-core.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/slider.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rPython’
Found the following significant warnings:
  bbobStructures.h:126:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bbobStructures.h:128:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bbobStructures.h:130:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bbobStructures.h:131:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bbobStructures.h:133:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarkshelper.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarkshelper.h:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarkshelper.h:18:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarkshelper.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarks.h:27:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarks.h:28:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarks.c:1637:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarks.c:1671:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarkshelper.c:192:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarkshelper.c:204:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarkshelper.c:304:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  benchmarkshelper.c:314:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smoof.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) hoods2dsmooth.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dmeitsjer.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dsmooth.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) smoothie-package.Rd:42: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘my_new_social_media_plot.png’
Unknown package ‘andrews’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  SnowballC_init.c:7:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  stem.c:59:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SnowballC.Rcheck/00install.out’ for details.
Found the following HTML validation problems:
makeGeneSet.html:95:15 (makeGeneSet.Rd:41): Error: <gene> is not recognized!
makeGeneSet.html:95:15 (makeGeneSet.Rd:41): Warning: discarding unexpected <gene>
Found the following HTML validation problems:
confint.selm.html:91:15 (confint.selm.Rd:52): Error: <param1> is not recognized!
confint.selm.html:91:15 (confint.selm.Rd:52): Warning: discarding unexpected <param1>
confint.selm.html:95:15 (confint.selm.Rd:53): Error: <param2> is not recognized!
confint.selm.html:95:15 (confint.selm.Rd:53): Warning: discarding unexpected <param2>
profile.selm.html:173:15 (profile.selm.Rd:121): Error: <param1> is not recognized!
profile.selm.html:173:15 (profile.selm.Rd:121): Warning: discarding unexpected <param1>
profile.selm.html:177:15 (profile.selm.Rd:122): Error: <param2> is not recognized!
profile.selm.html:177:15 (profile.selm.Rd:122): Warning: discarding unexpected <param2>
Package suggested but not available for checking: ‘MfUSampler’
Found the following calls to attach():
File ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘.R_Test’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  SoDA_init.c:5:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  crc32.c:161:23: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  digest_C.c:180:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SoDA.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.som.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) som.Rd:128: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘NLMR’
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
corrFamily.html:140:9 (corrFamily.Rd:77): Warning: <code> anchor "fixed" already defined
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘sparsebn’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RandomFields’
checkRd: (-1) grid2latlong.Rd:22: Escaped LaTeX specials: \$
checkRd: (-1) latlong2grid.Rd:22: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) sarorderedprobit.Rd:84: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RandomFields’
Unknown package ‘RandomFields’ in Rd xrefs
Running examples in ‘spatstat.core-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Emark
> ### Title: Diagnostics for random marking
> ### Aliases: Emark Vmark
> ### Keywords: spatial nonparametric
> 
> ### ** Examples
> 
>     plot(Emark(spruces))
>     E <- Emark(spruces, method="density", kernel="epanechnikov")
>     plot(Vmark(spruces))
> 
>     plot(Emark(finpines))
Loading required namespace: spatstat.explore
Failed with error:  ‘there is no package called ‘spatstat.explore’’
Error: Package 'spatstat.explore' is required for plotting objects of class 'fv'
Execution halted
Package suggested but not available for checking: ‘spatstat.model’
Package suggested but not available for checking: ‘spatstat.model’
Package suggested but not available for checking: ‘spatstat.model’
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.core',
  'spatstat.linnet', 'spatstat.data', 'spatstat', 'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages suggested but not available for checking:
  'RandomFields', 'spatstat.model'
Package unavailable to check Rd xrefs: ‘RandomFields’
Error(s) in re-building vignettes:
  ...
--- re-building ‘bugfixes.Rnw’ using Sweave
Loading required package: spatstat.data
Loading required package: spatstat.geom
spatstat.geom 3.0-3
Loading required package: spatstat.random
spatstat.random 3.0-1
Loading required package: spatstat.core
Loading required package: nlme
Loading required package: rpart
spatstat.core 2.4-4
Loading required package: spatstat.linnet
spatstat.linnet 2.3-2

spatstat 2.3-4       (nickname: ‘Watch this space’) 
For an introduction to spatstat, type ‘beginner’ 

--- finished re-building 'bugfixes.Rnw'

--- re-building 'datasets.Rnw' using Sweave
--- finished re-building 'datasets.Rnw'

--- re-building 'getstart.Rnw' using Sweave
--- finished re-building 'getstart.Rnw'

--- re-building 'replicated.Rnw' using Sweave
Loading required namespace: spatstat.explore
Failed with error:  'there is no package called 'spatstat.explore''

Error: processing vignette ‘replicated.Rnw’ failed with diagnostics:
 chunk 31 
Error : Package 'spatstat.explore' is required for plotting objects of class 'fv'

--- failed re-building 'replicated.Rnw'

--- re-building 'shapefiles.Rnw' using Sweave
--- finished re-building 'shapefiles.Rnw'

--- re-building 'updates.Rnw' using Sweave
--- finished re-building 'updates.Rnw'

