'LazyData' is specified without 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
Found the following HTML validation problems:
acled.api.html:145:40: Warning: missing </a> before <a>
acled.api.html:145:151: Warning: discarding unexpected </a>
get.api.regions.html:57:40: Warning: missing </a> before <a>
get.api.regions.html:57:151: Warning: discarding unexpected </a>
'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.
Problems with news in 'NEWS.md':
No news entries found.
Found the following HTML validation problems:
activityCounts-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
activityCounts-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without 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 package 'MHadaptive' in Rd xrefs
Found the following HTML validation problems:
adaptr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
adaptr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
checkRd: (-1) chickenk.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) multispati.Rd:54: Escaped LaTeX specials: \$
checkRd: (-1) randboot.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) HWE.Rd:22: Escaped LaTeX specials: \$
checkRd: (-1) accessors.Rd:79: Escaped LaTeX specials: \$ \$
checkRd: (-1) dist.genpop.Rd:91: Escaped LaTeX specials: \~
checkRd: (-1) genind.Rd:20: Escaped LaTeX specials: \$
checkRd: (-1) genpop.Rd:20: Escaped LaTeX specials: \$
checkRd: (-1) hybridize.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) selpopsize.Rd:20: Escaped LaTeX specials: \$
checkRd: (-1) seploc.Rd:47: Escaped LaTeX specials: \$
checkRd: (-1) spca.Rd:113: Escaped LaTeX specials: \$ \$
checkRd: (-1) truenames.Rd:28: Escaped LaTeX specials: \$ \$
checkRd: (-1) truenames.Rd:31: Escaped LaTeX specials: \$ \$
checkRd: (-1) truenames.Rd:32: Escaped LaTeX specials: \$
checkRd: (-1) kernelUD.Rd:210: Escaped LaTeX specials: \&
checkRd: (-1) orthobasis.Rd:106: Escaped LaTeX specials: \&
checkRd: (-1) orthobasis.Rd:110: Escaped LaTeX specials: \&
checkRd: (-1) treePart.Rd:33: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
checkRd: (-1) multispati.Rd:62: Escaped LaTeX specials: \$
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 math rendering problems:
daep.Rd:5-10: Unknown column alignment: * in ...{\begin{array}{*{20}c}
  \frac{1}...
fitaep.Rd:5-10: Unknown column alignment: * in ...{\begin{array}{*{20}c}
  \frac{1}...
paep.Rd:5-10: Unknown column alignment: * in ...{\begin{array}{*{20}c}
  \frac{1-...
qaep.Rd:5-10: Unknown column alignment: * in ...{\begin{array}{*{20}c}
  \mu-\sig...
raep.Rd:5-10: Unknown column alignment: * in ...{\begin{array}{*{20}c}
  \mu-\sig...
regaep.Rd:7-12: Unknown column alignment: * in ...{\begin{array}{*{20}c}
  \frac{1}...
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: \&
Found the following HTML validation problems:
AgroTech-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
AgroTech-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) adapt.Rd:41: Escaped LaTeX specials: \$
Found the following HTML validation problems:
dev.html:62:126: Warning: inserting implicit <p>
dev.html:62:126: Warning: trimming empty <p>
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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'stuve.pdf'
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
akc-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
akc-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
'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
checkRd: (-1) varrob.Rd:44: Escaped LaTeX specials: \^
Found the following HTML validation problems:
Introduction.html:162:66: Error: <name> is not recognized!
Introduction.html:162:66: Warning: discarding unexpected <name>
Found the following HTML validation problems:
crop.html:31:52: Warning: inserting implicit <p>
crop.html:31:52: Warning: trimming empty <p>
merge.html:59:70: Warning: inserting implicit <p>
merge.html:59:70: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ambient-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ambient-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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: \&
Package which this enhances but not available for checking: 'SparkR'
'LazyData' is specified without a 'data' directory
'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.
checkRd: (-1) diamonds.Rd:10: Escaped LaTeX specials: \$ \$
checkRd: (-1) msleep.Rd:15: Escaped LaTeX specials: \_
checkRd: (-1) msleep.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) msleep.Rd:17: Escaped LaTeX specials: \_
Found the following HTML validation problems:
stat_unique.html:110:1: Warning: trimming empty <li>
stat_unique.html:109:1: Warning: trimming empty <ul>
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tmg'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
AnnData.html:1390:1: Warning: <a> anchor "method-new" already defined
AnnData.html:1419:1: Warning: <a> anchor "method-copy" already defined
AnnData.html:1501:1: Warning: <a> anchor "method-print" already defined
AnnData.html:1571:1: Warning: <a> anchor "method-.set_py_object" already defined
AnnData.html:1600:1: Warning: <a> anchor "method-.get_py_object" already defined
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'
checkRd: (-1) AIDS-Functions.Rd:334: Escaped LaTeX specials: \&
checkRd: (-1) Logit-Functions.Rd:380: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
anyflights_description.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
anyflights_description.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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.
'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.
Found the following HTML validation problems:
mislabel.html:25:1: Warning: trimming empty <p>
raphylo.html:25:1: Warning: trimming empty <p>
sim_fun_on_tree.html:25:1: Warning: trimming empty <p>
'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'.
Found the following HTML validation problems:
applicable-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
applicable-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
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
Found the following HTML validation problems:
arcpullr-package.html:29:4: Warning: <img> attribute "align" not allowed for HTML5
arcpullr-package.html:29:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
mapApp.html:105:101: Warning: inserting implicit <p>
mapApp.html:105:101: Warning: trimming empty <p>
'LazyData' is specified without 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:
  aricode.cpp:22:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  aricode.cpp:41:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/aricode.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 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 math rendering problems:
chi.plot.Rd:27-28: Undefined control sequence: \emph in ...bda = 4 \times \emph{S} \times max[...
ci.prat.rd:94-95: Can't use function '$' in math mode in ...{\theta }_{0}}}$, and ${{X}^{2}...
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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
getCostsAndPresolvedStatus.html:55:38: Warning: <code> is probably intended as </code>
getCostsAndPresolvedStatus.html:55:74: Warning: discarding unexpected </code>
getCostsAndPresolvedStatus.html:55:82: Warning: discarding unexpected </code>
getCostsAndPresolvedStatus.html:59:38: Warning: <code> is probably intended as </code>
getCostsAndPresolvedStatus.html:59:75: Warning: discarding unexpected </code>
getCostsAndPresolvedStatus.html:59:83: Warning: discarding unexpected </code>
getCostsAndPresolvedStatus.html:63:38: Warning: <code> is probably intended as </code>
getCostsAndPresolvedStatus.html:63:67: Warning: discarding unexpected </code>
getCostsAndPresolvedStatus.html:63:75: Warning: discarding unexpected </code>
Found the following files/directories:
  'MSToutput.txt'
Package which this enhances but not available for checking: 'asreml'
checkRd: (-1) Ladybird.dat.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) infoCriteria.asreml.Rd:79: Escaped LaTeX specials: \&
Found the following HTML validation problems:
tsk_estimation.html:61:149: Warning: inserting implicit <p>
tsk_estimation.html:147:138: Warning: inserting implicit <p>
tsk_estimation.html:61:149: Warning: trimming empty <p>
tsk_estimation.html:147:138: Warning: trimming empty <p>
tsk_output.html:58:149: Warning: inserting implicit <p>
tsk_output.html:58:149: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
Found the following HTML validation problems:
gen.html:82:83: Warning: inserting implicit <p>
gen.html:87:54: Warning: inserting implicit <p>
gen.html:82:83: Warning: trimming empty <p>
gen.html:87:54: Warning: trimming empty <p>
'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
Found the following HTML validation problems:
attachment-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
attachment-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Found the following HTML validation problems:
aweSOM-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
aweSOM-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
'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 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 HTML validation problems:
rwnorm2.html:111:126: Warning: trimming empty <code>
rwnorm2.html:115:73: Warning: trimming empty <code>
rwnorm2.html:115:146: Warning: trimming empty <code>
rwnorm2.html:115:211: Warning: trimming empty <code>
rwnorm2.html:119:126: Warning: trimming empty <code>
'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 HTML validation problems:
img.html:24:1: Warning: <img> discarding newline in URI reference
Found the following HTML validation problems:
baseballr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
baseballr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
bref.html:72:105: Warning: inserting implicit <p>
bref.html:72:105: Warning: trimming empty <p>
'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
checkRd: (-1) bas.lm.Rd:425: Escaped LaTeX specials: \&
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: \$
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.
Found the following HTML validation problems:
getSamples.html:74:1: Warning: trimming empty <h3>
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Future development plan of the author's life
    Future development plan of this package
    Explanatory Variables
checkRd: (-1) check_rhat.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) snippet_for_BayesianFROC.Rd:22: Escaped LaTeX specials: \$
Found the following HTML validation problems:
error_MRMC.html:38:14: Warning: nested emphasis <strong>
'LazyData' is specified without 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:
WAIC.html:55:1: Warning: inserting implicit <p>
WAIC.html:58:1: Warning: inserting implicit <p>
WAIC.html:67:1: Warning: inserting implicit <p>
WAIC.html:55:1: Warning: trimming empty <p>
WAIC.html:58:1: Warning: trimming empty <p>
WAIC.html:67:1: Warning: trimming empty <p>
WAIC.html:54:1: Warning: <center> element removed from HTML5
WAIC.html:57:1: Warning: <center> element removed from HTML5
WAIC.html:63:1: Warning: <center> element removed from HTML5
WAIC.html:65:1: Warning: <center> element removed from HTML5
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
Found the following significant warnings:
  BayesReversePLLH.cpp:439:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BayesReversePLLH.cpp:1129:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BayesReversePLLH.cpp:1172:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BayesReversePLLH.cpp:3029:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BayesReversePLLH.Rcheck/00install.out' for details.
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 math rendering problems:
bayes.regress.Rd:92: Unknown column alignment: @ in \begin{array}{r@{\,}l}\beta | \...
bayes.regress.Rd:95-100: Unknown column alignment: @ in \begin{array}{r@{\,}l}
    \beta ...
checkRd: (-1) describe_posterior.Rd:194: Escaped LaTeX specials: \&
checkRd: (-1) diagnostic_posterior.Rd:103: Escaped LaTeX specials: \&
checkRd: (-1) estimate_density.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) point_estimate.Rd:113: Escaped LaTeX specials: \&
checkRd: (-1) sexit.Rd:91: Escaped LaTeX specials: \&
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
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: unable to re-encode 'bdc_clean_names.R' line 934
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bdc.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:
  'dump.txt'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'beast_plot_toy.pdf'
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
hill.html:23:30: Warning: <em> is probably intended as </em>
hill.html:25:72: Warning: discarding unexpected </em>
hill.html:28:23: Warning: discarding unexpected </em>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Checking should be performed on sources prepared by 'R CMD build'.
'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.
checkRd: (-1) scrHpd.Rd:30: Escaped LaTeX specials: \&
Found the following HTML validation problems:
bggCollection.html:70:6: Warning: missing </span> before <p>
bggCollection.html:70:93: Warning: inserting implicit <span>
bggCollection.html:73:6: Warning: missing </span> before <p>
bggCollection.html:73:92: Warning: inserting implicit <span>
bggCollection.html:76:6: Warning: missing </span> before <p>
bggCollection.html:76:103: Warning: inserting implicit <span>
bggCollection.html:70:6: Warning: trimming empty <span>
bggCollection.html:73:6: Warning: trimming empty <span>
bggCollection.html:76:6: Warning: trimming empty <span>
bggGames.html:68:6: Warning: missing </span> before <p>
bggGames.html:68:93: Warning: inserting implicit <span>
bggGames.html:71:6: Warning: missing </span> before <p>
bggGames.html:71:92: Warning: inserting implicit <span>
bggGames.html:74:6: Warning: missing </span> before <p>
bggGames.html:74:103: Warning: inserting implicit <span>
bggGames.html:68:6: Warning: trimming empty <span>
bggGames.html:71:6: Warning: trimming empty <span>
bggGames.html:74:6: Warning: trimming empty <span>
bggSearch.html:77:6: Warning: missing </span> before <p>
bggSearch.html:77:93: Warning: inserting implicit <span>
bggSearch.html:80:6: Warning: missing </span> before <p>
bggSearch.html:80:92: Warning: inserting implicit <span>
bggSearch.html:83:6: Warning: missing </span> before <p>
bggSearch.html:83:103: Warning: inserting implicit <span>
bggSearch.html:77:6: Warning: trimming empty <span>
bggSearch.html:80:6: Warning: trimming empty <span>
bggSearch.html:83:6: Warning: trimming empty <span>
'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: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ffbase'
Package suggested but not available for checking: 'INLA'
Found the following HTML validation problems:
air.density.html:65:38: Warning: nested emphasis <code>
decoupling.html:123:38: Warning: nested emphasis <code>
latent.heat.vaporization.html:55:38: Warning: nested emphasis <code>
psychrometric.constant.html:67:38: Warning: nested emphasis <code>
stability.parameter.html:100:38: Warning: nested emphasis <code>
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.
Checking should be performed on sources prepared by 'R CMD build'.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'outputs'
Found the following HTML validation problems:
snp_ldsc.html:122:1: Warning: trimming empty <dt>
Problems with news in 'NEWS.md':
No news entries found.
Found the following math rendering problems:
MDL.Rd:90-98: Expected '}', got '&' in ...n{pmatrix}
  {
  1 & 0 & 0 & 0 & .....
MDL.Rd:132: Expected '}', got '&' in ...{pmatrix} {1.1 & 0 & 1.3  \cr 0...
MDL.Rd:154: Expected '}', got '&' in ....1 * Rscale[1] & 0 & 1.3 * Rsca...
MDL.Rd:170: Expected '}', got '&' in ...pmatrix} {X' X & R_{aug}' \cr R...
MDL.Rd:212: Expected '}', got '&' in ...in{pmatrix} {0 & 1 & -3 & 3 & 1...
'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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) core.find.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) core.find.Rd:87: Escaped LaTeX specials: \^
checkRd: (-1) core.find.Rd:89: Escaped LaTeX specials: \^
checkRd: (-1) core.find.Rd:91: Escaped LaTeX specials: \^
checkRd: (-1) core.find.Rd:93: Escaped LaTeX specials: \^
checkRd: (-1) core.find.Rd:95: Escaped LaTeX specials: \^
checkRd: (-1) core.find.Rd:97: Escaped LaTeX specials: \^
'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'
Found the following HTML validation problems:
biogrowth-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
biogrowth-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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 HTML validation problems:
bioRad-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
bioRad-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
bioseq-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
bioseq-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) NOS.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) specieslevel.Rd:156: 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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
bittermelon.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
bittermelon.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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:
amlps.object.html:113:38: Warning: nested emphasis <code>
coxlps.baseline.html:84:38: Warning: nested emphasis <code>
coxlps.baseline.html:88:38: Warning: nested emphasis <code>
coxlps.object.html:74:38: Warning: nested emphasis <code>
cubicbs.html:65:38: Warning: nested emphasis <code>
curelps.object.html:68:38: Warning: nested emphasis <code>
gamlps.object.html:117:38: Warning: nested emphasis <code>
simsurvdata.html:108:38: Warning: nested emphasis <code>
snmatch.html:79:38: Warning: nested emphasis <code>
'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: \&
Found the following HTML validation problems:
ChiSquare.html:30:1: Warning: inserting implicit <p>
ChiSquare.html:109:1: Warning: inserting implicit <p>
ChiSquare.html:30:1: Warning: trimming empty <p>
ChiSquare.html:109:1: Warning: trimming empty <p>
FarringtonManning.html:32:1: Warning: inserting implicit <p>
FarringtonManning.html:101:1: Warning: inserting implicit <p>
FarringtonManning.html:32:1: Warning: trimming empty <p>
FarringtonManning.html:101:1: Warning: trimming empty <p>
Student.html:37:1: Warning: inserting implicit <p>
Student.html:113:1: Warning: inserting implicit <p>
Student.html:37:1: Warning: trimming empty <p>
Student.html:113:1: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Forest.cpp:350:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/blockForest.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.
Found the following HTML validation problems:
bmscstan.html:55:70: Warning: replacing unexpected i with </i>
bmscstan.html:55:89: Warning: inserting implicit <sub>
bmscstan.html:56:4: Warning: inserting implicit <sub>
bmscstan.html:58:1: Warning: inserting implicit <sub>
bmscstan.html:58:1: Warning: missing </sub> before <p>
bmscstan.html:58:4: Warning: inserting implicit <sub>
bmscstan.html:63:1: Warning: inserting implicit <sub>
bmscstan.html:63:1: Warning: missing </sub> before <h3>
bmscstan.html:63:5: Warning: inserting implicit <sub>
bmscstan.html:65:4: Warning: inserting implicit <sub>
bmscstan.html:70:1: Warning: inserting implicit <sub>
bmscstan.html:55:89: Warning: trimming empty <sub>
bmscstan.html:58:1: Warning: trimming empty <sub>
bmscstan.html:63:1: Warning: trimming empty <sub>
bmscstan.html:70:1: Warning: trimming empty <sub>
bmscstan.html:44:1: Warning: <center> element removed from HTML5
bmscstan.html:55:1: Warning: <center> element removed from HTML5
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:
  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
Found the following HTML validation problems:
bayes.lin.reg.html:27:32: Warning: trimming empty <code>
bayes.lin.reg.html:32:32: Warning: trimming empty <code>
Problems with news in 'NEWS.md':
No news entries found.
Found the following HTML validation problems:
BoneProfileR-package.html:39:1: Warning: <img> attribute "," lacks value
BoneProfileR-package.html:39:1: Warning: <img> attribute "align" not allowed for HTML5
BoneProfileR-package.html:39:1: Warning: <img> attribute "align" not allowed for HTML5
Found the following files/directories:
  'attractors.tex' 'cellcycle.sbml' 'cellcycle.txt' 'pajek_export.net'
  'sequence.txt' 'testNet.bn'
Found the following HTML validation problems:
boomer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
boomer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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: \&
GNU make is a SystemRequirements.
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
'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:
  exhaust_bic.cpp:269:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  exhaust_bic.cpp:290:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/breakfast.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) brew.Rd:41: Escaped LaTeX specials: \#
Found the following HTML validation problems:
Bridge.html:80:32: Warning: trimming empty <code>
Bridge.html:85:32: Warning: trimming empty <code>
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Found the following HTML validation problems:
fit_200.html:38:60: Warning: inserting implicit <p>
fit_200.html:38:60: Warning: trimming empty <p>
fit_200_light.html:37:61: Warning: inserting implicit <p>
fit_200_light.html:37:61: Warning: trimming empty <p>
Package suggested but not available for checking: 'glmmADMB'
checkRd: (-1) brr-package.Rd:33: Escaped LaTeX specials: \&
Found the following HTML validation problems:
bruceR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
bruceR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
Found the following significant warnings:
  simulate_toad.cpp:155:17: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  simulate_toad.cpp:182:17: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BSL.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: '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
Found the following HTML validation problems:
buildr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
buildr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following HTML validation problems:
bunching.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
bunching.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  opt.cpp:110:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  opt.cpp:110:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bzinb.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
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  calculus.cpp:6:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/calculus.Rcheck/00install.out' for details.
Found the following HTML validation problems:
calculus-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
calculus-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
'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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
carbon.html:48:55: Warning: <big> element removed from HTML5
carbon.html:57:55: Warning: <big> element removed from HTML5
carbon.html:73:55: Warning: <big> element removed from HTML5
carbon.html:105:55: Warning: <big> element removed from HTML5
carbon.html:133:55: Warning: <big> element removed from HTML5
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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
create_table.html:67:50: Warning: inserting implicit <p>
create_table.html:67:50: Warning: trimming empty <p>
'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 HTML validation problems:
catmaply-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
catmaply-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following files/directories:
  'catmapdata.fixed.effects.plot.pdf' 'catmapdata.funnel.plot.pdf'
  'catmapdata.output.txt' 'catmapdata.random.effects.plot.pdf'
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
Found the following significant warnings:
  kernel_calc.cpp:242:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  kernel_calc.cpp:246:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  kernel_calc.cpp:429:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  kernel_calc.cpp:433:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  kernel_calc.cpp:537:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/causalOT.Rcheck/00install.out' for details.
checkRd: (-1) causalPAFplot.Rd:47: Escaped LaTeX specials: \$ \$
checkRd: (-1) eval_make_formula.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) pointEstimate.Rd:43: Escaped LaTeX specials: \$ \$
checkRd: (-1) sim_outnode.Rd:20: Escaped LaTeX specials: \$ \$
checkRd: (-1) sim_outnode_2.Rd:26: Escaped LaTeX specials: \$ \$
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
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 math rendering problems:
discrim.index.Rd:52-55: Undefined control sequence: \boldmath in ...c{1}{2} \max_{ \boldmath{\alpha} }
  \lef...
discrim.index.Rd:56: Undefined control sequence: \boldmath in \boldmath{\alpha}^{(-k)}
discrim.index.Rd:56: Undefined control sequence: \boldmath in \boldmath{\alpha}
discrim.index.Rd:65-66: Undefined control sequence: \boldmath in IDI_j=\max_{ \boldmath{\alpha}_1,\bol...
gdina.Rd:354-356: Undefined control sequence: \boldmath in ...| \alpha_n ) ]=\boldmath{M}_j ( \alpha ...
gdina.Rd:357: Undefined control sequence: \boldmath in \boldmath{M}_j (\alpha _...
gdina.Rd:358: Undefined control sequence: \boldmath in \boldmath{\delta}_j
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
Found the following HTML validation problems:
cffr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
cffr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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 significant warnings:
  soft_impute.cpp:49:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/changepoints.Rcheck/00install.out' for details.
'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
Package suggested but not available for checking: '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.
Found the following HTML validation problems:
chillR-package.html:19:5: Warning: <img> attribute "align" not allowed for HTML5
chillR-package.html:19:5: Warning: <img> attribute "align" not allowed for HTML5
plot_phenology_trends.html:153:4: Warning: <img> attribute "align" not allowed for HTML5
plot_phenology_trends.html:153:4: Warning: <img> attribute "align" not allowed for HTML5
plot_scenarios.html:184:4: Warning: <img> attribute "align" not allowed for HTML5
plot_scenarios.html:184:4: Warning: <img> attribute "align" not allowed for HTML5
'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'
Found the following HTML validation problems:
chk-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
chk-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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'
*** caught segfault ***
address 0x18, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Found the following HTML validation problems:
Chrome.html:66:6: Warning: missing </span> before <p>
Chrome.html:66:89: Warning: inserting implicit <span>
Chrome.html:69:6: Warning: missing </span> before <p>
Chrome.html:69:92: Warning: inserting implicit <span>
Chrome.html:72:6: Warning: missing </span> before <p>
Chrome.html:72:92: Warning: inserting implicit <span>
Chrome.html:75:6: Warning: missing </span> before <p>
Chrome.html:75:95: Warning: inserting implicit <span>
Chrome.html:78:6: Warning: missing </span> before <p>
Chrome.html:78:92: Warning: inserting implicit <span>
Chrome.html:66:6: Warning: trimming empty <span>
Chrome.html:69:6: Warning: trimming empty <span>
Chrome.html:72:6: Warning: trimming empty <span>
Chrome.html:75:6: Warning: trimming empty <span>
Chrome.html:78:6: Warning: trimming empty <span>
ChromeRemote.html:55:6: Warning: missing </span> before <p>
ChromeRemote.html:55:89: Warning: inserting implicit <span>
ChromeRemote.html:58:6: Warning: missing </span> before <p>
ChromeRemote.html:58:92: Warning: inserting implicit <span>
ChromeRemote.html:61:6: Warning: missing </span> before <p>
ChromeRemote.html:61:92: Warning: inserting implicit <span>
ChromeRemote.html:64:6: Warning: missing </span> before <p>
ChromeRemote.html:64:95: Warning: inserting implicit <span>
ChromeRemote.html:67:6: Warning: missing </span> before <p>
ChromeRemote.html:67:92: Warning: inserting implicit <span>
ChromeRemote.html:55:6: Warning: trimming empty <span>
ChromeRemote.html:58:6: Warning: trimming empty <span>
ChromeRemote.html:61:6: Warning: trimming empty <span>
ChromeRemote.html:64:6: Warning: trimming empty <span>
ChromeRemote.html:67:6: Warning: trimming empty <span>
Chromote.html:40:39: Warning: inserting implicit <p>
Chromote.html:40:39: Warning: trimming empty <p>
'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
Package suggested but not available for checking: 'userfriendlyscience'
Found the following HTML validation problems:
browse_circle_token.html:68:81: Warning: inserting implicit <p>
browse_circle_token.html:68:81: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Found the following math rendering problems:
signature.Rd:52: Undefined control sequence: \cases in 
    e_i e_i = \cases{
    +1 & if $1\...
Found the following HTML validation problems:
climaemet-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
climaemet-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) diagwl.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) diagwl.Rd:5: Escaped LaTeX specials: \&
Found the following HTML validation problems:
climatrends.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
climatrends.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
ClimMobTools.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ClimMobTools.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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) dataADaMCDISCP01.Rd:48: Escaped LaTeX specials: \&
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
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
Package suggested but not available for checking: 'CRTSize'
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
'LazyData' is specified without 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.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Older versions
'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 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'
Found the following HTML validation problems:
write_codemeta.html:189:30: Warning: inserting implicit <p>
write_codemeta.html:189:30: Warning: trimming empty <p>
write_codemeta.html:184:1: Warning: <details> proprietary attribute "closed"
Found the following HTML validation problems:
coder-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
coder-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Error(s) in re-building vignettes:
  ...
--- re-building 'colorDF.Rmd' using rmarkdown
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
'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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'CAM'
Found the following HTML validation problems:
CompAREdesign-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
CompAREdesign-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) compareGroups-package.Rd:52: Escaped LaTeX specials: \~
checkRd: (-1) sumboxdata.Rd:12: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) sumboxmktCnt.Rd:10: Escaped LaTeX specials: \$ \$ \$
Found the following significant warnings:
  sprinkler.c:6:14037: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CompModels.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
concurve-package.html:38:43: Warning: <img> attribute "width" has invalid value "50px"
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
Found the following HTML validation problems:
conformalbayes-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
conformalbayes-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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.
'LazyData' is specified without 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 math rendering problems:
check-convergence.Rd:37: Can't use function '$' in math mode in $\hat(l)_n(t)=|\...
criterion.Rd:20: Can't use function '$' in math mode in $X_n-X$
criterion.Rd:21: Can't use function '$' in math mode in $p_n=P[|X_n-X|>\...
criterion.Rd:22-23: Can't use function '$' in math mode in $a_n=P[\exists k...
criterion.Rd:25: Can't use function '$' in math mode in $e_{n,r}=E|X_n-X...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: 'cec2005benchmark'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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) poss_local.Rd:21: Escaped LaTeX specials: \~
'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
Running examples in 'correlation-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: visualisation_recipe.easycor_test
> ### Title: Visualisation Recipe for 'correlation' Objects
> ### Aliases: visualisation_recipe.easycor_test
> ###   visualisation_recipe.easycormatrix
> ###   visualisation_recipe.easycorrelation
> 
> ### ** Examples
> 
> # ==============================================
> # Correlation Matrix
> # ==============================================
> if (require("see")) {
+   rez <- correlation(mtcars)
+ 
+   x <- cor_sort(as.matrix(rez))
+   layers <- visualisation_recipe(x)
+   layers
+   plot(layers)
+ 
+   #' Get more details using `summary()`
+   x <- summary(rez, redundant = TRUE, digits = 3)
+   plot(visualisation_recipe(x))
+ 
+   # Customize
+   x <- summary(rez)
+   layers <- visualisation_recipe(x,
+     show_data = "points",
+     scale = list(range = c(10, 20)),
+     scale_fill = list(
+       high = "#FF5722",
+       low = "#673AB7",
+       name = "r"
+     ),
+     text = list(color = "white"),
+     labs = list(title = "My Plot")
+   )
+   plot(layers) + theme_modern()
+ }
Loading required package: see
Warning: Argument `colnames_to` is deprecated. Please use `names_to` instead.
Error in colnames(data)[sapply(data, select)] : 
  invalid subscript type 'list'
Calls: visualisation_recipe ... visualisation_recipe.easycormatrix -> <Anonymous> -> .select_nse
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
corrr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
corrr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package required but not available: 'ctsem'

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 math rendering problems:
couples-class.Rd:95: Can't use function '$' in math mode in $||\mathbf{h}_{1...
couples-class.Rd:99: Can't use function '$' in math mode in $u_{1}^{2\alpha}...
covaprop-class.Rd:46: Can't use function '$' in math mode in C(h,u) - C...
covaprop-class.Rd:52: Can't use function '$' in math mode in C(h, u)/C(...
covaprop-class.Rd:60: Can't use function '$' in math mode in C(h,u)/C(h...
covaprop-class.Rd:62: Can't use function '$' in math mode in C(h,u)/C(h...
covaprop-class.Rd:68: Can't use function '$' in math mode in Af(G)=0$
Package suggested but not available for checking: 'spcov'
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'covfefe_inauguration.txt'
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [3s/79s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(covid19us)
  > 
  > test_check("covid19us")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  
  == Failed tests ================================================================
  -- Error (test-all.R:63:3): other funs work ------------------------------------
  Error in `get_info_covid19us()`: Data service unavailable.
  Backtrace:
      x
   1. \-covid19us::get_info_covid19us() at test-all.R:63:2
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial Release
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
covr-package.html:36:133: Warning: inserting implicit <p>
covr-package.html:36:133: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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
Package suggested but not available for checking: 'argosfilter'
'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
Found the following HTML validation problems:
plot-PseudoDualFlexiSimulations-missing-method.html:19:1: Warning: missing </h2> before <dl>
plot-PseudoDualFlexiSimulations-missing-method.html:32:28: Warning: discarding unexpected </h2>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
download_terraclimate.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
download_terraclimate.html:20:1: Warning: <img> proprietary attribute "logo"
eto_calibration.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
eto_calibration.html:20:1: Warning: <img> proprietary attribute "logo"
loadROI.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
loadROI.html:20:1: Warning: <img> proprietary attribute "logo"
monthly_stack.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
monthly_stack.html:20:1: Warning: <img> proprietary attribute "logo"
plot_AWC.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
plot_AWC.html:20:1: Warning: <img> proprietary attribute "logo"
ppt_calibration.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
ppt_calibration.html:20:1: Warning: <img> proprietary attribute "logo"
see_brazil_biomes.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
see_brazil_biomes.html:20:1: Warning: <img> proprietary attribute "logo"
see_brazil_states.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
see_brazil_states.html:20:1: Warning: <img> proprietary attribute "logo"
waterDemand.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
waterDemand.html:20:1: Warning: <img> proprietary attribute "logo"
'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
Found the following HTML validation problems:
ccrop_zoning.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
ccrop_zoning.html:20:1: Warning: <img> proprietary attribute "logo"
download_terraclimate.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
download_terraclimate.html:20:1: Warning: <img> proprietary attribute "logo"
loadROI.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
loadROI.html:20:1: Warning: <img> proprietary attribute "logo"
plot_ccrop_zoning.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
plot_ccrop_zoning.html:20:1: Warning: <img> proprietary attribute "logo"
see_brazil_biomes.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
see_brazil_biomes.html:20:1: Warning: <img> proprietary attribute "logo"
see_brazil_states.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
see_brazil_states.html:20:1: Warning: <img> proprietary attribute "logo"
tmax_calibration.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
tmax_calibration.html:20:1: Warning: <img> proprietary attribute "logo"
tmean.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
tmean.html:20:1: Warning: <img> proprietary attribute "logo"
tmean_monthly_stack.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
tmean_monthly_stack.html:20:1: Warning: <img> proprietary attribute "logo"
Found the following HTML validation problems:
crossmap-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
crossmap-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
crosstable-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
crosstable-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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 math rendering problems:
geeDREstimation.Rd:112: Can't use function '$' in math mode in ...ymbol U_i^{1/2}$ with $\boldsym...
geeDREstimation.Rd:120: Can't use function '$' in math mode in ...dsymbol \eta}_W$ in $\boldsymbo...
geeDREstimation.Rd:120: Can't use function '$' in math mode in ...dsymbol \eta}_B$ in $\boldsymbo...
Found the following HTML validation problems:
AsyncQueue.html:102:6: Warning: missing </span> before <p>
AsyncQueue.html:102:92: Warning: inserting implicit <span>
AsyncQueue.html:102:6: Warning: trimming empty <span>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
ctrdata-registers.html:85:230: Warning: <a> illegal characters found in URI
Package required but not available: 'ctsem'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ctsem.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:
  'Hello.csv'
GNU make is a SystemRequirements.
Found the following math rendering problems:
divonne.Rd:143: Can't use function '$' in math mode in $n=|key2|$
hcubature.Rd:124: Undefined control sequence: \L in \L_{\infty}
'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'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    CVXR pre-0.94-4
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following HTML validation problems:
spade.html:201:125: Warning: nested emphasis <strong>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
czso-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
czso-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following files/directories:
  'GRCh38_browser' 'GRCh38_map'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Found the following significant warnings:
  DTRegion3D.cpp:58:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  DTRegion3D.cpp:102:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DataGraph.Rcheck/00install.out' for details.
'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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    dataquieR (1.0.8)
    dataquieR (1.0.7)
    dataquieR (1.0.6)
    dataquieR (1.0.0)
Found the following HTML validation problems:
acc_robust_univariate_outlier.html:128:4: Warning: nested emphasis <em>
acc_univariate_outlier.html:128:4: Warning: nested emphasis <em>
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 HTML validation problems:
get_dated_otol_induced_subtree.html:53:1: Warning: trimming empty <dt>
get_otol_synthetic_tree.html:67:1: Warning: trimming empty <dt>
summary_matrix_to_phylo.html:89:1: Warning: trimming empty <dt>
Package suggested but not available for checking: 'SASxport'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
datos-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
datos-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
dbflobr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
dbflobr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    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
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
validate_arguments.html:83:111: Warning: inserting implicit <p>
validate_arguments.html:87:95: Warning: inserting implicit <p>
validate_arguments.html:94:51: Warning: inserting implicit <p>
validate_arguments.html:83:111: Warning: trimming empty <p>
validate_arguments.html:87:95: Warning: trimming empty <p>
validate_arguments.html:94:51: Warning: trimming empty <p>
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
GNU make is a SystemRequirements.
Found the following HTML validation problems:
fit.dl.html:19:1: Warning: missing </h2> before <ol>
fit.dl.html:34:1: Warning: discarding unexpected </h2>
Found the following files/directories:
  'res.pdf' 'res1.jpg'
'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 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
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'
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 math rendering problems:
BinomRatioCI.rd:88-89: Can't use function '$' in math mode in ...{\theta }_{0}}}$, and ${{X}^{2}...
StdCoef.Rd:71: Undefined control sequence: \var in ...^{*}=s_{X_{i}} \var{VIF}(X_i)^{-0....
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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) phihat.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) anova.dglm.Rd:41: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
dialr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
dialr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
diceR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
diceR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
did_imputation.html:125:104: Warning: inserting implicit <p>
did_imputation.html:133:96: Warning: inserting implicit <p>
did_imputation.html:146:99: Warning: inserting implicit <p>
did_imputation.html:169:78: Warning: inserting implicit <p>
did_imputation.html:125:104: Warning: trimming empty <p>
did_imputation.html:133:96: Warning: trimming empty <p>
did_imputation.html:146:99: Warning: trimming empty <p>
did_imputation.html:169:78: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
dimensio-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
dimensio-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
checkRd: (-1) eul2rot.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) multivm.mle.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) rot2eul.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) spml.mle.Rd:78: Escaped LaTeX specials: \&
'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'
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
fit_model.Rd:97: Can't use function '$' in math mode in \sigma_{min}$ and $\sigma_{p...
make_model_object.Rd:64: Can't use function '$' in math mode in \sigma_{min}$ and $\sigma_{p...
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
disastr.api.html:125:40: Warning: missing </a> before <a>
disastr.api.html:125:151: Warning: discarding unexpected </a>
checkRd: (-1) sammy.Rd:51: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'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
Found the following HTML validation problems:
amakihi.html:85:6: Warning: <a> illegal characters found in URI
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
DistAlgo.Rd:10: Undefined control sequence: \time in 6\times6\time4
GraphDistatisAll.Rd:24: Undefined control sequence: \time in I\time 1
GraphDistatisAll.Rd:26: Undefined control sequence: \time in I\time 1
GraphDistatisCompromise.Rd:21: Undefined control sequence: \time in I\time 1
GraphDistatisPartial.Rd:23: Undefined control sequence: \time in I\time 1
GraphDistatisPartial.Rd:25: Undefined control sequence: \time in I\time 1
GraphDistatisRv.Rd:27: Undefined control sequence: \time in I\time 1
Found the following HTML validation problems:
HEQueryCountMaster.html:88:6: Warning: missing </span> before <p>
HEQueryCountMaster.html:88:100: Warning: inserting implicit <span>
HEQueryCountMaster.html:91:6: Warning: missing </span> before <p>
HEQueryCountMaster.html:91:101: Warning: inserting implicit <span>
HEQueryCountMaster.html:88:6: Warning: trimming empty <span>
HEQueryCountMaster.html:91:6: Warning: trimming empty <span>
HEQueryCountWorker.html:74:6: Warning: missing </span> before <p>
HEQueryCountWorker.html:74:104: Warning: inserting implicit <span>
HEQueryCountWorker.html:77:6: Warning: missing </span> before <p>
HEQueryCountWorker.html:77:99: Warning: inserting implicit <span>
HEQueryCountWorker.html:74:6: Warning: trimming empty <span>
HEQueryCountWorker.html:77:6: Warning: trimming empty <span>
'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: \&
Found the following HTML validation problems:
create_theme.html:55:112: Warning: inserting implicit <p>
create_theme.html:64:58: Warning: inserting implicit <p>
create_theme.html:55:112: Warning: trimming empty <p>
create_theme.html:64:58: Warning: trimming empty <p>
distill-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
distill-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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:
  Engine.cpp:73:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:79:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:84:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:94:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:102:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:109:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:116:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:124:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:132:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:140:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:148:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:156:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:164:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/divDyn.Rcheck/00install.out' for details.
Found the following HTML validation problems:
divDyn.html:138:81: Warning: <em> is probably intended as </em>
divDyn.html:138:96: Warning: discarding unexpected </em>
divDyn.html:138:130: Warning: discarding unexpected </em>
divDyn.html:140:82: Warning: <em> is probably intended as </em>
divDyn.html:140:97: Warning: discarding unexpected </em>
divDyn.html:140:131: Warning: discarding unexpected </em>
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 math rendering problems:
Dixon.Rd:56-66: Unknown column alignment: [ in 
  \begin{array}[h]{lcl}
  f(r) & ...
'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
Found the following HTML validation problems:
make_index.html:92:55: Warning: nested emphasis <b>
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: \#
Found the following HTML validation problems:
dobin-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
dobin-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without 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'.
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
Found the following HTML validation problems:
downloadthis-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
downloadthis-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
across.html:114:90: Warning: inserting implicit <p>
across.html:114:90: Warning: trimming empty <p>
select.html:176:41: Warning: inserting implicit <p>
select.html:182:55: Warning: inserting implicit <p>
select.html:204:85: Warning: inserting implicit <p>
select.html:216:96: Warning: inserting implicit <p>
select.html:231:99: Warning: inserting implicit <p>
select.html:242:78: Warning: inserting implicit <p>
select.html:274:121: Warning: inserting implicit <p>
select.html:296:52: Warning: inserting implicit <p>
select.html:176:41: Warning: trimming empty <p>
select.html:182:55: Warning: trimming empty <p>
select.html:204:85: Warning: trimming empty <p>
select.html:216:96: Warning: trimming empty <p>
select.html:231:99: Warning: trimming empty <p>
select.html:242:78: Warning: trimming empty <p>
select.html:274:121: Warning: trimming empty <p>
select.html:296:52: Warning: trimming empty <p>
Found the following HTML validation problems:
LinearRegressionDP.html:86:6: Warning: missing </span> before <p>
LinearRegressionDP.html:86:113: Warning: inserting implicit <span>
LinearRegressionDP.html:86:6: Warning: trimming empty <span>
'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
Found the following HTML validation problems:
make.html:800:24: Warning: inserting implicit <p>
make.html:800:24: Warning: trimming empty <p>
Found the following HTML validation problems:
canvas.html:147:49: Warning: inserting implicit <p>
canvas.html:160:130: Warning: inserting implicit <p>
canvas.html:147:49: Warning: trimming empty <p>
canvas.html:160:130: Warning: trimming empty <p>
'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
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following math rendering problems:
cdfDRM.Rd:21: Undefined control sequence: \textsuperscript in \textsuperscript{th}
cdfDRM.Rd:42: Undefined control sequence: \textsuperscript in \textsuperscript{th}
densityDRM.Rd:12: Undefined control sequence: \textsuperscript in \textsuperscript{th}
quantileDRM.Rd:52: Undefined control sequence: \textsuperscript in \textsuperscript{th}
quantileDRM.Rd:77: Undefined control sequence: \textsuperscript in \textsuperscript{th}
quantileDRM.Rd:79: Undefined control sequence: \textsuperscript in \textsuperscript{th}
quantileDRM.Rd:89: Undefined control sequence: \textsuperscript in \textsuperscript{th}
quantileDRM.Rd:108: Undefined control sequence: \textsuperscript in \textsuperscript{th}
'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
Found the following HTML validation problems:
dtplyr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
dtplyr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
dttr2-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
dttr2-package.html:30:4: Warning: <img> attribute "align" not allowed for HTML5
dttr2-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
dttr2-package.html:30:4: Warning: <img> attribute "align" not allowed for HTML5
GNU make is a SystemRequirements.
Found the following HTML validation problems:
dual-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
dual-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without 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.
checkRd: (-1) dynaTree.Rd:265: Escaped LaTeX specials: \&
checkRd: (-1) dynaTree.Rd:270: Escaped LaTeX specials: \&
checkRd: (-1) relevance.dynaTree.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) sens.dynaTree.Rd:140: Escaped LaTeX specials: \&
'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
'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
'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
Found the following HTML validation problems:
easycensus-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
easycensus-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
EcoDiet-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
EcoDiet-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Package suggested but not available for checking: 'geoR'
Unknown package 'geoR' 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.
Package suggested but not available for checking: 'ecomix'
'LazyData' is specified without 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:
  'tmplp.dat'
'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
Found the following HTML validation problems:
edibble-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
edibble-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) eta_squared.Rd:164: Escaped LaTeX specials: \&
checkRd: (-1) eta_squared.Rd:321: Escaped LaTeX specials: \&
checkRd: (-1) interpret_gfi.Rd:133: Escaped LaTeX specials: \&
checkRd: (-1) interpret_gfi.Rd:135: Escaped LaTeX specials: \&
checkRd: (-1) interpret_gfi.Rd:137: Escaped LaTeX specials: \&
checkRd: (-1) interpret_icc.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) interpret_pd.Rd:45: Escaped LaTeX specials: \&
Found the following HTML validation problems:
interpret_bf.html:152:1: Warning: trimming empty <li>
interpret_bf.html:151:1: Warning: trimming empty <ol>
'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
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 HTML validation problems:
elbird-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
elbird-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
embryogrowth-package.html:27:1: Warning: <img> attribute "," lacks value
embryogrowth-package.html:27:1: Warning: <img> attribute "align" not allowed for HTML5
embryogrowth-package.html:27:1: Warning: <img> attribute "align" not allowed for HTML5
Package which this enhances but not available for checking: 'PPtree'
Found the following math rendering problems:
a0_project.on.2d.Rd:39: Undefined control sequence: \time in p \time 2
'LazyData' is specified without a 'data' directory
'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
Unknown package 'geoR' in Rd xrefs
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Cyclops'
Error(s) in re-building vignettes:
  ...
--- re-building 'EmpiricalCiCalibrationVignette.Rmd' using rmarkdown
--- finished re-building 'EmpiricalCiCalibrationVignette.Rmd'

--- re-building 'EmpiricalMaxSprtCalibrationVignette.Rmd' using rmarkdown
Quitting from lines 61-74 (EmpiricalMaxSprtCalibrationVignette.Rmd) 
Error: processing vignette 'EmpiricalMaxSprtCalibrationVignette.Rmd' failed with diagnostics:
there is no package called 'Cyclops'
--- failed re-building 'EmpiricalMaxSprtCalibrationVignette.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
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)'
'LazyData' is specified without a 'data' directory
checkRd: (-1) check_several.Rd:34: Escaped LaTeX specials: \#
checkRd: (-1) check_several.Rd:35: Escaped LaTeX specials: \#
Found the following HTML validation problems:
attach_source.html:105:96: Warning: inserting implicit <p>
attach_source.html:111:52: Warning: inserting implicit <p>
attach_source.html:119:55: Warning: inserting implicit <p>
attach_source.html:105:96: Warning: trimming empty <p>
attach_source.html:111:52: Warning: trimming empty <p>
attach_source.html:119:55: Warning: trimming empty <p>
set_library_default_pos.html:59:104: Warning: inserting implicit <p>
set_library_default_pos.html:59:104: Warning: trimming empty <p>
Found the following math rendering problems:
Mguttatus.Rd:35: Undefined control sequence: \emph in \emph{PLoS Biol}
eigenboot.Rd:101: Undefined control sequence: \emph in \emph{in prep}
eigenbootcanon.Rd:106: Undefined control sequence: \emph in \emph{in prep}
fit_boot_Efron.Rd:191: Undefined control sequence: \emph in \emph{in prep}
fit_boot_Efron.Rd:195: Undefined control sequence: \emph in \emph{in prep}
fit_boot_Efron.Rd:199: Undefined control sequence: \emph in \emph{JASA}
secondboot.Rd:154: Undefined control sequence: \emph in \emph{in prep}
secondboot.Rd:158: Undefined control sequence: \emph in \emph{in prep}
secondboot.Rd:162: Undefined control sequence: \emph in \emph{JASA}
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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'Net1-fromR.inp'
GNU make is a SystemRequirements.
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: 'EpiSoon'
'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
Found the following significant warnings:
  EqMult.cpp:542:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/equateMultiple.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
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:
  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.
checkRd: (-1) ergm-package.Rd:105: Escaped LaTeX specials: \#
checkRd: (-1) ergm.Rd:441: Escaped LaTeX specials: \#
checkRd: (-1) faux.mesa.high.Rd:45: Escaped LaTeX specials: \&
checkRd: (-1) florentine.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) florentine.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) florentine.Rd:39: Escaped LaTeX specials: \&
Found the following HTML validation problems:
Error.html:61:6: Warning: missing </span> before <p>
Error.html:61:88: Warning: inserting implicit <span>
Error.html:64:6: Warning: missing </span> before <p>
Error.html:64:86: Warning: inserting implicit <span>
Error.html:67:6: Warning: missing </span> before <p>
Error.html:67:86: Warning: inserting implicit <span>
Error.html:70:6: Warning: missing </span> before <p>
Error.html:70:86: Warning: inserting implicit <span>
Error.html:73:6: Warning: missing </span> before <p>
Error.html:73:87: Warning: inserting implicit <span>
Error.html:61:6: Warning: trimming empty <span>
Error.html:64:6: Warning: trimming empty <span>
Error.html:67:6: Warning: trimming empty <span>
Error.html:70:6: Warning: trimming empty <span>
Error.html:73:6: Warning: trimming empty <span>
Warning.html:58:6: Warning: missing </span> before <p>
Warning.html:58:88: Warning: inserting implicit <span>
Warning.html:61:6: Warning: missing </span> before <p>
Warning.html:61:86: Warning: inserting implicit <span>
Warning.html:64:6: Warning: missing </span> before <p>
Warning.html:64:86: Warning: inserting implicit <span>
Warning.html:67:6: Warning: missing </span> before <p>
Warning.html:67:86: Warning: inserting implicit <span>
Warning.html:70:6: Warning: missing </span> before <p>
Warning.html:70:87: Warning: inserting implicit <span>
Warning.html:58:6: Warning: trimming empty <span>
Warning.html:61:6: Warning: trimming empty <span>
Warning.html:64:6: Warning: trimming empty <span>
Warning.html:67:6: Warning: trimming empty <span>
Warning.html:70:6: Warning: trimming empty <span>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
ic.proporcion.html:77:4: Warning: <img> attribute with missing trailing quote mark
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
EstCRMitem.Rd:54-56: Undefined control sequence: \emph in 
  \emph{f}(z_{ij}|\the...
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
Found the following HTML validation problems:
ebc_allmeasures.html:41:4: Warning: <img> attribute "align" not allowed for HTML5
ebc_allmeasures.html:41:4: Warning: <img> attribute "align" not allowed for HTML5
'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: \&
checkRd: (-1) exams2blackboard.Rd:152: Escaped LaTeX specials: \&
checkRd: (-1) exams2qti12.Rd:186: 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
Found the following HTML validation problems:
exoplanets-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
exoplanets-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'
Found the following HTML validation problems:
exuber.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
exuber.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
'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 HTML validation problems:
fable-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
fable-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
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
Found the following math rendering problems:
simul.far.Rd:51-57: Unknown column alignment: [ in ...t(\begin{array}[c]{lc}%
      \co...
simul.far.Rd:82-88: Unknown column alignment: [ in ...t(\begin{array}[c]{lc}%
      m_2...
simul.far.wiener.Rd:34-40: Unknown column alignment: [ in ...t(\begin{array}[c]{lc}%
      \co...
simul.farx.Rd:81-87: Unknown column alignment: [ in ...t(\begin{array}[c]{lc}%
      d.r...
simul.farx.Rd:109-115: Unknown column alignment: [ in ...t(\begin{array}[c]{lc}%
      alp...
'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 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
Found the following significant warnings:
  FastHCS.cpp:88:5: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  FastHCS.cpp:127:5: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/FastHCS.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'coxKM'
'LazyData' is specified without 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 '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.
Found the following significant warnings:
  cor_struct.c:27:13: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/fastmatrix.Rcheck/00install.out' for details.
Found the following math rendering problems:
helmert.Rd:16-22: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
      1/...
kronecker.prod.Rd:17-21: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
      x_...
'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
Found the following significant warnings:
  code.cpp:64:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/fastqq.Rcheck/00install.out' for details.
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 HTML validation problems:
fastRhockey-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
fastRhockey-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
.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
Found the following significant warnings:
  clean.cc:18:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  clean.cc:29:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  clean.cc:70:25: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  clean.cc:74:25: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/fastTextR.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'NNLM'
GNU make is a SystemRequirements.
Found the following HTML validation problems:
fauxnaif-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
fauxnaif-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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'
GNU make is a SystemRequirements.
checkRd: (-1) summary.fdata.comp.Rd:44: Escaped LaTeX specials: \&
Found the following HTML validation problems:
GCCV.S.html:87:32: Warning: trimming empty <code>
Found the following math rendering problems:
fregre.plm.Rd:86-87: Undefined control sequence: \emph in y =\emph{r(X)}+\sum_{j=...
metric.kl.Rd:45-46: Undefined control sequence: \- in \left|f_i(t)\-g_i(t) \right|\...
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Other Changes
Found the following HTML validation problems:
dfddm.html:192:1: Warning: unescaped & or unknown entity "&#8734"
pfddm.html:56:2: Warning: unescaped & or unknown entity "&#8734"
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'vert.txt'
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
feasts-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
feasts-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'treesAll.txt'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./vector_converter.h:249:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ./vector_converter.h:259:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/FeatureHashing.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:
fec16.html:29:4: Warning: <img> attribute "align" not allowed for HTML5
fec16.html:29:4: Warning: <img> attribute "align" not allowed for HTML5
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
'LazyData' is specified without a 'data' directory
'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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    ffp (development version)
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: \_
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Fixes
Found the following HTML validation problems:
ffsimulator-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ffsimulator-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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:
plot_tag_status_by_subquadrat.html:92:96: Warning: inserting implicit <p>
plot_tag_status_by_subquadrat.html:92:96: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
add_subquad.html:54:75: Warning: inserting implicit <p>
add_subquad.html:54:75: Warning: trimming empty <p>
recode_subquad.html:39:45: Warning: inserting implicit <p>
recode_subquad.html:39:45: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'MicrobeDS'
Found the following HTML validation problems:
optimMaltipooCollapsed.html:173:41: Warning: <em> is probably intended as </em>
optimMaltipooCollapsed.html:173:68: Warning: discarding unexpected </em>
optimMaltipooCollapsed.html:173:76: Warning: discarding unexpected </em>
Found the following HTML validation problems:
fiery-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
fiery-package.html:23:4: 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:
    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
'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'
Found the following HTML validation problems:
finetune-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
finetune-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
tune_race_anova.html:139:103: Warning: inserting implicit <p>
tune_race_anova.html:155:93: Warning: inserting implicit <p>
tune_race_anova.html:180:47: Warning: inserting implicit <p>
tune_race_anova.html:200:63: Warning: inserting implicit <p>
tune_race_anova.html:220:50: Warning: inserting implicit <p>
tune_race_anova.html:139:103: Warning: trimming empty <p>
tune_race_anova.html:155:93: Warning: trimming empty <p>
tune_race_anova.html:180:47: Warning: trimming empty <p>
tune_race_anova.html:200:63: Warning: trimming empty <p>
tune_race_anova.html:220:50: Warning: trimming empty <p>
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'
Found the following HTML validation problems:
SpotRate-class.html:55:64: Warning: inserting implicit <p>
SpotRate-class.html:63:95: Warning: inserting implicit <p>
SpotRate-class.html:71:54: Warning: inserting implicit <p>
SpotRate-class.html:75:66: Warning: inserting implicit <p>
SpotRate-class.html:79:74: Warning: inserting implicit <p>
SpotRate-class.html:93:75: Warning: inserting implicit <p>
SpotRate-class.html:107:106: Warning: inserting implicit <p>
SpotRate-class.html:125:61: Warning: inserting implicit <p>
SpotRate-class.html:155:111: Warning: inserting implicit <p>
SpotRate-class.html:55:64: Warning: trimming empty <p>
SpotRate-class.html:63:95: Warning: trimming empty <p>
SpotRate-class.html:71:54: Warning: trimming empty <p>
SpotRate-class.html:75:66: Warning: trimming empty <p>
SpotRate-class.html:79:74: Warning: trimming empty <p>
SpotRate-class.html:93:75: Warning: trimming empty <p>
SpotRate-class.html:107:106: Warning: trimming empty <p>
SpotRate-class.html:125:61: Warning: trimming empty <p>
SpotRate-class.html:155:111: Warning: trimming empty <p>
Term-class.html:33:39: Warning: inserting implicit <p>
Term-class.html:38:102: Warning: inserting implicit <p>
Term-class.html:44:102: Warning: inserting implicit <p>
Term-class.html:49:62: Warning: inserting implicit <p>
Term-class.html:59:60: Warning: inserting implicit <p>
Term-class.html:33:39: Warning: trimming empty <p>
Term-class.html:38:102: Warning: trimming empty <p>
Term-class.html:44:102: Warning: trimming empty <p>
Term-class.html:49:62: Warning: trimming empty <p>
Term-class.html:59:60: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
checkRd: (-1) etable.Rd:494: Escaped LaTeX specials: \$
'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 HTML validation problems:
flexpolyline-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
flexpolyline-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
GNU make is a SystemRequirements.
Found the following HTML validation problems:
GenF.html:115:32: Warning: trimming empty <code>
'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:
flobr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
flobr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
flow-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
flow-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
Found the following HTML validation problems:
folio-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
folio-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Found the following HTML validation problems:
forcats-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
forcats-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
checkRd: (-1) fpColors.Rd:59: 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:
  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'
Found the following math rendering problems:
Approx.cfpt.density.rd:41-46: Undefined control sequence: \vspace in ...} x_0 < S(t_0) \vspace{5pt} \\
  \mbox{...
Approx.fpt.density.rd:66-71: Undefined control sequence: \vspace in ...(t_0) < S(t_0) \vspace{5pt} \\
  \mbox{...
FPTL.Rd:37-42: Undefined control sequence: \vspace in ...} x_0 < S(t_0) \vspace{5pt} \\
  P[ X(t...
Integration.Steps.Rd:42-43: Undefined control sequence: \smallskip in ...box{for i odd} \smallskip \\ t_{max, \thi...
Integration.Steps.Rd:67-71: Undefined control sequence: \vspace in ...{i,j}^* \leq 1 \vspace{0.25cm} \\
     ...
Integration.Steps.Rd:78-82: Undefined control sequence: \vspace in ...{0,j}^* \leq 1 \vspace{0.25cm} \\
     ...
Integration.Steps.Rd:91-95: Undefined control sequence: \vspace in ..._j,j}^* \leq 1 \vspace{0.25cm} \\
     ...
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
Found the following math rendering problems:
cov.structure.Rd:35: Can't use function '$' in math mode in ...sum_{t=1}^T X_t$ and $\hat\mu^Y...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CatalogueAccessors.Rd:249: Escaped LaTeX specials: \^ \^
checkRd: (-1) FrF2.Rd:574: Escaped LaTeX specials: \^
checkRd: (-1) FrF2.Rd:629: Escaped LaTeX specials: \^ \^
checkRd: (-1) IAPlot.Rd:87: Escaped LaTeX specials: \$
checkRd: (-1) block.Rd:121: Escaped LaTeX specials: \^
checkRd: (-1) block.Rd:150: Escaped LaTeX specials: \^ \^
checkRd: (-1) blockpick.Rd:114: Escaped LaTeX specials: \^ \^
Found the following HTML validation problems:
read_resource.html:125:57: Warning: inserting implicit <p>
read_resource.html:125:57: Warning: trimming empty <p>
Packages suggested but not available for checking: 'dggrids', 'INLA'
Found the following HTML validation problems:
SRE.html:290:1: Warning: inserting implicit <p>
SRE.html:321:1: Warning: inserting implicit <p>
SRE.html:290:1: Warning: trimming empty <p>
SRE.html:321:1: Warning: trimming empty <p>
Unknown package 'frm' in Rd xrefs
Unknown package 'frm' in Rd xrefs
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
fso.Rd:44: Can't use function '$' in math mode in (correlations $>=$ observed + ...
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.
Found the following HTML validation problems:
fd_fric.html:105:6: Warning: <a> illegal characters found in URI
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
furrr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
furrr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
fusen-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
fusen-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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'
Found the following HTML validation problems:
future.apply.html:77:104: Warning: inserting implicit <p>
future.apply.html:80:43: Warning: inserting implicit <p>
future.apply.html:84:48: Warning: inserting implicit <p>
future.apply.html:89:58: Warning: inserting implicit <p>
future.apply.html:95:94: Warning: inserting implicit <p>
future.apply.html:99:79: Warning: inserting implicit <p>
future.apply.html:77:104: Warning: trimming empty <p>
future.apply.html:80:43: Warning: trimming empty <p>
future.apply.html:84:48: Warning: trimming empty <p>
future.apply.html:89:58: Warning: trimming empty <p>
future.apply.html:95:94: Warning: trimming empty <p>
future.apply.html:99:79: Warning: trimming empty <p>
future_lapply.html:303:105: Warning: inserting implicit <p>
future_lapply.html:303:105: Warning: trimming empty <p>
Found the following HTML validation problems:
future.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
future.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
multiprocess.html:28:1: Warning: nested emphasis <em>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
FuzzyClass-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
FuzzyClass-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package 'cffdrs' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  proglikelihood.cc:279:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  proglikelihood.cc:368:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  proglikelihood.cc:371:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/gadget2.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'geoR'
Found the following HTML validation problems:
got.html:90:36: Warning: <img> attribute with missing trailing quote mark
got.html:91:1: Warning: inserting implicit <p>
got.html:91:1: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'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 math rendering problems:
DEL.Rd:47: Undefined control sequence: \matrix in ...=0}^{y} \left( \matrix{ y \cr j } \ri...
'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: \&
checkRd: (-1) mia.Rd:39: Escaped LaTeX specials: \#
Found the following significant warnings:
  genope.cpp:963:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  genope.cpp:1400:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/GA.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
Found the following HTML validation problems:
Gargle-class.html:112:6: Warning: missing </span> before <p>
Gargle-class.html:112:92: Warning: inserting implicit <span>
Gargle-class.html:115:6: Warning: missing </span> before <p>
Gargle-class.html:115:87: Warning: inserting implicit <span>
Gargle-class.html:118:6: Warning: missing </span> before <p>
Gargle-class.html:118:85: Warning: inserting implicit <span>
Gargle-class.html:121:6: Warning: missing </span> before <p>
Gargle-class.html:121:89: Warning: inserting implicit <span>
Gargle-class.html:112:6: Warning: trimming empty <span>
Gargle-class.html:115:6: Warning: trimming empty <span>
Gargle-class.html:118:6: Warning: trimming empty <span>
Gargle-class.html:121:6: Warning: trimming empty <span>
GceToken.html:80:6: Warning: missing </span> before <p>
GceToken.html:80:82: Warning: inserting implicit <span>
GceToken.html:83:6: Warning: missing </span> before <p>
GceToken.html:83:88: Warning: inserting implicit <span>
GceToken.html:86:6: Warning: missing </span> before <p>
GceToken.html:86:85: Warning: inserting implicit <span>
GceToken.html:89:6: Warning: missing </span> before <p>
GceToken.html:89:89: Warning: inserting implicit <span>
GceToken.html:80:6: Warning: trimming empty <span>
GceToken.html:83:6: Warning: trimming empty <span>
GceToken.html:86:6: Warning: trimming empty <span>
GceToken.html:89:6: Warning: trimming empty <span>
WifToken.html:88:6: Warning: missing </span> before <p>
WifToken.html:88:82: Warning: inserting implicit <span>
WifToken.html:91:6: Warning: missing </span> before <p>
WifToken.html:91:85: Warning: inserting implicit <span>
WifToken.html:88:6: Warning: trimming empty <span>
WifToken.html:91:6: Warning: trimming empty <span>
'LazyData' is specified without a 'data' directory
Running examples in 'gasper-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HPFVN
> ### Title: High Pass Filter Von Neumann Estimator.
> ### Aliases: HPFVN
> 
> ### ** Examples
> 
> matrixname <- "grid1"
> groupname <- "AG-Monien"
> graph <- download_graph(matrixname,groupname)
trying URL 'https://sparse.tamu.edu/MM/AG-Monien/grid1.tar.gz'
Warning in download.file(url, temp) :
  URL 'https://sparse.tamu.edu/MM/AG-Monien/grid1.tar.gz': status was 'SSL peer certificate or SSH remote key was not OK'
Error in download.file(url, temp) : 
  cannot open URL 'https://sparse.tamu.edu/MM/AG-Monien/grid1.tar.gz'
Calls: download_graph -> download.file
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'gasper_vignette.rmd' using rmarkdown
trying URL 'https://sparse.tamu.edu/MM/AG-Monien/grid1.tar.gz'
Quitting from lines 52-56 (gasper_vignette.rmd) 
Error: processing vignette 'gasper_vignette.rmd' failed with diagnostics:
cannot open URL 'https://sparse.tamu.edu/MM/AG-Monien/grid1.tar.gz'
--- failed re-building 'gasper_vignette.rmd'

SUMMARY: processing the following file failed:
  'gasper_vignette.rmd'

Error: Vignette re-building failed.
Execution halted
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 HTML validation problems:
gbfs.html:32:4: Warning: <img> attribute "align" not allowed for HTML5
gbfs.html:32:4: Warning: <img> attribute "align" not allowed for HTML5
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'.
Found the following math rendering problems:
GDINA.Rd:367: Can't use function '$' in math mode in ...,\cdots,K_j^*-1$, and $k^{''}>k...
Found the following HTML validation problems:
gdistance.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
gdistance.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following significant warnings:
  gdpc_auxfunc.cpp:79:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/gdpc.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'gdxrrw'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'geoR'
'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) 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
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.
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 HTML validation problems:
geniusr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
geniusr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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.
Found the following significant warnings:
  mdr.cpp:684:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:686:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:688:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:690:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:719:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:721:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:723:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:725:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:755:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:757:18: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:759:18: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:761:18: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:791:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:793:18: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:795:18: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:797:18: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/GenomicTools.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
Package suggested but not available for checking: 'geoR'
Unknown package 'geoR' 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 math rendering problems:
geo_fkf.Rd:19: Undefined control sequence: \- in [\-pi, \pi]
checkRd: (-1) predict.geoGAM.Rd:86: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
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
Found the following HTML validation problems:
extprod3d.html:24:32: Warning: trimming empty <code>
extprod3d.html:29:32: Warning: trimming empty <code>
Found the following HTML validation problems:
geomtextpath-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
geomtextpath-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following math rendering problems:
pendulum.Rd:19: Undefined control sequence: \time in n \time 2
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
Found the following HTML validation problems:
WeightGermPercent.html:78:1: Warning: <em> is probably intended as </em>
WeightGermPercent.html:78:143: Warning: discarding unexpected </em>
WeightGermPercent.html:78:162: Warning: discarding unexpected </em>
germination.indices.html:445:1: Warning: <em> is probably intended as </em>
germination.indices.html:445:143: Warning: discarding unexpected </em>
germination.indices.html:445:162: Warning: discarding unexpected </em>
'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
Found the following HTML validation problems:
gganimate-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
gganimate-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
ggbraid-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggbraid-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ggforce-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggforce-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
ggfx-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggfx-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
object_support.html:69:131: Warning: inserting implicit <p>
object_support.html:93:53: Warning: inserting implicit <p>
object_support.html:110:77: Warning: inserting implicit <p>
object_support.html:125:23: Warning: inserting implicit <p>
object_support.html:143:67: Warning: inserting implicit <p>
object_support.html:150:88: Warning: inserting implicit <p>
object_support.html:161:28: Warning: inserting implicit <p>
object_support.html:69:131: Warning: trimming empty <p>
object_support.html:93:53: Warning: trimming empty <p>
object_support.html:110:77: Warning: trimming empty <p>
object_support.html:125:23: Warning: trimming empty <p>
object_support.html:143:67: Warning: trimming empty <p>
object_support.html:150:88: Warning: trimming empty <p>
object_support.html:161:28: Warning: trimming empty <p>
'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:
ggh4x-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggh4x-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
gghdr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
gghdr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ggip-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggip-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
guide_bins_interactive.html:50:23: Warning: nested emphasis <em>
guide_colourbar_interactive.html:52:23: Warning: nested emphasis <em>
guide_coloursteps_interactive.html:52:23: Warning: nested emphasis <em>
guide_legend_interactive.html:50:23: Warning: nested emphasis <em>
ipar.html:104:23: Warning: nested emphasis <em>
scale_alpha_interactive.html:70:23: Warning: nested emphasis <em>
scale_colour_brewer_interactive.html:73:23: Warning: nested emphasis <em>
scale_colour_interactive.html:105:23: Warning: nested emphasis <em>
scale_colour_steps_interactive.html:73:23: Warning: nested emphasis <em>
scale_gradient_interactive.html:73:23: Warning: nested emphasis <em>
scale_linetype_interactive.html:61:23: Warning: nested emphasis <em>
scale_manual_interactive.html:72:23: Warning: nested emphasis <em>
scale_shape_interactive.html:64:23: Warning: nested emphasis <em>
scale_size_interactive.html:79:23: Warning: nested emphasis <em>
scale_viridis_interactive.html:81:23: Warning: nested emphasis <em>
'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: \&
Found the following HTML validation problems:
ggmulti-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggmulti-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
ggnewscale-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggnewscale-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Found the following HTML validation problems:
ggpattern.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggpattern.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ggperiodic.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggperiodic.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) diamonds.Rd:10: Escaped LaTeX specials: \$ \$
Found the following HTML validation problems:
ggplot2-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggplot2-package.html:23:4: 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
Package suggested but not available for checking: 'lixoftConnectors'
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ggpointless-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggpointless-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
checkRd: (-1) interaction_data.Rd:174: Escaped LaTeX specials: \&
checkRd: (-1) partial_data.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) rfsrc_data.Rd:154: Escaped LaTeX specials: \&
checkRd: (-1) varsel_data.Rd:156: Escaped LaTeX specials: \&
Found the following HTML validation problems:
interaction_data.html:19:1: Warning: missing </h2> before <ul>
interaction_data.html:38:1: Warning: discarding unexpected </h2>
partial_coplot_data.html:19:1: Warning: missing </h2> before <ul>
partial_coplot_data.html:29:1: Warning: discarding unexpected </h2>
partial_data.html:19:1: Warning: missing </h2> before <ul>
partial_data.html:37:1: Warning: discarding unexpected </h2>
partial_surface_data.html:19:1: Warning: missing </h2> before <ul>
partial_surface_data.html:37:1: Warning: discarding unexpected </h2>
varsel_data.html:19:1: Warning: missing </h2> before <ul>
varsel_data.html:37:1: Warning: discarding unexpected </h2>
Error(s) in re-building vignettes:
  ...
--- re-building 'Edges.Rmd' using rmarkdown
Loading required package: ggplot2

Attaching package: 'tidygraph'

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

    filter


Attaching package: 'rlang'

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

    %@%, as_function, flatten, flatten_chr, flatten_dbl, flatten_int,
    flatten_lgl, flatten_raw, invoke, splice

--- finished re-building 'Edges.Rmd'

--- re-building 'Layouts.Rmd' using rmarkdown
Using `stress` as default layout
--- finished re-building 'Layouts.Rmd'

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

--- re-building 'tidygraph.Rmd' using rmarkdown
Quitting from lines 99-102 (tidygraph.Rmd) 
Error: processing vignette 'tidygraph.Rmd' failed with diagnostics:
At core/layout/fruchterman_reingold.c:401 : Weights must be positive for Fruchterman-Reingold layout. Invalid value
--- failed re-building 'tidygraph.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following HTML validation problems:
ggraph-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggraph-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial Release (0.1.0)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ggspectra-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggspectra-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Found the following HTML validation problems:
ghibli-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ghibli-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
gh_whoami.html:68:83: Warning: inserting implicit <p>
gh_whoami.html:68:83: Warning: trimming empty <p>
'LazyData' is specified without 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'
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
ConfidenceInterval.Rd:25: Undefined control sequence: \boldmath in ...athcal{D}} =\{(\boldmath{x}_i,y_i)\} 
KdCor.Rd:27-31: Undefined control sequence: \label in ...}(Y,Y')\right].\label{dCovkk}
    \end...
KdCov.Rd:22-26: Undefined control sequence: \label in ...prime})\right].\label{dCovkk}
      \e...
KdCov.Rd:28-32: Undefined control sequence: \label in \label{setdiff}
      \...
KdCov.Rd:36: Undefined control sequence: \label in ...rime}) \right].\label{dCovk}
KgCor.Rd:24-26: Undefined control sequence: \label in ..._\kappa(X,X')}.\label{gCork}
KgCov.Rd:24-26: Undefined control sequence: \label in ...a(X,X')\right],\label{gCovk}
Unknown package 'IC2' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
giscoR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
giscoR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
gitcreds_get.html:129:26: Warning: inserting implicit <p>
gitcreds_get.html:129:26: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
gitlabr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
gitlabr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
checkRd: (-1) starship.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) starship.adaptivegrid.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) starship.adaptivegrid.Rd:54: Escaped LaTeX specials: \&
checkRd: (-1) starship.adaptivegrid.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) starship.obj.Rd:25: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'mlr3proba'
'LazyData' is specified without a 'data' directory
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 math rendering problems:
breakdown.Rd:22: Can't use function '$' in math mode in $8\times 4$
'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'
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
checkRd: (-1) congagvp.Rd:46: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
AIC.html:31:1: Warning: inserting implicit <p>
AIC.html:31:1: Warning: trimming empty <p>
BIC.html:34:1: Warning: inserting implicit <p>
BIC.html:34:1: Warning: trimming empty <p>
gmbn.html:52:1: Warning: inserting implicit <p>
gmbn.html:52:1: Warning: trimming empty <p>
gmdbn.html:40:1: Warning: inserting implicit <p>
gmdbn.html:40:1: Warning: trimming empty <p>
gmm.html:45:1: Warning: inserting implicit <p>
gmm.html:45:1: Warning: trimming empty <p>
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building 'gmm_with_R.rnw' using knitr
Warning in nlminb(P$t0, .obj1, x = x, w = w, ...) :
  NA/NaN function evaluation
Warning in nlminb(P$t0, .obj1, x = x, w = w, ...) :
  NA/NaN function evaluation
Warning: The provided gradv is not used when smooth=TRUE
Error: processing vignette 'gmm_with_R.rnw' failed with diagnostics:
Running 'texi2dvi' on 'gmm_with_R.tex' failed.
LaTeX errors:
! Argument of Â has an extra }.
<inserted text> 
                \par 
l.122 \section{Introduction}
                            
! Emergency stop.
<inserted text> 
                \par 
l.122 \section{Introduction}
                            
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'gmm_with_R.rnw'

SUMMARY: processing the following file failed:
  'gmm_with_R.rnw'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
Found the following HTML validation problems:
cond_moments.html:277:38: Warning: nested emphasis <code>
cond_moments.html:282:38: Warning: nested emphasis <code>
cond_moments.html:288:38: Warning: nested emphasis <code>
cond_moments.html:293:38: Warning: nested emphasis <code>
cond_moments.html:298:38: Warning: nested emphasis <code>
loglikelihood_int.html:292:38: Warning: nested emphasis <code>
loglikelihood_int.html:296:38: Warning: nested emphasis <code>
loglikelihood_int.html:301:38: Warning: nested emphasis <code>
loglikelihood_int.html:305:38: Warning: nested emphasis <code>
loglikelihood_int.html:310:38: Warning: nested emphasis <code>
loglikelihood_int.html:315:38: Warning: nested emphasis <code>
loglikelihood_int.html:321:38: Warning: nested emphasis <code>
loglikelihood_int.html:326:38: Warning: nested emphasis <code>
loglikelihood_int.html:331:38: Warning: nested emphasis <code>
loglikelihood_int.html:337:38: Warning: nested emphasis <code>
'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
Found the following math rendering problems:
flm_stat.Rd:51-54: Unexpected end of input in a macro argument, expected '}' in ...mathrm{tr}(\hat\mathbf{E}_q' \mathbf{...
flm_stat.Rd:57: Unexpected end of input in a macro argument, expected '}' in \hat\mathbf{E}_q
'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
Running 'testthat.R' [11s/15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(goodpractice)
  > 
  > test_check("goodpractice")
  Preparing: covr
  Preparing: description
  Preparing: covr
  Preparing: description
  Preparing: desc
  Preparing: lintr
  Preparing: lintr
  Preparing: lintr
  Preparing: namespace
  Preparing: namespace
  Preparing: namespace
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 36 ]
  
  == Skipped tests ===============================================================
  * On CRAN (1)
  
  == Failed tests ================================================================
  -- Failure (test-print.R:27:3): print with default and explicit positions.limit --
  gsub(...) (`actual`) not equal to gsub(...) (`expected`).
  
  actual vs expected
  - "-- GP badpackage --------------------------------------------------------------- It is good practice to x avoid 'T' and 'F', as they are just variables which are set to the logicals 'TRUE' and 'FALSE' by default, but are not reserved words and hence can be overwritten by the user. Hence, one should always use 'TRUE' and 'FALSE' for the logicals. R/tf.R:NA:NA R/tf.R:NA:NA R/tf.R:NA:NA R/tf.R:NA:NA R/tf.R:NA:NA ... and 4 more lines -------------------------------------------------------------------------------- "
  + "-- GP badpackage --------------------------------------------------------------- It is good practice to & avoid 'T' and 'F', as they are just variables which are set to the logicals 'TRUE' and 'FALSE' by default, but are not reserved words and hence can be overwritten by the user. Hence, one should always use 'TRUE' and 'FALSE' for the logicals. R/tf.R:NA:NA R/tf.R:NA:NA R/tf.R:NA:NA R/tf.R:NA:NA R/tf.R:NA:NA ... and 4 more lines -------------------------------------------------------------------------------- "
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 36 ]
  Error: Test failures
  Execution halted
Found the following HTML validation problems:
cr_run.html:115:1: Warning: trimming empty <dt>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
googlesheets4-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
googlesheets4-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
gosset.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
gosset.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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) rotations.Rd:103: Escaped LaTeX specials: \^
Package suggested but not available for checking: 'gvcm.cat'
Unknown package 'gvcm.cat' in Rd xrefs
Found the following HTML validation problems:
exponential_anisotropic3D_alt.html:70:1: Warning: trimming empty <h3>
'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: \&
Running examples in 'gprofiler2-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gconvert
> ### Title: Gene ID conversion.
> ### Aliases: gconvert
> 
> ### ** Examples
> 
> gconvert(c("POU5F1", "SOX2", "NANOG"), organism = "hsapiens", target="AFFY_HG_U133_PLUS_2")
Error in gconvert(c("POU5F1", "SOX2", "NANOG"), organism = "hsapiens",  : 
  Bad request, response code 502
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'gprofiler2.Rmd' using rmarkdown
Quitting from lines 113-120 (gprofiler2.Rmd) 
Error: processing vignette 'gprofiler2.Rmd' failed with diagnostics:
Bad request, response code 502
--- failed re-building 'gprofiler2.Rmd'