SUMMARY: processing the following file failed:
  'replicated.Rnw'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘spatstat.model’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spDataLarge’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
SpectraInTime-class.html:114:9 (SpectraInTime-class.Rd:65): Warning: <code> anchor "object" already defined
SpectraInTime-class.html:118:9 (SpectraInTime-class.Rd:67): Warning: <code> anchor "summaryFunctions" already defined
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.neig’
Running examples in ‘spFSR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: spFeatureSelection
> ### Title: SPSA-FSR for Feature Selection and Ranking
> ### Aliases: spFeatureSelection
> 
> ### ** Examples
> 
> 
> library(mlr3)          # load the mlr3 package
> library(mlr3learners) # load the mlr3learners package
> 
> task    <- tsk('iris') # define task
> wrapper <- lrn('classif.rpart')                # define wrapper
> measure <- msr('classif.acc')
> 
> # run spsa
> spsaMod <- spFeatureSelection( task = task,
+                                wrapper = wrapper,
+                                scoring = measure,
+                                num.features.selected = 3,
+                                n.jobs = 1,
+                                iters.max = 2,
+                                num.grad.avg = 1)
Warning: Package 'ranger' required but not installed for Learner 'classif.ranger'
Error: The following packages could not be loaded: ranger
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘AlphaGA_3.txt’ ‘AlphaML_3.txt’ ‘BetaGA_3.txt’ ‘BetaML_3.txt’
  ‘Performance_GA_ML_ 3 .pdf’ ‘SPIGA_3Pmon.Pm_St1.pdf’
  ‘SPIGA_3Pmon.Pm_St2.pdf’ ‘SPI_AG_3.txt’ ‘SPI_ML_3.txt’
  ‘SPI_ML_3Pm_St1.pdf’ ‘SPI_ML_3Pm_St2.pdf’ ‘SPI_ML_3Pm_St3.pdf’
  ‘SPI_ML_3Pm_St4.pdf’ ‘SPI_PARAM_3.txt’ ‘SPI_PARAM_3Pm_St1.pdf’
  ‘SPI_PARAM_3Pm_St2.pdf’ ‘SPI_PARAM_3Pm_St3.pdf’
  ‘SPI_PARAM_3Pm_St4.pdf’
checkRd: (-1) PimaIndiansDiabetes_long.Rd:14: Escaped LaTeX specials: \^
checkRd: (-1) PimaIndiansDiabetes_wide.Rd:16: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
Found the following significant warnings:
  timeObj.c:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  timeObj.c:63:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zoneObj.c:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zoneObj.c:52:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/splusTimeDate.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  spMC.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  spMC.c:303:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spMC.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  maqmap.h:62:9: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  maqmap.c:15:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spp.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  mathematics.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mathematics.h:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spTDyn.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) B_sraAutoreg.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) C_sraMechanistic.Rd:68: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘SRTsim.Rmd’ using rmarkdown
Quitting from lines 26-47 (SRTsim.Rmd) 
Error: processing vignette ‘SRTsim.Rmd’ failed with diagnostics:
there is no package called 'BiocFileCache'
--- failed re-building ‘SRTsim.Rmd’

SUMMARY: processing the following file failed:
  ‘SRTsim.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Snacks.Rd:6: Escaped LaTeX specials: \~
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Bug fixes
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) katrina.Rd:36: Escaped LaTeX specials: \&
Found the following significant warnings:
  include/misc/adaptiveRadixTree.h:54:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  misc_adaptiveRadixTree.c:195:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/stan4bart.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    To do
Package suggested but not available for checking: ‘starsdata’
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘testmat.sdml’ ‘testmat2.sdml’
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package required but not available: ‘tergm’

Packages suggested but not available for checking: 'EpiModel', 'networksis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘INLA’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [53s/87s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stevedore)
  > 
  > test_check("stevedore")
  [ FAIL 1 | WARN 0 | SKIP 162 | PASS 3273 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (20)
  • df containers output looks broken to me (1)
  • docker using tests not enabled (STEVEDORE_TEST_USE_DOCKER) (125)
  • does not work in covr (1)
  • events this needs some streaming support (1)
  • httppipe cannot be loaded (1)
  • httppipe needs update for new python/reticulate (8)
  • might also work? (1)
  • not yet tested (2)
  • wip (1)
  • work in progress (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-util.R:490'): parse_timestamp ────────────────────────────────
  `t` not identical to `cmp`.
  Objects equal but not identical
  