SUMMARY: processing the following file failed:
  'gprofiler2.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  U_NZentries.cpp:27:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/GPvecchia.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 Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
grainchanger-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
grainchanger-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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: \~
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
Found the following significant warnings:
  SimpleIclCoModel.cpp:219:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  SimpleIclCoModel.cpp:223:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/greed.Rcheck/00install.out' for details.
Found the following HTML validation problems:
summary_greek.html:58:1: Warning: trimming empty <dt>
'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.
Found the following HTML validation problems:
gridpattern-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
gridpattern-package.html:23:4: 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:
    News
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
sample_session_duration.Rd:30: Undefined control sequence: \k in ...lambda ~ Gamma(\k, \theta)
'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 math rendering problems:
fit_easylinear.Rd:39: Can't use function '$' in math mode in $b_{max}$
fit_easylinear.Rd:41: Can't use function '$' in math mode in $quota \cdot b_{...
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.
Found the following HTML validation problems:
gsheet2tbl.html:31:5: Warning: trimming empty <p>
gsheet2tbl.html:31:1: Warning: trimming empty <li>
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Found the following HTML validation problems:
GSODR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
GSODR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
checkRd: (-1) fit.variogram.Rd:91: Escaped LaTeX specials: \&
checkRd: (-1) fit.variogram.gls.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) gstat.Rd:117: Escaped LaTeX specials: \&
checkRd: (-1) hscat.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) krige.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) krigeST.Rd:85: Escaped LaTeX specials: \&
checkRd: (-1) meuse.all.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) predict.gstat.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) variogram.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) variogramST.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) vgm.Rd:116: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) gsym.point.Rd:143: Escaped LaTeX specials: \&
Found the following HTML validation problems:
gtable-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
gtable-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
gt_plt_summary.html:62:1: Warning: <img> lacks "alt" attribute
gt_plt_winloss.html:99:1: Warning: <img> lacks "alt" attribute
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'RRprof.out'
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
gutenberg_get_mirror.html:25:1: Warning: <a> illegal characters found in URI
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
Found the following HTML validation problems:
gwasrapidd-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
gwasrapidd-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) luzdat.Rd:21: Escaped LaTeX specials: \~
Found the following HTML validation problems:
gedit.html:139:6: Warning: trimming empty <p>
gedit.html:139:1: Warning: trimming empty <li>
'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
Found the following HTML validation problems:
gyrodemos.html:50:1: Warning: inserting implicit <p>
gyrodemos.html:50:1: Warning: trimming empty <p>
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    v.0.2.2
'LazyData' is specified without 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:
cf_key_meson_3pt.html:19:1: Warning: missing </h2> before <ul>
cf_key_meson_3pt.html:72:1: Warning: discarding unexpected </h2>
correlators_key_meson_3pt.html:19:1: Warning: missing </h2> before <ul>
correlators_key_meson_3pt.html:72:1: Warning: discarding unexpected </h2>
gevp.html:84:45: Warning: trimming empty <code>
gevp.html:85:17: Warning: trimming empty <code>
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: \&
'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.
Found the following HTML validation problems:
haven-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
haven-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
'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':
  Cannot extract version info from the following section titles:
    TODO:
    "GW", "OLO"
    seriate(cophenetic(dend), method = "OLO", control = list(hclust = as.hclust(dend)))
    the downside in using cophenetic is that seriate has to go through running hclust all over again
    but we'll just have to accept it...
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rgho'
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
HelpersMG-package.html:41:1: Warning: <img> attribute "," lacks value
HelpersMG-package.html:41:1: Warning: <img> attribute "align" not allowed for HTML5
HelpersMG-package.html:41:1: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'synbreed'
Found the following HTML validation problems:
IndivCtstmTrans.html:116:6: Warning: missing </span> before <p>
IndivCtstmTrans.html:116:93: Warning: inserting implicit <span>
IndivCtstmTrans.html:119:6: Warning: missing </span> before <p>
IndivCtstmTrans.html:119:90: Warning: inserting implicit <span>
IndivCtstmTrans.html:116:6: Warning: trimming empty <span>
IndivCtstmTrans.html:119:6: Warning: trimming empty <span>
'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
Found the following HTML validation problems:
get_breaks.html:78:1: Warning: trimming empty <dt>
'LazyData' is specified without a 'data' directory
checkRd: (-1) bivariateNormal.Rd:42: Escaped LaTeX specials: \&
':::' 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
Problems with news in 'NEWS.md':
No news entries found.
Found the following math rendering problems:
rCholCov.Rd:55: Can't use function '$' in math mode in ...au^{b}_j}^{(2)}$. Set $\hat{h}_...
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) trans.dens.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) Snow.Rd:118: Escaped LaTeX specials: \&
checkRd: (-1) Snow.Rd:142: Escaped LaTeX specials: \&
checkRd: (-1) Yeast.Rd:56: Escaped LaTeX specials: \&
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
Package suggested but not available for checking: 'FGN'
Problems with news in 'NEWS.md':
No news entries found.
Found the following math rendering problems:
rcorr.cens.Rd:14: Undefined control sequence: \var in \var{Dxy}=2(\var{c}...
rcspline.plot.Rd:44: Undefined control sequence: \var in 1 - \var{f}
rcspline.plot.Rd:45: Undefined control sequence: \var in \var{f} = \frac{10}...
rcspline.restate.Rd:32: Undefined control sequence: \var in \var{k}-1
rm.boot.Rd:122: Undefined control sequence: \var in \var{k} - 1
rm.boot.Rd:345: Undefined control sequence: \var in \var{m} > \var{n}
rm.boot.Rd:347: Undefined control sequence: \var in \var{m} < \var{n}
rm.boot.Rd:348-349: Undefined control sequence: \var in \var{n} -
    \var{m}
scat1d.Rd:19: Undefined control sequence: \var in \code{eps}*\var{w}
scat1d.Rd:22-23: Undefined control sequence: \var in ...\code{jitfrac}*\var{w},
    \code{ji...
scat1d.Rd:178: Undefined control sequence: \var in \max{(.1, 125/\var{n})}
scat1d.Rd:230-231: Undefined control sequence: \var in ...de{fill}*\min{(\var{u}-\var{d},\va...
scat1d.Rd:236-237: Undefined control sequence: \var in ...de{fill}*\min{(\var{u}-\var{d},\va...
scat1d.Rd:239: Undefined control sequence: \var in \min{(\var{u}-\var{d},\va...
scat1d.Rd:283: Undefined control sequence: \var in \var{l}<\var{d}<\va...
transace.Rd:87: Undefined control sequence: \var in \var{ginverse}(\var...
transace.Rd:101-102: Undefined control sequence: \var in \var{ginverse}(\var...
transace.Rd:250: Undefined control sequence: \var in \var{ginverse}(\var...
transcan.Rd:272: Undefined control sequence: \var in \var{n} < 30
transcan.Rd:273: Undefined control sequence: \var in 30 <= \var{n} < 100
transcan.Rd:274: Undefined control sequence: \var in \var{n} \ge 100
transcan.Rd:770-771: Undefined control sequence: \var in ...rac{1-\frac{(1-\var{R2})(\var{n}-1...
transcan.Rd:783: Undefined control sequence: \var in + \var{m}
transcan.Rd:788-789: Undefined control sequence: \var in 1-\frac{(1-\var{R2})(\var{n}-1...
transcan.Rd:797: Undefined control sequence: \var in \sqrt{\var{n}-1}
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: \&
Found the following HTML validation problems:
hms-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
hms-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
hmstimer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
hmstimer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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: \&
Found the following HTML validation problems:
hockeystick-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
hockeystick-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ars_demo.cpp:39:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/HTLR.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: 'CensRegMod'
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
'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
'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
Problems with news in 'NEWS.md':
No news entries found.
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 HTML validation problems:
cldr_currencies.html:91:70: Warning: inserting implicit <p>
cldr_currencies.html:91:70: Warning: trimming empty <p>
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'
'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: '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: \$
Packages suggested but not available for checking: 'glrt', 'MIICD'
Found the following math rendering problems:
loglogistic.Rd:31-42: Unknown column alignment: @ in ...\begin{array}{r@{\;=\;}ll}
    \m...
checkRd: (-1) dmahal.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
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
Found the following HTML validation problems:
idiogramFISH-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
idiogramFISH-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
idmodelr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
idmodelr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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:
  ifs.c:751:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ifs.Rcheck/00install.out' for details.
checkRd: (-1) ifsm.w.maps.Rd:15: Escaped LaTeX specials: \^
Found the following HTML validation problems:
igoR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
igoR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor fix
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
h.fn.exp.html:19:1: Warning: missing </h2> before <p>
h.fn.exp.html:22:109: Warning: discarding unexpected </h2>
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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    BUG FIXES
Found the following HTML validation problems:
imagefluency-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
imagefluency-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  engines.cpp:337:14: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  engines.cpp:351:14: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  engines.cpp:365:14: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  engines.cpp:379:14: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  engines.cpp:401:16: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/imagine.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 math rendering problems:
USPSdigits.Rd:41: Undefined control sequence: \textsuperscript in 2\textsuperscript{nd}
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
immer_latent_regression.Rd:45: Unexpected end of input in a macro argument, expected '}' at end of input: \bold
'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
checkRd: (-1) tsAirgap.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) tsAirgapComplete.Rd:11: Escaped LaTeX specials: \&
Found the following HTML validation problems:
imputeTS-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
imputeTS-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building 'congress.Rmd' using rmarkdown

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

trying URL 'https://www.govinfo.gov/bulkdata/BILLSTATUS/115/sres/BILLSTATUS-115-sres.zip'
Content type 'application/zip' length 2208123 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

trying URL 'https://www.govinfo.gov/bulkdata/BILLSTATUS/115/sres/BILLSTATUS-115-sres.zip'
Warning in utils::download.file(paste0("https://www.govinfo.gov/bulkdata/BILLSTATUS/",  :
  URL 'https://www.govinfo.gov/bulkdata/BILLSTATUS/115/sres/BILLSTATUS-115-sres.zip': status was 'SSL connect error'
Quitting from lines 95-96 (congress.Rmd) 
Error: processing vignette 'congress.Rmd' failed with diagnostics:
cannot open URL 'https://www.govinfo.gov/bulkdata/BILLSTATUS/115/sres/BILLSTATUS-115-sres.zip'
--- failed re-building 'congress.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
fit.infer.html:126:35: Warning: inserting implicit <p>
fit.infer.html:147:45: Warning: inserting implicit <p>
fit.infer.html:126:35: Warning: trimming empty <p>
fit.infer.html:147:45: Warning: trimming empty <p>
generate.html:112:35: Warning: inserting implicit <p>
generate.html:133:45: Warning: inserting implicit <p>
generate.html:112:35: Warning: trimming empty <p>
generate.html:133:45: Warning: trimming empty <p>
infer.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
infer.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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: \&
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 math rendering problems:
topo.Rd:20: Undefined control sequence: \textsuperscript in \textsuperscript{TM}
Found the following HTML validation problems:
DeepLift.html:93:6: Warning: missing </span> before <p>
DeepLift.html:93:105: Warning: inserting implicit <span>
DeepLift.html:93:6: Warning: trimming empty <span>
Gradient.html:64:6: Warning: missing </span> before <p>
Gradient.html:64:105: Warning: inserting implicit <span>
Gradient.html:67:6: Warning: missing </span> before <p>
Gradient.html:67:97: Warning: inserting implicit <span>
Gradient.html:70:6: Warning: missing </span> before <p>
Gradient.html:70:94: Warning: inserting implicit <span>
Gradient.html:64:6: Warning: trimming empty <span>
Gradient.html:67:6: Warning: trimming empty <span>
Gradient.html:70:6: Warning: trimming empty <span>
GradientBased.html:84:6: Warning: missing </span> before <p>
GradientBased.html:84:105: Warning: inserting implicit <span>
GradientBased.html:84:6: Warning: trimming empty <span>
LRP.html:89:6: Warning: missing </span> before <p>
LRP.html:89:105: Warning: inserting implicit <span>
LRP.html:89:6: Warning: trimming empty <span>
SmoothGrad.html:74:6: Warning: missing </span> before <p>
SmoothGrad.html:74:105: Warning: inserting implicit <span>
SmoothGrad.html:77:6: Warning: missing </span> before <p>
SmoothGrad.html:77:97: Warning: inserting implicit <span>
SmoothGrad.html:80:6: Warning: missing </span> before <p>
SmoothGrad.html:80:94: Warning: inserting implicit <span>
SmoothGrad.html:74:6: Warning: trimming empty <span>
SmoothGrad.html:77:6: Warning: trimming empty <span>
SmoothGrad.html:80:6: Warning: trimming empty <span>
'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: \_
'LazyData' is specified without 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:
invctr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
invctr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
aggregateData.html:94:372: Warning: inserting implicit <p>
aggregateData.html:94:372: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
iotables_read_tempdir.html:19:1: Warning: missing </h2> before <ul>
iotables_read_tempdir.html:63:1: Warning: discarding unexpected </h2>
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.
Found the following HTML validation problems:
ipaddress-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ipaddress-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Problems with news in 'NEWS.md':
No news entries found.
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
Found the following HTML validation problems:
aFiles.html:52:78: Warning: inserting implicit <p>
aFiles.html:52:78: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
checkRd: (-1) pine.Rd:20: Escaped LaTeX specials: \&
'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: \$
Package suggested but not available for checking: 'RandomFields'
Unknown package 'RandomFields' in Rd xrefs
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  Genetics.cpp:363:20: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Genetics.cpp:376:20: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Genetics.cpp:376:51: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/isqg.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
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.
Found the following significant warnings:
  jacobi.cpp:683:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  jacobi.cpp:684:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/jacobi.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:
  javaGD.c:153:9: warning: expression which evaluates to zero treated as a null pointer constant of type 'newJavaGDDesc *' [-Wnon-literal-null-conversion]
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.
Found the following HTML validation problems:
JirAgileR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
JirAgileR-package.html:23:4: 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:
    joineR <1.1
Package which this enhances but not available for checking: 'remMap'
Found the following HTML validation problems:
hc_rdslope_info.html:56:86: Warning: inserting implicit <p>
hc_rdslope_info.html:56:86: Warning: trimming empty <p>
hc_rdslope_interact.html:54:86: Warning: inserting implicit <p>
hc_rdslope_interact.html:54:86: Warning: trimming empty <p>
model_imp.html:402:100: Warning: inserting implicit <p>
model_imp.html:405:46: Warning: inserting implicit <p>
model_imp.html:437:39: Warning: inserting implicit <p>
model_imp.html:468:93: Warning: inserting implicit <p>
model_imp.html:479:83: Warning: inserting implicit <p>
model_imp.html:484:47: Warning: inserting implicit <p>
model_imp.html:518:73: Warning: inserting implicit <p>
model_imp.html:937:99: Warning: inserting implicit <p>
model_imp.html:942:118: Warning: inserting implicit <p>
model_imp.html:967:35: Warning: inserting implicit <p>
model_imp.html:974:38: Warning: inserting implicit <p>
model_imp.html:983:83: Warning: inserting implicit <p>
model_imp.html:989:59: Warning: inserting implicit <p>
model_imp.html:402:100: Warning: trimming empty <p>
model_imp.html:405:46: Warning: trimming empty <p>
model_imp.html:437:39: Warning: trimming empty <p>
model_imp.html:468:93: Warning: trimming empty <p>
model_imp.html:479:83: Warning: trimming empty <p>
model_imp.html:484:47: Warning: trimming empty <p>
model_imp.html:518:73: Warning: trimming empty <p>
model_imp.html:937:99: Warning: trimming empty <p>
model_imp.html:942:118: Warning: trimming empty <p>
model_imp.html:967:35: Warning: trimming empty <p>
model_imp.html:974:38: Warning: trimming empty <p>
model_imp.html:983:83: Warning: trimming empty <p>
model_imp.html:989:59: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  jomo1C.c:377:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  jomo1C.c:385:17: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  jomo1ranC.c:520:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  jomo1ranC.c:528:17: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  jomo1ranhrC.c:679:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  jomo1ranhrC.c:687:19: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  jomo1ranhrC.c:751:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  jomo1ranhrC.c:758:18: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  jomo2comC.c:843:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  jomo2comC.c:851:17: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  jomo2hrC.c:982:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  jomo2hrC.c:990:19: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  jomo2hrC.c:1054:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  jomo2hrC.c:1061:18: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/jomo.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) 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
'LazyData' is specified without a 'data' directory
'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'
'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:
  evaluators.cpp:52:13: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/kdevine.Rcheck/00install.out' for details.
'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
Found the following HTML validation problems:
MLP.html:77:6: Warning: missing </span> before <p>
MLP.html:77:90: Warning: inserting implicit <span>
MLP.html:77:6: Warning: trimming empty <span>
RBF.html:77:6: Warning: missing </span> before <p>
RBF.html:77:90: Warning: inserting implicit <span>
RBF.html:77:6: Warning: trimming empty <span>
'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
Found the following math rendering problems:
consensusmatrix.Rd:34-36: Undefined control sequence: \emph in\em...
'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
Found the following significant warnings:
  ProteinSequence.cpp:347:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/krm.Rcheck/00install.out' for details.
'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'
Found the following HTML validation problems:
lactater-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
lactater-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
metab.kalman.Rd:51: Undefined control sequence: \do in ... + \beta_{t-1}*\do.obs_{t-1} + \e...
metab.mle.Rd:48: Undefined control sequence: \do in ... + \beta_{t-1}*\do.obs_{t-1} + \e...
Found the following HTML validation problems:
handle_event_error.html:36:89: Warning: inserting implicit <p>
handle_event_error.html:36:89: Warning: trimming empty <p>
html_response.html:24:45: Warning: inserting implicit <p>
html_response.html:24:45: Warning: trimming empty <p>
lambdr.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
lambdr.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
post_lambda_error.html:27:48: Warning: inserting implicit <p>
post_lambda_error.html:27:48: Warning: trimming empty <p>
Found the following HTML validation problems:
Gaussianize.html:136:38: Warning: nested emphasis <code>
Gaussianize.html:140:38: Warning: nested emphasis <code>
Gaussianize.html:145:38: Warning: nested emphasis <code>
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: \&
Problems with news in 'NEWS.md':
No news entries found.
Found the following files/directories:
  'example.llo'
Found the following significant warnings:
  ExportedFunctions.cpp:101:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ExportedFunctions.cpp:106:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/LassoBacktracking.Rcheck/00install.out' for details.
'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.
'LazyData' is specified without a 'data' directory
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'
checkRd: (-1) Col.Rd:17: Escaped LaTeX specials: \#
checkRd: (-1) regression-set.Rd:103: Escaped LaTeX specials: \$
Found the following HTML validation problems:
gini.index.html:82:1: Warning: nested emphasis <em>
'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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'fitted.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:
  em.cpp:103:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ldsep.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
'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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
annotate_axis.html:91:1: Warning: trimming empty <h3>
'LazyData' is specified without 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) hydro.Rd:17: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
TariffTypeSingleEnum-class.html:19:1: Warning: missing </h2> before <dl>
TariffTypeSingleEnum-class.html:51:1: Warning: discarding unexpected </h2>
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', '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
Found the following HTML validation problems:
lime-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
lime-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Problems with news in 'NEWS.md':
No news entries found.
Found the following math rendering problems:
WLindley.Rd:54: Undefined control sequence: \label in ...e^{-\theta x}  \label{density-weight...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
lmn_post.Rd:30-34: Undefined control sequence: \vspace in 
  \vspace{-1em}
  
lmn_prior.Rd:54-58: Undefined control sequence: \vspace in 
  \vspace{-1em}
Found the following math rendering problems:
Lcomoment.matrix.Rd:16-17: Undefined control sequence: \boldmath in  \mbox{\boldmath $\Lambda_k$} = ...
lmomgld.Rd:17-18: Undefined control sequence: \boldmath in \mbox{\boldmath $Y$} = 2\xi + \...
lmomgld.Rd:19-22: Undefined control sequence: \boldmath in ...mbda_3 = \mbox{\boldmath $Y$} + 6\alpha
  ...
lmomgld.Rd:25-27: Undefined control sequence: \boldmath in \mbox{\boldmath $Y$} = \frac{-3...
lmomgld.Rd:28-29: Undefined control sequence: \boldmath in \mbox{\boldmath $Z$} = \frac{20...
lmomgld.Rd:30-32: Undefined control sequence: \boldmath in ...mbda_4 = \mbox{\boldmath $Z$} -
          ...
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: \_
'LazyData' is specified without a 'data' directory
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: \^ \^
Found the following HTML validation problems:
UPSLTDdist.html:54:1: Warning: trimming empty <dt>
plot.LocalControlCR.html:63:1: Warning: trimming empty <dt>
plot.LocalControlCS.html:59:1: Warning: trimming empty <dt>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
checkRd: (-1) logreg.myown.Rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:20: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:24: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:99: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:120: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:132: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:133: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:134: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:172: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:182: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:184: Escaped LaTeX specials: \_ \_
Found the following HTML validation problems:
dx.html:74:38: Warning: nested emphasis <code>
dx.html:81:38: Warning: nested emphasis <code>
dx.html:92:38: Warning: nested emphasis <code>
dx.html:100:38: Warning: nested emphasis <code>
dx.html:112:38: Warning: nested emphasis <code>
dx.html:148:38: Warning: nested emphasis <code>
dx.html:170:38: Warning: nested emphasis <code>
dx.html:229:38: Warning: nested emphasis <code>
dx.html:240:38: Warning: nested emphasis <code>
dx.html:251:38: Warning: nested emphasis <code>
dx.html:269:38: Warning: nested emphasis <code>
dx.html:282:38: Warning: nested emphasis <code>
plotGlm.html:219:38: Warning: nested emphasis <code>
plotGlm.html:225:38: Warning: nested emphasis <code>
plotGlm.html:233:38: Warning: nested emphasis <code>
plotGlm.html:240:38: Warning: nested emphasis <code>
plotGlm.html:248:38: Warning: nested emphasis <code>
plotGlm.html:271:38: Warning: nested emphasis <code>
plotGlm.html:279:38: Warning: nested emphasis <code>
plotGlm.html:286:38: Warning: nested emphasis <code>
'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:
set_log_name_path.html:19:1: Warning: missing </h2> before <ol>
set_log_name_path.html:31:1: Warning: discarding unexpected </h2>
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
events_long.html:19:1: Warning: missing </h2> before <ul>
events_long.html:35:1: Warning: discarding unexpected </h2>
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 HTML validation problems:
lookout-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
lookout-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
loon.ggplot-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
loon.ggplot-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
loon.shiny-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
loon.shiny-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
'LazyData' is specified without a 'data' directory
Checking should be performed on sources prepared by 'R CMD build'.
'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
checkRd: (-1) lp.Rd:4: Escaped LaTeX specials: \_
checkRd: (-1) lp.Rd:53: Escaped LaTeX specials: \_
checkRd: (-1) lp.assign.Rd:4: Escaped LaTeX specials: \_
checkRd: (-1) lp.transport.Rd:4: Escaped LaTeX specials: \_
'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'
Found the following HTML validation problems:
evaluate.html:100:31: Warning: inserting implicit <p>
evaluate.html:100:31: Warning: trimming empty <p>
luz_callback.html:79:95: Warning: inserting implicit <p>
luz_callback.html:108:57: Warning: inserting implicit <p>
luz_callback.html:79:95: Warning: trimming empty <p>
luz_callback.html:108:57: Warning: trimming empty <p>
luz_metric.html:105:51: Warning: inserting implicit <p>
luz_metric.html:105:51: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: \#
Found the following significant warnings:
  code.cpp:45:43: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  code.cpp:69:45: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  code.cpp:121:25: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/MagmaClustR.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
Found the following HTML validation problems:
mailmerge-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
mailmerge-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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 math rendering problems:
estimateD0.Rd:40: Undefined control sequence: \link in \link[base]{trigamma...
estimateD0Robust.Rd:80: Undefined control sequence: \link in \link[base]{trigamma...
Package suggested but not available for checking: 'RGtk2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) china.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) china.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) japan.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) japan.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) nzHires.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) nzHires.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) rivers.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) rivers.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) world2Hires.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) world2Hires.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) worldHires.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) worldHires.Rd:52: Escaped LaTeX specials: \&
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
checkRd: (-1) mapproject.Rd:203: Escaped LaTeX specials: \_
checkRd: (-1) mapproject.Rd:204: Escaped LaTeX specials: \_
checkRd: (-1) mapproject.Rd:210: Escaped LaTeX specials: \&
'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
Found the following HTML validation problems:
mapSpain-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
mapSpain-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) county.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) county.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) france.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) france.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) italy.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) italy.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) match.map.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) nz.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) nz.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) state.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) state.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) state.carto.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) state.carto.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) state.vbm.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) state.vbm.Rd:45: Escaped LaTeX specials: \&
checkRd: (-1) usa.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) usa.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) world.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) world.Rd:45: Escaped LaTeX specials: \&
checkRd: (-1) world2.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) world2.Rd:54: Escaped LaTeX specials: \&
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'
'LazyData' is specified without 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: 'RItools'
checkRd: (-1) GerberGreenImai.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) GerberGreenImai.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) GerberGreenImai.Rd:34: Escaped LaTeX specials: \#
checkRd: (-1) GerberGreenImai.Rd:35: Escaped LaTeX specials: \#
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: \_
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
E.matrices.Rd:17-19: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
    {{{\...
H.matrices.Rd:16-18: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
    {{{\...
H.matrices.Rd:21-23: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
    {{{\...
T.matrices.Rd:19-22: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
  {{{\bf...
creation.matrix.Rd:18-25: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
  0&0&0&...
direct.prod.Rd:18-23: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
  {{x_{1...
direct.sum.Rd:20-23: Unknown column alignment: * in ...{\begin{array}{*{20}c}
     {\bf{...
entrywise.norm.Rd:16-18: Invalid size: '-' in ... \right.
   \kern-\nulldelimiters...
fibonacci.matrix.Rd:19-22: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
  {{f_{i...
frobenius.matrix.Rd:17-24: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}0&0& \c...
hadamard.prod.Rd:17-22: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
  {{x_{1...
hilbert.matrix.Rd:15-17: Invalid size: '-' in ... \right.
   \kern-\nulldelimiters...
s.Rd:20-23: Unknown column alignment: * in ...{\begin{array}{*{20}c}
     {\bf{...
spectral.norm.Rd:17-19: Unknown column alignment: * in ...{\begin{array}{*{20}c}
     {\lam...
stirling.matrix.Rd:20: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}i\\j\en...
stirling.matrix.Rd:27-33: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
  {S_0^0...
symmetric.pascal.matrix.Rd:16-18: Invalid size: '-' in ... \right.
   \kern-\nulldelimiters...
vandermonde.matrix.Rd:16-18: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
  {{\alp...
vandermonde.matrix.Rd:19-25: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
  1&{{\a...
'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) USCounties.Rd:26: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'utilities.R'
'LazyData' is specified without a 'data' directory
checkRd: (-1) maxControl.Rd:83: 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:
  '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
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
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
'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: \& \$
checkRd: (-1) hydraulics_supplyfunctions.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) hydraulics_supplyfunctions.Rd:218: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
  'LazyDataCompression' is specified without a 'data' directory
Found the following HTML validation problems:
PlotMandala.html:82:4: Warning: <img> attribute "width" has invalid value "480px"
'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
checkRd: (-1) toLatexExtra.Rd:147: 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.
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
Found the following significant warnings:
  meshed_betalambdatau_sampler.cpp:126:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  meshed_lambda_sampler.cpp:225:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  meshed_w_sampler.cpp:296:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/meshed.Rcheck/00install.out' for details.
'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.
Found the following HTML validation problems:
metabolic-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
metabolic-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
Found the following math rendering problems:
rma.mv.Rd:76: Undefined control sequence: \vspace in ...t{struct="UN"} \vspace{1ex} \\ \left[...
rma.mv.Rd:86: Undefined control sequence: \vspace in ...{struct="CAR"} \vspace{1ex} \\ \left[...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
fat.Rd:52: Unexpected end of input in a macro argument, expected '}' in ...a_1\, \widehat \mathrm{SE}(\hat{b}_k)...
fat.Rd:56: Unexpected end of input in a macro argument, expected '}' in \widehat \mathrm{SE}(\hat{b}_k)
fat.Rd:60: Unexpected end of input in a macro argument, expected '}' in ...+ b\, \widehat \mathrm{SE}(\hat{\beta...
fat.Rd:72: Unexpected end of input in a macro argument, expected '}' in ...hi \; \widehat \mathrm{var}(\hat{\bet...
fat.Rd:74: Unexpected end of input in a macro argument, expected '}' in \widehat \mathrm{var}(\hat{b}_k...
fat.Rd:89: Unexpected end of input in a macro argument, expected '}' in ...hi \; \widehat \mathrm{var}(\hat{\bet...
fat.Rd:91: Unexpected end of input in a macro argument, expected '}' in \widehat \mathrm{var}(\hat{\bet...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following HTML validation problems:
metathis-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
metathis-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  landutils.cpp:114:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  precipitation.cpp:136:21: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  relativehumidity.cpp:97:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  relativehumidity.cpp:114:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  relativehumidity.cpp:204:21: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  temperature.cpp:78:21: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  wind.cpp:70:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  wind.cpp:217:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/meteoland.Rcheck/00install.out' for details.
checkRd: (-1) penman.Rd:48: Escaped LaTeX specials: \&
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: \&
Found the following HTML validation problems:
BA.est.html:149:32: Warning: trimming empty <code>
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'MetProc_output.pdf' 'sample_removed.csv' 'sample_retained.csv'
Found the following HTML validation problems:
metR.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
metR.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following significant warnings:
  fastcox.cpp:778:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  fastcox.cpp:779:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  fastcox.cpp:803:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  fastcox.cpp:804:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  fastcox.cpp:1735:77: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  fastcox.cpp:1735:42: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) gam.fit3.Rd:4: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) mHMM.Rd:423: Escaped LaTeX specials: \&
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'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'
Found the following math rendering problems:
ml_mcmc.Rd:210-211: Undefined control sequence: \boldmath in y=\boldmath{X}\boldmath{be...
checkRd: (-1) IPDNa.Rd:42: Escaped LaTeX specials: \&
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checkRd: (-1) mice.impute.cart.Rd:61: Escaped LaTeX specials: \&
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checkRd: (-1) pmm.match.Rd:41: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
Package suggested but not available for checking: 'microcontax.data'
Package unavailable to check Rd xrefs: 'microcontax.data'
checkRd: (-1) ees2010.Rd:30: Escaped LaTeX specials: \~
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Found the following HTML validation problems:
add_service.html:59:1: Warning: inserting implicit <p>
add_service.html:64:1: Warning: inserting implicit <p>
add_service.html:73:65: Warning: inserting implicit <p>
add_service.html:77:51: Warning: inserting implicit <p>
add_service.html:59:1: Warning: trimming empty <p>
add_service.html:64:1: Warning: trimming empty <p>
add_service.html:73:65: Warning: trimming empty <p>
add_service.html:77:51: Warning: trimming empty <p>
use_microservice.html:58:65: Warning: inserting implicit <p>
use_microservice.html:65:51: Warning: inserting implicit <p>
use_microservice.html:187:1: Warning: inserting implicit <p>
use_microservice.html:58:65: Warning: trimming empty <p>
use_microservice.html:65:51: Warning: trimming empty <p>
use_microservice.html:187:1: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: 'gurobi'
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'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
Found the following math rendering problems:
test.cor.Rd:54: Undefined control sequence: \emph in \emph{E}(\textbf{z})...
test.cor.Rd:58: Undefined control sequence: \emph in \emph{E}(\textbf{z})...
'LazyData' is specified without a 'data' directory
checkRd: (-1) AKMCS.Rd:215: Escaped LaTeX specials: \&
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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: \&
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checkRd: (-1) oscillator_d6.Rd:14: Escaped LaTeX specials: \&
Found the following HTML validation problems:
Bm.html:19:1: Warning: missing </h2> before <p>
Bm.html:22:1: Warning: discarding unexpected </h2>
Found the following math rendering problems:
NMixMCMC.Rd:133: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:134: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:138: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:139: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:142: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:143: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:155: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:156: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:177: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:178: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:197: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:224: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:229: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:234: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:239: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:252: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:256: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:271: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:276: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:281: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:287: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
Found the following math rendering problems:
mixEMM.Rd:22: Unexpected end of input in a macro argument, expected '}' in \bar\mathbf{y}_{i}
mixEMM.Rd:53-54: Unexpected end of input in a macro argument, expected '}' in ...} - \gamma \bar\mathbf{y}_{i}
  \right)...
mixEMM.Rd:55: Unexpected end of input in a macro argument, expected '}' in \bar\mathbf{y}_{i}
mixEMM.Rd:63: Unexpected end of input in a macro argument, expected '}' in \bar\mathbf{y}_{i}
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: \&
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Package suggested but not available for checking: 'mixRasch'
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checkRd: (-1) RTdata2.Rd:3: Escaped LaTeX specials: \#
checkRd: (-1) boot.comp.Rd:64: Escaped LaTeX specials: \&
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checkRd: (-1) ssize.propCI.Rd:38: Escaped LaTeX specials: \&
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: \&
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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
Found the following significant warnings:
  ./mlpack/core/tree/rectangle_tree/x_tree_split_impl.hpp:152:17: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./mlpack/core/tree/rectangle_tree/x_tree_split_impl.hpp:167:19: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mlpack.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
mlr3benchmark-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
mlr3benchmark-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
DataBackendDplyr.html:110:6: Warning: missing </span> before <p>
DataBackendDplyr.html:110:90: Warning: inserting implicit <span>
DataBackendDplyr.html:113:6: Warning: missing </span> before <p>
DataBackendDplyr.html:113:89: Warning: inserting implicit <span>
DataBackendDplyr.html:110:6: Warning: trimming empty <span>
DataBackendDplyr.html:113:6: Warning: trimming empty <span>
DataBackendDuckDB.html:114:6: Warning: missing </span> before <p>
DataBackendDuckDB.html:114:90: Warning: inserting implicit <span>
DataBackendDuckDB.html:117:6: Warning: missing </span> before <p>
DataBackendDuckDB.html:117:89: Warning: inserting implicit <span>
DataBackendDuckDB.html:114:6: Warning: trimming empty <span>
DataBackendDuckDB.html:117:6: Warning: trimming empty <span>
Found the following HTML validation problems:
mlr3misc-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
mlr3misc-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Package suggested but not available for checking: 'mlr3proba'
Found the following HTML validation problems:
DataBackendRaster.html:138:6: Warning: missing </span> before <p>
DataBackendRaster.html:138:90: Warning: inserting implicit <span>
DataBackendRaster.html:141:6: Warning: missing </span> before <p>
DataBackendRaster.html:141:89: Warning: inserting implicit <span>
DataBackendRaster.html:138:6: Warning: trimming empty <span>
DataBackendRaster.html:141:6: Warning: trimming empty <span>
DataBackendVector.html:102:6: Warning: missing </span> before <p>
DataBackendVector.html:102:90: Warning: inserting implicit <span>
DataBackendVector.html:105:6: Warning: missing </span> before <p>
DataBackendVector.html:105:89: Warning: inserting implicit <span>
DataBackendVector.html:102:6: Warning: trimming empty <span>
DataBackendVector.html:105:6: Warning: trimming empty <span>
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'DiscriMiner', 'extraTrees', 'nodeHarvest', 'rknn', 'rrlda'
Found the following HTML validation problems:
extractFDAFeatures.html:107:38: Warning: <code> is probably intended as </code>
extractFDAFeatures.html:107:73: Warning: discarding unexpected </code>
extractFDAFeatures.html:107:81: Warning: discarding unexpected </code>
impute.html:171:38: Warning: <code> is probably intended as </code>
impute.html:171:70: Warning: discarding unexpected </code>
impute.html:171:78: Warning: discarding unexpected </code>
mlr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
mlr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 math rendering problems:
MNIW.Rd:40-48: Undefined control sequence: \arraycolsep in 
  \arraycolsep=1.4pt
  \begin{a...
MNIW.Rd:49-53: Undefined control sequence: \vspace in 
  \vspace{-1em}
  
mniw-package.Rd:13-21: Undefined control sequence: \arraycolsep in 
  \arraycolsep=1.4pt
  \begin{a...
mniw-package.Rd:22-26: Undefined control sequence: \vspace in 
  \vspace{-1em}
  
rRxNorm.Rd:25-33: Undefined control sequence: \arraycolsep in 
  \arraycolsep=1.4pt
  \begin{a...
rRxNorm.Rd:34-38: Undefined control sequence: \vspace in 
  \vspace{-2em}
'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'
Found the following math rendering problems:
residuals.moc.Rd:22-24: Invalid delimiter type 'ordgroup' in ...um_{i=1}^n\Bigl{(}\frac{\hat{h}_j...
residuals.moc.Rd:26-28: Invalid delimiter type 'ordgroup' in ...um_{i=1}^n\Bigl{(}\frac{d\hat{F}(...
residuals.moc.Rd:89-92: Invalid delimiter type 'ordgroup' in ...eviance = \Bigl{\lbrace}2\cdot wt\cdot
  ...
'LazyData' is specified without a 'data' directory
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
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Running examples in 'modelbased-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estimate_slopes
> ### Title: Estimate Marginal Effects
> ### Aliases: estimate_slopes
> 
> ### ** Examples
> 
> if (require("emmeans")) {
+   # Get an idea of the data
+   if (require("ggplot2")) {
+     ggplot(iris, aes(x = Petal.Length, y = Sepal.Width)) +
+       geom_point(aes(color = Species)) +
+       geom_smooth(color = "black", se = FALSE) +
+       geom_smooth(aes(color = Species), linetype = "dotted", se = FALSE) +
+       geom_smooth(aes(color = Species), method = "lm", se = FALSE)
+   }
+ 
+   # Model it
+   model <- lm(Sepal.Width ~ Species * Petal.Length, data = iris)
+   # Compute the marginal effect of Petal.Length at each level of Species
+   slopes <- estimate_slopes(model, trend = "Petal.Length", at = "Species")
+   slopes
+   if (require("see")) {
+     plot(slopes)
+   }
+   standardize(slopes)
+ 
+   if (require("mgcv") && require("see")) {
+     model <- mgcv::gam(Sepal.Width ~ s(Petal.Length), data = iris)
+     slopes <- estimate_slopes(model, at = "Petal.Length", length = 50)
+     summary(slopes)
+     plot(slopes)
+ 
+     model <- mgcv::gam(Sepal.Width ~ s(Petal.Length, by = Species), data = iris)
+     slopes <- estimate_slopes(model,
+       trend = "Petal.Length",
+       at = c("Petal.Length", "Species"), length = 20
+     )
+     summary(slopes)
+     plot(slopes)
+   }
+ }
Loading required package: emmeans
Loading required package: ggplot2
Loading required package: see
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-40. For overview type 'help("mgcv-package")'.
No numeric variable was specified for slope estimation. Selecting `trend = "Petal.Length"`.
Error in emmeans::emtrends(model, specs = args$emmeans_specs, var = args$trend,  : 
  Variable 'Petal.Length' is not in the dataset
Calls: estimate_slopes -> get_emtrends -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ames.html:35:83: Warning: inserting implicit <p>
ames.html:35:83: Warning: trimming empty <p>
Found the following HTML validation problems:
modeldb-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
modeldb-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'BIO_TCandNLCD_NLCD.jpg' 'BIO_TCandNLCD_TCB.jpg'
  'BIO_TCandNLCD_TCG.jpg' 'BIO_TCandNLCD_TCW.jpg'
  'BIO_TCandNLCD_corrplot.jpg' 'BIO_TCandNLCD_mask_all_predictors.jpg'
  'BIO_TCandNLCD_projections.txt' 'RF_BIO_TCandNLCD_01.img'
  'RF_BIO_TCandNLCD_01.img.aux.xml'
  'RF_BIO_TCandNLCD_01_mapmake_arguments.txt'
  'RF_BIO_TCandNLCD_01_projections.txt' 'RF_BIO_TCandNLCD_OOB.csv'
  'RF_BIO_TCandNLCD_OOB_corrplot.jpg'
  'RF_BIO_TCandNLCD_OOB_corrplot.pdf' 'RF_BIO_TCandNLCD_OOB_error.jpg'
  'RF_BIO_TCandNLCD_OOB_error.pdf'
  'RF_BIO_TCandNLCD_OOB_importance.jpg'
  'RF_BIO_TCandNLCD_OOB_importance.pdf'
  'RF_BIO_TCandNLCD_OOB_scatterplot.jpg'
  'RF_BIO_TCandNLCD_OOB_scatterplot.pdf'
  'RF_BIO_TCandNLCD_model_building_arguments.txt'
  'RF_Bio_TC_model_building_arguments.txt' 'example.test.csv'
  'example.train.csv'
Found the following HTML validation problems:
modelr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
modelr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without 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
'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
checkRd: (-1) bmonomvn.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) bmonomvn.Rd:149: Escaped LaTeX specials: \&
checkRd: (-1) returns.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) returns.Rd:37: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
moodleR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
moodleR-package.html:27:4: Warning: <img> attribute "align" not allowed for HTML5
moodleR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
moodleR-package.html:27:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without 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:
  exhaust_bic.cpp:269:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  exhaust_bic.cpp:290:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mosum.Rcheck/00install.out' for details.
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: \&
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
atleast.one.endpoint.Rd:28: Can't use function '$' in math mode in $\mu_{Tk}-\mu_{C...
atleast.one.endpoint.Rd:29: Can't use function '$' in math mode in $k\in\{1,\ldots,...
mpe.t.test.Rd:22: Can't use function '$' in math mode in $\mu_{Tk}-\mu_{C...
mpe.t.test.Rd:23: Can't use function '$' in math mode in $k\in\{1,\ldots,...
mpe.z.test.Rd:23: Can't use function '$' in math mode in $\mu_{Tk}-\mu_{C...
mpe.z.test.Rd:24: Can't use function '$' in math mode in $k\in\{1,\ldots,...
power.known.var.Rd:29: Can't use function '$' in math mode in $\mu_{Tk}-\mu_{C...
power.known.var.Rd:30: Can't use function '$' in math mode in $k\in\{1,\ldots,...
power.unknown.var.Rd:33: Can't use function '$' in math mode in $\mu_{Tk}-\mu_{C...
power.unknown.var.Rd:34: Can't use function '$' in math mode in $k\in\{1,\ldots,...
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
Found the following HTML validation problems:
detfct.fit.html:132:1: Warning: trimming empty <li>
detfct.fit.opt.html:133:1: Warning: trimming empty <li>
Found the following files/directories:
  'MRH_lung'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
FindMaxHomoOptimalPartitions.html:90:38: Warning: nested emphasis <code>
FindMaxHomoOptimalPartitions.html:94:38: Warning: nested emphasis <code>
FindMaxHomoOptimalPartitions.html:98:38: Warning: nested emphasis <code>
FindMaxHomoOptimalPartitions.html:102:38: Warning: nested emphasis <code>
FindMaxHomoOptimalPartitions.html:108:38: Warning: nested emphasis <code>
FindMaxHomoOptimalPartitions.html:114:38: Warning: nested emphasis <code>
linearModelTraining.html:80:38: Warning: nested emphasis <code>
'LazyData' is specified without 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
Found the following significant warnings:
  Cmicrosim.c:789:18: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Cmicrosim.c:798:18: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Cmicrosim.c:965:16: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Cmicrosim.c:1018:16: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Cmicrosim.c:1068:16: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mSimCC.Rcheck/00install.out' for details.
'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
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
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
multilinguer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
multilinguer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following HTML validation problems:
multinma-package.html:24:4: Warning: <img> attribute "align" not allowed for HTML5
multinma-package.html:24:4: Warning: <img> attribute "align" not allowed for HTML5
Package suggested but not available for checking: 'rPorta'
Found the following HTML validation problems:
multinomineq-package.html:24:4: Warning: <img> attribute "align" not allowed for HTML5
multinomineq-package.html:24:4: Warning: <img> attribute "align" not allowed for HTML5
multinomineq-package.html:24:4: Warning: <img> attribute "hspace" not allowed for HTML5
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
Found the following math rendering problems:
r.squaredLR.Rd:82: Unknown accent ' <U+0305>' in R<U+0305>² = R² / max(R²...
std.coef.Rd:61: Undefined control sequence: \var in ...^{*}=s_{X_{i}} \var{VIF}(X_i)^{-0....
'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
checkRd: (-1) MXM-package.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) MXM-package.Rd:100: Escaped LaTeX specials: \&
checkRd: (-1) MXMCondIndTests.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) MXMCondIndTests.Rd:174: Escaped LaTeX specials: \&
checkRd: (-1) MXMCondIndTests.Rd:212: Escaped LaTeX specials: \&
checkRd: (-1) MXMCondIndTests.Rd:242: Escaped LaTeX specials: \&
checkRd: (-1) MXMCondIndTests.Rd:276: Escaped LaTeX specials: \&
checkRd: (-1) SES.glmm.Rd:222: Escaped LaTeX specials: \&
checkRd: (-1) SES.glmm.Rd:224: Escaped LaTeX specials: \&
checkRd: (-1) cond.regs.Rd:109: Escaped LaTeX specials: \&
checkRd: (-1) cv.fbed.lmm.reg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) cv.ses.Rd:236: Escaped LaTeX specials: \&
checkRd: (-1) ebic.glmm.bsreg.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) ebic.regs.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) fbed.gee.reg.Rd:112: Escaped LaTeX specials: \&
checkRd: (-1) fbed.glmm.reg.Rd:110: Escaped LaTeX specials: \&
checkRd: (-1) glmm.bsreg.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) glmm.ci.mm.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) mmhc.skel.Rd:122: Escaped LaTeX specials: \&
checkRd: (-1) mmpc.glmm.model.Rd:108: Escaped LaTeX specials: \&
checkRd: (-1) mmpc.glmm.model.Rd:110: Escaped LaTeX specials: \&
checkRd: (-1) mmpc.glmm2.Rd:138: Escaped LaTeX specials: \&
checkRd: (-1) mmpc.glmm2.Rd:140: Escaped LaTeX specials: \&
checkRd: (-1) pc.skel.Rd:203: Escaped LaTeX specials: \&
checkRd: (-1) testIndGEEReg.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) testIndGLMMReg.Rd:124: Escaped LaTeX specials: \&
checkRd: (-1) testIndGLMMReg.Rd:126: Escaped LaTeX specials: \&
checkRd: (-1) univregs.Rd:157: 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
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 HTML validation problems:
namedropR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
namedropR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor changes
Found the following HTML validation problems:
nasapower-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
nasapower-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
Found the following significant warnings:
  energypot.cpp:14:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/nbody.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
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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Slightly modified tests
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'ndvtest.Rmd' using rmarkdown
Quitting from lines 641-648 (ndvtest.Rmd) 
Error: processing vignette 'ndvtest.Rmd' failed with diagnostics:
input string 2 is invalid
--- failed re-building 'ndvtest.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  subsetAndUpdate.cpp:13:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  subsetAndUpdate.cpp:35:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  subsetAndUpdate.cpp:118:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  subsetAndUpdateTime.cpp:13:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  subsetAndUpdateTime.cpp:35:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  subsetAndUpdateTime.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/neatRanges.Rcheck/00install.out' for details.
'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.
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) netCoin-package.Rd:38: Escaped LaTeX specials: \&
Found the following significant warnings:
  netdiffuser_extra.cpp:84:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  netdiffuser_extra.cpp:85:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  netdiffuser_extra.cpp:86:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  netdiffuser_extra.cpp:87:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  netdiffuser_extra.cpp:88:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  netdiffuser_extra.cpp:89:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  netdiffuser_extra.cpp:90:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  netdiffuser_extra.cpp:91:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  netdiffuser_extra.cpp:92:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  plot.cpp:70:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  plot.cpp:70:58: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  plot.cpp:70:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  rgraph.cpp:257:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/netdiffuseR.Rcheck/00install.out' for details.
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
Found the following significant warnings:
  rcpp_lin_alg.cpp:9:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  rcpp_lin_alg.cpp:9:35: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  rcpp_lin_alg.cpp:30:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  rcpp_lin_alg.cpp:48:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  rcpp_lin_alg.cpp:48:35: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/netgsa.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'fastshp'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Dependency changes
    Bugfixes
'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.
Found the following significant warnings:
  checkPairs.cpp:15:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  checkPairs.cpp:15:41: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  checkPairs.cpp:15:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  checkPairs.cpp:18:15: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  checkPairs.cpp:18:46: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  checkPairs.cpp:18:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  checkPairs.cpp:21:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  checkPairs.cpp:24:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  listingIdeals.cpp:50:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/netrankr.Rcheck/00install.out' for details.
Found the following HTML validation problems:
netseg-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
netseg-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Found the following math rendering problems:
nBartlett.Rd:45-50: Undefined control sequence: \raise in ... }
      \over {{\raise0.7ex\hbox{$1$}...
Found the following HTML validation problems:
nfl4th-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
nfl4th-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
nflplotR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
nflplotR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
asym_m_ng.html:117:38: Warning: nested emphasis <code>
asym_m_ng.html:123:38: Warning: nested emphasis <code>
m_ng.html:123:38: Warning: nested emphasis <code>
m_ng.html:129:38: Warning: nested emphasis <code>
'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:
  rcpp_rmultinom.cpp:40:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/NHMM.Rcheck/00install.out' for details.
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
tsp_solver.Rd:54: Can't use function '$' in math mode in i=1,\ldots,p,$ $p=n(n-1)
'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
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) NMextractText.Rd:41: Escaped LaTeX specials: \$
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: \#
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
pm.Rd:35: Undefined control sequence: \emph in \emph{x}
pm.Rd:35: Undefined control sequence: \emph in \emph{n}
pm.Rd:46: Undefined control sequence: \emph in \emph{t}
pm.Rd:47: Undefined control sequence: \emph in \emph{e}
'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:
    Other ideas
'LazyData' is specified without a 'data' directory
checkRd: (-1) euc.dist.Rd:50: Escaped LaTeX specials: \&
Found the following math rendering problems:
funsW345values.Rd:28-29: Undefined control sequence: \boldmath in ...ymbol \delta^t \boldmath A(\theta)) \bol...
funsW345values.Rd:30: Undefined control sequence: \boldmath in \boldmath A(\theta) = (a_...
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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    norgeo (development version)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
cub_spline_est.rd:40: Can't use function '$' in math mode in ...^T \alpha\leq 0$, $j=0,1,\ldots...
checkRd: (-1) prepareplot.Rd:64: Escaped LaTeX specials: \#
checkRd: (-1) prepareplot.Rd:68: Escaped LaTeX specials: \#
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
Error(s) in re-building vignettes:
  ...
--- re-building 'entropy_np.Rnw' using Sweave
Nonparametric Kernel Methods for Mixed Datatypes (version 0.60-11)
[vignette("np_faq",package="np") provides answers to frequently asked questions]
[vignette("np",package="np") an overview]
[vignette("entropy_np",package="np") an overview of entropy-based methods]
Error: processing vignette 'entropy_np.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'entropy_np.tex' failed.
LaTeX errors:
! Argument of Â has an extra }.
<inserted text> 
                \par 
l.57 \begin{document}
                     
! Emergency stop.
<inserted text> 
                \par 
l.57 \begin{document}
                     
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'entropy_np.Rnw'

--- re-building 'np.Rnw' using Sweave
Warning in Ops.factor(dfemale + dmarried + educ + exper + tenure, female) :
  '|' not meaningful for factors
Error: processing vignette 'np.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'np.tex' failed.
LaTeX errors:
! Argument of Â has an extra }.
<inserted text> 
                \par 
l.77 \begin{document}
                     
! Emergency stop.
<inserted text> 
                \par 
l.77 \begin{document}
                     
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'np.Rnw'

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

SUMMARY: processing the following files failed:
  'entropy_np.Rnw' 'np.Rnw'

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) frfast.Rd:172: Escaped LaTeX specials: \~
checkRd: (-1) globaltest.Rd:114: Escaped LaTeX specials: \~
checkRd: (-1) localtest.Rd:139: Escaped LaTeX specials: \~
Found the following math rendering problems:
globaltest.Rd:97-98: Undefined control sequence: \emph in ...m{some}
   \quad \emph{i}, \emph{j} \...
localtest.Rd:115-116: Undefined control sequence: \emph in ...{some}} \quad 
  \emph{i}, \emph{j} \...
'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
checkRd: (-1) Ardechedata.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) nsRFA-package.Rd:231: 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
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) dataca20.Rd:23: Escaped LaTeX specials: \~
checkRd: (-1) dataca20.Rd:23: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'OBL-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: blockboot
> ### Title: OBL: Optimal Block Length Compute Optimal Block Length for
> ###   Non-overlapping, Overlapping, Circular Block, tapered moving, and
> ###   tapered circular Block Bootstrap method
> ### Aliases: blockboot
> 
> ### ** Examples
> 
>   set.seed(289805)
>   ts <- arima.sim(n = 3, model = list(ar = 0.8, order = c(1, 0, 0)), sd = 1)
>   blockboot(ts = ts, R = 5, seed = 6, n_cores = 2)
Error in { : task 1 failed - "32 simultaneous processes spawned"
Calls: blockboot -> nbb -> %dopar% -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
Overbeck2.Rd:52: Can't use function '$' in math mode in $K$
Overbeck2.Rd:53: Can't use function '$' in math mode in $X_{i}$
Overbeck2.Rd:55: Can't use function '$' in math mode in $X$
Found the following HTML validation problems:
soi.html:37:100: Warning: inserting implicit <p>
soi.html:37:100: Warning: trimming empty <p>
Running 'testthat.R' [58s/63s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(oce)
  Loading required package: gsw
  > 
  > test_check("oce")
  [ FAIL 1 | WARN 18 | SKIP 9 | PASS 2688 ]
  
  == Skipped tests ===============================================================
  * On CRAN (3)
  * empty test (6)
  
  == Failed tests ================================================================
  -- Error (test_ctd_ssda.R:8:5): read.ctd.ssda() works (discussions/1929) -------
  Error in `1L:dataStart`: argument of length 0
  Backtrace:
      x
   1. \-oce::read.oce(file) at test_ctd_ssda.R:8:4
   2.   \-oce::read.ctd.ssda(...)
  
  [ FAIL 1 | WARN 18 | SKIP 9 | PASS 2688 ]
  Error: Test failures
  Execution halted
Found the following HTML validation problems:
swTFreeze.html:114:1: Warning: trimming empty <li>
Found the following math rendering problems:
swSpecificHeat.Rd:35: Got group of unknown type: 'internal'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'morse'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  ./oneclust.h:24:21: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/oneclust.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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp500_1950_2018.Rd:6: Escaped LaTeX specials: \&
Found the following HTML validation problems:
openintro-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
openintro-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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:
  omxRAMExpectation.cpp:677:24: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  omxRAMExpectation.cpp:682:25: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/OpenMx.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Older changes
    trunk
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'openNLPmodels.en'
Found the following significant warnings:
  load_workbook.cpp:122:15: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  load_workbook.cpp:142:17: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  read_workbook.cpp:640:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  write_data.cpp:106:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  write_data.cpp:137:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  write_file.cpp:251:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/openxlsx.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'gurobi'
Found the following significant warnings:
  functions.cpp:103:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  rcpp_funded_projects.cpp:18:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  rcpp_random_solution.cpp:90:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/oppr.Rcheck/00install.out' for details.
checkRd: (-1) problem.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) problem.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) problem.Rd:45: Escaped LaTeX specials: \$
'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
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RItools', 'rrelaxiv'
checkRd: (-1) match_on-methods.Rd:149: Escaped LaTeX specials: \&
checkRd: (-1) scores.Rd:29: Escaped LaTeX specials: \&
Error(s) in re-building vignettes:
  ...
--- re-building 'fullmatch-vignette.Rmd' using rmarkdown
Quitting from lines 72-74 (fullmatch-vignette.Rmd) 
Error: processing vignette 'fullmatch-vignette.Rmd' failed with diagnostics:
there is no package called 'RItools'
--- failed re-building 'fullmatch-vignette.Rmd'

--- re-building 'matching-from-foreign-software.Rmd' using rmarkdown
--- finished re-building 'matching-from-foreign-software.Rmd'

--- re-building 'matching-within-subgroups.Rmd' using rmarkdown
--- finished re-building 'matching-within-subgroups.Rmd'

SUMMARY: processing the following file failed:
  'fullmatch-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
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
'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'
checkRd: (-1) compartmentalModel.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) multilinearReferenceTissueModel.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) simplifiedReferenceTissueModel.Rd:60: Escaped LaTeX specials: \&
Found the following math rendering problems:
chebyshev.c.inner.products.Rd:18-22: Unknown column alignment: * in ...{\begin{array}{*{20}c}
     {4\,\...
chebyshev.t.inner.products.Rd:18-23: Unknown column alignment: * in ...{\begin{array}{*{20}c}
     {\fra...
gegenbauer.inner.products.Rd:19-25: Unknown column alignment: * in ...{\begin{array}{*{20}c}
     {\fra...
schebyshev.t.inner.products.Rd:18-23: Unknown column alignment: * in ...{\begin{array}{*{20}c}
     {\fra...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
    development version
Found the following HTML validation problems:
macos_keychain.html:220:35: Warning: inserting implicit <p>
macos_keychain.html:225:88: Warning: inserting implicit <p>
macos_keychain.html:234:79: Warning: inserting implicit <p>
macos_keychain.html:240:109: Warning: inserting implicit <p>
macos_keychain.html:250:95: Warning: inserting implicit <p>
macos_keychain.html:265:62: Warning: inserting implicit <p>
macos_keychain.html:445:104: Warning: inserting implicit <p>
macos_keychain.html:462:98: Warning: inserting implicit <p>
macos_keychain.html:474:58: Warning: inserting implicit <p>
macos_keychain.html:220:35: Warning: trimming empty <p>
macos_keychain.html:225:88: Warning: trimming empty <p>
macos_keychain.html:234:79: Warning: trimming empty <p>
macos_keychain.html:240:109: Warning: trimming empty <p>
macos_keychain.html:250:95: Warning: trimming empty <p>
macos_keychain.html:265:62: Warning: trimming empty <p>
macos_keychain.html:445:104: Warning: trimming empty <p>
macos_keychain.html:462:98: Warning: trimming empty <p>
macos_keychain.html:474:58: Warning: trimming empty <p>
windows_credentials.html:172:33: Warning: inserting implicit <p>
windows_credentials.html:183:62: Warning: inserting implicit <p>
windows_credentials.html:196:69: Warning: inserting implicit <p>
windows_credentials.html:204:102: Warning: inserting implicit <p>
windows_credentials.html:212:71: Warning: inserting implicit <p>
windows_credentials.html:220:50: Warning: inserting implicit <p>
windows_credentials.html:172:33: Warning: trimming empty <p>
windows_credentials.html:183:62: Warning: trimming empty <p>
windows_credentials.html:196:69: Warning: trimming empty <p>
windows_credentials.html:204:102: Warning: trimming empty <p>
windows_credentials.html:212:71: Warning: trimming empty <p>
windows_credentials.html:220:50: Warning: trimming empty <p>
Found the following HTML validation problems:
osmextract-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
osmextract-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following math rendering problems:
plot.osmose.Rd:501: Can't use function '$' in math mode in freq = 1/x$model$start
plot.osmose.config.Rd:141: Can't use function '$' in math mode in freq = 1/x$model$start
'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
Found the following HTML validation problems:
eff.html:65:38: Warning: nested emphasis <code>
eff.html:71:38: Warning: nested emphasis <code>
'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: \$
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pad_int
'LazyData' is specified without 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) eseq.Rd:36: Escaped LaTeX specials: \_
checkRd: (-1) eseq.Rd:38: Escaped LaTeX specials: \_
Found the following math rendering problems:
specialg.Rd:62: Can't use function '$' in math mode in a_i \leq b_i$,$i=1, \ldots, ...
Found the following HTML validation problems:
pairwise-package.html:64:184: Warning: <a> illegal characters found in URI
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
handle_package_not_found.html:49:102: Warning: inserting implicit <p>
handle_package_not_found.html:49:102: Warning: trimming empty <p>
pak_package_sources.html:32:39: Warning: inserting implicit <p>
pak_package_sources.html:55:39: Warning: inserting implicit <p>
pak_package_sources.html:98:61: Warning: inserting implicit <p>
pak_package_sources.html:104:35: Warning: inserting implicit <p>
pak_package_sources.html:32:39: Warning: trimming empty <p>
pak_package_sources.html:55:39: Warning: trimming empty <p>
pak_package_sources.html:98:61: Warning: trimming empty <p>
pak_package_sources.html:104:35: Warning: trimming empty <p>
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
Found the following HTML validation problems:
timePaleoPhy.html:262:4: Warning: nested emphasis <em>
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Bug fixes
    Other changes
Found the following HTML validation problems:
paletteer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
paletteer-package.html:30:4: Warning: <img> attribute "align" not allowed for HTML5
paletteer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
paletteer-package.html:30:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
palmerpenguins-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
palmerpenguins-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
document.html:43:1: Warning: trimming empty <dt>
document.html:45:1: Warning: trimming empty <dt>
document.html:46:1: Warning: trimming empty <dt>
document.html:56:1: Warning: trimming empty <dt>
document.html:58:1: Warning: trimming empty <dt>
document.html:59:1: Warning: trimming empty <dt>
document.html:62:1: Warning: trimming empty <dt>
document.html:64:1: Warning: trimming empty <dt>
document.html:65:1: Warning: trimming empty <dt>
document.html:68:1: Warning: trimming empty <dt>
document.html:69:1: Warning: trimming empty <dt>
document.html:72:1: Warning: trimming empty <dt>
document.html:73:1: Warning: trimming empty <dt>
document.html:76:1: Warning: trimming empty <dt>
document.html:78:1: Warning: trimming empty <dt>
document.html:79:1: Warning: trimming empty <dt>
document.html:89:1: Warning: trimming empty <dt>
document.html:91:1: Warning: trimming empty <dt>
document.html:92:1: Warning: trimming empty <dt>
document.html:95:1: Warning: trimming empty <dt>
document.html:97:1: Warning: trimming empty <dt>
document.html:98:1: Warning: trimming empty <dt>
document.html:107:1: Warning: trimming empty <dt>
document.html:114:1: Warning: trimming empty <dt>
document.html:121:1: Warning: trimming empty <dt>
document.html:128:1: Warning: trimming empty <dt>
document.html:135:1: Warning: trimming empty <dt>
document.html:142:1: Warning: trimming empty <dt>
document.html:149:1: Warning: trimming empty <dt>
document.html:156:1: Warning: trimming empty <dt>
document.html:163:1: Warning: trimming empty <dt>
document.html:170:1: Warning: trimming empty <dt>
document.html:177:1: Warning: trimming empty <dt>
document.html:184:1: Warning: trimming empty <dt>
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: \_
Found the following HTML validation problems:
pvargmm.html:141:1: Warning: <center> element removed from HTML5
'LazyData' is specified without a 'data' directory
checkRd: (-1) pan.bd.Rd:65: Escaped LaTeX specials: \$
Found the following HTML validation problems:
apa_barplot.html:83:1: Warning: trimming empty <dt>
apa_beeplot.html:84:1: Warning: trimming empty <dt>
apa_interval.html:96:1: Warning: trimming empty <dt>
apa_lineplot.html:84:1: Warning: trimming empty <dt>
apa_print.emmGrid.html:77:1: Warning: trimming empty <dt>
apa_print.glm.html:107:1: Warning: trimming empty <dt>
apa_print.htest.html:90:1: Warning: trimming empty <dt>
apa_print.papaja_wsci.html:50:1: Warning: trimming empty <dt>
revision_letter_pdf.html:48:1: Warning: trimming empty <dt>
Found the following HTML validation problems:
param6-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
param6-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Missing or unexported object: 'datawizard::data_rescale'
checkRd: (-1) model_parameters.principal.Rd:117: Escaped LaTeX specials: \&
checkRd: (-1) reduce_parameters.Rd:89: Escaped LaTeX specials: \&
Running examples in 'parameters-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cluster_analysis
> ### Title: Cluster Analysis
> ### Aliases: cluster_analysis
> 
> ### ** Examples
> 
> set.seed(33)
> # K-Means ====================================================
> rez <- cluster_analysis(iris[1:4], n = 3, method = "kmeans")
Error: Could not find variable '4' in data.
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.
Found the following math rendering problems:
parfm.Rd:112-113: Undefined control sequence: \slash in ...exp \left( - u \slash \theta \right)}...
Found the following files/directories:
  'NUL'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
particles-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
particles-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Found the following HTML validation problems:
patchwork-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
patchwork-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
pathviewr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
pathviewr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Checking should be performed on sources prepared by 'R CMD build'.
GNU make is a SystemRequirements.
checkRd: (-1) plot-methods.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) plot-methods.Rd:125: Escaped LaTeX specials: \_
Found the following math rendering problems:
find_astar.Rd:5: Can't use function '$' in math mode in $\alpha^*$
find_astar.Rd:18: Can't use function '$' in math mode in $\alpha^*$
find_astar.Rd:14: Can't use function '$' in math mode in $\alpha^*$
find_astar.Rd:22: Can't use function '$' in math mode in $\alpha$
summary.colspace.Rd:42: Can't use function '$' in math mode in $\alpha$
summary.colspace.Rd:73: Can't use function '$' in math mode in $\alpha$
tcsplot.Rd:81: Can't use function '$' in math mode in $\alpha^*$
vol.Rd:28: Can't use function '$' in math mode in $\alpha^*$
vol.Rd:77: Can't use function '$' in math mode in $\alpha$
voloverlap.Rd:34: Can't use function '$' in math mode in $\alpha^*$
voloverlap.Rd:127: Can't use function '$' in math mode in $\alpha$
checkRd: (-1) glue_search_tables.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) mq_update_broker.Rd:28: Escaped LaTeX specials: \#
Found the following HTML validation problems:
swf_register_activity_type.html:154:8: Warning: nested emphasis <em>
checkRd: (-1) ec2_create_key_pair.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:27: 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: \#
'LazyData' is specified without 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 math rendering problems:
calcArea.Rd:33: Undefined control sequence: \emph in -186 + 6\emph{i}^\circ < x \...
convUL.Rd:28-29: Undefined control sequence: \emph in -186 + 6\emph{i}^\circ < x \...
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
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
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 in Depends field not imported from: 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  'A.txt' 'Ainv.txt'
'LazyData' is specified without a 'data' directory
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
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: \&
Found the following HTML validation problems:
Return.Geltner.html:58:32: Warning: trimming empty <code>
centeredmoments.html:24:32: Warning: trimming empty <code>
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
Found the following HTML validation problems:
personalr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
personalr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Found the following math rendering problems:
fingerprint.regression.Rd:87: Can't use function '$' in math mode in $\lambda$
fingerprint.regression.Rd:88: Can't use function '$' in math mode in $\delta$
fingerprint.regression.Rd:88: Can't use function '$' in math mode in $\kappa$
pez.evenness.Rd:47: Can't use function '$' in math mode in $\lambda$
pez.evenness.Rd:47: Can't use function '$' in math mode in $\delta$
pez.evenness.Rd:48: Can't use function '$' in math mode in $\kappa$
phy.signal.Rd:13: Can't use function '$' in math mode in $\lambda$
phy.signal.Rd:13: Can't use function '$' in math mode in $\delta$
phy.signal.Rd:14: Can't use function '$' in math mode in $\kappa$
sim.meta.Rd:43: Can't use function '$' in math mode in $\lambda$
sim.meta.Rd:47: Can't use function '$' in math mode in $\lambda$
sim.meta.Rd:51: Can't use function '$' in math mode in $\lambda$
sim.phy.Rd:94-96: Can't use function '$' in math mode in $p(speciate)_i =...
sim.phy.Rd:96-98: Can't use function '$' in math mode in $p(extinct)_i = ...
sim.phy.Rd:98: Can't use function '$' in math mode in $i$
Found the following math rendering problems:
pgam.likelihood.Rd:20-21: Undefined control sequence: \cr in ...t)-\log y_{t}!-\cr
  \log \Gamma\lef...
'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
'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
SIR.html:67:1: Warning: <center> element removed from HTML5
competition.html:72:1: Warning: <center> element removed from HTML5
example1.html:62:1: Warning: <center> element removed from HTML5
example10.html:62:1: Warning: <center> element removed from HTML5
example11.html:62:1: Warning: <center> element removed from HTML5
example12.html:62:1: Warning: <center> element removed from HTML5
example13.html:62:1: Warning: <center> element removed from HTML5
example14.html:62:1: Warning: <center> element removed from HTML5
example15.html:62:1: Warning: <center> element removed from HTML5
example2.html:62:1: Warning: <center> element removed from HTML5
example3.html:62:1: Warning: <center> element removed from HTML5
example4.html:62:1: Warning: <center> element removed from HTML5
example5.html:62:1: Warning: <center> element removed from HTML5
example6.html:62:1: Warning: <center> element removed from HTML5
example7.html:62:1: Warning: <center> element removed from HTML5
example8.html:62:1: Warning: <center> element removed from HTML5
example9.html:62:1: Warning: <center> element removed from HTML5
exponential.html:65:1: Warning: <center> element removed from HTML5
lindemannMechanism.html:65:1: Warning: <center> element removed from HTML5
logistic.html:67:1: Warning: <center> element removed from HTML5
lotkaVolterra.html:69:1: Warning: <center> element removed from HTML5
monomolecular.html:67:1: Warning: <center> element removed from HTML5
morrisLecar.html:67:1: Warning: <center> element removed from HTML5
morrisLecar.html:70:1: Warning: <center> element removed from HTML5
simplePendulum.html:65:1: Warning: <center> element removed from HTML5
toggle.html:68:1: Warning: <center> element removed from HTML5
vanDerPol.html:65:1: Warning: <center> element removed from HTML5
vonBertalanffy.html:67:1: Warning: <center> element removed from HTML5
Found the following files/directories:
  'test.pdf'
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
phenology-package.html:28:1: Warning: <img> attribute "," lacks value
phenology-package.html:28:1: Warning: <img> attribute "align" not allowed for HTML5
phenology-package.html:28:1: Warning: <img> attribute "align" not allowed for HTML5
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.
Found the following HTML validation problems:
estimate.probability.html:33:1: Warning: trimming empty <li>
estimate.probability.html:35:1: Warning: trimming empty <li>
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  '1khz.wav' 'snd.wav'
Found the following HTML validation problems:
photobiologyInOut-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
photobiologyInOut-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
photobiologyLamps-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
photobiologyLamps-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
photobiologyLEDs-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
photobiologyLEDs-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
photobiologyWavebands-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
photobiologyWavebands-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) 11_d.EMControl.Rd:52: Escaped LaTeX specials: \_
checkRd: (-1) plotdots.Rd:33: Escaped LaTeX specials: \#
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
Found the following HTML validation problems:
piecepackr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
piecepackr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
board_rsconnect.html:128:59: Warning: inserting implicit <p>
board_rsconnect.html:134:92: Warning: inserting implicit <p>
board_rsconnect.html:128:59: Warning: trimming empty <p>
board_rsconnect.html:134:92: Warning: trimming empty <p>
pins-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
pins-package.html:23:4: 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':
No news entries found.
Package suggested but not available for checking: 'ggsubplot'
'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
checkRd: (-1) sanitize_latex.Rd:49: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
pkgcache-package.html:38:78: Warning: inserting implicit <p>
pkgcache-package.html:51:62: Warning: inserting implicit <p>
pkgcache-package.html:93:146: Warning: inserting implicit <p>
pkgcache-package.html:38:78: Warning: trimming empty <p>
pkgcache-package.html:51:62: Warning: trimming empty <p>
pkgcache-package.html:93:146: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following HTML validation problems:
pkglite-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
pkglite-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
DependencyReporter.html:35:1: Warning: trimming empty <dt>
FunctionReporter.html:101:1: Warning: trimming empty <dt>
InheritanceReporter.html:79:1: Warning: trimming empty <dt>
PackageReporters.html:34:1: Warning: trimming empty <dt>
SummaryReporter.html:33:1: Warning: trimming empty <dt>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
PL94171-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
PL94171-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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'
Found the following HTML validation problems:
mus_b_trans.html:19:1: Warning: missing </h2> before <dl>
mus_b_trans.html:34:1: Warning: discarding unexpected </h2>
vdj_length_prob.html:19:1: Warning: missing </h2> before <dl>
vdj_length_prob.html:36:1: Warning: discarding unexpected </h2>
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
palettes.html:90:1: Warning: trimming empty <li>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 math rendering problems:
plsim.MAVE.Rd:35: Undefined control sequence: \boldmath in \boldmath{\alpha}_0
plsim.MAVE.Rd:36: Undefined control sequence: \boldmath in \boldmath{\beta}_0
plsim.MAVE.Rd:55: Undefined control sequence: \boldmath in \hat{\eta}(Z^T\boldmath{\hat{\alpha} }...
plsim.MAVE.Rd:64: Undefined control sequence: \boldmath in Z^T\boldmath{\hat{\alpha}}
plsim.bw.Rd:50: Undefined control sequence: \boldmath in \boldmath{\alpha}_0
plsim.bw.Rd:51: Undefined control sequence: \boldmath in \boldmath{\beta}_0
plsim.est.Rd:33: Undefined control sequence: \boldmath in \boldmath{\alpha}_0
plsim.est.Rd:34: Undefined control sequence: \boldmath in \boldmath{\beta}_0
plsim.est.Rd:49: Undefined control sequence: \boldmath in \hat{\eta}(Z^T\boldmath{\hat{\alpha} }...
plsim.est.Rd:57: Undefined control sequence: \boldmath in Z^T\boldmath{\hat{\alpha}}
plsim.ini.Rd:34: Undefined control sequence: \boldmath in \boldmath{\alpha}_0
plsim.ini.Rd:35: Undefined control sequence: \boldmath in \boldmath{\beta}_0
plsim.lam.Rd:32: Undefined control sequence: \boldmath in \boldmath{\alpha}_0
plsim.lam.Rd:33: Undefined control sequence: \boldmath in \boldmath{\beta}_0
plsim.vs.hard.Rd:39: Undefined control sequence: \boldmath in \boldmath{\alpha}_0
plsim.vs.hard.Rd:40: Undefined control sequence: \boldmath in \boldmath{\beta}_0
plsim.vs.soft.Rd:34: Undefined control sequence: \boldmath in \boldmath{\alpha}_0
plsim.vs.soft.Rd:35: Undefined control sequence: \boldmath in \boldmath{\beta}_0
plsim.vs.soft.Rd:57: Undefined control sequence: \boldmath in \hat{\eta}(Z^T\boldmath{\hat{\alpha} }...
plsim.vs.soft.Rd:66: Undefined control sequence: \boldmath in Z^T\boldmath{\hat{\alpha}}
Found the following HTML validation problems:
plsmod-package.html:37:98: Warning: inserting implicit <p>
plsmod-package.html:50:99: Warning: inserting implicit <p>
plsmod-package.html:55:71: Warning: inserting implicit <p>
plsmod-package.html:62:47: Warning: inserting implicit <p>
plsmod-package.html:37:98: Warning: trimming empty <p>
plsmod-package.html:50:99: Warning: trimming empty <p>
plsmod-package.html:55:71: Warning: trimming empty <p>
plsmod-package.html:62:47: Warning: trimming empty <p>
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
Found the following HTML validation problems:
plu-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
plu-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 math rendering problems:
1dpoilog.Rd:31: Undefined control sequence: \emph in \code{nu}\,\emph{y}
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
poissonreg-package.html:38:90: Warning: inserting implicit <p>
poissonreg-package.html:74:31: Warning: inserting implicit <p>
poissonreg-package.html:38:90: Warning: trimming empty <p>
poissonreg-package.html:74:31: Warning: trimming empty <p>
'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: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'pollimetrydata'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Documentation
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'polyfreqs-mcmc.out'
'LazyData' is specified without a 'data' directory
'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
Found the following HTML validation problems:
poorman.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
poorman.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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'
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'
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
Found the following math rendering problems:
cachet.Rd:126-127: Undefined control sequence: \textbackslash in ...a_{idx} \cup X \textbackslash
    A_a)
calct.Rd:64-65: Undefined control sequence: \textbackslash in t(y \cup X \textbackslash
    A_a)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
powerjoin-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
powerjoin-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    [1.7.3]
    [1.7.2]
    [1.7.1]
    [1.7.0]
    [1.6.1]
    [1.6.0]
    [1.5.2]
    [1.5.1]
    [1.5.0]
    [1.4.0]
    [1.3.0]
    [1.2.0]
    [1.1.1]
    [1.1.0]
    [1.0.0]
    [0.2.0]
    [0.1.1]
    [0.1.0]
Found the following HTML validation problems:
plot.Method.html:107:1: Warning: inserting implicit <p>
plot.Method.html:112:1: Warning: inserting implicit <p>
plot.Method.html:118:1: Warning: inserting implicit <p>
plot.Method.html:104:1: Warning: trimming empty <p>
plot.Method.html:107:1: Warning: trimming empty <p>
plot.Method.html:109:1: Warning: trimming empty <p>
plot.Method.html:112:1: Warning: trimming empty <p>
plot.Method.html:114:1: Warning: trimming empty <p>
plot.Method.html:118:1: Warning: trimming empty <p>
plot.StepOne.html:86:1: Warning: inserting implicit <p>
plot.StepOne.html:86:1: Warning: trimming empty <p>
plot.StepThree.html:86:1: Warning: inserting implicit <p>
plot.StepThree.html:86:1: Warning: trimming empty <p>
plot.StepTwo.html:86:1: Warning: inserting implicit <p>
plot.StepTwo.html:86:1: Warning: trimming empty <p>
plot.Validation.html:92:1: Warning: inserting implicit <p>
plot.Validation.html:92:1: Warning: trimming empty <p>
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
Found the following HTML validation problems:
leukemia.html:19:1: Warning: missing </h2> before <ul>
leukemia.html:29:1: Warning: discarding unexpected </h2>
'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
Running 'testthat.R' [20s/12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(praznik)
  > 
  > test_check("praznik")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 311 ]
  
  == Failed tests ================================================================
  -- Failure (test-native-pure.R:41:4): Native NJMIM works like pure NJMIM with spoiler --
  `pure` (`actual`) not equal to `native` (`expected`).
  