  [ FAIL 1 | WARN 0 | SKIP 162 | PASS 3273 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘corrviz.html’
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial TODO
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘myNewStrat.R’
Package suggested but not available for checking: ‘StrathE2E2examples’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Found the following significant warnings:
  ../inst/include/sundials/sundials_nvector.h:163:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_nonlinearsolver.h:131:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_matrix.h:106:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_linearsolver.h:137:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_linearsolver.c:28:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_matrix.c:29:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_nonlinearsolver.c:26:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_nvector.c:28:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sundialr.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘extraTrees’
Unknown package ‘extraTrees’ in Rd xrefs
Package suggested but not available for checking: ‘extraTrees’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) estweights.Rd:42: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘gurobi’
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘distr6’
Unknown package ‘distr6’ in Rd xrefs
Found the following HTML validation problems:
coxph_mpl.object.html:112:9 (coxph_mpl.object.Rd:70): Warning: <code> anchor "iter" already defined
Package required but not available: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  agsurv3.c:66:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  agsurv3.c:260:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  chinv3.c:58:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cox_Rcallback.c:20:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  survreg6.c:67:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  survreg7.c:76:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  survregc1.c:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/survival.Rcheck/00install.out’ for details.
Found the following significant warnings:
  survivalROC.c:16:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/survivalROC.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
DNF: multiple local function definitions for ‘mu_x’ with different
  formal arguments
DNF: multiple local function definitions for ‘mu_y’ with different
  formal arguments
DNF: multiple local function definitions for ‘sigma_x’ with different
  formal arguments
DNF: multiple local function definitions for ‘sigma_y’ with different
  formal arguments
DNFOptim : MLE_f: multiple local function definitions for ‘mu_x’ with
  different formal arguments
DNFOptim : MLE_f: multiple local function definitions for ‘mu_y’ with
  different formal arguments
DNFOptim : MLE_f: multiple local function definitions for ‘sigma_x’
  with different formal arguments
DNFOptim : MLE_f: multiple local function definitions for ‘sigma_y’
  with different formal arguments
modelSim: multiple local function definitions for ‘mu_x’ with different
  formal arguments
modelSim: multiple local function definitions for ‘mu_y’ with different
  formal arguments
modelSim: multiple local function definitions for ‘sigma_x’ with
  different formal arguments
modelSim: multiple local function definitions for ‘sigma_y’ with
  different formal arguments
'LazyData' is specified without a 'data' directory
checkRd: (-1) diabetes.Rd:18: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘swephRdata’
Found the following significant warnings:
  libswe/swephlib.h:120:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  libswe/swephlib.h:130:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  libswe/swepcalc.h:120:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  libswe/swepcalc.c:373:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  libswe/sweph.c:7099:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  libswe/swephlib.c:3033:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/swephR.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    CRAN release
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cplexAPI’
Packages suggested but not available for checking: 'cplexAPI', 'clpAPI'
Found the following math rendering problems:
optObj-class.Rd:240: Undefined control sequence: \boldmath in \mbox{\boldmath$Sv$\unboldmath...
robAna.Rd:53-67: Undefined control sequence: \boldmath in ...       & \mbox{\boldmath$c$\unboldmath}...
setRhsZero-methods.Rd:18: Undefined control sequence: \boldmath in \mbox{\boldmath$Sv$\unboldmath...
sysBiolAlg_fba-class.Rd:114-126: Undefined control sequence: \boldmath in ...       & \mbox{\boldmath$c$\unboldmath}...
sysBiolAlg_fba-class.Rd:132-135: Undefined control sequence: \boldmath in 
        \mbox{\boldmath$c$\unboldmath}...
sysBiolAlg_fbaEasyConstraint-class.Rd:93-105: Undefined control sequence: \boldmath in ...       & \mbox{\boldmath$c$\unboldmath}...
sysBiolAlg_fbaEasyConstraint-class.Rd:111-114: Undefined control sequence: \boldmath in 
        \mbox{\boldmath$c$\unboldmath}...
sysBiolAlg_fv-class.Rd:139-152: Undefined control sequence: \boldmath in ...       & \mbox{\boldmath$Sv$\unboldmath...
sysBiolAlg_lmoma-class.Rd:145-165: No such environment: minipage in ...       & \begin{minipage}[b]{5em}
        ...
sysBiolAlg_lmoma-class.Rd:167-169: Undefined control sequence: \boldmath in 
      \mbox{\boldmath$v$\unboldmath}...
sysBiolAlg_lmoma-class.Rd:177-205: No such environment: minipage in ...       & \begin{minipage}[b]{5em}
        ...
sysBiolAlg_moma-class.Rd:131-148: No such environment: minipage in ...       & \begin{minipage}[b]{5em}
        ...
sysBiolAlg_moma-class.Rd:155-157: Undefined control sequence: \boldmath in 
      \mbox{\boldmath$v$\unboldmath}...
sysBiolAlg_mtf-class.Rd:160-179: No such environment: minipage in ...      &  \begin{minipage}[b]{2.5em}
      ...
sysBiolAlg_mtf-class.Rd:181-184: Undefined control sequence: \boldmath in 
        \mbox{\boldmath$c$\unboldmath}...
sysBiolAlg_room-class.Rd:157-177: No such environment: minipage in ...       & \begin{minipage}[b]{5em}
        ...
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
checkRd: (-1) HINoV.SDA.rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  SymTS.c:22:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  SymTS.c:28:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SymTS.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.csv’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.xls’ ‘attenu.xls’ ‘chick1.xls’ ‘chick2.xls’ ‘generic1.xls’
  ‘hands.xls’ ‘table1.xls’
'LazyData' is specified without a 'data' directory
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘R2wd’
checkRd: (-1) R2txt.Rd:164: Escaped LaTeX specials: \#
checkRd: (-1) bct.Rd:18: Escaped LaTeX specials: \^
checkRd: (-1) bct.Rd:19: Escaped LaTeX specials: \^
checkRd: (-1) ineq.Rd:10: Escaped LaTeX specials: \&
checkRd: (-1) put.points.demo.Rd:39: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:10: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:31: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘tergm’

Package suggested but not available for checking: ‘EpiModel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tergm.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  proj_conf_test.c:5:5: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/terra.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: multiple methods tables found for ‘bootstrap’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tesselle.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Problems with news in ‘inst/NEWS.Rd’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Unknown package ‘textreadr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘theft.Rmd’ using rmarkdown
No IDs removed. All value vectors good for feature extraction.
Running computations for catch22...
Warning: As of 0.1.14 the feature 'CO_f1ecac' returns a double instead of int
This warning is displayed once per session.

Calculations completed for catch22.
Null testing method 'model free shuffles' is fast. Consider running more permutations for more reliable results. N = 10000 is recommended.
Quitting from lines 283-301 (theft.Rmd) 
Error: processing vignette ‘theft.Rmd’ failed with diagnostics:
argument is of length zero
--- failed re-building ‘theft.Rmd’

SUMMARY: processing the following file failed:
  ‘theft.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  thor.h:18:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  thor.h:21:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  thor.h:23:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  thor.h:106:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  thor.c:9:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  thor.c:23:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  thor.c:35:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  thor.c:748:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/thor.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
estimate.html:44:9 (estimate.Rd:14): Warning: <code> anchor "x" already defined
'LazyData' is specified without a 'data' directory
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3dimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [128s/193s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidytags)
  > 
  > test_check("tidytags")
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 284 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-8-get_url_domain.R:3'): get_url_domain() works on a variety of domains ──
  Error in `vapply(interactions, function(x) {
      sprintf("%s => %s", request_summary(Request$new()$from_hash(x$request)), 
          response_summary(VcrResponse$new()$from_hash(x$response)))
  }, "")`: values must be length 1,
   but FUN(X[[1]]) result is length 0
  Backtrace:
      ▆
   1. └─vcr::use_cassette(...) at test-8-get_url_domain.R:3:2
   2.   └─vcr::insert_cassette(...)
   3.     └─Cassette$new(...)
   4.       └─vcr (local) initialize(...)
   5.         └─self$http_interactions()
   6.           └─HTTPInteractionList$new(...)
   7.             └─vcr (local) initialize(...)
   8.               └─base::vapply(...)
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 284 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  common.c:36:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tiff.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ntr.c:65:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ntr.c:91:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TIMP.Rcheck/00install.out’ for details.
checkRd: (-1) dat-class.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) dat-class.Rd:48: Escaped LaTeX specials: \_
checkRd: (-1) dat-class.Rd:49: Escaped LaTeX specials: \_
checkRd: (-1) dat-class.Rd:50: Escaped LaTeX specials: \_
Found the following files/directories:
  ‘_paramEst.txt’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  external_metis.c:102:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TMB.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running examples in ‘tm.plugin.dc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tm_map.DCorpus
> ### Title: Transformations on Distributed Corpora
> ### Aliases: tm_map.DCorpus
> 
> ### ** Examples
> 
> data("crude")
> tm_map(as.DCorpus(crude), content_transformer(tolower))
Warning in file(con, "w") :
  cannot open file '/home/hornik/tmp/scratch/Rtmpwwr8qb/DSL-20221108-023332-ydgabwknrs/chunk-2d69975c6d4987': No such file or directory
Error in file(con, "w") : cannot open the connection
Calls: tm_map ... DS_write_lines -> <Anonymous> -> <Anonymous> -> file
Execution halted
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'lasso2', 'corpus.JSS.papers'
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Found the following significant warnings:
  topmodel.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:14:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:16:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:18:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:21:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:23:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  topmodel.h:26:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/topmodel.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘p3state.msm’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Enhancements
    Other changes
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taxidata’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TraMineR.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘V01_get_started.Rmd’ using rmarkdown
Loading required package: stars
Loading required package: abind
Loading required package: sf
Linking to GEOS 3.11.0, GDAL 3.5.2, PROJ 9.1.0; sf_use_s2() is TRUE
--- finished re-building ‘V01_get_started.Rmd’

--- re-building ‘V02_inputs_preparation_stars.Rmd’ using rmarkdown
udunits database from /usr/share/xml/udunits/udunits2.xml
--- finished re-building ‘V02_inputs_preparation_stars.Rmd’

--- re-building ‘V03_inputs_preparation_whitebox.Rmd’ using rmarkdown
Quitting from lines 45-66 (V03_inputs_preparation_whitebox.Rmd) 
Error: processing vignette ‘V03_inputs_preparation_whitebox.Rmd’ failed with diagnostics:
there is no package called 'rgdal'
--- failed re-building ‘V03_inputs_preparation_whitebox.Rmd’

SUMMARY: processing the following file failed:
  ‘V03_inputs_preparation_whitebox.Rmd’