  `names(actual$selection)`:   "spoiler" "Sepal.Length" "Petal.Length"
  `names(expected$selection)`: "spoiler" "Sepal.Length" "Petal.Width" 
  
    `actual$selection`: 7 1 3
  `expected$selection`: 7 1 4
  
  `names(actual$score)`:   "spoiler" "Sepal.Length" "Petal.Length"
  `names(expected$score)`: "spoiler" "Sepal.Length" "Petal.Width" 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 311 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'PerfMeas'
'LazyData' is specified without a 'data' directory
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
checkRd: (-1) PReMiuM-package.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) profRegr.Rd:156: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
preregr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
preregr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Problems with news in 'NEWS.md':
No news entries found.
Found the following HTML validation problems:
presize-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
presize-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
new_app.html:119:43: Warning: inserting implicit <p>
new_app.html:205:35: Warning: inserting implicit <p>
new_app.html:237:40: Warning: inserting implicit <p>
new_app.html:329:21: Warning: inserting implicit <p>
new_app.html:344:82: Warning: inserting implicit <p>
new_app.html:352:65: Warning: inserting implicit <p>
new_app.html:395:72: Warning: inserting implicit <p>
new_app.html:119:43: Warning: trimming empty <p>
new_app.html:205:35: Warning: trimming empty <p>
new_app.html:237:40: Warning: trimming empty <p>
new_app.html:329:21: Warning: trimming empty <p>
new_app.html:344:82: Warning: trimming empty <p>
new_app.html:352:65: Warning: trimming empty <p>
new_app.html:395:72: Warning: trimming empty <p>
new_app_process.html:75:88: Warning: inserting implicit <p>
new_app_process.html:75:88: Warning: trimming empty <p>
'LazyData' is specified without 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
Packages suggested but not available for checking: 'geoR', 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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:
  'RandomFields', 'gurobi', 'rcbc', 'cplexAPI'
Found the following significant warnings:
  rcpp_boundary_data.cpp:45:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  rcpp_boundary_data.cpp:132:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  rcpp_summarize_exactextractr.cpp:22:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/prioritizr.Rcheck/00install.out' for details.
Unknown package 'RandomFields' in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
prismatic-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
prismatic-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
proceduralnames-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
proceduralnames-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
prodigenr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
prodigenr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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: \&
'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:
handlers.html:80:4: Warning: nested emphasis <em>
with_progress.html:102:4: Warning: nested emphasis <em>
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
refmodel-init-get.html:313:36: Warning: inserting implicit <p>
refmodel-init-get.html:313:36: Warning: trimming empty <p>
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'
Package suggested but not available for checking: 'cin'
Found the following HTML validation problems:
prospectr-package.html:25:1: Warning: <img> attribute "align" not allowed for HTML5
prospectr-package.html:25:1: Warning: <img> attribute "align" not allowed for HTML5
Packages suggested but not available for checking: 'rdtLite', 'rdt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rdtLite', 'rdt'
Packages suggested but not available for checking: 'rdt', 'rdtLite'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rdt', 'rdtLite'
Package in Depends field not imported from: 'rpart'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'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: 'WebPower'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
dot-integrate_dmod.Rd:53: Undefined control sequence: \link in ...p f_{2}(X)\left\link[=X\left(b_{1_{...
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: \&
checkRd: (-1) cor.plot.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) mediate.Rd:94: Escaped LaTeX specials: \&
checkRd: (-1) multilevel.reliability.Rd:120: Escaped LaTeX specials: \&
checkRd: (-1) testRetest.Rd:47: Escaped LaTeX specials: \&
Found the following HTML validation problems:
psymonitor-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
psymonitor-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ptvapi.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ptvapi.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
CVDictionarySingleton.html:64:6: Warning: missing </span> before <p>
CVDictionarySingleton.html:64:91: Warning: inserting implicit <span>
CVDictionarySingleton.html:64:6: Warning: trimming empty <span>
QCMetaFilenames.html:64:6: Warning: missing </span> before <p>
QCMetaFilenames.html:64:91: Warning: inserting implicit <span>
QCMetaFilenames.html:64:6: Warning: trimming empty <span>
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
Found the following HTML validation problems:
purrr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
purrr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
reduce.html:108:68: Warning: inserting implicit <p>
reduce.html:108:68: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  pvarC.cpp:344:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  pvarC.cpp:591:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/pvar.Rcheck/00install.out' for details.
'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 files/directories:
  'lambda.pdf' 'qqplot.pdf'
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
qrandommaxint.Rd:6: Can't use function '$' in math mode in U(-.Machine$integer.max,.Ma...
qrandommaxint.Rd:14: Can't use function '$' in math mode in U(-.Machine$integer.max,.Ma...
qrandommaxint.Rd:27: Can't use function '$' in math mode in U(-.Machine$integer.max,.Ma...
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
GEV.Rd:37-41: Undefined control sequence: \cases in F(x) = \cases{
      \exp(-(1-...
GPD.Rd:49-53: Undefined control sequence: \cases in F(x) = \cases{
      1-(1+\xi ...
risk_measures.Rd:85: Can't use function '$' in math mode in $t$
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 HTML validation problems:
quadmesh-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
quadmesh-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
bounded.reg.html:204:33: Warning: unescaped & or unknown entity "&beta"
bounded.reg.html:213:1: Warning: inserting implicit <p>
bounded.reg.html:213:1: Warning: trimming empty <p>
bounded.reg.html:201:34: Warning: <center> element removed from HTML5
elastic.net.html:210:33: Warning: unescaped & or unknown entity "&beta"
elastic.net.html:219:1: Warning: inserting implicit <p>
elastic.net.html:219:1: Warning: trimming empty <p>
elastic.net.html:207:48: Warning: <center> element removed from HTML5
quadrupen-package.html:57:33: Warning: unescaped & or unknown entity "&beta"
quadrupen-package.html:67:1: Warning: inserting implicit <p>
quadrupen-package.html:67:1: Warning: trimming empty <p>
quadrupen-package.html:55:2: Warning: <center> element removed from HTML5
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
'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:
  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
Package suggested but not available for checking: 'fastshp'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
frame_fn_obs.Rd:24: Can't use function '$' in math mode in ...=r[\tau-I(r<0)]$ for $\tau \in ...
frame_fn_path.Rd:24: Can't use function '$' in math mode in ...=r[\tau-I(r<0)]$ for $\tau \in ...
'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
Found the following HTML validation problems:
prioritize.html:71:98: Warning: inserting implicit <p>
prioritize.html:107:71: Warning: inserting implicit <p>
prioritize.html:71:98: Warning: trimming empty <p>
prioritize.html:107:71: Warning: trimming empty <p>
'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
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File 'R2WinBUGS/R/attach.all.R':
  attach(x, name = name)
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
NullObject.html:47:1: Warning: inserting implicit <p>
NullObject.html:51:1: Warning: inserting implicit <p>
NullObject.html:56:1: Warning: inserting implicit <p>
NullObject.html:47:1: Warning: trimming empty <p>
NullObject.html:51:1: Warning: trimming empty <p>
NullObject.html:56:1: Warning: trimming empty <p>
Singleton.html:86:1: Warning: inserting implicit <p>
Singleton.html:92:1: Warning: inserting implicit <p>
Singleton.html:86:1: Warning: trimming empty <p>
Singleton.html:92:1: Warning: trimming empty <p>
ValueObject.html:61:1: Warning: inserting implicit <p>
ValueObject.html:98:73: Warning: inserting implicit <p>
ValueObject.html:110:37: Warning: inserting implicit <p>
ValueObject.html:115:34: Warning: inserting implicit <p>
ValueObject.html:182:78: Warning: inserting implicit <p>
ValueObject.html:270:1: Warning: inserting implicit <p>
ValueObject.html:61:1: Warning: trimming empty <p>
ValueObject.html:98:73: Warning: trimming empty <p>
ValueObject.html:110:37: Warning: trimming empty <p>
ValueObject.html:115:34: Warning: trimming empty <p>
ValueObject.html:182:78: Warning: trimming empty <p>
ValueObject.html:270:1: Warning: trimming empty <p>
'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
Found the following HTML validation problems:
ragg-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ragg-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) fdepth.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) fdepth.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
'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
'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.
checkRd: (-1) pseudoRNG.Rd:74: Escaped LaTeX specials: \_
Found the following math rendering problems:
colltest.Rd:34-38: Got group of unknown type: 'internal'
colltest.Rd:39: Got group of unknown type: 'internal'
colltestsparse.Rd:31-35: Got group of unknown type: 'internal'
colltestsparse.Rd:36: Got group of unknown type: 'internal'
Found the following HTML validation problems:
rangeMapper.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rangeMapper.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Package suggested but not available for checking: '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
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 HTML validation problems:
rasterly-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rasterly-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following math rendering problems:
RPT.Rd:47: Can't use function '$' in math mode in \sigma^2(P)$ when $X_1,\dot...
'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 HTML validation problems:
yc_get.html:38:1: Warning: trimming empty <li>
Found the following HTML validation problems:
getblock.html:58:1: Warning: trimming empty <h3>
getrawtransaction.html:57:1: Warning: trimming empty <h3>
'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':
  Cannot extract version info from the following section titles:
    names consisting of just one part, family, were missing processing of escaped
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'fts'
Found the following notes/warnings:
  Non-staged installation was used
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rblpapi.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
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
Found the following HTML validation problems:
getblock.html:58:1: Warning: trimming empty <h3>
getrawtransaction.html:57:1: Warning: trimming empty <h3>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'rcanvec.cache'
checkRd: (-1) Example_Data.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) Example_Data.Rd:22: Escaped LaTeX specials: \&
checkRd: (-1) Example_Data.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) Reference_Data.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) Reference_Data.Rd:45: Escaped LaTeX specials: \&
checkRd: (-1) Reference_Data.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) Reference_Data.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Reference_Data.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) Reference_Data.Rd:57: Escaped LaTeX specials: \&
'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'
'LazyData' is specified without 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:
rchie-package.html:23:4: Warning: <img> attribute "width" has invalid value "120px"
rchie-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rchie-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following files/directories:
  'data.csv'
'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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'conics'
Found the following significant warnings:
  myDerivs4.cc:45:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  myParms4.cc:79:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RCPmod.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
Found the following HTML validation problems:
colorMaps.html:79:1: Warning: inserting implicit <p>
colorMaps.html:79:1: Warning: trimming empty <p>
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'
Found the following significant warnings:
  ../inst/include/RcppSimdJson/../simdjson.h:8817:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ../inst/include/simdjson.h:8817:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RcppSimdJson.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.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Todo
Found the following HTML validation problems:
cal_knee_point.html:81:62: Warning: nested emphasis <em>
cal_knee_point.html:81:89: Warning: nested emphasis <em>
estimate_dataset_bmr.html:82:62: Warning: nested emphasis <em>
estimate_dataset_bmr.html:82:89: Warning: nested emphasis <em>
'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:
  decline_interface.cpp:34:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rdca.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) nonlinear_MVE.Rd:73: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
Rdistance-package.html:19:1: Warning: missing </h2> before <ul>
Rdistance-package.html:68:1: Warning: discarding unexpected </h2>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  Source.cpp:389:13: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RDSsamplesize.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'example.pdf'
'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
'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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
readthat-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
readthat-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
readxl-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
readxl-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
GeneratedPipeline.html:85:6: Warning: missing </span> before <p>
GeneratedPipeline.html:85:88: Warning: inserting implicit <span>
GeneratedPipeline.html:85:6: Warning: trimming empty <span>
GeneratedTransformation.html:89:6: Warning: missing </span> before <p>
GeneratedTransformation.html:89:94: Warning: inserting implicit <span>
GeneratedTransformation.html:89:6: Warning: trimming empty <span>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  ecocrop.cpp:95:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Recocrop.Rcheck/00install.out' for details.
'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':
  Cannot extract version info from the following section titles:
    GitHub Commits and Releases
Found the following HTML validation problems:
redcap_read_oneshot.html:205:1: Warning: nested emphasis <em>
Found the following files/directories:
  'Filled.RData' 'cleaned.RData' 'days' 'gridded'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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
checkRd: (-1) rcpp_grad_ram.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) rcpp_grad_ram.Rd:48: Escaped LaTeX specials: \&
'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':
  Cannot extract version info from the following section titles:
    DEPRECATED AND DEFUNCT
Found the following HTML validation problems:
copulaCorrection.html:85:1: Warning: inserting implicit <p>
copulaCorrection.html:96:1: Warning: inserting implicit <p>
copulaCorrection.html:85:1: Warning: trimming empty <p>
copulaCorrection.html:96:1: Warning: trimming empty <p>
hetErrorsIV.html:66:1: Warning: inserting implicit <p>
hetErrorsIV.html:66:1: Warning: trimming empty <p>
higherMomentsIV.html:62:1: Warning: inserting implicit <p>
higherMomentsIV.html:62:1: Warning: trimming empty <p>
latentIV.html:75:1: Warning: inserting implicit <p>
latentIV.html:92:1: Warning: inserting implicit <p>
latentIV.html:75:1: Warning: trimming empty <p>
latentIV.html:92:1: Warning: trimming empty <p>
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
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 HTML validation problems:
replaceVals.html:84:31: Warning: <em> is probably intended as </em>
replaceVals.html:84:69: Warning: discarding unexpected </em>
replaceVals.html:84:93: Warning: discarding unexpected </em>
'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:
Dbf4myc.html:68:20: Warning: <a> illegal characters found in URI
Dbf4myc.html:69:12: Warning: <a> illegal characters found in URI
MFAseq.html:68:38: Warning: <a> illegal characters found in URI
MFAseq.html:69:29: Warning: <a> illegal characters found in URI
W303.html:66:20: Warning: <a> illegal characters found in URI
W303.html:67:12: Warning: <a> illegal characters found in URI
W303_G2.html:58:4: Warning: <a> illegal characters found in URI
W303_S.html:58:4: Warning: <a> illegal characters found in URI
W303norm.html:68:20: Warning: <a> illegal characters found in URI
W303norm.html:69:12: Warning: <a> illegal characters found in URI
sortSeq.html:77:28: Warning: <a> illegal characters found in URI
sortSeq.html:78:20: Warning: <a> illegal characters found in URI
sortSeq.html:79:16: Warning: <a> illegal characters found in URI
sortSeq.html:80:17: Warning: <a> illegal characters found in URI
Found the following files/directories:
  'PackageCites.bib'
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
.find_regression_estimate: no visible global function definition for
  'data_findcols'
report_table.MixMod: no visible global function definition for
  'data_findcols'
report_table.anova: no visible global function definition for
  'data_findcols'
report_table.aov: no visible global function definition for
  'data_findcols'
report_table.aovlist: no visible global function definition for
  'data_findcols'
report_table.brmsfit: no visible global function definition for
  'data_findcols'
report_table.glm: no visible global function definition for
  'data_findcols'
report_table.glmmTMB: no visible global function definition for
  'data_findcols'
report_table.ivreg: no visible global function definition for
  'data_findcols'
report_table.lavaan: no visible global function definition for
  'data_findcols'
report_table.lm: no visible global function definition for
  'data_findcols'
report_table.lme: no visible global function definition for
  'data_findcols'
report_table.merMod: no visible global function definition for
  'data_findcols'
report_table.stanreg: no visible global function definition for
  'data_findcols'
report_table.survreg: no visible global function definition for
  'data_findcols'
report_table.zeroinfl: no visible global function definition for
  'data_findcols'
Undefined global functions or variables:
  data_findcols
Running examples in 'report-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: report.default
> ### Title: Template to add report support for new objects
> ### Aliases: report.default report_effectsize.default report_table.default
> ###   report_statistics.default report_parameters.default
> ###   report_intercept.default report_model.default report_random.default
> ###   report_priors.default report_performance.default report_info.default
> ###   report_text.default
> 
> ### ** Examples
> 
> library(report)
> 
> # Add a reproducible example instead of the following
> model <- lm(Sepal.Length ~ Petal.Length * Species, data = iris)
> r <- report(model)
Error in data_findcols(table, candidates) : 
  could not find function "data_findcols"
Calls: report ... report_statistics -> report_statistics.lm -> .find_regression_estimate
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'cite_packages.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 'cite_packages.Rmd'

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

--- re-building 'report.Rmd' using rmarkdown
Warning: Following variable(s) were not found: n_Obs
Warning: Following variable(s) were not found: n_Obs
Warning: Following variable(s) were not found: n_Obs
Warning in .effectsize_t.test(model, type = type, verbose = verbose, ...) :
  Unable to retrieve data from htest object. Using t_to_d() approximation.
Quitting from lines 105-108 (report.Rmd) 
Error: processing vignette 'report.Rmd' failed with diagnostics:
could not find function "data_findcols"
--- failed re-building 'report.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [20m/24m]
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
Found the following significant warnings:
  within_category_compare.cpp:52:21: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/representr.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
reprex-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
reprex-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) KitchenhamEtAl.CorrelationsAmongParticipants.Madeyski10.Rd:7: Escaped LaTeX specials: \&
checkRd: (-1) KitchenhamEtAl.CorrelationsAmongParticipants.Madeyski10.Rd:56: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'gdalUtils'
'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:
    reqres (development version)
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
reqres-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
reqres-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Found the following HTML validation problems:
resemble-package.html:26:4: Warning: <img> attribute "align" not allowed for HTML5
resemble-package.html:26:4: Warning: <img> attribute "align" not allowed for HTML5
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.
Found the following HTML validation problems:
RestRserve-package.html:91:34: Warning: inserting implicit <p>
RestRserve-package.html:105:62: Warning: inserting implicit <p>
RestRserve-package.html:137:71: Warning: inserting implicit <p>
RestRserve-package.html:157:74: Warning: inserting implicit <p>
RestRserve-package.html:196:79: Warning: inserting implicit <p>
RestRserve-package.html:205:65: Warning: inserting implicit <p>
RestRserve-package.html:118:1: Warning: <img> lacks "alt" attribute
RestRserve-package.html:91:34: Warning: trimming empty <p>
RestRserve-package.html:105:62: Warning: trimming empty <p>
RestRserve-package.html:137:71: Warning: trimming empty <p>
RestRserve-package.html:157:74: Warning: trimming empty <p>
RestRserve-package.html:196:79: Warning: trimming empty <p>
RestRserve-package.html:205:65: Warning: trimming empty <p>
RestRserve-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
RestRserve-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Problems with news in 'NEWS.md':
No news entries found.
Found the following HTML validation problems:
py_iterator.html:56:154: Warning: inserting implicit <p>
py_iterator.html:65:87: Warning: inserting implicit <p>
py_iterator.html:82:35: Warning: inserting implicit <p>
py_iterator.html:56:154: Warning: trimming empty <p>
py_iterator.html:65:87: Warning: trimming empty <p>
py_iterator.html:82:35: Warning: trimming empty <p>
Packages suggested but not available for checking:
  'gWidgets2RGtk2', 'cairoDevice', 'RGtk2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'evdbayes'
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
Found the following HTML validation problems:
read_facts.html:70:56: Warning: inserting implicit <p>
read_facts.html:79:63: Warning: inserting implicit <p>
read_facts.html:70:56: Warning: trimming empty <p>
read_facts.html:79:63: Warning: trimming empty <p>
write_facts.html:90:56: Warning: inserting implicit <p>
write_facts.html:100:62: Warning: inserting implicit <p>
write_facts.html:90:56: Warning: trimming empty <p>
write_facts.html:100:62: Warning: trimming empty <p>
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
Found the following HTML validation problems:
RfEmpImp-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
RfEmpImp-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
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
checkRd: (-1) Rglpk_read_file.Rd:6: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
rgoogleads-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rgoogleads-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Found the following HTML validation problems:
rgraph6-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rgraph6-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
rgugik-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rgugik-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
build_js.html:51:53: Warning: inserting implicit <p>
build_js.html:54:76: Warning: inserting implicit <p>
build_js.html:57:78: Warning: inserting implicit <p>
build_js.html:60:85: Warning: inserting implicit <p>
build_js.html:51:53: Warning: trimming empty <p>
build_js.html:54:76: Warning: trimming empty <p>
build_js.html:57:78: Warning: trimming empty <p>
build_js.html:60:85: Warning: trimming empty <p>
lint_js.html:54:106: Warning: inserting implicit <p>
lint_js.html:54:106: Warning: trimming empty <p>
'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
Found the following HTML validation problems:
rhub-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rhub-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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'
'LazyData' is specified without a 'data' directory
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 HTML validation problems:
ringostat-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ringostat-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    References
Found the following files/directories:
  'B110711CD4.CSV' 'inputparam2.txt' 'itcout0.pdf' 'itcout1.eps'
  'origin_data.csv'
Installation failed.
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RItools.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
FitCbmRoc.Rd:49: Undefined control sequence: \eqn in N(\eqn{mu},1)
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
Error(s) in re-building vignettes:
  ...
--- re-building 'rkafka.Rnw' using Sweave
Error: processing vignette 'rkafka.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'rkafka.tex' failed.
LaTeX errors:
! Argument of Â has an extra }.
<inserted text> 
                \par 
l.23  pdfsubject={rkafka package}}
                                  
! Emergency stop.
<inserted text> 
                \par 
l.23  pdfsubject={rkafka package}}
                                  
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'rkafka.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
RKorAPClient-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
RKorAPClient-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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.
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
theta.html:19:1: Warning: missing </h2> before <p>
theta.html:22:1: Warning: discarding unexpected </h2>
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
Found the following HTML validation problems:
1._The_MATLAB_server_running_in_MATLAB.html:482:8: Warning: trimming empty <p>
1._The_MATLAB_server_running_in_MATLAB.html:563:8: Warning: trimming empty <p>
R.matlab-package.html:103:1: Warning: trimming empty <p>
GNU make is a SystemRequirements.
Found the following HTML validation problems:
rmHDI.html:230:38: Warning: nested emphasis <code>
rmHDI.html:234:38: Warning: nested emphasis <code>
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
Found the following HTML validation problems:
ci.html:142:38: Warning: nested emphasis <code>
medci.html:136:38: Warning: nested emphasis <code>
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
Found the following significant warnings:
  ClusteringInputHandling.cpp:61:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ClusteringInputHandling.cpp:72:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rmixmod.Rcheck/00install.out' for details.
Found the following significant warnings:
  lib/Composer/MixtureComposer.h:247:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  optim/include/cppoptlib/solver/../linesearch/morethuente.h:175:20: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RMixtCompIO.Rcheck/00install.out' for details.
Found the following HTML validation problems:
rmoo-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rmoo-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major changes
checkRd: (-1) wr.Rd:2: Escaped LaTeX specials: \&
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: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) rNOMADS-package.Rd:28: 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 math rendering problems:
makeIC-methods.Rd:56: Undefined control sequence: \boldmath in \mathop{\mbox{\boldmath$E$}}[{\rm IC}]...
makeIC-methods.Rd:57: Undefined control sequence: \boldmath in \mathop{\mbox{\boldmath$E$}}[{\rm IC}\...
'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
checkRd: (-1) hybrid.filter.Rd:159: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) aircraft.Rd:8: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'heavy', 'robustvarComp'
Unknown packages 'heavy', 'robustvarComp' in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
cellCycleKO.html:19:1: Warning: missing </h2> before <ol>
cellCycleKO.html:36:1: Warning: discarding unexpected </h2>
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
'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
'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
Found the following HTML validation problems:
routr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
routr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'geoR', 'RandomFields'
'LazyData' is specified without a 'data' directory
checkRd: (-1) post.rpart.Rd:45: Escaped LaTeX specials: \# \#
checkRd: (-1) post.rpart.Rd:46: Escaped LaTeX specials: \#
checkRd: (-1) text.rpart.Rd:52: Escaped LaTeX specials: \# \#
checkRd: (-1) text.rpart.Rd:53: Escaped LaTeX specials: \#
Found the following files/directories:
  'Rpdb.pdb'
'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:
    IMPROVEMENTS AND ### BUG FIXES
'LazyData' is specified without a 'data' directory
checkRd: (-1) ractive.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) ractive.test.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) random.active.test.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) random.benchmark.Rd:49: Escaped LaTeX specials: \&
Found the following math rendering problems:
random.benchmark.Rd:35-37: Invalid size: '-' in ... \right.
   \kern-\nulldelimiters...
random.bounded.Rd:21-23: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
    {{x_...
random.bounded.test.Rd:21-23: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
    {{x_...
'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
Found the following files/directories:
  'HL_H0.pdf' 'pi0infer.pdf' 'rate.txt' 'summary.txt'
Found the following math rendering problems:
PcaHubert.Rd:93: Undefined control sequence: \l in l_1, \dots, \l_k
Found the following HTML validation problems:
rrd-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rrd-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Found the following HTML validation problems:
rRofex-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rRofex-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
rSAFE-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rSAFE-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Package suggested but not available for checking: 'gdalUtils'
'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:
  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]
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
checkRd: (-1) DOsgram.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) MTM.drive.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) MTMdisp.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) MTMgabor.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) doGABOR.AR.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) doGABOR.MTM.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) evolMTM.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) get.slepians.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) mtapspec.Rd:45: Escaped LaTeX specials: \&
checkRd: (-1) plt.MTM0.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) save.wpix.Rd:15: Escaped LaTeX specials: \$
Package suggested but not available for checking: 'Rcompression'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Rserv.c:2560:16: warning: 'd2i_RSAPrivateKey' is deprecated [-Wdeprecated-declarations]
  Rserv.c:2572:16: warning: 'RSA_new' is deprecated [-Wdeprecated-declarations]
  Rserv.c:2580:13: warning: 'RSA_free' is deprecated [-Wdeprecated-declarations]
  Rserv.c:2585:7: warning: 'RSA_generate_key_ex' is deprecated [-Wdeprecated-declarations]
  Rserv.c:2587:4: warning: 'RSA_free' is deprecated [-Wdeprecated-declarations]
  Rserv.c:2619:7: warning: 'i2d_RSAPublicKey' is deprecated [-Wdeprecated-declarations]
  Rserv.c:2627:21: warning: 'RSA_size' is deprecated [-Wdeprecated-declarations]
  Rserv.c:2630:11: warning: 'RSA_private_decrypt' is deprecated [-Wdeprecated-declarations]
  ./Rserv.c:2560:16: warning: 'd2i_RSAPrivateKey' is deprecated [-Wdeprecated-declarations]
  ./Rserv.c:2572:16: warning: 'RSA_new' is deprecated [-Wdeprecated-declarations]
  ./Rserv.c:2580:13: warning: 'RSA_free' is deprecated [-Wdeprecated-declarations]
  ./Rserv.c:2585:7: warning: 'RSA_generate_key_ex' is deprecated [-Wdeprecated-declarations]
  ./Rserv.c:2587:4: warning: 'RSA_free' is deprecated [-Wdeprecated-declarations]
  ./Rserv.c:2619:7: warning: 'i2d_RSAPublicKey' is deprecated [-Wdeprecated-declarations]
  ./Rserv.c:2627:21: warning: 'RSA_size' is deprecated [-Wdeprecated-declarations]
  ./Rserv.c:2630:11: warning: 'RSA_private_decrypt' is deprecated [-Wdeprecated-declarations]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rserve.Rcheck/00install.out' for details.
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
Found the following significant warnings:
  model/ml/MLSimulation.cpp:1073:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  model/ml/MLSimulation.cpp:1588:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  model/variables/DependentVariable.cpp:1780:13: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  model/effects/EffectFactory.cpp:1414:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  model/effects/DiffusionRateEffect.cpp:57:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  model/effects/DiffusionRateEffect.cpp:126:13: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  model/StatisticCalculator.cpp:1665:13: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  model/effects/SettingSizeEffect.cpp:48:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RSiena.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: 'Vdgraph'
Unknown package 'Vdgraph' in Rd xrefs
'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:
LinearFlow.html:79:6: Warning: missing </span> before <p>
LinearFlow.html:79:113: Warning: inserting implicit <span>
LinearFlow.html:79:6: Warning: trimming empty <span>
PureSVD.html:60:6: Warning: missing </span> before <p>
PureSVD.html:60:113: Warning: inserting implicit <span>
PureSVD.html:60:6: Warning: trimming empty <span>
WRMF.html:62:6: Warning: missing </span> before <p>
WRMF.html:62:113: Warning: inserting implicit <span>
WRMF.html:62:6: Warning: trimming empty <span>
'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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Known limitations / tasks for future development
Found the following HTML validation problems:
rsprite2-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rsprite2-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
hmatr.Rd:56-60: Got group of unknown type: 'internal'
'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 HTML validation problems:
build-tools.html:57:53: Warning: inserting implicit <p>
build-tools.html:57:53: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
rTCRBCRr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rTCRBCRr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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'
Found the following HTML validation problems:
rtgstat-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rtgstat-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
GNU make is a SystemRequirements.
Found the following HTML validation problems:
rticles-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rticles-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
rticulate-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rticulate-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
'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'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) sp500ret.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) spyreal.Rd:6: 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:
    rUM (development version)
'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: \$
Found the following significant warnings:
  lag_run.cpp:31:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  lag_run.cpp:42:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  lag_run.cpp:53:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  lag_run.cpp:64:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./vector_funs.h:167:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./vector_funs.h:178:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./vector_funs.h:193:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./vector_funs.h:206:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./vector_funs.h:351:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./vector_funs.h:364:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./vector_funs.h:382:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./vector_funs.h:397:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/runner.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 which this enhances but not available for checking: 'glmmADMB'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
rversions-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rversions-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
rvest-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rvest-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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.
Found the following notes/warnings:
  Non-staged installation was used
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RVowpalWabbit.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) DOG.Rd:32: Escaped LaTeX specials: \_ \_
checkRd: (-1) DOG.Rd:33: Escaped LaTeX specials: \_
checkRd: (-1) DOG.Rd:48: Escaped LaTeX specials: \_ \_
checkRd: (-1) DOG.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) cgt.Rd:36: Escaped LaTeX specials: \_ \_
checkRd: (-1) cwt.Rd:29: Escaped LaTeX specials: \_ \_
checkRd: (-1) cwt.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) cwt.Rd:43: Escaped LaTeX specials: \_ \_
checkRd: (-1) cwt.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) cwtimage.Rd:25: Escaped LaTeX specials: \_ \_
checkRd: (-1) cwtimage.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) cwtpolar.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
checkRd: (-1) mapBubbles.Rd:62: Escaped LaTeX specials: \$
Malformed Title field: should not end in a period.
Package suggested but not available for checking: 'cranly'
'LazyData' is specified without a 'data' directory
checkRd: (-1) Analyze.Rd:344: Escaped LaTeX specials: \&
checkRd: (-1) Analyze.Rd:337: Escaped LaTeX specials: \&
checkRd: (-1) AnalyzeWithExitPoll.Rd:285: Escaped LaTeX specials: \&
checkRd: (-1) AnalyzeWithExitPoll.Rd:278: Escaped LaTeX specials: \&
checkRd: (-1) RxCEcolInf-package.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) RxCEcolInf-package.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) Tune.Rd:206: Escaped LaTeX specials: \&
checkRd: (-1) Tune.Rd:203: Escaped LaTeX specials: \&
checkRd: (-1) TuneWithExitPoll.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) TuneWithExitPoll.Rd:220: Escaped LaTeX specials: \&
checkRd: (-1) gendata.ep.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) gendata.ep.Rd:289: Escaped LaTeX specials: \&
checkRd: (-1) gendata.ep.Rd:286: Escaped LaTeX specials: \&
checkRd: (-1) add.dosing.Rd:147: Escaped LaTeX specials: \&
checkRd: (-1) add.sampling.Rd:113: Escaped LaTeX specials: \&
checkRd: (-1) et.Rd:243: Escaped LaTeX specials: \&
checkRd: (-1) etRbind.Rd:146: Escaped LaTeX specials: \&
checkRd: (-1) etRep.Rd:164: Escaped LaTeX specials: \&
checkRd: (-1) etSeq.Rd:143: Escaped LaTeX specials: \&
checkRd: (-1) add.dosing.Rd:147: Escaped LaTeX specials: \&
checkRd: (-1) add.sampling.Rd:113: Escaped LaTeX specials: \&
checkRd: (-1) et.Rd:243: Escaped LaTeX specials: \&
checkRd: (-1) etRbind.Rd:146: Escaped LaTeX specials: \&
checkRd: (-1) etRep.Rd:164: Escaped LaTeX specials: \&
checkRd: (-1) etSeq.Rd:143: 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) 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: \$
Found the following HTML validation problems:
S3FileResourceGetter.html:75:6: Warning: missing </span> before <p>
S3FileResourceGetter.html:75:111: Warning: inserting implicit <span>
S3FileResourceGetter.html:78:6: Warning: missing </span> before <p>
S3FileResourceGetter.html:78:111: Warning: inserting implicit <span>
S3FileResourceGetter.html:75:6: Warning: trimming empty <span>
S3FileResourceGetter.html:78:6: Warning: trimming empty <span>
Found the following HTML validation problems:
sabre-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
sabre-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
Running 'testthat.R' [7s/175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(safedata)
  SAFE package reminder: Please set SAFE data directory using set_safe_dir()
  > 
  > test_check("safedata")
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 46 ]
  
  == Skipped tests ===============================================================
  * On CRAN (3)
  
  == Failed tests ================================================================
  -- Failure (test-load_safe.R:65:5): Download dataset fails gracefully on Zenodo down --
  `download_safe_files(1198475, confirm = FALSE)` produced unexpected messages.
  Expected match: Failed to download data:
  Actual values:
  * 1 files requested from 1 records
   - 0 local (0 bytes)
   - 0 embargoed or restricted (0 bytes)
   - 1 to download (34.4 Kb)
  
  * Downloading 1 record metadata files
  
  
  * Failed to download metadata: 1198475
  
  * URL timed out
  
  * Could not download metadata, aborting download: 
  
  * 
  
  -- Failure (test-load_safe.R:71:5): Download dataset fails gracefully on Zenodo down --
  `success` has length 1, not length 0.
  