Error: Vignette re-building failed.
Execution halted
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘TreeDistData’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug fixes
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggtree’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) ltriangle.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) triangle.Rd:70: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggtern’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sepIdGaps.Rd:18: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updates for the development version (0.1.0.9000) on Github
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) lindner.Rd:44: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘sl3’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  interface.c:114:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ucminf.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ursa.c:3714:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ursa.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘USAboundariesData’
Package suggested but not available for checking: ‘USA.state.boundaries.data’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) arctic.oscillations.Rd:19: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) arctic.oscillations.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) babies.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:43: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) exec.pay.Rd:5: Escaped LaTeX specials: \$
checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) sp500.excess.Rd:6: Escaped LaTeX specials: \&
Running ‘testthat.R’ [8s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(usmap)
  > 
  > test_check("usmap")
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 163 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plot.R:138'): singular regions can be used ───────────────────
  plot_usmap(regions = "states")$layers not equal to plot_usmap(regions = "state")$layers.
  Component 1: Component 12: Component 5: Component 21: Component 11: 1 string mismatch
  Component 1: Component 12: Component 5: Component 21: Component 12: 1 string mismatch
  Component 2: Component 12: Component 5: Component 21: Component 11: 1 string mismatch
  Component 2: Component 12: Component 5: Component 21: Component 12: 1 string mismatch
  ── Failure ('test-plot.R:140'): singular regions can be used ───────────────────
  plot_usmap(regions = "counties")$layers not equal to plot_usmap(regions = "county")$layers.
  Component 1: Component 12: Component 5: Component 21: Component 11: 1 string mismatch
  Component 1: Component 12: Component 5: Component 21: Component 12: 1 string mismatch
  Component 2: Component 12: Component 5: Component 21: Component 11: 1 string mismatch
  Component 2: Component 12: Component 5: Component 21: Component 12: 1 string mismatch
  
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 163 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rand.c:90:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rand.c:92:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rand.c:103:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rand.c:138:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/uuid.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) irf.Rd:111: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glass.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) Glass.Rd:22: Escaped LaTeX specials: \&
checkRd: (-1) Glass.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) Glass.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) Glass.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) Glass.Rd:28: Escaped LaTeX specials: \&
Running ‘testthat.R’ [98s/153s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(vctrs)
  > 
  > test_check("vctrs")
  [ FAIL 2 | WARN 0 | SKIP 256 | PASS 5057 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Can't profile memory on this system. (2)
  • FIXME: dimnames of matrices are not properly concatenated (1)
  • Factors now have a `c()` method (1)
  • Not testing performance (2)
  • On CRAN (246)
  • data.table cannot be loaded (3)
  • sf cannot be loaded (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-slice-assign.R:536'): can optionally assign names ────────────
  `actual` (vec_assign_params(oo_x, 2, oo_y, assign_names = TRUE)) not identical to `expected` (`oo_out`).
  
  `attr(actual, 'balanced')`:   <NA>
  `attr(expected, 'balanced')`: TRUE
  Backtrace:
      ▆
   1. └─vctrs:::expect_identical(...) at test-slice-assign.R:536:2
   2.   └─vctrs:::expect_waldo_equal("identical", act, exp, info, ...) at tests/testthat/helper-vctrs.R:43:2
  ── Failure ('test-slice-assign.R:561'): can optionally assign names ────────────
  `actual` (vec_assign_params(nested_x, 2, nested_y, assign_names = TRUE)) not identical to `expected` (`nested_out`).
  
  `attr(actual$oo, 'balanced')`:   <NA>
  `attr(expected$oo, 'balanced')`: TRUE
  Backtrace:
      ▆
   1. └─vctrs:::expect_identical(...) at test-slice-assign.R:561:2
   2.   └─vctrs:::expect_waldo_equal("identical", act, exp, info, ...) at tests/testthat/helper-vctrs.R:43:2
  
  [ FAIL 2 | WARN 0 | SKIP 256 | PASS 5057 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggtern’
Found the following significant warnings:
  computeCox.c:15:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vdra.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex125.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
‘gs+qpdf’ made some significant size reductions:
     compacted ‘How_to_work_with_package_VFP.pdf’ from 383Kb to 131Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
checkRd: (-1) huse.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) checkTS.VGAMextra.Rd:176: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    NEW FEATURES
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    NEWS UPDATES:
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Package required but not available: ‘ecospat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  functions.c:75:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  functions.c:101:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  functions.c:189:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  functions.c:220:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  functions.c:221:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  functions.c:295:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrow.c:34:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrow.c:54:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrow.c:134:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrow.c:157:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrow.c:219:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/waveband.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘sfdep’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:20:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wdnet.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘prepr’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/WeightedCluster.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ATE’
Unknown package ‘ATE’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  corFunctions.c:59:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  networkFunctions.c:182:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/WGCNA.Rcheck/00install.out’ for details.
checkRd: (-1) rgcolors.func.Rd:27: Escaped LaTeX specials: \#
Found the following HTML validation problems:
overlapTableUsingKME.html:112:20 (overlapTableUsingKME.Rd:54): Warning: <name1> attribute "/2" lacks value
overlapTableUsingKME.html:112:20 (overlapTableUsingKME.Rd:54): Error: <name1> is not recognized!
overlapTableUsingKME.html:112:20 (overlapTableUsingKME.Rd:54): Warning: discarding unexpected <name1>
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
tag2delim.html:40:9 (tag2delim.Rd:12): Warning: <code> anchor "tag" already defined
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  random_wrap.c:9:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wnominate.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘aphiainfo.csv’ ‘tax.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  wrassp.h:197:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  types.c:10:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  types.c:38:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  types.c:65:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrassp_init.c:20:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrassp_init.c:21:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  wrassp_init.c:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wrassp.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RP2_data_1.txt’ ‘RP2_data_4.txt’ ‘RP2_qtl_1.txt’ ‘RP2_qtl_4.txt’
  ‘hp1_effect_qtl.txt’ ‘hp1_freq_mrk.txt’ ‘hp1_freq_qtl.txt’
  ‘hp1_genome.txt’ ‘hp1_last_hp_data.txt’ ‘hp1_lm_mrk.txt’
  ‘hp1_lm_qtl.txt’ ‘hp1_lm_qtl_mrk.txt’ ‘hp1_mrk.txt’ ‘hp1_qtl.txt’
  ‘hp2_effect_qtl.txt’ ‘hp2_freq_mrk.txt’ ‘hp2_freq_qtl.txt’
  ‘hp2_genome.txt’ ‘hp2_last_hp_data.txt’ ‘hp2_lm_mrk.txt’
  ‘hp2_lm_qtl.txt’ ‘hp2_lm_qtl_mrk.txt’ ‘hp2_mrk.txt’ ‘hp2_qtl.txt’
  ‘my_RP_data_1.txt’ ‘my_RP_data_4.txt’ ‘my_RP_mrk_1.txt’
  ‘my_RP_mrk_4.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xgb.txt’
Found the following significant warnings:
  init.c:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/xgboost.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:24:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:71:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:72:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/xml2.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) read.npc.vpc.results.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) read.npc.vpc.results.Rd:19: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_
checkRd: (-1) read.npc.vpc.results.Rd:22: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
Found the following files/directories:
  ‘OPT.csv’ ‘testTecan_defaultLiquid.csv’ ‘testTecan_setLiquid.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggtree’
Error(s) in re-building vignettes:
  ...
--- re-building ‘gammaproteobacteria.Rmd’ using rmarkdown
Quitting from lines 24-27 (gammaproteobacteria.Rmd) 
Error: processing vignette ‘gammaproteobacteria.Rmd’ failed with diagnostics:
there is no package called 'ggtree'
--- failed re-building ‘gammaproteobacteria.Rmd’

SUMMARY: processing the following file failed:
  ‘gammaproteobacteria.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Running ‘test-all.R’ [3s/4s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("zbank")
  Loading required package: zbank
  [ FAIL 1 | WARN 1 | SKIP 22 | PASS 36 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (22)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-zb_publications.R:4'): high level works ────────────────────────
  Error: lexical error: invalid char in json text.
                                         W3sgInJlZmVyZW5jZXV1aWQiOiI0Mjd
                       (right here) ------^
  
  Backtrace:
      ▆
   1. ├─vcr::use_cassette(...) at test-zb_publications.R:4:2
   2. │ └─cassette$call_block(...)
   3. └─zbank::zb_publications(id = "427D7953-E8FC-41E8-BEA7-8AE644E6DE77") at test-zb_publications.R:5:4
   4.   └─zbank:::zb_parse(zb_publications_(id, query, ...), parse)
   5.     └─jsonlite::fromJSON(x, parse)
   6.       └─jsonlite:::parse_and_simplify(...)
   7.         └─jsonlite:::parseJSON(txt, bigint_as_char)
   8.           └─jsonlite:::parse_string(txt, bigint_as_char)
  