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 46 ]
  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 HTML validation problems:
sageR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
sageR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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) nvcovOfAcf.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) whiteNoiseTest.Rd:33: Escaped LaTeX specials: \&
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
Found the following files/directories:
  'stateLung-R01.pdf' 'stateLung-R01.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
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.
Found the following HTML validation problems:
scales-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
scales-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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 HTML validation problems:
heatFilter.html:19:1: Warning: missing </h2> before <p>
heatFilter.html:21:1: Warning: discarding unexpected </h2>
'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
Found the following HTML validation problems:
scico-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
scico-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Found the following math rendering problems:
bias_quantile.Rd:39: Can't use function '$' in math mode in ..., 0} = - \infty$ and $q_{t,1} =...
'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.
'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'
Found the following significant warnings:
  utils.cpp:364:35: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/sctransform.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/sdcMicro.Rcheck/00install.out' for details.
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.
Found the following HTML validation problems:
SDMtune-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
SDMtune-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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) detectfn.Rd:183: Escaped LaTeX specials: \&
checkRd: (-1) sim.popn.Rd:25: Escaped LaTeX specials: \^
checkRd: (-1) utility.Rd:47: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Found the following math rendering problems:
RSE.Rd:30: Undefined control sequence: \var in ... = \sqrt {\exp(\var (\beta))-1}
Rsurface.Rd:85-86: Can't use function '\bold' in text mode in d = |\mbox{\bold{x}} - \mbox{\b...
Rsurface.Rd:92: Can't use function '\bold' in text mode in z(\mbox{\bold{x}})
Rsurface.Rd:94-95: Can't use function '\bold' in text mode in R(\mbox{\bold{s}}) = \sum_x ...
Rsurface.Rd:100-101: Can't use function '\bold' in text mode in R'(\mbox{\bold{s}}) = R(\mbox...
Rsurface.Rd:102: Can't use function '\bold' in text mode in R'(\mbox{\bold{s}})
Rsurface.Rd:104-105: Can't use function '\bold' in text mode in 1 /
    R'(\mbox{\bold{s}})
Rsurface.Rd:106: Can't use function '\bold' in text mode in 1 / R(\mbox{\bold{s}})
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Missing or unexported object: 'datawizard::data_rescale'
Running examples in 'see-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coord_radar
> ### Title: Radar coordinate system
> ### Aliases: coord_radar
> 
> ### ** Examples
> 
> # Create a radar/spider chart with ggplot:
> if (require("poorman") && require("ggplot2")) {
+   data <- iris[-5] %>%
+     aggregate(list(Species = iris$Species), mean) %>%
+     datawizard::reshape_longer(2:5)
+ 
+   data %>%
+     ggplot(aes(x = Name, y = Value, color = Species, group = Species)) +
+     geom_polygon(fill = NA, size = 2) +
+     coord_radar(start = -pi / 4)
+ }
Loading required package: poorman

  I'd seen my father. He was a poor man, and I watched him do astonishing things.
    - Sidney Poitier

Attaching package: 'poorman'

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

    filter, lag

Loading required package: ggplot2
Error in FUN(X[[i]], ...) : object 'Name' not found
Calls: <Anonymous> ... <Anonymous> -> f -> scales_add_defaults -> lapply -> FUN
Execution halted
'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
Found the following math rendering problems:
multistagegain.each.Rd:29: Can't use function '$' in math mode in ...ta G_2(y), ...)$ where $\Delta ...
'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 'semPlot-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: modelMatrices
> ### Title: Extract SEM model matrices
> ### Aliases: modelMatrices
> 
> ### ** Examples
> 
> ## Mplus user guide SEM example:
> outfile <- tempfile(fileext=".out")
> tryres <- try({
+   download.file("http://www.statmodel.com/usersguide/chap5/ex5.11.out",outfile)
+ })
trying URL 'http://www.statmodel.com/usersguide/chap5/ex5.11.out'
> 
> if (!is(tryres,"try-error")){
+   # Plot model:
+   semPaths(outfile, intercepts = FALSE)
+ 
+   # Extract RAM:
+   RAM <- modelMatrices(outfile, "ram")
+   semPaths(do.call(ramModel, RAM), as.expression = "edges", intercepts = FALSE)
+ 
+   # Extract LISREL:
+   LISREL <- modelMatrices(outfile, "lisrel")
+   semPaths(do.call(lisrelModel, LISREL), as.expression = "edges", intercepts = FALSE)
+ }
Loading required namespace: MplusAutomation
Warning in extractInput_1file(rawtext, curfile) :
  Could not find beginning of input for: /tmp/Rtmp2lSv2h/file141d3f3a255a3a.out
Warning in extractWarningsErrors_1file(outfiletext, curfile, input = inp) :
  Could not identify bounds of input section: /tmp/Rtmp2lSv2h/file141d3f3a255a3a.out
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: li line 131 and ul
Opening and ending tag mismatch: li line 130 and body
Opening and ending tag mismatch: li line 129 and html
Premature end of data in tag li line 128
Warning in semPlotModel_Amos(object) :
  (Residual) variances of Amos model is not yet supported
Error in semPlotModel.default("/tmp/Rtmp2lSv2h/file141d3f3a255a3a.out",  : 
  Object not recognized as SEM model
Calls: semPaths -> do.call -> <Anonymous> -> semPlotModel.default
Execution halted
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
Found the following HTML validation problems:
sendgridr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
sendgridr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) morris.Rd:220: Escaped LaTeX specials: \&
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: \_ \_
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
Found the following HTML validation problems:
st_as_edges.html:59:261: Warning: inserting implicit <p>
st_as_edges.html:59:261: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
sfnetworks-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
sfnetworks-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'foreign' which was already attached by Depends.
  Please remove these calls from your code.
checkRd: (-1) shapefiles.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) shapefiles.Rd:96: 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
Found the following HTML validation problems:
shapviz-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
shapviz-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Package suggested but not available for checking: 'hydromad'
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
get_arg_help.html:43:1: Warning: trimming empty <dt>
get_desc_help.html:43:1: Warning: trimming empty <dt>
get_usage_help.html:43:1: Warning: trimming empty <dt>
'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
Found the following HTML validation problems:
shinyFiles-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
shinyFiles-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'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'
*** caught segfault ***
address 0x18, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Found the following HTML validation problems:
AppDriver.html:71:42: Warning: inserting implicit <p>
AppDriver.html:120:67: Warning: inserting implicit <p>
AppDriver.html:71:42: Warning: trimming empty <p>
AppDriver.html:120:67: Warning: trimming empty <p>
test_app.html:67:44: Warning: inserting implicit <p>
test_app.html:106:50: Warning: inserting implicit <p>
test_app.html:67:44: Warning: trimming empty <p>
test_app.html:106:50: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  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.
Found the following significant warnings:
  TG_sampling_functions.cpp:50:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  cpp_utilities.cpp:33:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  do_rgig1.cpp:149:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  shrinkTVP.cpp:146:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  shrinkTVP.cpp:151:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  shrinkTVP.cpp:156:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  shrinkTVP.cpp:161:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  shrinkTVP.cpp:620:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  shrinkTVP.cpp:624:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  shrinkTVP.cpp:628:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  shrinkTVP.cpp:632:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/shrinkTVP.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
Found the following files/directories:
  'MM.csv' 'Simul.csv' 'catalytic.csv'
Found the following significant warnings:
  optimBlocks.cpp:12:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  optimBlocks.cpp:15:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  optimBlocks.cpp:30:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  optimBlocks.cpp:33:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  optimBlocks.cpp:36:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  optimBlocks.cpp:39:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  optimBlocks.cpp:48:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  optimBlocks.cpp:51:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  optimBlocks.cpp:54:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  optimBlocks.cpp:57:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  optimBlocksGen.cpp:12:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  optimBlocksGen.cpp:20:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  triadCensus.cpp:53:26: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/signnet.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 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
Found the following significant warnings:
  genotype.cpp:475:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  genotype.cpp:672:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  pedigree.cpp:193:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/simer.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
range_delta.Rd:26: Undefined control sequence: \link in ...function \code{\link{mut.E.indirect...
'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 HTML validation problems:
simlandr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
simlandr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
Found the following HTML validation problems:
simts-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
simts-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Invalid NAMESPACE file, parsing gives:
Error in parseNamespaceFile(basename(pkgdir), dirname(pkgdir)): unable to re-encode some lines in NAMESPACE file

See section 'Package namespaces' 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: \&
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
Found the following HTML validation problems:
print.spscan.html:49:1: Warning: trimming empty <dt>
summary.spscan.html:48:1: Warning: trimming empty <dt>
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
Found the following HTML validation problems:
summary.smerc_cluster.html:48:1: Warning: trimming empty <dt>
'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:
cv.smog.html:165:1: Warning: trimming empty <h4>
smog.default.html:178:1: Warning: trimming empty <h4>
Package suggested but not available for checking: 'rPython'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
shr.Rd:13: Undefined control sequence: \texttildelow in \texttildelow
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) selm.fit.Rd:212: Escaped LaTeX specials: \&
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
'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
Found the following significant warnings:
  sorcering.cpp:247:29: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  sorcering.cpp:251:34: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  sorcering.cpp:255:34: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/sorcering.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
sortable.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
sortable.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SciencesPo'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'r2cytoscape'
'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 HTML validation problems:
SpaDES.core-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
SpaDES.core-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
SpaDES-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
SpaDES-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Packages suggested but not available for checking:
  'ffbase', 'gdalUtils', 'RandomFields'
Found the following HTML validation problems:
SpaDES.tools-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
SpaDES.tools-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Package suggested but not available for checking: 'earlywarnings'
Unknown package 'earlywarnings' in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
varpro_3_para_opts.html:19:1: Warning: missing </h2> before <ul>
varpro_3_para_opts.html:31:1: Warning: discarding unexpected </h2>
'LazyData' is specified without 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:
    Data
Found the following HTML validation problems:
stream_lag.html:45:1: Error: <destination> is not recognized!
stream_lag.html:45:1: Warning: discarding unexpected <destination>
stream_lag.html:45:42: Error: <offset> is not recognized!
stream_lag.html:45:42: Warning: discarding unexpected <offset>
stream_lag.html:45:24: Warning: <source> proprietary attribute "column"
'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
'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: \$
Packages suggested but not available for checking: 'INLA', 'geoR', 'SDraw'
Package suggested but not available for checking: 'INLA'
checkRd: (-1) sarorderedprobit.Rd:84: Escaped LaTeX specials: \#
Found the following HTML validation problems:
plant_richness_df.html:93:76: Warning: <a> illegal characters found in URI
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RandomFields'
Unknown package 'RandomFields' in Rd xrefs
checkRd: (-1) ants.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) ants.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) ants.Rd:36: Escaped LaTeX specials: \& \&
checkRd: (-1) ants.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) ants.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) ants.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) ants.Rd:124: Escaped LaTeX specials: \&
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.
Package suggested but not available for checking: 'RandomFields'
Unknown package 'RandomFields' in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
spcosa-package.Rd:12: Can't use function '$' in math mode in $k$
spcosa-package.Rd:15: Can't use function '$' in math mode in $k$
spcosa-package.Rd:39: Can't use function '$' in math mode in $k$
stratify-methods.Rd:13: Can't use function '$' in math mode in $k$
stratify-methods.Rd:60: Can't use function '$' in math mode in $k$
checkRd: (-1) euklid.ewma.arl.Rd:23: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'spDataLarge'
checkRd: (-1) columbus.Rd:21: Escaped LaTeX specials: \$
checkRd: (-1) columbus.Rd:22: Escaped LaTeX specials: \$
Found the following HTML validation problems:
boston.html:111:310: Warning: <a> illegal characters found in URI
Found the following HTML validation problems:
speakr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
speakr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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'
Found the following HTML validation problems:
sperrorest.html:259:71: Warning: inserting implicit <p>
sperrorest.html:259:71: Warning: trimming empty <p>
Found the following HTML validation problems:
glmFilter.html:166:27: Warning: <em> is probably intended as </em>
glmFilter.html:166:99: Warning: discarding unexpected </em>
glmFilter.html:166:104: Warning: discarding unexpected </em>
lmFilter.html:154:27: Warning: <em> is probably intended as </em>
lmFilter.html:154:99: Warning: discarding unexpected </em>
lmFilter.html:154:104: Warning: discarding unexpected </em>
'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:
  '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
checkRd: (-1) mSpline.Rd:164: 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:
    Feature 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
Found the following HTML validation problems:
spots-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
spots-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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.
Found the following HTML validation problems:
onNextInput.html:65:51: Warning: inserting implicit <p>
onNextInput.html:65:51: Warning: trimming empty <p>
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
Found the following math rendering problems:
spain.covid.Rd:69-81: No such environment: tabular in ...ac{ 
      \begin{tabular}{c}
        \text...
spain.covid.Rd:99-108: No such environment: tabular in ...{ 
        \begin{tabular}{c}
           \t...
'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) B_sraAutoreg.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) C_sraMechanistic.Rd:68: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  SRM_RCPP_SRM_ARBSRM.cpp:83:18: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  SRM_RCPP_SRM_ARBSRM.cpp:90:18: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  SRM_RCPP_SRM_ARBSRM.cpp:189:17: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  SRM_RCPP_SRM_ARBSRM.cpp:190:21: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  SRM_RCPP_SRM_ARBSRM.cpp:230:17: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  SRM_RCPP_SRM_ARBSRM.cpp:231:21: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  SRM_RCPP_SRM_ARBSRM.cpp:235:21: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  SRM_RCPP_SRM_ARBSRM.cpp:238:21: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/srm.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
Rowsums_cpp.Rd:21: Undefined control sequence: \time in P \in R^{2m \time n}
'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.
Found the following HTML validation problems:
sspm-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
sspm-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'scanstatistics'
Found the following HTML validation problems:
sss-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
sss-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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: \&
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
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'
Found the following HTML validation problems:
create_symlink.html:55:1: Warning: trimming empty <dt>
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'
Found the following math rendering problems:
gxeVarCov.Rd:64: Can't use function '$' in math mode in ...+ \sigma_{GE}^2$ | $\sigma_{GE}...
Package suggested but not available for checking: 'asreml'
Found the following significant warnings:
  calcIBD.cpp:116:18: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/statgenIBD.Rcheck/00install.out' for details.
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 math rendering problems:
remlscor.Rd:33: Undefined control sequence: \var in s_i=\var(y_i)
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Enhancements to existing utilities
    Miscellaneous changes
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: \&
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.
Found the following significant warnings:
  rcpp_cov_est1d.cpp:45:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  rcpp_cov_est1d.cpp:50:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/stfit.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:
  'corrviz.html'
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial TODO
Running 'testthat.R' [3s/7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(stockfish)
  > 
  > test_check("stockfish")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 17 ]
  
  == Failed tests ================================================================
  -- Failure (test-fish.R:30:3): engine works ------------------------------------
  engine$ucinewgame() (`actual`) not equal to "readyok" (`expected`).
  
  `actual` is NULL
  `expected` is a character vector ('readyok')
  -- Failure (test-fish.R:31:3): engine works ------------------------------------
  engine$setoption("Clear Hash") is not NULL
  
  `actual` is a character vector ('readyok')
  `expected` is NULL
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 17 ]
  Error: Test failures
  Execution halted
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.
Running examples in 'stppSim-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: artif_spo
> ### Title: Artificial spatial origins
> ### Aliases: artif_spo
> 
> ### ** Examples
> 
> #load boundary of Camden
> load(file = system.file("extdata", "camden.rda",
+ package="stppSim"))
> boundary = camden$boundary # get boundary
> landuse <- camden$landuse
> spo <- artif_spo(poly = boundary, n_origin = 50,
+ restriction_feat = landuse, n_foci=5, foci_separation = 0,
+ mfocal = NULL, conc_type = "dispersed", p_ratio=20)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'obj' in selecting a method for function 'bbox': assignment of an object of class "character" is not valid for slot 'proj4string' in an object of class "Spatial"; is(value, "CRS") is not TRUE
Calls: artif_spo ... bbox -> as -> asMethod -> slot<- -> checkSlotAssignment
Execution halted
'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
Found the following HTML validation problems:
stringr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
stringr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'STRaitRazoR'
Found the following HTML validation problems:
RSTRmodel.html:218:1: Warning: trimming empty <p>
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: \&
Installation failed.
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/StrucDiv.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) is_shebang.Rd:14: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) anneal.Rd:261: Escaped LaTeX specials: \&
checkRd: (-1) genetic.Rd:254: Escaped LaTeX specials: \&
checkRd: (-1) improve.Rd:231: Escaped LaTeX specials: \&
Found the following math rendering problems:
anneal.Rd:22: Can't use function '$' in math mode in $\exp^{\frac{ac-...
glmHmat.Rd:33: Can't use function '$' in math mode in $W_{excv} = W_{a...
wald.Rd:29: Can't use function '$' in math mode in $W_{excv} = W_{a...
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
sugarbag-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
sugarbag-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'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'
Found the following HTML validation problems:
RandomSearchCV.html:75:6: Warning: missing </span> before <p>
RandomSearchCV.html:75:102: Warning: inserting implicit <span>
RandomSearchCV.html:75:6: Warning: trimming empty <span>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
SurvSurv.Rd:34: Undefined control sequence: \eqn in I(T,S)=\eqn{1}{n}G^2
'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: \&
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
computeFrac.html:77:1: Warning: <center> element removed from HTML5
computeFrac.html:82:1: Warning: <center> element removed from HTML5
computeFrac.html:86:1: Warning: <center> element removed from HTML5
Package suggested but not available for checking: 'INLA'
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
modelSim.Rd:103-105: Undefined control sequence: \label inriskAFT}
    ...
'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:
  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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) diabetes.Rd:18: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
svmplus.Rd:13: Can't use function '$' in math mode in $(x_1, y_1), ......
svmplus.Rd:20: Can't use function '$' in math mode in $(x_1,x_1^*, y_1...
svmplus.Rd:26: Can't use function '$' in math mode in $\xi_i = (w^*)^T...
svmplus.Rd:32-33: Can't use function '$' in math mode in $ \min_{w,b} \le...
svmplus.Rd:36: Can't use function '$' in math mode in $ s. t. \quad y_...
svmplus.Rd:39: Can't use function '$' in math mode in $ (w^*)^T z_i^* ...
svmplus.Rd:45-47: Can't use function '$' in math mode in $ \max_{w,b} \le...
svmplus.Rd:50: Can't use function '$' in math mode in $s. t. \quad \su...
svmplus.Rd:53: Can't use function '$' in math mode in $ \alpha_i \geq ...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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'
Found the following math rendering problems:
sysBiolAlg_ccFBA-class.Rd:114-126: Undefined control sequence: \boldmath in ...       & \mbox{\boldmath$c$\unboldmath}...
sysBiolAlg_ccFBA-class.Rd:132-135: Undefined control sequence: \boldmath in 
        \mbox{\boldmath$c$\unboldmath}...
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
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 math rendering problems:
centroid_3d_sq_dist.Rd:16-20: Unexpected end of input in a macro argument, expected '}' at end of input: ...2 + (z-z_m)^2}
'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
'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'
Found the following HTML validation problems:
EagerExprBuilder.html:59:6: Warning: missing </span> before <p>
EagerExprBuilder.html:59:97: Warning: inserting implicit <span>
EagerExprBuilder.html:62:6: Warning: missing </span> before <p>
EagerExprBuilder.html:62:98: Warning: inserting implicit <span>
EagerExprBuilder.html:65:6: Warning: missing </span> before <p>
EagerExprBuilder.html:65:109: Warning: inserting implicit <span>
EagerExprBuilder.html:68:6: Warning: missing </span> before <p>
EagerExprBuilder.html:68:99: Warning: inserting implicit <span>
EagerExprBuilder.html:71:6: Warning: missing </span> before <p>
EagerExprBuilder.html:71:98: Warning: inserting implicit <span>
EagerExprBuilder.html:74:6: Warning: missing </span> before <p>
EagerExprBuilder.html:74:98: Warning: inserting implicit <span>
EagerExprBuilder.html:77:6: Warning: missing </span> before <p>
EagerExprBuilder.html:77:104: Warning: inserting implicit <span>
EagerExprBuilder.html:59:6: Warning: trimming empty <span>
EagerExprBuilder.html:62:6: Warning: trimming empty <span>
EagerExprBuilder.html:65:6: Warning: trimming empty <span>
EagerExprBuilder.html:68:6: Warning: trimming empty <span>
EagerExprBuilder.html:71:6: Warning: trimming empty <span>
EagerExprBuilder.html:74:6: Warning: trimming empty <span>
EagerExprBuilder.html:77:6: Warning: trimming empty <span>
'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
'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
Running 'testthat.R' [7s/7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # browseURL("https://kbroman.org/pkg_primer/pages/tests.html")
  > # browseURL(file.path("https://walczak.org/2017/06",
  > # 		"how-to-add-code-coverage-codecov-to-your-r-package/"))
  > 
  > library(testthat)
  > library(taxlist)
  > 
  > test_check("taxlist")
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 124 ]
  
  == Failed tests ================================================================
  -- Failure (test-indented_list.R:12:4): Summaries are produced -----------------
  grepl("Cyperus", result$output) not equal to TRUE.
  1 element mismatch
  -- Failure (test-merge_taxa.R:12:4): taxa are merged ---------------------------
  grepl("Cyperus", result$output) not equal to TRUE.
  1 element mismatch
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 124 ]
  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
Malformed Description field: should contain one or more complete sentences.
Running examples in 'tcsinvest-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sandboxRegister
> ### Title: Working with sandbox. Register account
> ### Aliases: sandboxRegister
> 
> ### ** Examples
> 
> token = 'your_token_from_tcs_account'
> sandboxRegister(token)
No encoding supplied: defaulting to UTF-8.
[1] ""
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("sandboxRegister", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.314 0.057 3.78 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')

 *** caught segfault ***
address 0x18, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
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
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
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following HTML validation problems:
as_tensor.html:35:1: Warning: trimming empty <li>
'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 HTML validation problems:
terrainr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
terrainr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
tesselle-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
tesselle-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
testdat-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
testdat-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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 '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'
Found the following HTML validation problems:
text2map-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
text2map-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Error(s) in re-building vignettes:
  ...
--- re-building 'text2sdg.Rmd' using rmarkdown
Quitting from lines 58-64 (text2sdg.Rmd) 
Error: processing vignette 'text2sdg.Rmd' failed with diagnostics:
input string 7001 is invalid
--- failed re-building 'text2sdg.Rmd'

SUMMARY: processing the following file failed:
  'text2sdg.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
textdata-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
textdata-package.html:23:4: 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':
No news entries found.
Found the following HTML validation problems:
read_transcript.html:174:4: Warning: <a> converting backslash in URI to slash
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
layer_dense_variational.html:27:38: Warning: inserting implicit <p>
layer_dense_variational.html:27:38: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
write_run_metadata.html:106:67: Warning: inserting implicit <p>
write_run_metadata.html:106:67: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) btgp.Rd:2: Escaped LaTeX specials: \&
checkRd: (-1) btgp.Rd:382: Escaped LaTeX specials: \&
checkRd: (-1) btgp.Rd:387: Escaped LaTeX specials: \&
checkRd: (-1) default.itemps.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) default.itemps.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) friedman.1.data.Rd:82: Escaped LaTeX specials: \&
checkRd: (-1) tgp.design.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) tgp.design.Rd:77: Escaped LaTeX specials: \&
Found the following math rendering problems:
btgp.Rd:66: Undefined control sequence: \boldmath in ...thbf{X}) \mbox{\boldmath $\beta$} + W(\m...
tgp.default.params.Rd:20: Undefined control sequence: \boldmath in ...thbf{X}) \mbox{\boldmath $\beta$} + W(\m...
tgp.default.params.Rd:51-52: Undefined control sequence: \boldmath in \mbox{\boldmath
  	 $\beta$}
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
thinkr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
thinkr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
CatalogNode.html:80:6: Warning: missing </span> before <p>
CatalogNode.html:80:93: Warning: inserting implicit <span>
CatalogNode.html:83:6: Warning: missing </span> before <p>
CatalogNode.html:83:101: Warning: inserting implicit <span>
CatalogNode.html:86:6: Warning: missing </span> before <p>
CatalogNode.html:86:90: Warning: inserting implicit <span>
CatalogNode.html:89:6: Warning: missing </span> before <p>
CatalogNode.html:89:97: Warning: inserting implicit <span>
CatalogNode.html:80:6: Warning: trimming empty <span>
CatalogNode.html:83:6: Warning: trimming empty <span>
CatalogNode.html:86:6: Warning: trimming empty <span>
CatalogNode.html:89:6: Warning: trimming empty <span>
DatasetNode.html:81:6: Warning: missing </span> before <p>
DatasetNode.html:81:93: Warning: inserting implicit <span>
DatasetNode.html:84:6: Warning: missing </span> before <p>
DatasetNode.html:84:101: Warning: inserting implicit <span>
DatasetNode.html:81:6: Warning: trimming empty <span>
DatasetNode.html:84:6: Warning: trimming empty <span>
ServiceNode.html:72:6: Warning: missing </span> before <p>
ServiceNode.html:72:93: Warning: inserting implicit <span>
ServiceNode.html:75:6: Warning: missing </span> before <p>
ServiceNode.html:75:101: Warning: inserting implicit <span>
ServiceNode.html:78:6: Warning: missing </span> before <p>
ServiceNode.html:78:90: Warning: inserting implicit <span>
ServiceNode.html:72:6: Warning: trimming empty <span>
ServiceNode.html:75:6: Warning: trimming empty <span>
ServiceNode.html:78:6: Warning: trimming empty <span>
'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.
Found the following significant warnings:
  sorted_range_search.cpp:34:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tibbletime.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
tidyBdE-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
tidyBdE-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
Found the following HTML validation problems:
tidygraph-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
tidygraph-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
tidyhydat-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
tidyhydat-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor changes:
Found the following HTML validation problems:
tidymv-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
tidymv-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
excel_if_functions.html:126:5: Warning: <em> is probably intended as </em>
excel_if_functions.html:126:60: Warning: discarding unexpected </em>
excel_if_functions.html:126:65: Warning: discarding unexpected </em>
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    tidyREDCap (development version)
Found the following HTML validation problems:
tidyr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
tidyr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
generate_control.html:87:1: Warning: trimming empty <li>
generate_control.html:86:1: Warning: trimming empty <ol>
generate_weights.html:220:1: Warning: trimming empty <li>
generate_weights.html:219:1: Warning: trimming empty <ol>
'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:
dynreg.html:141:33: Warning: trimming empty <code>
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
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'
Found the following math rendering problems:
Tinflex.setup.Rd:62-67: Unknown column alignment: @ in ...\begin{array}{l@{\quad}l}%
      ...
'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 math rendering problems:
sdreport.Rd:66-69: Undefined control sequence: \pmatrix in V \pmatrix{ \hat u - u \c...
sdreport.Rd:72: Undefined control sequence: \pmatrix in \pmatrix{\hat u(\theta)...
sdreport.Rd:80-81: Undefined control sequence: \pmatrix in ...x \nabla\phi V \pmatrix{
  \hat u - u \c...
sdreport.Rd:85-86: Undefined control sequence: \pmatrix in V
  \pmatrix{ \hat u - u \c...
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'
Found the following significant warnings:
  cppfunctions.cpp:202:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TMTI.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.JSS.papers'
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Found the following math rendering problems:
TopKListsGUI.Rd:43: Can't use function '$' in math mode in p=1,2,\ldots$, $L-1
aggmap.Rd:8: Can't use function '$' in math mode in p=1,2,\ldots$, $L-1
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'toscaData'
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
tourr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
tourr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'taxidata'
'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:
transformr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
transformr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
Found the following significant warnings:
  betaMPT.cpp:59:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:59:39: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:59:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:61:15: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:61:45: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:61:17: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:85:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:85:39: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:85:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:87:15: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:87:45: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:87:17: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TreeBUGS.Rcheck/00install.out' for details.
Found the following HTML validation problems:
TreeBUGS-package.html:24:4: Warning: <img> attribute "align" not allowed for HTML5
TreeBUGS-package.html:24:4: Warning: <img> attribute "align" not allowed for HTML5
TreeBUGS-package.html:24:4: Warning: <img> attribute "hspace" not allowed for HTML5
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
Found the following HTML validation problems:
Tb_mussel.html:100:6: Warning: <a> illegal characters found in URI
Tb_mussel.html:100:133: Warning: <a> illegal characters found in URI
Tb_snail.html:90:6: Warning: <a> illegal characters found in URI
Tb_snail.html:90:133: Warning: <a> illegal characters found in URI
Tbed_mussel.html:86:6: Warning: <a> illegal characters found in URI
Tbed_mussel.html:86:133: Warning: <a> illegal characters found in URI
'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
Found the following HTML validation problems:
ypr_sel.html:113:1: Warning: trimming empty <li>
ypr_sel.html:112:1: Warning: trimming empty <ul>
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
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: 'TScompare'
Unknown package 'TScompare' in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Found the following math rendering problems:
STSDistance.Rd:32: Got function '\sum' with no arguments as argument to '\sqrt' in STS= \sqrt \sum (((y_{k+1} - y_...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
tsibbledata-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
tsibbledata-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
tsibble-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
tsibble-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
'LazyData' is specified without a 'data' directory
checkRd: (-1) lindner.Rd:44: Escaped LaTeX specials: \_
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
tweenr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
tweenr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
twenty48-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
twenty48-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
'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
Found the following HTML validation problems:
Fischbein_wt.html:62:49: Warning: inserting implicit <p>
Fischbein_wt.html:62:49: Warning: trimming empty <p>
oddsratio.html:54:119: Warning: inserting implicit <p>
oddsratio.html:54:119: Warning: trimming empty <p>
umxModify.html:122:84: Warning: inserting implicit <p>
umxModify.html:122:84: Warning: trimming empty <p>
umxRAM.html:46:110: Warning: inserting implicit <p>
umxRAM.html:53:131: Warning: inserting implicit <p>
umxRAM.html:46:110: Warning: trimming empty <p>
umxRAM.html:53:131: Warning: trimming empty <p>
'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) unf.Rd:180: Escaped LaTeX specials: \&
checkRd: (-1) unf.Rd:182: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
unheadr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
unheadr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
unifir-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
unifir-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Found the following HTML validation problems:
Century.html:62:6: Warning: missing </span> before <p>
Century.html:62:99: Warning: inserting implicit <span>
Century.html:65:6: Warning: missing </span> before <p>
Century.html:65:90: Warning: inserting implicit <span>
Century.html:62:6: Warning: trimming empty <span>
Century.html:65:6: Warning: trimming empty <span>
Decade.html:62:6: Warning: missing </span> before <p>
Decade.html:62:99: Warning: inserting implicit <span>
Decade.html:65:6: Warning: missing </span> before <p>
Decade.html:65:90: Warning: inserting implicit <span>
Decade.html:62:6: Warning: trimming empty <span>
Decade.html:65:6: Warning: trimming empty <span>
Year.html:65:6: Warning: missing </span> before <p>
Year.html:65:99: Warning: inserting implicit <span>
Year.html:65:6: Warning: trimming empty <span>
'LazyData' is specified without 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 math rendering problems:
ur.kpss.Rd:21-22: Undefined control sequence: \root in \root 4 \of {4
        ...
ur.kpss.Rd:23-24: Undefined control sequence: \root in \root 4 \of
      {12 \...
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
Found the following HTML validation problems:
add_service.html:59:1: Warning: inserting implicit <p>
add_service.html:64:1: Warning: inserting implicit <p>
add_service.html:73:65: Warning: inserting implicit <p>
add_service.html:77:51: Warning: inserting implicit <p>
add_service.html:59:1: Warning: trimming empty <p>
add_service.html:64:1: Warning: trimming empty <p>
add_service.html:73:65: Warning: trimming empty <p>
add_service.html:77:51: Warning: trimming empty <p>
use_microservice.html:57:65: Warning: inserting implicit <p>
use_microservice.html:64:51: Warning: inserting implicit <p>
use_microservice.html:186:1: Warning: inserting implicit <p>
use_microservice.html:57:65: Warning: trimming empty <p>
use_microservice.html:64:51: Warning: trimming empty <p>
use_microservice.html:186:1: Warning: trimming empty <p>
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
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
Found the following significant warnings:
  ../inst/include/gdalgeometry/gdalgeometry.h:230:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ../inst/include/gdalgeometry/gdalgeometry.h:241:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ../inst/include/gdalgeometry/gdalgeometry.h:291:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ../inst/include/gdalgeometry/gdalgeometry.h:302:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ../inst/include/gdalgeometry/gdalgeometry.h:354:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ../inst/include/gdalgeometry/gdalgeometry.h:365:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ../inst/include/gdalgeometry/gdalgeometry.h:421:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ../inst/include/gdalgeometry/gdalgeometry.h:432:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/vapour.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
Found the following math rendering problems:
aep.Rd:8-56: Undefined control sequence: \eqn in ...t], & \mbox{if \eqn{x > 0},}
  \end{...
ast.Rd:8-41: Undefined control sequence: \eqn in ...}}, &
  \mbox{if \eqn{x > 0},}
  \end{...
asypower.Rd:8-66: Undefined control sequence: \eqn in ...t], & \mbox{if \eqn{x > 0},}
  \end{...
'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: 'geoR'
Unknown package 'geoR' in Rd xrefs
'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: \&
Found the following math rendering problems:
ACtest.Rd:89-92: Undefined control sequence: \label in ...bold{\psi }},  \label{LMstat}
  
ACtest.Rd:116-120: Undefined control sequence: \label in ...I}_{K})^{-1},  \label{HCCME}
'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: Warning: missing </span> before <p>
RequestHandlerCrul.html:50:92: Warning: inserting implicit <span>
RequestHandlerCrul.html:53:6: Warning: missing </span> before <p>
RequestHandlerCrul.html:53:96: Warning: inserting implicit <span>
RequestHandlerCrul.html:50:6: Warning: trimming empty <span>
RequestHandlerCrul.html:53:6: Warning: trimming empty <span>
RequestHandlerHttr.html:53:6: Warning: missing </span> before <p>
RequestHandlerHttr.html:53:92: Warning: inserting implicit <span>
RequestHandlerHttr.html:53:6: Warning: trimming empty <span>
lightswitch.html:113:79: Warning: inserting implicit <p>
lightswitch.html:150:58: Warning: inserting implicit <p>
lightswitch.html:181:33: Warning: inserting implicit <p>
lightswitch.html:202:42: Warning: inserting implicit <p>
lightswitch.html:113:79: Warning: trimming empty <p>
lightswitch.html:150:58: Warning: trimming empty <p>
lightswitch.html:181:33: Warning: trimming empty <p>
lightswitch.html:202:42: Warning: trimming empty <p>
request-matching.html:83:57: Warning: inserting implicit <p>
request-matching.html:83:57: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) MOStest.Rd:9: Escaped LaTeX specials: \&
Found the following HTML validation problems:
vein-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
vein-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
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.
Found the following math rendering problems:
colSequence.Rd:16: Can't use function '$' in math mode in $[0,1]$
matrixplot.Rd:91: Can't use function '$' in math mode in $[0,1]$
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
RVineClarkeTest.html:56:32: Warning: trimming empty <code>
RVineClarkeTest.html:68:32: Warning: trimming empty <code>
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
Found the following HTML validation problems:
viridis.html:116:1: Warning: inserting implicit <p>
viridis.html:116:1: Warning: trimming empty <p>
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
Found the following HTML validation problems:
vistime-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
vistime-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
vitae-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
vitae-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Found the following HTML validation problems:
virtualboxOptions.html:46:43: Warning: inserting implicit <p>
virtualboxOptions.html:87:44: Warning: inserting implicit <p>
virtualboxOptions.html:46:43: Warning: trimming empty <p>
virtualboxOptions.html:87:44: Warning: trimming empty <p>
Problems with news in 'NEWS.md':
No news entries found.
Found the following math rendering problems:
anonymise.Rd:28: Can't use function '$' in math mode in s_1,...,s_n$ s.t. $s_1
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
Found the following HTML validation problems:
vroom-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
vroom-package.html:23:4: 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':
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
walrus-package.html:76:4: Warning: <img> attribute "width" has invalid value "72px"
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'linout.csv' 'linout.pdf' 'out.csv' 'out.pdf' 'tabel_out.csv'
Found the following HTML validation problems:
data.SW1.html:19:1: Warning: missing </h2> before <p>
data.SW1.html:21:1: Warning: discarding unexpected </h2>
data.SW3.html:19:1: Warning: missing </h2> before <p>
data.SW3.html:21:1: Warning: discarding unexpected </h2>
'LazyData' is specified without 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'
Found the following math rendering problems:
dwpt.sim.Rd:32: Can't use function '$' in math mode in $M>N$
'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:
wdnr.gis-package.html:30:4: Warning: <img> attribute "align" not allowed for HTML5
wdnr.gis-package.html:30:4: Warning: <img> attribute "align" not allowed for HTML5
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
Found the following HTML validation problems:
httpbin_app.html:25:73: Warning: inserting implicit <p>
httpbin_app.html:25:73: Warning: trimming empty <p>
new_app.html:119:43: Warning: inserting implicit <p>
new_app.html:209:35: Warning: inserting implicit <p>
new_app.html:241:40: Warning: inserting implicit <p>
new_app.html:333:21: Warning: inserting implicit <p>
new_app.html:348:82: Warning: inserting implicit <p>
new_app.html:356:65: Warning: inserting implicit <p>
new_app.html:405:73: Warning: inserting implicit <p>
new_app.html:119:43: Warning: trimming empty <p>
new_app.html:209:35: Warning: trimming empty <p>
new_app.html:241:40: Warning: trimming empty <p>
new_app.html:333:21: Warning: trimming empty <p>
new_app.html:348:82: Warning: trimming empty <p>
new_app.html:356:65: Warning: trimming empty <p>
new_app.html:405:73: Warning: trimming empty <p>
new_app_process.html:88:89: Warning: inserting implicit <p>
new_app_process.html:88:89: Warning: trimming empty <p>
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
Adapter.html:83:6: Warning: missing </span> before <p>
Adapter.html:83:91: Warning: inserting implicit <span>
Adapter.html:86:6: Warning: missing </span> before <p>
Adapter.html:86:90: Warning: inserting implicit <span>
Adapter.html:89:6: Warning: missing </span> before <p>
Adapter.html:89:98: Warning: inserting implicit <span>
Adapter.html:92:6: Warning: missing </span> before <p>
Adapter.html:92:94: Warning: inserting implicit <span>
Adapter.html:95:6: Warning: missing </span> before <p>
Adapter.html:95:96: Warning: inserting implicit <span>
Adapter.html:169:6: Warning: missing </span> before <p>
Adapter.html:169:91: Warning: inserting implicit <span>
Adapter.html:172:6: Warning: missing </span> before <p>
Adapter.html:172:90: Warning: inserting implicit <span>
Adapter.html:175:6: Warning: missing </span> before <p>
Adapter.html:175:98: Warning: inserting implicit <span>
Adapter.html:178:6: Warning: missing </span> before <p>
Adapter.html:178:94: Warning: inserting implicit <span>
Adapter.html:181:6: Warning: missing </span> before <p>
Adapter.html:181:96: Warning: inserting implicit <span>
Adapter.html:188:1: Warning: <a> anchor "method-clone" already defined
Adapter.html:408:1: Warning: <a> anchor "method-clone" already defined
Adapter.html:83:6: Warning: trimming empty <span>
Adapter.html:86:6: Warning: trimming empty <span>
Adapter.html:89:6: Warning: trimming empty <span>
Adapter.html:92:6: Warning: trimming empty <span>
Adapter.html:95:6: Warning: trimming empty <span>
Adapter.html:169:6: Warning: trimming empty <span>
Adapter.html:172:6: Warning: trimming empty <span>
Adapter.html:175:6: Warning: trimming empty <span>
Adapter.html:178:6: Warning: trimming empty <span>
Adapter.html:181:6: Warning: trimming empty <span>
'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: 'ATE'
Unknown package 'ATE' in Rd xrefs
'LazyData' is specified without a 'data' directory
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
Found the following HTML validation problems:
whippr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
whippr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
Found the following HTML validation problems:
benefits.html:96:1: Warning: trimming empty <h3>
beveridge.html:66:1: Warning: trimming empty <h3>
happiness.html:141:1: Warning: trimming empty <h3>
hprice3.html:99:1: Warning: trimming empty <h3>
checkRd: (-1) DSM_VerbNounTriples_BNC.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) eval_clustering.Rd:54: Escaped LaTeX specials: \&
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.
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:
style_duo.html:618:87: Warning: inserting implicit <p>
style_duo.html:618:87: Warning: trimming empty <p>
style_duo_accent.html:641:87: Warning: inserting implicit <p>
style_duo_accent.html:641:87: Warning: trimming empty <p>
style_duo_accent_inverse.html:643:87: Warning: inserting implicit <p>
style_duo_accent_inverse.html:643:87: Warning: trimming empty <p>
style_mono_accent.html:624:87: Warning: inserting implicit <p>
style_mono_accent.html:624:87: Warning: trimming empty <p>
style_mono_accent_inverse.html:625:87: Warning: inserting implicit <p>
style_mono_accent_inverse.html:625:87: Warning: trimming empty <p>
style_mono_dark.html:625:87: Warning: inserting implicit <p>
style_mono_dark.html:625:87: Warning: trimming empty <p>
style_mono_light.html:625:87: Warning: inserting implicit <p>
style_mono_light.html:625:87: Warning: trimming empty <p>
style_solarized_dark.html:600:87: Warning: inserting implicit <p>
style_solarized_dark.html:600:87: Warning: trimming empty <p>
style_solarized_light.html:600:87: Warning: inserting implicit <p>
style_solarized_light.html:600:87: Warning: trimming empty <p>
style_xaringan.html:615:87: Warning: inserting implicit <p>
style_xaringan.html:615:87: Warning: trimming empty <p>
xaringanthemer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
xaringanthemer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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'
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 math rendering problems:
mmeta.Rd:61-64: Invalid delimiter type 'ordgroup' in ...log \left( \Big{|}\sum_{i=1}^m \b...
'LazyData' is specified without 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
'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
Package suggested but not available for checking: 'fts'
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [19s/25s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(yamlet)
  
  Attaching package: 'yamlet'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("yamlet")
   'dvec' int [1:4] 0 1 0 1
   - attr(*, "label")= chr "sex"
   - attr(*, "guide")=List of 2
    ..$ female: int 0
    ..$ male  : int 1
   'dvec' int [1:4] 0 1 0 1
   - attr(*, "label")= chr "sex"
   - attr(*, "guide")=List of 2
    ..$ female: int 0
    ..$ male  : int 1
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 299 ]
  
  == Skipped tests ===============================================================
  * empty test (2)
  * l10n_info()$`UTF-8` is not TRUE (2)
  