  [ FAIL 1 | WARN 1 | SKIP 22 | PASS 36 ]
  Error: Test failures
  Execution halted
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘zdat’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    NEW DEPENDENCIES
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:74: Escaped LaTeX specials: \_
checkRd: (-1) zid.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
Package suggested but not available for checking: ‘SDMTools’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 134469 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Undeclared package ‘CCA’ in Rd xrefs
Found the following files/directories:
  ‘acceldata2.RData’
File ‘acc/libs/acc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  getLL.c:133:22: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  getLL.c:257:22: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See ‘/data/gannet/ripley/R/packages/tests-clang/ACDm.Rcheck/00install.out’ for details.
File ‘ACDm/libs/ACDm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
File ‘acepack/libs/acepack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘hunspell’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘acrt/libs/acrt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
‘configure’: /bin/bash is not portable
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R  13.9Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘patchwork’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 305 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘HI’, ‘MHadaptive’ in Rd xrefs
Unknown packages ‘HI’, ‘MHadaptive’ in Rd xrefs
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       3.0Mb
    pictures   2.1Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
Undeclared packages ‘timereg’, ‘rms’, ‘ranger’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ADMMnet/libs/ADMMnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    tutorials   5.6Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘Hmisc’ ‘WRS2’ ‘boot’ ‘car’ ‘dplyr’ ‘effects’
  ‘effsize’ ‘forcats’ ‘ggplot2’ ‘lm.beta’ ‘nlme’ ‘readr’ ‘robust’
  ‘sandwich’ ‘sjstats’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘table_AeRobiology’
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘mFilter’ ‘regclass’ ‘writexl’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Undeclared packages ‘epiR’, ‘cccrm’ in Rd xrefs
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BerryMielke.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) BlairLacy.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) Kvalseth.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) consensus.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) dsquared.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) l.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) lsquared.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) lsquared.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) var.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) adapt.Rd:41: Escaped LaTeX specials: \$
File ‘ahaz/libs/ahaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘RandomFields’
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘randomNames’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘multcomp’, ‘gmodels’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘ans_19-2.jpg’ ‘display2d_19-2.jpg’ ‘dist(3)_19-2.jpg’
  ‘dist(4)_19-2.jpg’ ‘dist(mirror)_19-2.jpg’ ‘dist(mirror2)_19-2.jpg’
Namespaces in Imports field not imported from:
  ‘Rsolnp’ ‘SuperLearner’ ‘future.apply’ ‘ggplot2’ ‘progressr’ ‘stats’
  ‘utils’
  All declared Imports should be used.
Note: found 53 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
Undeclared package ‘SnowballC’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  fun_sublr.cpp:18:22: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/ALassoSurvIC.Rcheck/00install.out’ for details.
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘AlgDesign/libs/AlgDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘hyperSpec’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘alphabetr/libs/alphabetr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following HTML validation problems:
mapLevels.html:111:9 (mapLevels.Rd:93): Warning: <code> anchor "codes" already defined
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Note: found 171 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metaboliteIDmapping’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Zelig’
Found the following significant warnings:
  em.cpp:89:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  em.cpp:89:53: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/Amelia.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘dplyr’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘vegan’ in Rd xrefs
checkRd: (-1) deshrink.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) deshrink.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) plot.mat.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) plot.wa.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) predict.prcurve.Rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘BH-0.05-ListOfGenes.txt’ ‘BH-0.05-VM-ListOfGenes.txt’
  ‘CompleteListOfGenes.txt’ ‘GenesOutOfAnalysis.txt’
  ‘GenesOutOfAnalysis_NotEnoughObs.txt’
  ‘GenesOutOfAnalysis_NullVar.txt’ ‘VM-CompleteListOfGenes.txt’
  ‘bonferroni-0.05-ListOfGenes.txt’
  ‘bonferroni-0.05-VM-ListOfGenes.txt’
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Note: found 231 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    test_v8    2.0Mb
    testdata   2.3Mb
Package suggested but not available for checking: ‘SportsAnalytics’
Found the following significant warnings:
  init.c:11:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/Anthropometry.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./header.h:50:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  bicriterion_iterated_local_search_call.c:510:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/anticlust.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mcclust’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘geepack’, ‘dispmod’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  get_subplot_boundary_pixels.cpp:37:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  polygonize_class.cpp:52:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  polygonize_class.cpp:78:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  polygonize_class.cpp:99:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  polygonize_class.cpp:102:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/APAtree.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘AER’ ‘ChainLadder’ ‘ISLR’ ‘ggplot2’
  All declared Imports should be used.
Found the following significant warnings:
  ./me.h:122:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  me.c:234:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/ape.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ViterbiC.cpp:217:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ViterbiC.cpp:528:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ViterbiC.cpp:814:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ViterbiC.cpp:1104:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ViterbiC.cpp:1242:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:45:40: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:59:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:60:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:61:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:62:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:63:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:64:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:65:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:66:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:67:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/aphid.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ../inst/include/tree_meat.hpp:375:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/aphylo.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
File ‘APIS/libs/APIS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘ggtree’
Running examples in ‘aplot-Ex.R’ failed
The error most likely occurred in:

> ### Name: insert_left
> ### Title: plot-insertion
> ### Aliases: insert_left insert_right insert_top insert_bottom
> 
> ### ** Examples
> 
> library(ggplot2)
> library(aplot)
> 
> p <- ggplot(mtcars, aes(mpg, disp)) + geom_point()
> p2 <- ggplot(mtcars, aes(mpg)) + 
+     geom_density(fill='steelblue', alpha=.5) + 
+         ggtree::theme_dendrogram()
Error in loadNamespace(x) : there is no package called ‘ggtree’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Package suggested but not available for checking: ‘BayesianTools’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Unknown package ‘BayesianTools’ in Rd xrefs
Found the following files/directories:
  ‘APBinary_PPV.csv’ ‘APBinary_TPF.csv’
  ‘APBinary_ap_summary(method=perturbation,B=1500).csv’
  ‘APBinary_auc_summary(method=perturbation,B=1500).csv’
  ‘APSurv_PPV.csv’ ‘APSurv_TPF.csv’
  ‘APSurv_ap_summary(method=bootstrap,B=500).csv’
  ‘APSurv_auc_summary(method=bootstrap,B=500).csv’
  ‘CompareAP_Binary_dap_summary(method=none).csv’
  ‘CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
checkRd: (-1) AQuadtree-package.Rd:11: Escaped LaTeX specials: \$
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Undeclared package ‘RCurl’ in Rd xrefs
Note: found 76 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘bannerCommenter’ ‘config’ ‘feather’ ‘here’ ‘knitr’ ‘log4r’ ‘ps’
  ‘rmarkdown’ ‘skimr’ ‘snakecase’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘rmarkdown’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘methods’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Undeclared packages ‘survey’, ‘Matching’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.1Mb
    testScripts   1.3Mb
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Found the following HTML validation problems:
writeDataFrame.AromaUnitSignalBinaryFile.html:82:9 (writeDataFrame.AromaUnitSignalBinaryFile.Rd:44): Warning: <code> anchor "sep" already defined
writeDataFrame.AromaUnitTabularBinaryFile.html:82:9 (writeDataFrame.AromaUnitTabularBinaryFile.Rd:44): Warning: <code> anchor "sep" already defined
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
installed size is 43.6Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    libs  38.2Mb
Undeclared package ‘readr’ in Rd xrefs
Note: found 1409 marked UTF-8 strings
Package which this enhances but not available for checking: ‘ARTP’
Found the following significant warnings:
  ARTP2_init.c:17:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/ARTP2.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
Found the following significant warnings:
  ptree.c:32:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ptree.c:192:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ptree.c:200:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ptree.c:768:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/arulesSequences.Rcheck/00install.out’ for details.
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
Note: found 328 marked UTF-8 strings
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ash/libs/ash.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MSToutput.txt’
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
Undeclared packages ‘assertive.properties’, ‘assertive.types’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘rstudioapi’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘sets’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘pryr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Found the following HTML validation problems:
ASSISTant-internal.html:86:9 (ASSISTant-internal.Rd:40): Warning: <code> anchor "low" already defined
ASSISTant-internal.html:90:9 (ASSISTant-internal.Rd:42): Warning: <code> anchor "high" already defined
ASSISTant-internal.html:94:9 (ASSISTant-internal.Rd:44): Warning: <code> anchor "low" already defined
ASSISTant-internal.html:98:9 (ASSISTant-internal.Rd:46): Warning: <code> anchor "high" already defined
ASSISTant-internal.html:102:9 (ASSISTant-internal.Rd:48): Warning: <code> anchor "low" already defined
ASSISTant-internal.html:106:9 (ASSISTant-internal.Rd:50): Warning: <code> anchor "high" already defined
Package suggested but not available for checking: ‘asteRiskData’
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘lubridate’ ‘openair’ ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘snpar’ in Rd xrefs
Unknown package ‘snpar’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dlnm’ ‘ggplot2’ ‘lubridate’ ‘mvmeta’ ‘pbs’ ‘tsModel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  driver.c:114:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  driver.c:161:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  driver.c:199:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/audio.Rcheck/00install.out’ for details.
Undeclared package ‘gtable’ in Rd xrefs
Note: found 1 marked UTF-8 string
Note: found 899 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 552 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘tensorflow’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.rsp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinycssloaders’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘readxl’ ‘reshape2’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘rclipboard’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MixAll’ ‘dplyr’ ‘lqmm’ ‘matrixcalc’ ‘rmutil’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
Undeclared package ‘AzureAuth’ in Rd xrefs
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jose’ ‘openssl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httr’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Package suggested but not available for checking: ‘lixoftConnectors’
Note: found 64209 marked UTF-8 strings
Note: found 133353 marked UTF-8 strings
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.3Mb
Namespace in Imports field not imported from: ‘glpkAPI’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘InvariantCausalPrediction’, ‘CompareCausalNetworks’ in Rd xrefs
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 260 marked UTF-8 strings
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Found the following files/directories:
  ‘exemplary_input1.txt’ ‘exemplary_input2.txt’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./utilities.h:67:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./utilities.h:68:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./utilities.h:83:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./Ball_omp.h:6:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./Ball_omp.h:7:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./Ball_omp.h:8:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  bd_gwas.c:260:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  utilities.c:1438:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  utilities.c:1446:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  utilities.c:1455:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/Ball.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘fs’ ‘testthat’
  All declared Imports should be used.
Found the following significant warnings:
  bamlss_functions.c:117:10: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/bamlss.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.3Mb
    doc    1.8Mb
Undeclared package ‘akima’ in Rd xrefs
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
Note: found 148 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
Undeclared package ‘YaleToolkit’ in Rd xrefs
Note: found 13825 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
File ‘Barnard/libs/Barnard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Crashpad’
Namespace in Imports field not imported from: ‘mvnfast’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.4Mb
Found the following significant warnings:
  init.c:16:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/BART.Rcheck/00install.out’ for details.
Undeclared package ‘Rraven’ in Rd xrefs
File ‘base64enc/libs/base64enc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dbplyr’ ‘dotenv’ ‘googleAuthR’ ‘writexl’ ‘xml2’
  All declared Imports should be used.
Undeclared packages ‘jsonlite’, ‘arrow’ in Rd xrefs