  == Failed tests ================================================================
  -- Failure (test-yamlet.R:823:1): ggplot.resolved is stable --------------------
  x %>% decorations(value) has changed from known value recorded in '085.rds'.
  Component "value": Names: 1 string mismatch
  Backtrace:
      x
   1. \-testthat::expect_equal_to_reference(file = "085.rds", x %>% decorations(value)) at test-yamlet.R:823:0
   2.   \-testthat::expect_known_value(..., update = update)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 299 ]
  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
Found the following HTML validation problems:
listGroupInput.html:113:161: Warning: inserting implicit <p>
listGroupInput.html:113:161: Warning: trimming empty <p>
navInput.html:114:92: Warning: inserting implicit <p>
navInput.html:114:92: Warning: trimming empty <p>
toast.html:117:57: Warning: inserting implicit <p>
toast.html:117:57: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
yowie-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
yowie-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Found the following HTML validation problems:
ypr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ypr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ae.cpp:8:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/yuima.Rcheck/00install.out' for details.
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.
Found the following HTML validation problems:
jholiday.html:70:62: Warning: inserting implicit <p>
jholiday.html:70:62: Warning: trimming empty <p>
kana.html:65:1: Warning: trimming empty <dt>
'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.
Found the following HTML validation problems:
zip.html:153:56: Warning: inserting implicit <p>
zip.html:176:81: Warning: inserting implicit <p>
zip.html:153:56: Warning: trimming empty <p>
zip.html:176:81: Warning: trimming empty <p>
'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: \_
Found the following HTML validation problems:
referencesDatabase.html:234:42: Warning: inserting implicit <p>
referencesDatabase.html:283:27: Warning: inserting implicit <p>
referencesDatabase.html:321:65: Warning: inserting implicit <p>
referencesDatabase.html:234:42: Warning: trimming empty <p>
referencesDatabase.html:283:27: Warning: trimming empty <p>
referencesDatabase.html:321:65: Warning: trimming empty <p>
Package suggested but not available for checking: 'SDMTools'
Package suggested but not available for checking: 'fts'
Unknown package 'fts' in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  fnToExport.cpp:415:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ZVCV.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
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’
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> \text 
                 {min}(-1/2*x^TB^Tx + \gamma p(y): ||x||_2 \leq 1, DNx = y)
l.1924 ...\gamma p(y): ||x||_2 \leq 1, DNx = y)}{}
Found the following files/directories:
  ‘accSDA-manual.tex’
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:
acled.api.html:145:40: Warning: missing </a> before <a>
acled.api.html:145:151: Warning: discarding unexpected </a>
get.api.regions.html:57:40: Warning: missing </a> before <a>
get.api.regions.html:57:151: Warning: discarding unexpected </a>
'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.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following HTML validation problems:
activityCounts-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
activityCounts-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without 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 package ‘MHadaptive’ in Rd xrefs
Found the following HTML validation problems:
adaptr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
adaptr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
checkRd: (-1) chickenk.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) multispati.Rd:54: Escaped LaTeX specials: \$
checkRd: (-1) randboot.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) HWE.Rd:22: Escaped LaTeX specials: \$
checkRd: (-1) accessors.Rd:79: Escaped LaTeX specials: \$ \$
checkRd: (-1) dist.genpop.Rd:91: Escaped LaTeX specials: \~
checkRd: (-1) genind.Rd:20: Escaped LaTeX specials: \$
checkRd: (-1) genpop.Rd:20: Escaped LaTeX specials: \$
checkRd: (-1) hybridize.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) selpopsize.Rd:20: Escaped LaTeX specials: \$
checkRd: (-1) seploc.Rd:47: Escaped LaTeX specials: \$
checkRd: (-1) spca.Rd:113: Escaped LaTeX specials: \$ \$
checkRd: (-1) truenames.Rd:28: Escaped LaTeX specials: \$ \$
checkRd: (-1) truenames.Rd:31: Escaped LaTeX specials: \$ \$
checkRd: (-1) truenames.Rd:32: Escaped LaTeX specials: \$
checkRd: (-1) kernelUD.Rd:210: Escaped LaTeX specials: \&
checkRd: (-1) orthobasis.Rd:106: Escaped LaTeX specials: \&
checkRd: (-1) orthobasis.Rd:110: Escaped LaTeX specials: \&
checkRd: (-1) treePart.Rd:33: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
checkRd: (-1) multispati.Rd:62: Escaped LaTeX specials: \$
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 math rendering problems:
daep.Rd:5-10: Unknown column alignment: * in ...{\begin{array}{*{20}c}
  \frac{1}...
fitaep.Rd:5-10: Unknown column alignment: * in ...{\begin{array}{*{20}c}
  \frac{1}...
paep.Rd:5-10: Unknown column alignment: * in ...{\begin{array}{*{20}c}
  \frac{1-...
qaep.Rd:5-10: Unknown column alignment: * in ...{\begin{array}{*{20}c}
  \mu-\sig...
raep.Rd:5-10: Unknown column alignment: * in ...{\begin{array}{*{20}c}
  \mu-\sig...
regaep.Rd:7-12: Unknown column alignment: * in ...{\begin{array}{*{20}c}
  \frac{1}...
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: \&
Found the following HTML validation problems:
AgroTech-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
AgroTech-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) adapt.Rd:41: Escaped LaTeX specials: \$
Found the following HTML validation problems:
dev.html:62:126: Warning: inserting implicit <p>
dev.html:62:126: Warning: trimming empty <p>
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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
akc-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
akc-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
'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
checkRd: (-1) varrob.Rd:44: Escaped LaTeX specials: \^
Found the following HTML validation problems:
Introduction.html:162:66: Error: <name> is not recognized!
Introduction.html:162:66: Warning: discarding unexpected <name>
Found the following HTML validation problems:
crop.html:31:52: Warning: inserting implicit <p>
crop.html:31:52: Warning: trimming empty <p>
merge.html:59:70: Warning: inserting implicit <p>
merge.html:59:70: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ambient-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ambient-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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: \&
Package which this enhances but not available for checking: ‘SparkR’
'LazyData' is specified without a 'data' directory
'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.
checkRd: (-1) diamonds.Rd:10: Escaped LaTeX specials: \$ \$
checkRd: (-1) msleep.Rd:15: Escaped LaTeX specials: \_
checkRd: (-1) msleep.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) msleep.Rd:17: Escaped LaTeX specials: \_
Found the following HTML validation problems:
stat_unique.html:110:1: Warning: trimming empty <li>
stat_unique.html:109:1: Warning: trimming empty <ul>
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tmg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
AnnData.html:1390:1: Warning: <a> anchor "method-new" already defined
AnnData.html:1419:1: Warning: <a> anchor "method-copy" already defined
AnnData.html:1501:1: Warning: <a> anchor "method-print" already defined
AnnData.html:1571:1: Warning: <a> anchor "method-.set_py_object" already defined
AnnData.html:1600:1: Warning: <a> anchor "method-.get_py_object" already defined
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’
checkRd: (-1) AIDS-Functions.Rd:334: Escaped LaTeX specials: \&
checkRd: (-1) Logit-Functions.Rd:380: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
anyflights_description.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
anyflights_description.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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 HTML validation problems:
mislabel.html:25:1: Warning: trimming empty <p>
raphylo.html:25:1: Warning: trimming empty <p>
sim_fun_on_tree.html:25:1: Warning: trimming empty <p>
'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’.
Found the following HTML validation problems:
applicable-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
applicable-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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
Found the following HTML validation problems:
arcpullr-package.html:29:4: Warning: <img> attribute "align" not allowed for HTML5
arcpullr-package.html:29:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
mapApp.html:105:101: Warning: inserting implicit <p>
mapApp.html:105:101: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 math rendering problems:
chi.plot.Rd:27-28: Undefined control sequence: \emph in ...bda = 4 \times \emph{S} \times max[...
ci.prat.rd:94-95: Can't use function '$' in math mode in ...{\theta }_{0}}}$, and ${{X}^{2}...
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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
getCostsAndPresolvedStatus.html:55:38: Warning: <code> is probably intended as </code>
getCostsAndPresolvedStatus.html:55:74: Warning: discarding unexpected </code>
getCostsAndPresolvedStatus.html:55:82: Warning: discarding unexpected </code>
getCostsAndPresolvedStatus.html:59:38: Warning: <code> is probably intended as </code>
getCostsAndPresolvedStatus.html:59:75: Warning: discarding unexpected </code>
getCostsAndPresolvedStatus.html:59:83: Warning: discarding unexpected </code>
getCostsAndPresolvedStatus.html:63:38: Warning: <code> is probably intended as </code>
getCostsAndPresolvedStatus.html:63:67: Warning: discarding unexpected </code>
getCostsAndPresolvedStatus.html:63:75: Warning: discarding unexpected </code>
Found the following files/directories:
  ‘MSToutput.txt’
Package which this enhances but not available for checking: ‘asreml’
checkRd: (-1) Ladybird.dat.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) infoCriteria.asreml.Rd:79: Escaped LaTeX specials: \&
Found the following HTML validation problems:
tsk_estimation.html:61:149: Warning: inserting implicit <p>
tsk_estimation.html:147:138: Warning: inserting implicit <p>
tsk_estimation.html:61:149: Warning: trimming empty <p>
tsk_estimation.html:147:138: Warning: trimming empty <p>
tsk_output.html:58:149: Warning: inserting implicit <p>
tsk_output.html:58:149: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
Found the following HTML validation problems:
gen.html:82:83: Warning: inserting implicit <p>
gen.html:87:54: Warning: inserting implicit <p>
gen.html:82:83: Warning: trimming empty <p>
gen.html:87:54: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Unknown package ‘snpar’ in Rd xrefs
Found the following HTML validation problems:
attachment-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
attachment-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Package required but not available: ‘gbm’

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
Found the following HTML validation problems:
aweSOM-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
aweSOM-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
'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 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 HTML validation problems:
rwnorm2.html:111:126: Warning: trimming empty <code>
rwnorm2.html:115:73: Warning: trimming empty <code>
rwnorm2.html:115:146: Warning: trimming empty <code>
rwnorm2.html:115:211: Warning: trimming empty <code>
rwnorm2.html:119:126: Warning: trimming empty <code>
'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 HTML validation problems:
img.html:24:1: Warning: <img> discarding newline in URI reference
Found the following HTML validation problems:
baseballr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
baseballr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
bref.html:72:105: Warning: inserting implicit <p>
bref.html:72:105: Warning: trimming empty <p>
'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
checkRd: (-1) bas.lm.Rd:425: Escaped LaTeX specials: \&
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: \$
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.
Found the following HTML validation problems:
getSamples.html:74:1: Warning: trimming empty <h3>
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Future development plan of the author's life
    Future development plan of this package
    Explanatory Variables
checkRd: (-1) check_rhat.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) snippet_for_BayesianFROC.Rd:22: Escaped LaTeX specials: \$
Found the following HTML validation problems:
error_MRMC.html:38:14: Warning: nested emphasis <strong>
'LazyData' is specified without 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:
WAIC.html:55:1: Warning: inserting implicit <p>
WAIC.html:58:1: Warning: inserting implicit <p>
WAIC.html:67:1: Warning: inserting implicit <p>
WAIC.html:55:1: Warning: trimming empty <p>
WAIC.html:58:1: Warning: trimming empty <p>
WAIC.html:67:1: Warning: trimming empty <p>
WAIC.html:54:1: Warning: <center> element removed from HTML5
WAIC.html:57:1: Warning: <center> element removed from HTML5
WAIC.html:63:1: Warning: <center> element removed from HTML5
WAIC.html:65:1: Warning: <center> element removed from HTML5
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 math rendering problems:
bayes.regress.Rd:92: Unknown column alignment: @ in \begin{array}{r@{\,}l}\beta | \...
bayes.regress.Rd:95-100: Unknown column alignment: @ in \begin{array}{r@{\,}l}
    \beta ...
checkRd: (-1) describe_posterior.Rd:194: Escaped LaTeX specials: \&
checkRd: (-1) diagnostic_posterior.Rd:103: Escaped LaTeX specials: \&
checkRd: (-1) estimate_density.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) point_estimate.Rd:113: Escaped LaTeX specials: \&
checkRd: (-1) sexit.Rd:91: Escaped LaTeX specials: \&
checkRd: (-1) bart.Rd:271: Escaped LaTeX specials: \_
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
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kBET', 'lisi', '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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
hill.html:23:30: Warning: <em> is probably intended as </em>
hill.html:25:72: Warning: discarding unexpected </em>
hill.html:28:23: Warning: discarding unexpected </em>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Checking should be performed on sources prepared by ‘R CMD build’.
'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.
checkRd: (-1) scrHpd.Rd:30: Escaped LaTeX specials: \&
Found the following HTML validation problems:
bggCollection.html:70:6: Warning: missing </span> before <p>
bggCollection.html:70:93: Warning: inserting implicit <span>
bggCollection.html:73:6: Warning: missing </span> before <p>
bggCollection.html:73:92: Warning: inserting implicit <span>
bggCollection.html:76:6: Warning: missing </span> before <p>
bggCollection.html:76:103: Warning: inserting implicit <span>
bggCollection.html:70:6: Warning: trimming empty <span>
bggCollection.html:73:6: Warning: trimming empty <span>
bggCollection.html:76:6: Warning: trimming empty <span>
bggGames.html:68:6: Warning: missing </span> before <p>
bggGames.html:68:93: Warning: inserting implicit <span>
bggGames.html:71:6: Warning: missing </span> before <p>
bggGames.html:71:92: Warning: inserting implicit <span>
bggGames.html:74:6: Warning: missing </span> before <p>
bggGames.html:74:103: Warning: inserting implicit <span>
bggGames.html:68:6: Warning: trimming empty <span>
bggGames.html:71:6: Warning: trimming empty <span>
bggGames.html:74:6: Warning: trimming empty <span>
bggSearch.html:77:6: Warning: missing </span> before <p>
bggSearch.html:77:93: Warning: inserting implicit <span>
bggSearch.html:80:6: Warning: missing </span> before <p>
bggSearch.html:80:92: Warning: inserting implicit <span>
bggSearch.html:83:6: Warning: missing </span> before <p>
bggSearch.html:83:103: Warning: inserting implicit <span>
bggSearch.html:77:6: Warning: trimming empty <span>
bggSearch.html:80:6: Warning: trimming empty <span>
bggSearch.html:83:6: Warning: trimming empty <span>
'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: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ffbase’
Package suggested but not available for checking: ‘INLA’
Found the following HTML validation problems:
air.density.html:65:38: Warning: nested emphasis <code>
decoupling.html:123:38: Warning: nested emphasis <code>
latent.heat.vaporization.html:55:38: Warning: nested emphasis <code>
psychrometric.constant.html:67:38: Warning: nested emphasis <code>
stability.parameter.html:100:38: Warning: nested emphasis <code>
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 files/directories:
  ‘outputs’
Found the following HTML validation problems:
snp_ldsc.html:122:1: Warning: trimming empty <dt>
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following math rendering problems:
MDL.Rd:90-98: Expected '}', got '&' in ...n{pmatrix}
  {
  1 & 0 & 0 & 0 & .....
MDL.Rd:132: Expected '}', got '&' in ...{pmatrix} {1.1 & 0 & 1.3  \cr 0...
MDL.Rd:154: Expected '}', got '&' in ....1 * Rscale[1] & 0 & 1.3 * Rsca...
MDL.Rd:170: Expected '}', got '&' in ...pmatrix} {X' X & R_{aug}' \cr R...
MDL.Rd:212: Expected '}', got '&' in ...in{pmatrix} {0 & 1 & -3 & 3 & 1...
'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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) core.find.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) core.find.Rd:87: Escaped LaTeX specials: \^
checkRd: (-1) core.find.Rd:89: Escaped LaTeX specials: \^
checkRd: (-1) core.find.Rd:91: Escaped LaTeX specials: \^
checkRd: (-1) core.find.Rd:93: Escaped LaTeX specials: \^
checkRd: (-1) core.find.Rd:95: Escaped LaTeX specials: \^
checkRd: (-1) core.find.Rd:97: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gbm’
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’
Found the following HTML validation problems:
biogrowth-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
biogrowth-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
Package required but not available: ‘gbm’

Package suggested but not available for checking: ‘ecospat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
bioRad-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
bioRad-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
bioseq-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
bioseq-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) NOS.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) specieslevel.Rd:156: 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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
bittermelon.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
bittermelon.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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:
amlps.object.html:113:38: Warning: nested emphasis <code>
coxlps.baseline.html:84:38: Warning: nested emphasis <code>
coxlps.baseline.html:88:38: Warning: nested emphasis <code>
coxlps.object.html:74:38: Warning: nested emphasis <code>
cubicbs.html:65:38: Warning: nested emphasis <code>
curelps.object.html:68:38: Warning: nested emphasis <code>
gamlps.object.html:117:38: Warning: nested emphasis <code>
simsurvdata.html:108:38: Warning: nested emphasis <code>
snmatch.html:79:38: Warning: nested emphasis <code>
'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: \&
Found the following HTML validation problems:
ChiSquare.html:30:1: Warning: inserting implicit <p>
ChiSquare.html:109:1: Warning: inserting implicit <p>
ChiSquare.html:30:1: Warning: trimming empty <p>
ChiSquare.html:109:1: Warning: trimming empty <p>
FarringtonManning.html:32:1: Warning: inserting implicit <p>
FarringtonManning.html:101:1: Warning: inserting implicit <p>
FarringtonManning.html:32:1: Warning: trimming empty <p>
FarringtonManning.html:101:1: Warning: trimming empty <p>
Student.html:37:1: Warning: inserting implicit <p>
Student.html:113:1: Warning: inserting implicit <p>
Student.html:37:1: Warning: trimming empty <p>
Student.html:113:1: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
Found the following HTML validation problems:
bmscstan.html:55:70: Warning: replacing unexpected i with </i>
bmscstan.html:55:89: Warning: inserting implicit <sub>
bmscstan.html:56:4: Warning: inserting implicit <sub>
bmscstan.html:58:1: Warning: inserting implicit <sub>
bmscstan.html:58:1: Warning: missing </sub> before <p>
bmscstan.html:58:4: Warning: inserting implicit <sub>
bmscstan.html:63:1: Warning: inserting implicit <sub>
bmscstan.html:63:1: Warning: missing </sub> before <h3>
bmscstan.html:63:5: Warning: inserting implicit <sub>
bmscstan.html:65:4: Warning: inserting implicit <sub>
bmscstan.html:70:1: Warning: inserting implicit <sub>
bmscstan.html:55:89: Warning: trimming empty <sub>
bmscstan.html:58:1: Warning: trimming empty <sub>
bmscstan.html:63:1: Warning: trimming empty <sub>
bmscstan.html:70:1: Warning: trimming empty <sub>
bmscstan.html:44:1: Warning: <center> element removed from HTML5
bmscstan.html:55:1: Warning: <center> element removed from HTML5
Package suggested but not available for checking: ‘INLA’
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: ‘gbm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following HTML validation problems:
bayes.lin.reg.html:27:32: Warning: trimming empty <code>
bayes.lin.reg.html:32:32: Warning: trimming empty <code>
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following HTML validation problems:
BoneProfileR-package.html:39:1: Warning: <img> attribute "," lacks value
BoneProfileR-package.html:39:1: Warning: <img> attribute "align" not allowed for HTML5
BoneProfileR-package.html:39:1: Warning: <img> attribute "align" not allowed for HTML5
Found the following files/directories:
  ‘attractors.tex’ ‘cellcycle.sbml’ ‘cellcycle.txt’ ‘pajek_export.net’
  ‘sequence.txt’ ‘testNet.bn’
Found the following HTML validation problems:
boomer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
boomer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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: \&
GNU make is a SystemRequirements.
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
'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.
checkRd: (-1) brew.Rd:41: Escaped LaTeX specials: \#
Found the following HTML validation problems:
Bridge.html:80:32: Warning: trimming empty <code>
Bridge.html:85:32: Warning: trimming empty <code>
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Found the following HTML validation problems:
fit_200.html:38:60: Warning: inserting implicit <p>
fit_200.html:38:60: Warning: trimming empty <p>
fit_200_light.html:37:61: Warning: inserting implicit <p>
fit_200_light.html:37:61: Warning: trimming empty <p>
Package suggested but not available for checking: ‘glmmADMB’
checkRd: (-1) brr-package.Rd:33: Escaped LaTeX specials: \&
Found the following HTML validation problems:
bruceR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
bruceR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
'LazyData' is specified without a 'data' directory
Package required but not available: ‘gbm’

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: ‘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
Found the following HTML validation problems:
buildr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
buildr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Packages required but not available: 'mpath', 'gbm', 'bst'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following HTML validation problems:
bunching.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
bunching.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
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) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
calculus-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
calculus-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
Found the following files/directories:
  ‘callr-manual.tex’
'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:
  ‘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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
carbon.html:48:55: Warning: <big> element removed from HTML5
carbon.html:57:55: Warning: <big> element removed from HTML5
carbon.html:73:55: Warning: <big> element removed from HTML5
carbon.html:105:55: Warning: <big> element removed from HTML5
carbon.html:133:55: Warning: <big> element removed from HTML5
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
Package suggested but not available for checking: ‘gbm’
Running ‘testthat.R’ [48s/74s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(caretEnsemble)
  > 
  > test_check("caretEnsemble")
  [ FAIL 1 | WARN 4 | SKIP 20 | PASS 164 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Basic skip failed (1)
  • On CRAN (16)
  • empty test (1)
  • gbm cannot be loaded (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-caretList.R:4:1): (code run outside of `test_that()`) ───────────
  <packageNotFoundError/error/condition>
  Error in `library("gbm")`: there is no package called 'gbm'
  Backtrace:
      ▆
   1. ├─base::suppressMessages(...) at test-caretList.R:4:0
   2. │ └─base::withCallingHandlers(...)
   3. └─base::library("gbm") at test-caretList.R:8:2
  
  [ FAIL 1 | WARN 4 | SKIP 20 | PASS 164 ]
  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) 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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
create_table.html:67:50: Warning: inserting implicit <p>
create_table.html:67:50: Warning: trimming empty <p>
'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 HTML validation problems:
catmaply-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
catmaply-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
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
Running examples in ‘CauchyCP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CauchyCP
> ### Title: A robust test under non-proportional hazards using Cauchy
> ###   combination of change-point Cox regressions.
> ### Aliases: CauchyCP
> 
> ### ** Examples
> 
> data(gast)
> CauchyCP(time=gast$time, status=gast$status, x=gast$trt)
Error in pvals[1] <- anova(fit0, fit1, test = "LRT")[2, "P(>|Chi|)"] : 
  replacement has length zero
Calls: CauchyCP
Execution halted
Package required but not available: ‘PSweight’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) causalPAFplot.Rd:47: Escaped LaTeX specials: \$ \$
checkRd: (-1) eval_make_formula.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) pointEstimate.Rd:43: Escaped LaTeX specials: \$ \$
checkRd: (-1) sim_outnode.Rd:20: Escaped LaTeX specials: \$ \$
checkRd: (-1) sim_outnode_2.Rd:26: Escaped LaTeX specials: \$ \$
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character − (U+2212)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character − (U+2212)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
Found the following files/directories:
  ‘causalPAF-manual.tex’
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
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 math rendering problems:
discrim.index.Rd:52-55: Undefined control sequence: \boldmath in ...c{1}{2} \max_{ \boldmath{\alpha} }
  \lef...
discrim.index.Rd:56: Undefined control sequence: \boldmath in \boldmath{\alpha}^{(-k)}
discrim.index.Rd:56: Undefined control sequence: \boldmath in \boldmath{\alpha}
discrim.index.Rd:65-66: Undefined control sequence: \boldmath in IDI_j=\max_{ \boldmath{\alpha}_1,\bol...
gdina.Rd:354-356: Undefined control sequence: \boldmath in ...| \alpha_n ) ]=\boldmath{M}_j ( \alpha ...
gdina.Rd:357: Undefined control sequence: \boldmath in \boldmath{M}_j (\alpha _...
gdina.Rd:358: Undefined control sequence: \boldmath in \boldmath{\delta}_j
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 required but not available: ‘twang’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Found the following HTML validation problems:
cffr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
cffr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cheddar.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘gbm’
Running examples in ‘cheem-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gbm.unify
> ### Title: Unify GBM model
> ### Aliases: gbm.unify
> 
> ### ** Examples
> 
> library(cheem)
> 
> ## Regression setup:
> dat  <- amesHousing2018_NorthAmes
> X    <- dat[, 1:9]
> Y    <- dat$SalePrice
> clas <- dat$SubclassMS
> 
> ## Fit a model:
> gbm_model <- gbm::gbm(
+   formula = Y ~ .,
+   data = data.frame(X, Y),
+   distribution = "gaussian",
+   n.trees = 50,
+   interaction.depth = 4,
+   n.cores = 1)
Error in loadNamespace(x) : there is no package called ‘gbm’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
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:
chillR-package.html:19:5: Warning: <img> attribute "align" not allowed for HTML5
chillR-package.html:19:5: Warning: <img> attribute "align" not allowed for HTML5
plot_phenology_trends.html:153:4: Warning: <img> attribute "align" not allowed for HTML5
plot_phenology_trends.html:153:4: Warning: <img> attribute "align" not allowed for HTML5
plot_scenarios.html:184:4: Warning: <img> attribute "align" not allowed for HTML5
plot_scenarios.html:184:4: Warning: <img> attribute "align" not allowed for HTML5
'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’
Found the following HTML validation problems:
chk-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
chk-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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’
*** caught segfault ***
address 0x18, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Found the following HTML validation problems:
Chrome.html:66:6: Warning: missing </span> before <p>
Chrome.html:66:89: Warning: inserting implicit <span>
Chrome.html:69:6: Warning: missing </span> before <p>
Chrome.html:69:92: Warning: inserting implicit <span>
Chrome.html:72:6: Warning: missing </span> before <p>
Chrome.html:72:92: Warning: inserting implicit <span>
Chrome.html:75:6: Warning: missing </span> before <p>
Chrome.html:75:95: Warning: inserting implicit <span>
Chrome.html:78:6: Warning: missing </span> before <p>
Chrome.html:78:92: Warning: inserting implicit <span>
Chrome.html:66:6: Warning: trimming empty <span>
Chrome.html:69:6: Warning: trimming empty <span>
Chrome.html:72:6: Warning: trimming empty <span>
Chrome.html:75:6: Warning: trimming empty <span>
Chrome.html:78:6: Warning: trimming empty <span>
ChromeRemote.html:55:6: Warning: missing </span> before <p>
ChromeRemote.html:55:89: Warning: inserting implicit <span>
ChromeRemote.html:58:6: Warning: missing </span> before <p>
ChromeRemote.html:58:92: Warning: inserting implicit <span>
ChromeRemote.html:61:6: Warning: missing </span> before <p>
ChromeRemote.html:61:92: Warning: inserting implicit <span>
ChromeRemote.html:64:6: Warning: missing </span> before <p>
ChromeRemote.html:64:95: Warning: inserting implicit <span>
ChromeRemote.html:67:6: Warning: missing </span> before <p>
ChromeRemote.html:67:92: Warning: inserting implicit <span>
ChromeRemote.html:55:6: Warning: trimming empty <span>
ChromeRemote.html:58:6: Warning: trimming empty <span>
ChromeRemote.html:61:6: Warning: trimming empty <span>
ChromeRemote.html:64:6: Warning: trimming empty <span>
ChromeRemote.html:67:6: Warning: trimming empty <span>
Chromote.html:40:39: Warning: inserting implicit <p>
Chromote.html:40:39: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘twang’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘userfriendlyscience’
Found the following HTML validation problems:
browse_circle_token.html:68:81: Warning: inserting implicit <p>
browse_circle_token.html:68:81: Warning: trimming empty <p>
'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: ‘gbm’
Running examples in ‘ciu-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ciu.blackbox.new
> ### Title: Create CIU.BlackBox object
> ### Aliases: ciu.blackbox.new
> 
> ### ** Examples
> 
> # Create CIU.BlackBox wrapper for Gradient Boosting
> library(MASS) # Just in case Boston is not already available
> library(gbm)
Error in library(gbm) : there is no package called ‘gbm’
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
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: There's no line here to end.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...
Found the following files/directories:
  ‘cleanr-manual.tex’
Package suggested but not available for checking: ‘lasso2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘clere.Rnw’ using Sweave

Error: processing vignette ‘clere.Rnw’ failed with diagnostics:
 chunk 3 
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘lasso2’

--- failed re-building ‘clere.Rnw’

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

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:
    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
Found the following math rendering problems:
signature.Rd:52: Undefined control sequence: \cases in 
    e_i e_i = \cases{
    +1 & if $1\...
Found the following HTML validation problems:
climaemet-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
climaemet-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) diagwl.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) diagwl.Rd:5: Escaped LaTeX specials: \&
Found the following HTML validation problems:
climatrends.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
climatrends.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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) dataADaMCDISCP01.Rd:48: Escaped LaTeX specials: \&
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
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
Package suggested but not available for checking: ‘CRTSize’
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
'LazyData' is specified without 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: ‘twang’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Older versions
'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 suggested but not available for checking: ‘twang’
'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’
Found the following HTML validation problems:
write_codemeta.html:189:30: Warning: inserting implicit <p>
write_codemeta.html:189:30: Warning: trimming empty <p>
write_codemeta.html:184:1: Warning: <details> proprietary attribute "closed"
Found the following HTML validation problems:
coder-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
coder-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
'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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘CAM’
Found the following HTML validation problems:
CompAREdesign-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
CompAREdesign-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) compareGroups-package.Rd:52: Escaped LaTeX specials: \~
checkRd: (-1) sumboxdata.Rd:12: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) sumboxmktCnt.Rd:10: Escaped LaTeX specials: \$ \$ \$
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
concurve-package.html:38:43: Warning: <img> attribute "width" has invalid value "50px"
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
Package suggested but not available for checking: ‘gbm’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
conformalbayes-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
conformalbayes-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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.
'LazyData' is specified without 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 math rendering problems:
check-convergence.Rd:37: Can't use function '$' in math mode in $\hat(l)_n(t)=|\...
criterion.Rd:20: Can't use function '$' in math mode in $X_n-X$
criterion.Rd:21: Can't use function '$' in math mode in $p_n=P[|X_n-X|>\...
criterion.Rd:22-23: Can't use function '$' in math mode in $a_n=P[\exists k...
criterion.Rd:25: Can't use function '$' in math mode in $e_{n,r}=E|X_n-X...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
checkRd: (-1) poss_local.Rd:21: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [4s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(CorporaCoCo)
  > 
  > test_check("CorporaCoCo")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 147 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-corp_text.R:102:5): corp_text_rbindlist-real-example ──────────
  corp_list[[1]]$tokens[100]$type (`actual`) not equal to "date" (`expected`).
  
  `actual`:   "engraved"
  `expected`: "date"    
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 147 ]
  Error: Test failures
  Execution halted
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
Package suggested but not available for checking: ‘gbm’
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
corrr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
corrr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
couples-class.Rd:95: Can't use function '$' in math mode in $||\mathbf{h}_{1...
couples-class.Rd:99: Can't use function '$' in math mode in $u_{1}^{2\alpha}...
covaprop-class.Rd:46: Can't use function '$' in math mode in C(h,u) - C...
covaprop-class.Rd:52: Can't use function '$' in math mode in C(h, u)/C(...
covaprop-class.Rd:60: Can't use function '$' in math mode in C(h,u)/C(h...
covaprop-class.Rd:62: Can't use function '$' in math mode in C(h,u)/C(h...
covaprop-class.Rd:68: Can't use function '$' in math mode in Af(G)=0$
Package suggested but not available for checking: ‘spcov’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘covfefe_inauguration.txt’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
covr-package.html:36:133: Warning: inserting implicit <p>
covr-package.html:36:133: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Non-visible changes:
Package suggested but not available for checking: ‘L1pack’
'LazyData' is specified without a 'data' directory
Running examples in ‘cpss-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cpss.custom
> ### Title: Detecting changes in uers-customized models
> ### Aliases: cpss.custom
> 
> ### ** Examples
> 
> library("cpss")
> if (!requireNamespace("L1pack", quietly = TRUE)) {
+   stop("Please install the package \"L1pack\".")
+ }
Error: Please install the package "L1pack".
Execution halted
'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: ‘argosfilter’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gbm’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gbm’
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
Package required but not available: ‘gbm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following HTML validation problems:
plot-PseudoDualFlexiSimulations-missing-method.html:19:1: Warning: missing </h2> before <dl>
plot-PseudoDualFlexiSimulations-missing-method.html:32:28: Warning: discarding unexpected </h2>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
download_terraclimate.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
download_terraclimate.html:20:1: Warning: <img> proprietary attribute "logo"
eto_calibration.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
eto_calibration.html:20:1: Warning: <img> proprietary attribute "logo"
loadROI.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
loadROI.html:20:1: Warning: <img> proprietary attribute "logo"
monthly_stack.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
monthly_stack.html:20:1: Warning: <img> proprietary attribute "logo"
plot_AWC.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
plot_AWC.html:20:1: Warning: <img> proprietary attribute "logo"
ppt_calibration.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
ppt_calibration.html:20:1: Warning: <img> proprietary attribute "logo"
see_brazil_biomes.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
see_brazil_biomes.html:20:1: Warning: <img> proprietary attribute "logo"
see_brazil_states.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
see_brazil_states.html:20:1: Warning: <img> proprietary attribute "logo"
waterDemand.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
waterDemand.html:20:1: Warning: <img> proprietary attribute "logo"
'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
Found the following HTML validation problems:
ccrop_zoning.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
ccrop_zoning.html:20:1: Warning: <img> proprietary attribute "logo"
download_terraclimate.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
download_terraclimate.html:20:1: Warning: <img> proprietary attribute "logo"
loadROI.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
loadROI.html:20:1: Warning: <img> proprietary attribute "logo"
plot_ccrop_zoning.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
plot_ccrop_zoning.html:20:1: Warning: <img> proprietary attribute "logo"
see_brazil_biomes.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
see_brazil_biomes.html:20:1: Warning: <img> proprietary attribute "logo"
see_brazil_states.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
see_brazil_states.html:20:1: Warning: <img> proprietary attribute "logo"
tmax_calibration.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
tmax_calibration.html:20:1: Warning: <img> proprietary attribute "logo"
tmean.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
tmean.html:20:1: Warning: <img> proprietary attribute "logo"
tmean_monthly_stack.html:20:1: Warning: <img> attribute "width" has invalid value "auto"
tmean_monthly_stack.html:20:1: Warning: <img> proprietary attribute "logo"
Found the following HTML validation problems:
crossmap-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
crossmap-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
crosstable-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
crosstable-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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 math rendering problems:
geeDREstimation.Rd:112: Can't use function '$' in math mode in ...ymbol U_i^{1/2}$ with $\boldsym...
geeDREstimation.Rd:120: Can't use function '$' in math mode in ...dsymbol \eta}_W$ in $\boldsymbo...
geeDREstimation.Rd:120: Can't use function '$' in math mode in ...dsymbol \eta}_B$ in $\boldsymbo...
Found the following HTML validation problems:
AsyncQueue.html:102:6: Warning: missing </span> before <p>
AsyncQueue.html:102:92: Warning: inserting implicit <span>
AsyncQueue.html:102:6: Warning: trimming empty <span>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ctrdata-registers.html:85:230: Warning: <a> illegal characters found in URI
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Hello.csv’
GNU make is a SystemRequirements.
Found the following math rendering problems:
divonne.Rd:143: Can't use function '$' in math mode in $n=|key2|$
hcubature.Rd:124: Undefined control sequence: \L in \L_{\infty}
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘relsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Running ‘testthat.R’ [112s/173s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cvms)
  > 
  > test_check("cvms")
  [ FAIL 1 | WARN 0 | SKIP 70 | PASS 3622 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Fails in check - IMPROVE THESE TESTS (1)
  • On CRAN (58)
  • Skipping check for CRAN release due to r_hub failure (1)
  • Skipping parallel tests (3)
  • empty test (1)
  • keras and tensorflow take too long and have too many dependencies (1)
  • mac and ubuntu give different warnings (4)
  • tidymodels have too many dependencies (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_cross_validate.R:3476:5): varying number of folds in repeated cv with cross_validate() ──
  CV$Coefficients not equal to list(...).
  Component 1: Attributes: < Names: 19 string mismatches >
  Component 1: Attributes: < Length mismatch: comparison on first 32 components >
  Component 1: Attributes: < Component "ci_method": 1 string mismatch >
  Component 1: Attributes: < Component "df_method": 1 string mismatch >
  Component 1: Attributes: < Component 15: Modes: logical, character >
  Component 1: Attributes: < Component 15: target is logical, current is character >
  Component 1: Attributes: < Component 16: Modes: logical, character >
  Component 1: Attributes: < Component 16: target is logical, current is character >
  Component 1: Attributes: < Component 17: Modes: logical, numeric >
  ...
  
  [ FAIL 1 | WARN 0 | SKIP 70 | PASS 3622 ]
  Error: Test failures
  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.
Package suggested but not available for checking: ‘gbm’
Error(s) in re-building vignettes:
  ...
--- re-building ‘computeError.Rmd’ using rmarkdown
Loading required package: Matrix
Loaded glmnet 4.1-4

Attaching package: 'cvwrapr'

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

    coxnet.deviance

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

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

Attaching package: 'pls'

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

    loadings

Quitting from lines 233-253 (kfoldcv.Rmd) 
Error: processing vignette ‘kfoldcv.Rmd’ failed with diagnostics:
there is no package called 'gbm'
--- failed re-building ‘kfoldcv.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages which this enhances but not available for checking:
  'gurobi', 'rcbc'
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    CVXR pre-0.94-4
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following HTML validation problems:
spade.html:201:125: Warning: nested emphasis <strong>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
czso-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
czso-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following files/directories:
  ‘GRCh38_browser’ ‘GRCh38_map’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘gbm’
Running examples in ‘DALEXtra-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: explain_mlr
> ### Title: Create explainer from your mlr model
> ### Aliases: explain_mlr
> 
> ### ** Examples
> 
> library("DALEXtra")
> titanic_test <- read.csv(system.file("extdata", "titanic_test.csv", package = "DALEXtra"))
> titanic_train <- read.csv(system.file("extdata", "titanic_train.csv", package = "DALEXtra"))
> library("mlr")
Loading required package: ParamHelpers
Warning message: 'mlr' is in 'maintenance-only' mode since July 2019.
Future development will only happen in 'mlr3'
(<https://mlr3.mlr-org.com>). Due to the focus on 'mlr3' there might be
uncaught bugs meanwhile in {mlr} - please consider switching.
> task <- mlr::makeClassifTask(
+ id = "R",
+ data = titanic_train,
+ target = "survived"
+ )
> learner <- mlr::makeLearner(
+   "classif.gbm",
+   par.vals = list(
+     distribution = "bernoulli",
+     n.trees = 500,
+     interaction.depth = 4,
+     n.minobsinnode = 12,
+     shrinkage = 0.001,
+     bag.fraction = 0.5,
+     train.fraction = 1
+   ),
+   predict.type = "prob"
+ )
Error in requirePackages(package, why = stri_paste("learner", id, sep = " "),  : 
  For learner classif.gbm please install the following packages: gbm
Calls: <Anonymous> ... addClasses -> makeRLearnerInternal -> requirePackages -> stopf
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 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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    dataquieR (1.0.8)
    dataquieR (1.0.7)
    dataquieR (1.0.6)
    dataquieR (1.0.0)
Found the following HTML validation problems:
acc_robust_univariate_outlier.html:128:4: Warning: nested emphasis <em>
acc_univariate_outlier.html:128:4: Warning: nested emphasis <em>
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:
  fread.c:1278:38: warning: the comparison will always evaluate as ‘false’ for the pointer operand in ‘nastr + 8’ must not be NULL [-Waddress]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/data.table.Rcheck/00install.out’ for details.
Found the following HTML validation problems:
get_dated_otol_induced_subtree.html:53:1: Warning: trimming empty <dt>
get_otol_synthetic_tree.html:67:1: Warning: trimming empty <dt>
summary_matrix_to_phylo.html:89:1: Warning: trimming empty <dt>
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
datos-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
datos-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
dbflobr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
dbflobr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    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
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.
'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 ‘chytrid_dede_example.Rmd’ using rmarkdown
Loading required package: deSolve
Order of initial conditions is  C, S, Z
initial posterior probability = -13968.8205931737
Quitting from lines 201-204 (chytrid_dede_example.Rmd) 
Error: processing vignette ‘chytrid_dede_example.Rmd’ failed with diagnostics:
bandwidths must be strictly positive
--- failed re-building ‘chytrid_dede_example.Rmd’

--- re-building ‘logistic_ode_example.Rmd’ using rmarkdown
Order of initial conditions is  N
initial posterior probability = -7868.61983481059
--- finished re-building ‘logistic_ode_example.Rmd’

--- re-building ‘deBInfer_compiled_code.pdf.asis’ using asis
--- finished re-building ‘deBInfer_compiled_code.pdf.asis’

SUMMARY: processing the following file failed:
  ‘chytrid_dede_example.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
Found the following HTML validation problems:
validate_arguments.html:83:111: Warning: inserting implicit <p>
validate_arguments.html:87:95: Warning: inserting implicit <p>
validate_arguments.html:94:51: Warning: inserting implicit <p>
validate_arguments.html:83:111: Warning: trimming empty <p>
validate_arguments.html:87:95: Warning: trimming empty <p>
validate_arguments.html:94:51: Warning: trimming empty <p>
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
GNU make is a SystemRequirements.
Found the following HTML validation problems:
fit.dl.html:19:1: Warning: missing </h2> before <ol>
fit.dl.html:34:1: Warning: discarding unexpected </h2>
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'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 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
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’
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 math rendering problems:
BinomRatioCI.rd:88-89: Can't use function '$' in math mode in ...{\theta }_{0}}}$, and ${{X}^{2}...
StdCoef.Rd:71: Undefined control sequence: \var in ...^{*}=s_{X_{i}} \var{VIF}(X_i)^{-0....
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 required but not available: ‘MLInterfaces’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) phihat.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) anova.dglm.Rd:41: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
dialr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
dialr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
diceR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
diceR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
did_imputation.html:125:104: Warning: inserting implicit <p>
did_imputation.html:133:96: Warning: inserting implicit <p>
did_imputation.html:146:99: Warning: inserting implicit <p>
did_imputation.html:169:78: Warning: inserting implicit <p>
did_imputation.html:125:104: Warning: trimming empty <p>
did_imputation.html:133:96: Warning: trimming empty <p>
did_imputation.html:146:99: Warning: trimming empty <p>
did_imputation.html:169:78: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
dimensio-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
dimensio-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) eul2rot.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) multivm.mle.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) rot2eul.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) spml.mle.Rd:78: Escaped LaTeX specials: \&
'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’
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
fit_model.Rd:97: Can't use function '$' in math mode in \sigma_{min}$ and $\sigma_{p...
make_model_object.Rd:64: Can't use function '$' in math mode in \sigma_{min}$ and $\sigma_{p...
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
disastr.api.html:125:40: Warning: missing </a> before <a>
disastr.api.html:125:151: Warning: discarding unexpected </a>
checkRd: (-1) sammy.Rd:51: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'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
Package suggested but not available for checking: ‘gbm’
Running examples in ‘dismo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gbm.step
> ### Title: gbm step
> ### Aliases: gbm.step
> ### Keywords: spatial
> 
> ### ** Examples
> 
> data(Anguilla_train)
> # reduce data set to speed things up a bit
> Anguilla_train = Anguilla_train[1:200,]
> angaus.tc5.lr01 <- gbm.step(data=Anguilla_train, gbm.x = 3:14, gbm.y = 2, family = "bernoulli",
+        tree.complexity = 5, learning.rate = 0.01, bag.fraction = 0.5)
Loading required namespace: gbm
Failed with error:  ‘there is no package called ‘gbm’’
Error in gbm.step(data = Anguilla_train, gbm.x = 3:14, gbm.y = 2, family = "bernoulli",  : 
  you need to install the gbm package to run this function
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
amakihi.html:85:6: Warning: <a> illegal characters found in URI
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
DistAlgo.Rd:10: Undefined control sequence: \time in 6\times6\time4
GraphDistatisAll.Rd:24: Undefined control sequence: \time in I\time 1
GraphDistatisAll.Rd:26: Undefined control sequence: \time in I\time 1
GraphDistatisCompromise.Rd:21: Undefined control sequence: \time in I\time 1
GraphDistatisPartial.Rd:23: Undefined control sequence: \time in I\time 1
GraphDistatisPartial.Rd:25: Undefined control sequence: \time in I\time 1
GraphDistatisRv.Rd:27: Undefined control sequence: \time in I\time 1
Found the following HTML validation problems:
HEQueryCountMaster.html:88:6: Warning: missing </span> before <p>
HEQueryCountMaster.html:88:100: Warning: inserting implicit <span>
HEQueryCountMaster.html:91:6: Warning: missing </span> before <p>
HEQueryCountMaster.html:91:101: Warning: inserting implicit <span>
HEQueryCountMaster.html:88:6: Warning: trimming empty <span>
HEQueryCountMaster.html:91:6: Warning: trimming empty <span>
HEQueryCountWorker.html:74:6: Warning: missing </span> before <p>
HEQueryCountWorker.html:74:104: Warning: inserting implicit <span>
HEQueryCountWorker.html:77:6: Warning: missing </span> before <p>
HEQueryCountWorker.html:77:99: Warning: inserting implicit <span>
HEQueryCountWorker.html:74:6: Warning: trimming empty <span>
HEQueryCountWorker.html:77:6: Warning: trimming empty <span>
'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: \&
Found the following HTML validation problems:
create_theme.html:55:112: Warning: inserting implicit <p>
create_theme.html:64:58: Warning: inserting implicit <p>
create_theme.html:55:112: Warning: trimming empty <p>
create_theme.html:64:58: Warning: trimming empty <p>
distill-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
distill-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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 HTML validation problems:
divDyn.html:138:81: Warning: <em> is probably intended as </em>
divDyn.html:138:96: Warning: discarding unexpected </em>
divDyn.html:138:130: Warning: discarding unexpected </em>
divDyn.html:140:82: Warning: <em> is probably intended as </em>
divDyn.html:140:97: Warning: discarding unexpected </em>
divDyn.html:140:131: Warning: discarding unexpected </em>
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 math rendering problems:
Dixon.Rd:56-66: Unknown column alignment: [ in 
  \begin{array}[h]{lcl}
  f(r) & ...
'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
Found the following HTML validation problems:
make_index.html:92:55: Warning: nested emphasis <b>
Package required but not available: ‘gbm’

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
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: \#
Found the following HTML validation problems:
dobin-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
dobin-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without 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’.
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
Found the following HTML validation problems:
downloadthis-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
downloadthis-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
across.html:114:90: Warning: inserting implicit <p>
across.html:114:90: Warning: trimming empty <p>
select.html:176:41: Warning: inserting implicit <p>
select.html:182:55: Warning: inserting implicit <p>
select.html:204:85: Warning: inserting implicit <p>
select.html:216:96: Warning: inserting implicit <p>
select.html:231:99: Warning: inserting implicit <p>
select.html:242:78: Warning: inserting implicit <p>
select.html:274:121: Warning: inserting implicit <p>
select.html:296:52: Warning: inserting implicit <p>
select.html:176:41: Warning: trimming empty <p>
select.html:182:55: Warning: trimming empty <p>
select.html:204:85: Warning: trimming empty <p>
select.html:216:96: Warning: trimming empty <p>
select.html:231:99: Warning: trimming empty <p>
select.html:242:78: Warning: trimming empty <p>
select.html:274:121: Warning: trimming empty <p>
select.html:296:52: Warning: trimming empty <p>
Found the following HTML validation problems:
LinearRegressionDP.html:86:6: Warning: missing </span> before <p>
LinearRegressionDP.html:86:113: Warning: inserting implicit <span>
LinearRegressionDP.html:86:6: Warning: trimming empty <span>
'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
Found the following HTML validation problems:
make.html:800:24: Warning: inserting implicit <p>
make.html:800:24: Warning: trimming empty <p>
Found the following HTML validation problems:
canvas.html:147:49: Warning: inserting implicit <p>
canvas.html:160:130: Warning: inserting implicit <p>
canvas.html:147:49: Warning: trimming empty <p>
canvas.html:160:130: Warning: trimming empty <p>
'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
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following math rendering problems:
cdfDRM.Rd:21: Undefined control sequence: \textsuperscript in \textsuperscript{th}
cdfDRM.Rd:42: Undefined control sequence: \textsuperscript in \textsuperscript{th}
densityDRM.Rd:12: Undefined control sequence: \textsuperscript in \textsuperscript{th}
quantileDRM.Rd:52: Undefined control sequence: \textsuperscript in \textsuperscript{th}
quantileDRM.Rd:77: Undefined control sequence: \textsuperscript in \textsuperscript{th}
quantileDRM.Rd:79: Undefined control sequence: \textsuperscript in \textsuperscript{th}
quantileDRM.Rd:89: Undefined control sequence: \textsuperscript in \textsuperscript{th}
quantileDRM.Rd:108: Undefined control sequence: \textsuperscript in \textsuperscript{th}
'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
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
Found the following HTML validation problems:
dtplyr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
dtplyr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
dttr2-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
dttr2-package.html:30:4: Warning: <img> attribute "align" not allowed for HTML5
dttr2-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
dttr2-package.html:30:4: Warning: <img> attribute "align" not allowed for HTML5
GNU make is a SystemRequirements.
Found the following HTML validation problems:
dual-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
dual-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without 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.
checkRd: (-1) dynaTree.Rd:265: Escaped LaTeX specials: \&
checkRd: (-1) dynaTree.Rd:270: Escaped LaTeX specials: \&
checkRd: (-1) relevance.dynaTree.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) sens.dynaTree.Rd:140: Escaped LaTeX specials: \&
'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
'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
'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
Found the following HTML validation problems:
easycensus-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
easycensus-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: There's no line here to end.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...
Found the following files/directories:
  ‘eat-manual.tex’
Package required but not available: ‘gbm’

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: ‘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
Found the following HTML validation problems:
EcoDiet-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
EcoDiet-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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.
Packages required but not available: 'gbm', 'biomod2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ecomix’
'LazyData' is specified without 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:
  ‘tmplp.dat’
'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
Found the following HTML validation problems:
edibble-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
edibble-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [13s/37s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(EDIutils)
  > 
  > test_check("EDIutils")
  [ FAIL 1 | WARN 0 | SKIP 15 | PASS 144 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Not run when logged out. Login with 'login()'. (12)
  • empty test (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_utilities.R:91:3): xml2df() works ───────────────────────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [pasta.lternet.edu] Connection timeout after 10001 ms
  Backtrace:
      ▆
   1. └─EDIutils::read_data_package_report_resource_metadata(...) at test_utilities.R:91:2
   2.   └─httr::GET(url, set_user_agent(), handle = httr::handle(""))
   3.     └─httr:::request_perform(req, hu$handle$handle)
   4.       ├─httr:::request_fetch(req$output, req$url, handle)
   5.       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   6.         └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 0 | SKIP 15 | PASS 144 ]
  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 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
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 HTML validation problems:
elbird-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
elbird-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
embryogrowth-package.html:27:1: Warning: <img> attribute "," lacks value
embryogrowth-package.html:27:1: Warning: <img> attribute "align" not allowed for HTML5
embryogrowth-package.html:27:1: Warning: <img> attribute "align" not allowed for HTML5
Package which this enhances but not available for checking: ‘PPtree’
Found the following math rendering problems:
a0_project.on.2d.Rd:39: Undefined control sequence: \time in p \time 2
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  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
'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’
Package required but not available: ‘gbm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EnsembleBase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EnsembleBase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EnsembleBase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) check_several.Rd:34: Escaped LaTeX specials: \#
checkRd: (-1) check_several.Rd:35: Escaped LaTeX specials: \#
Found the following HTML validation problems:
attach_source.html:105:96: Warning: inserting implicit <p>
attach_source.html:111:52: Warning: inserting implicit <p>
attach_source.html:119:55: Warning: inserting implicit <p>
attach_source.html:105:96: Warning: trimming empty <p>
attach_source.html:111:52: Warning: trimming empty <p>
attach_source.html:119:55: Warning: trimming empty <p>
set_library_default_pos.html:59:104: Warning: inserting implicit <p>
set_library_default_pos.html:59:104: Warning: trimming empty <p>
Found the following math rendering problems:
Mguttatus.Rd:35: Undefined control sequence: \emph in \emph{PLoS Biol}
eigenboot.Rd:101: Undefined control sequence: \emph in \emph{in prep}
eigenbootcanon.Rd:106: Undefined control sequence: \emph in \emph{in prep}
fit_boot_Efron.Rd:191: Undefined control sequence: \emph in \emph{in prep}
fit_boot_Efron.Rd:195: Undefined control sequence: \emph in \emph{in prep}
fit_boot_Efron.Rd:199: Undefined control sequence: \emph in \emph{JASA}
secondboot.Rd:154: Undefined control sequence: \emph in \emph{in prep}
secondboot.Rd:158: Undefined control sequence: \emph in \emph{in prep}
secondboot.Rd:162: Undefined control sequence: \emph in \emph{JASA}
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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
GNU make is a SystemRequirements.
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: ‘EpiSoon’
'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
checkRd: (-1) ergm-package.Rd:105: Escaped LaTeX specials: \#
checkRd: (-1) ergm.Rd:441: Escaped LaTeX specials: \#
checkRd: (-1) faux.mesa.high.Rd:45: Escaped LaTeX specials: \&
checkRd: (-1) florentine.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) florentine.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) florentine.Rd:39: Escaped LaTeX specials: \&
Found the following HTML validation problems:
Error.html:61:6: Warning: missing </span> before <p>
Error.html:61:88: Warning: inserting implicit <span>
Error.html:64:6: Warning: missing </span> before <p>
Error.html:64:86: Warning: inserting implicit <span>
Error.html:67:6: Warning: missing </span> before <p>
Error.html:67:86: Warning: inserting implicit <span>
Error.html:70:6: Warning: missing </span> before <p>
Error.html:70:86: Warning: inserting implicit <span>
Error.html:73:6: Warning: missing </span> before <p>
Error.html:73:87: Warning: inserting implicit <span>
Error.html:61:6: Warning: trimming empty <span>
Error.html:64:6: Warning: trimming empty <span>
Error.html:67:6: Warning: trimming empty <span>
Error.html:70:6: Warning: trimming empty <span>
Error.html:73:6: Warning: trimming empty <span>
Warning.html:58:6: Warning: missing </span> before <p>
Warning.html:58:88: Warning: inserting implicit <span>
Warning.html:61:6: Warning: missing </span> before <p>
Warning.html:61:86: Warning: inserting implicit <span>
Warning.html:64:6: Warning: missing </span> before <p>
Warning.html:64:86: Warning: inserting implicit <span>
Warning.html:67:6: Warning: missing </span> before <p>
Warning.html:67:86: Warning: inserting implicit <span>
Warning.html:70:6: Warning: missing </span> before <p>
Warning.html:70:87: Warning: inserting implicit <span>
Warning.html:58:6: Warning: trimming empty <span>
Warning.html:61:6: Warning: trimming empty <span>
Warning.html:64:6: Warning: trimming empty <span>
Warning.html:67:6: Warning: trimming empty <span>
Warning.html:70:6: Warning: trimming empty <span>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
ic.proporcion.html:77:4: Warning: <img> attribute with missing trailing quote mark
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
EstCRMitem.Rd:54-56: Undefined control sequence: \emph in 
  \emph{f}(z_{ij}|\the...
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
Found the following HTML validation problems:
ebc_allmeasures.html:41:4: Warning: <img> attribute "align" not allowed for HTML5
ebc_allmeasures.html:41:4: Warning: <img> attribute "align" not allowed for HTML5
'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: \&
checkRd: (-1) exams2blackboard.Rd:152: Escaped LaTeX specials: \&
checkRd: (-1) exams2qti12.Rd:186: 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
Found the following HTML validation problems:
exoplanets-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
exoplanets-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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’
Found the following HTML validation problems:
exuber.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
exuber.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
'LazyData' is specified without a 'data' directory
Package required but not available: ‘gbm’

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
Found the following HTML validation problems:
fable-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
fable-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Package suggested but not available for checking: ‘gbm’
Running examples in ‘fairmodels-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: reweight
> ### Title: Reweight
> ### Aliases: reweight
> 
> ### ** Examples
> 
> data("german")
> 
> data <- german
> data$Age <- as.factor(ifelse(data$Age <= 25, "young", "old"))
> data$Risk <- as.numeric(data$Risk) - 1
> 
> # training 2 models
> weights <- reweight(protected = data$Age, y = data$Risk)
> 
> gbm_model <- gbm::gbm(Risk ~ ., data = data)
Error in loadNamespace(x) : there is no package called ‘gbm’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fairmodels)
  > 
  > 
  > test_check("fairmodels")
  Welcome to DALEX (version: 2.4.2).
  Find examples and detailed introduction at: http://ema.drwhy.ai/
  Additional features will be available after installation of: ggpubr.
  Use 'install_dependencies()' to get all suggested dependencies
  Error in library("gbm") : there is no package called 'gbm'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Advanced_tutorial.Rmd’ using rmarkdown
Quitting from lines 49-67 (Advanced_tutorial.Rmd) 
Error: processing vignette ‘Advanced_tutorial.Rmd’ failed with diagnostics:
there is no package called 'gbm'
--- failed re-building ‘Advanced_tutorial.Rmd’

--- re-building ‘Basic_tutorial.Rmd’ using rmarkdown
Welcome to DALEX (version: 2.4.2).
Find examples and detailed introduction at: http://ema.drwhy.ai/

Quitting from lines 125-150 (Basic_tutorial.Rmd) 
Error: processing vignette ‘Basic_tutorial.Rmd’ failed with diagnostics:
there is no package called 'gbm'
--- failed re-building ‘Basic_tutorial.Rmd’

SUMMARY: processing the following files failed:
  ‘Advanced_tutorial.Rmd’ ‘Basic_tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
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
Found the following math rendering problems:
simul.far.Rd:51-57: Unknown column alignment: [ in ...t(\begin{array}[c]{lc}%
      \co...
simul.far.Rd:82-88: Unknown column alignment: [ in ...t(\begin{array}[c]{lc}%
      m_2...
simul.far.wiener.Rd:34-40: Unknown column alignment: [ in ...t(\begin{array}[c]{lc}%
      \co...
simul.farx.Rd:81-87: Unknown column alignment: [ in ...t(\begin{array}[c]{lc}%
      d.r...
simul.farx.Rd:109-115: Unknown column alignment: [ in ...t(\begin{array}[c]{lc}%
      alp...
'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 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
'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
'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 HTML validation problems:
fastRhockey-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
fastRhockey-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
.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 HTML validation problems:
fauxnaif-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
fauxnaif-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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’
GNU make is a SystemRequirements.
checkRd: (-1) summary.fdata.comp.Rd:44: Escaped LaTeX specials: \&
Found the following HTML validation problems:
GCCV.S.html:87:32: Warning: trimming empty <code>
Found the following math rendering problems:
fregre.plm.Rd:86-87: Undefined control sequence: \emph in y =\emph{r(X)}+\sum_{j=...
metric.kl.Rd:45-46: Undefined control sequence: \- in \left|f_i(t)\-g_i(t) \right|\...
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Other Changes
Found the following HTML validation problems:
dfddm.html:192:1: Warning: unescaped & or unknown entity "&#8734"
pfddm.html:56:2: Warning: unescaped & or unknown entity "&#8734"
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘vert.txt’
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
feasts-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
feasts-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gbm’
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
Found the following HTML validation problems:
fec16.html:29:4: Warning: <img> attribute "align" not allowed for HTML5
fec16.html:29:4: Warning: <img> attribute "align" not allowed for HTML5
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
'LazyData' is specified without a 'data' directory
'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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    ffp (development version)
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: \_
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixes
Found the following HTML validation problems:
ffsimulator-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ffsimulator-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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:
plot_tag_status_by_subquadrat.html:92:96: Warning: inserting implicit <p>
plot_tag_status_by_subquadrat.html:92:96: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
add_subquad.html:54:75: Warning: inserting implicit <p>
add_subquad.html:54:75: Warning: trimming empty <p>
recode_subquad.html:39:45: Warning: inserting implicit <p>
recode_subquad.html:39:45: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MicrobeDS’
Found the following HTML validation problems:
optimMaltipooCollapsed.html:173:41: Warning: <em> is probably intended as </em>
optimMaltipooCollapsed.html:173:68: Warning: discarding unexpected </em>
optimMaltipooCollapsed.html:173:76: Warning: discarding unexpected </em>
Found the following HTML validation problems:
fiery-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
fiery-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
Found the following HTML validation problems:
finetune-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
finetune-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
tune_race_anova.html:139:103: Warning: inserting implicit <p>
tune_race_anova.html:155:93: Warning: inserting implicit <p>
tune_race_anova.html:180:47: Warning: inserting implicit <p>
tune_race_anova.html:200:63: Warning: inserting implicit <p>
tune_race_anova.html:220:50: Warning: inserting implicit <p>
tune_race_anova.html:139:103: Warning: trimming empty <p>
tune_race_anova.html:155:93: Warning: trimming empty <p>
tune_race_anova.html:180:47: Warning: trimming empty <p>
tune_race_anova.html:200:63: Warning: trimming empty <p>
tune_race_anova.html:220:50: Warning: trimming empty <p>
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’
Found the following HTML validation problems:
SpotRate-class.html:55:64: Warning: inserting implicit <p>
SpotRate-class.html:63:95: Warning: inserting implicit <p>
SpotRate-class.html:71:54: Warning: inserting implicit <p>
SpotRate-class.html:75:66: Warning: inserting implicit <p>
SpotRate-class.html:79:74: Warning: inserting implicit <p>
SpotRate-class.html:93:75: Warning: inserting implicit <p>
SpotRate-class.html:107:106: Warning: inserting implicit <p>
SpotRate-class.html:125:61: Warning: inserting implicit <p>
SpotRate-class.html:155:111: Warning: inserting implicit <p>
SpotRate-class.html:55:64: Warning: trimming empty <p>
SpotRate-class.html:63:95: Warning: trimming empty <p>
SpotRate-class.html:71:54: Warning: trimming empty <p>
SpotRate-class.html:75:66: Warning: trimming empty <p>
SpotRate-class.html:79:74: Warning: trimming empty <p>
SpotRate-class.html:93:75: Warning: trimming empty <p>
SpotRate-class.html:107:106: Warning: trimming empty <p>
SpotRate-class.html:125:61: Warning: trimming empty <p>
SpotRate-class.html:155:111: Warning: trimming empty <p>
Term-class.html:33:39: Warning: inserting implicit <p>
Term-class.html:38:102: Warning: inserting implicit <p>
Term-class.html:44:102: Warning: inserting implicit <p>
Term-class.html:49:62: Warning: inserting implicit <p>
Term-class.html:59:60: Warning: inserting implicit <p>
Term-class.html:33:39: Warning: trimming empty <p>
Term-class.html:38:102: Warning: trimming empty <p>
Term-class.html:44:102: Warning: trimming empty <p>
Term-class.html:49:62: Warning: trimming empty <p>
Term-class.html:59:60: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
checkRd: (-1) etable.Rd:494: Escaped LaTeX specials: \$
'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 HTML validation problems:
flexpolyline-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
flexpolyline-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘relsurv’
Running examples in ‘flexrsurv-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getBrassHazardFromTable
> ### Title: Compute expected hazards with respect to a corrected reference
> ###   life table
> ### Aliases: getBrassHazardFromTable getBrassPseudoHazardFromTable
> ### Keywords: survival
> 
> ### ** Examples
> 
> require(date)
Loading required package: date
> # data from package relsurv
> data(rdata, package="relsurv")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘relsurv’
Calls: data -> find.package
Execution halted
Found the following HTML validation problems:
GenF.html:115:32: Warning: trimming empty <code>
'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:
flobr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
flobr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
flow-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
flow-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
Found the following HTML validation problems:
folio-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
folio-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Found the following HTML validation problems:
forcats-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
forcats-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
checkRd: (-1) fpColors.Rd:59: 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
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
Found the following math rendering problems:
Approx.cfpt.density.rd:41-46: Undefined control sequence: \vspace in ...} x_0 < S(t_0) \vspace{5pt} \\
  \mbox{...
Approx.fpt.density.rd:66-71: Undefined control sequence: \vspace in ...(t_0) < S(t_0) \vspace{5pt} \\
  \mbox{...
FPTL.Rd:37-42: Undefined control sequence: \vspace in ...} x_0 < S(t_0) \vspace{5pt} \\
  P[ X(t...
Integration.Steps.Rd:42-43: Undefined control sequence: \smallskip in ...box{for i odd} \smallskip \\ t_{max, \thi...
Integration.Steps.Rd:67-71: Undefined control sequence: \vspace in ...{i,j}^* \leq 1 \vspace{0.25cm} \\
     ...
Integration.Steps.Rd:78-82: Undefined control sequence: \vspace in ...{0,j}^* \leq 1 \vspace{0.25cm} \\
     ...
Integration.Steps.Rd:91-95: Undefined control sequence: \vspace in ..._j,j}^* \leq 1 \vspace{0.25cm} \\
     ...
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
Found the following math rendering problems:
cov.structure.Rd:35: Can't use function '$' in math mode in ...sum_{t=1}^T X_t$ and $\hat\mu^Y...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CatalogueAccessors.Rd:249: Escaped LaTeX specials: \^ \^
checkRd: (-1) FrF2.Rd:574: Escaped LaTeX specials: \^
checkRd: (-1) FrF2.Rd:629: Escaped LaTeX specials: \^ \^
checkRd: (-1) IAPlot.Rd:87: Escaped LaTeX specials: \$
checkRd: (-1) block.Rd:121: Escaped LaTeX specials: \^
checkRd: (-1) block.Rd:150: Escaped LaTeX specials: \^ \^
checkRd: (-1) blockpick.Rd:114: Escaped LaTeX specials: \^ \^
Found the following HTML validation problems:
read_resource.html:125:57: Warning: inserting implicit <p>
read_resource.html:125:57: Warning: trimming empty <p>
Packages suggested but not available for checking: 'dggrids', 'INLA'
Found the following HTML validation problems:
SRE.html:290:1: Warning: inserting implicit <p>
SRE.html:321:1: Warning: inserting implicit <p>
SRE.html:290:1: Warning: trimming empty <p>
SRE.html:321:1: Warning: trimming empty <p>
Unknown package ‘frm’ in Rd xrefs
Unknown package ‘frm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'bst', 'extraTrees', 'foba', 'gbm', 'nodeHarvest', 'obliqueRF',
  'relaxo', 'rrlda'
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
fso.Rd:44: Can't use function '$' in math mode in (correlations $>=$ observed + ...
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.
Found the following HTML validation problems:
fd_fric.html:105:6: Warning: <a> illegal characters found in URI
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
furrr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
furrr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
fusen-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
fusen-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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’
Found the following HTML validation problems:
future.apply.html:77:104: Warning: inserting implicit <p>
future.apply.html:80:43: Warning: inserting implicit <p>
future.apply.html:84:48: Warning: inserting implicit <p>
future.apply.html:89:58: Warning: inserting implicit <p>
future.apply.html:95:94: Warning: inserting implicit <p>
future.apply.html:99:79: Warning: inserting implicit <p>
future.apply.html:77:104: Warning: trimming empty <p>
future.apply.html:80:43: Warning: trimming empty <p>
future.apply.html:84:48: Warning: trimming empty <p>
future.apply.html:89:58: Warning: trimming empty <p>
future.apply.html:95:94: Warning: trimming empty <p>
future.apply.html:99:79: Warning: trimming empty <p>
future_lapply.html:303:105: Warning: inserting implicit <p>
future_lapply.html:303:105: Warning: trimming empty <p>
Found the following HTML validation problems:
future.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
future.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
multiprocess.html:28:1: Warning: nested emphasis <em>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
FuzzyClass-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
FuzzyClass-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without 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:
got.html:90:36: Warning: <img> attribute with missing trailing quote mark
got.html:91:1: Warning: inserting implicit <p>
got.html:91:1: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'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 math rendering problems:
DEL.Rd:47: Undefined control sequence: \matrix in ...=0}^{y} \left( \matrix{ y \cr j } \ri...
'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: \&
checkRd: (-1) mia.Rd:39: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following HTML validation problems:
Gargle-class.html:112:6: Warning: missing </span> before <p>
Gargle-class.html:112:92: Warning: inserting implicit <span>
Gargle-class.html:115:6: Warning: missing </span> before <p>
Gargle-class.html:115:87: Warning: inserting implicit <span>
Gargle-class.html:118:6: Warning: missing </span> before <p>
Gargle-class.html:118:85: Warning: inserting implicit <span>
Gargle-class.html:121:6: Warning: missing </span> before <p>
Gargle-class.html:121:89: Warning: inserting implicit <span>
Gargle-class.html:112:6: Warning: trimming empty <span>
Gargle-class.html:115:6: Warning: trimming empty <span>
Gargle-class.html:118:6: Warning: trimming empty <span>
Gargle-class.html:121:6: Warning: trimming empty <span>
GceToken.html:80:6: Warning: missing </span> before <p>
GceToken.html:80:82: Warning: inserting implicit <span>
GceToken.html:83:6: Warning: missing </span> before <p>
GceToken.html:83:88: Warning: inserting implicit <span>
GceToken.html:86:6: Warning: missing </span> before <p>
GceToken.html:86:85: Warning: inserting implicit <span>
GceToken.html:89:6: Warning: missing </span> before <p>
GceToken.html:89:89: Warning: inserting implicit <span>
GceToken.html:80:6: Warning: trimming empty <span>
GceToken.html:83:6: Warning: trimming empty <span>
GceToken.html:86:6: Warning: trimming empty <span>
GceToken.html:89:6: Warning: trimming empty <span>
WifToken.html:88:6: Warning: missing </span> before <p>
WifToken.html:88:82: Warning: inserting implicit <span>
WifToken.html:91:6: Warning: missing </span> before <p>
WifToken.html:91:85: Warning: inserting implicit <span>
WifToken.html:88:6: Warning: trimming empty <span>
WifToken.html:91:6: Warning: trimming empty <span>
'LazyData' is specified without a 'data' directory
Running examples in ‘gasper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HPFVN
> ### Title: High Pass Filter Von Neumann Estimator.
> ### Aliases: HPFVN
> 
> ### ** Examples
> 
> matrixname <- "grid1"
> groupname <- "AG-Monien"
> graph <- download_graph(matrixname,groupname)
trying URL 'https://sparse.tamu.edu/MM/AG-Monien/grid1.tar.gz'
Warning in download.file(url, temp) :
  URL 'https://sparse.tamu.edu/MM/AG-Monien/grid1.tar.gz': status was 'SSL peer certificate or SSH remote key was not OK'
Error in download.file(url, temp) : 
  cannot open URL 'https://sparse.tamu.edu/MM/AG-Monien/grid1.tar.gz'
Calls: download_graph -> download.file
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gasper_vignette.rmd’ using rmarkdown
trying URL ‘https://sparse.tamu.edu/MM/AG-Monien/grid1.tar.gz’
Quitting from lines 52-56 (gasper_vignette.rmd) 
Error: processing vignette ‘gasper_vignette.rmd’ failed with diagnostics:
cannot open URL ‘https://sparse.tamu.edu/MM/AG-Monien/grid1.tar.gz’
--- failed re-building ‘gasper_vignette.rmd’

SUMMARY: processing the following file failed:
  ‘gasper_vignette.rmd’

Error: Vignette re-building failed.
Execution halted
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 HTML validation problems:
gbfs.html:32:4: Warning: <img> attribute "align" not allowed for HTML5
gbfs.html:32:4: Warning: <img> attribute "align" not allowed for HTML5
Package required but not available: ‘gbm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gbm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gbm.Rcheck/00install.out’ for details.
'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 required but not available: ‘gbm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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’.
Found the following math rendering problems:
GDINA.Rd:367: Can't use function '$' in math mode in ...,\cdots,K_j^*-1$, and $k^{''}>k...
Found the following HTML validation problems:
gdistance.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
gdistance.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Package suggested but not available for checking: ‘gdxrrw’
'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) 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
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.
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 HTML validation problems:
geniusr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
geniusr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [87s/142s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(GenomeAdmixR) # nolint
  > 
  > test_check("GenomeAdmixR")
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |===================================                                   |  50%
    |                                                                            
    |======================================================================| 100%[ FAIL 1 | WARN 0 | SKIP 0 | PASS 454 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-simulate_admixture_data.R:202:3): simulate_admixture_data_recombination_map ──
  `all_j` not equal to `expected_num_j`.
  1/1 mismatches
  [1] 68 - 100 == -32
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 454 ]
  Error: Test failures
  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
'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 math rendering problems:
geo_fkf.Rd:19: Undefined control sequence: \- in [\-pi, \pi]
checkRd: (-1) predict.geoGAM.Rd:86: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘geomarocdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Paragraph ended before \Rd@code@wrk was complete.
<to be read again> 
                   \par 
l.308 
      
! Paragraph ended before \Rd@code@wrk was complete.
<to be read again> 
                   \par 
l.316 
      
! Paragraph ended before \Rd@code@wrk was complete.
<to be read again> 
                   \par 
l.323 
      
! Paragraph ended before \Rd@code@wrk was complete.
<to be read again> 
                   \par 
l.343
Found the following files/directories:
  ‘geomedb-manual.tex’
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
extprod3d.html:24:32: Warning: trimming empty <code>
extprod3d.html:29:32: Warning: trimming empty <code>
Found the following HTML validation problems:
geomtextpath-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
geomtextpath-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following math rendering problems:
pendulum.Rd:19: Undefined control sequence: \time in n \time 2
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
Found the following HTML validation problems:
WeightGermPercent.html:78:1: Warning: <em> is probably intended as </em>
WeightGermPercent.html:78:143: Warning: discarding unexpected </em>
WeightGermPercent.html:78:162: Warning: discarding unexpected </em>
germination.indices.html:445:1: Warning: <em> is probably intended as </em>
germination.indices.html:445:143: Warning: discarding unexpected </em>
germination.indices.html:445:162: Warning: discarding unexpected </em>
'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
Found the following HTML validation problems:
gganimate-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
gganimate-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
ggbraid-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggbraid-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘RSDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ggforce-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggforce-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
ggfx-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggfx-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
object_support.html:69:131: Warning: inserting implicit <p>
object_support.html:93:53: Warning: inserting implicit <p>
object_support.html:110:77: Warning: inserting implicit <p>
object_support.html:125:23: Warning: inserting implicit <p>
object_support.html:143:67: Warning: inserting implicit <p>
object_support.html:150:88: Warning: inserting implicit <p>
object_support.html:161:28: Warning: inserting implicit <p>
object_support.html:69:131: Warning: trimming empty <p>
object_support.html:93:53: Warning: trimming empty <p>
object_support.html:110:77: Warning: trimming empty <p>
object_support.html:125:23: Warning: trimming empty <p>
object_support.html:143:67: Warning: trimming empty <p>
object_support.html:150:88: Warning: trimming empty <p>
object_support.html:161:28: Warning: trimming empty <p>
'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:
ggh4x-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggh4x-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
gghdr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
gghdr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ggip-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggip-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
guide_bins_interactive.html:50:23: Warning: nested emphasis <em>
guide_colourbar_interactive.html:52:23: Warning: nested emphasis <em>
guide_coloursteps_interactive.html:52:23: Warning: nested emphasis <em>
guide_legend_interactive.html:50:23: Warning: nested emphasis <em>
ipar.html:104:23: Warning: nested emphasis <em>
scale_alpha_interactive.html:70:23: Warning: nested emphasis <em>
scale_colour_brewer_interactive.html:73:23: Warning: nested emphasis <em>
scale_colour_interactive.html:105:23: Warning: nested emphasis <em>
scale_colour_steps_interactive.html:73:23: Warning: nested emphasis <em>
scale_gradient_interactive.html:73:23: Warning: nested emphasis <em>
scale_linetype_interactive.html:61:23: Warning: nested emphasis <em>
scale_manual_interactive.html:72:23: Warning: nested emphasis <em>
scale_shape_interactive.html:64:23: Warning: nested emphasis <em>
scale_size_interactive.html:79:23: Warning: nested emphasis <em>
scale_viridis_interactive.html:81:23: Warning: nested emphasis <em>
'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: \&
Found the following HTML validation problems:
ggmulti-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggmulti-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
ggnewscale-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggnewscale-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Found the following HTML validation problems:
ggpattern.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggpattern.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ggperiodic.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggperiodic.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) diamonds.Rd:10: Escaped LaTeX specials: \$ \$
Found the following HTML validation problems:
ggplot2-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggplot2-package.html:23:4: 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
Package suggested but not available for checking: ‘lixoftConnectors’
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ggpointless-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggpointless-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
checkRd: (-1) interaction_data.Rd:174: Escaped LaTeX specials: \&
checkRd: (-1) partial_data.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) rfsrc_data.Rd:154: Escaped LaTeX specials: \&
checkRd: (-1) varsel_data.Rd:156: Escaped LaTeX specials: \&
Found the following HTML validation problems:
interaction_data.html:19:1: Warning: missing </h2> before <ul>
interaction_data.html:38:1: Warning: discarding unexpected </h2>
partial_coplot_data.html:19:1: Warning: missing </h2> before <ul>
partial_coplot_data.html:29:1: Warning: discarding unexpected </h2>
partial_data.html:19:1: Warning: missing </h2> before <ul>
partial_data.html:37:1: Warning: discarding unexpected </h2>
partial_surface_data.html:19:1: Warning: missing </h2> before <ul>
partial_surface_data.html:37:1: Warning: discarding unexpected </h2>
varsel_data.html:19:1: Warning: missing </h2> before <ul>
varsel_data.html:37:1: Warning: discarding unexpected </h2>
'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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (0.1.0)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ggspectra-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ggspectra-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Found the following HTML validation problems:
ghibli-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ghibli-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
gh_whoami.html:68:83: Warning: inserting implicit <p>
gh_whoami.html:68:83: Warning: trimming empty <p>
'LazyData' is specified without 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’
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
ConfidenceInterval.Rd:25: Undefined control sequence: \boldmath in ...athcal{D}} =\{(\boldmath{x}_i,y_i)\} 
KdCor.Rd:27-31: Undefined control sequence: \label in ...}(Y,Y')\right].\label{dCovkk}
    \end...
KdCov.Rd:22-26: Undefined control sequence: \label in ...prime})\right].\label{dCovkk}
      \e...
KdCov.Rd:28-32: Undefined control sequence: \label in \label{setdiff}
      \...
KdCov.Rd:36: Undefined control sequence: \label in ...rime}) \right].\label{dCovk}
KgCor.Rd:24-26: Undefined control sequence: \label in ..._\kappa(X,X')}.\label{gCork}
KgCov.Rd:24-26: Undefined control sequence: \label in ...a(X,X')\right],\label{gCovk}
Unknown package ‘IC2’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
giscoR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
giscoR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
gitcreds_get.html:129:26: Warning: inserting implicit <p>
gitcreds_get.html:129:26: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
gitlabr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
gitlabr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
checkRd: (-1) starship.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) starship.adaptivegrid.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) starship.adaptivegrid.Rd:54: Escaped LaTeX specials: \&
checkRd: (-1) starship.adaptivegrid.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) starship.obj.Rd:25: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘mlr3proba’
'LazyData' is specified without a 'data' directory
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 math rendering problems:
breakdown.Rd:22: Can't use function '$' in math mode in $8\times 4$
'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’
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
checkRd: (-1) congagvp.Rd:46: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
AIC.html:31:1: Warning: inserting implicit <p>
AIC.html:31:1: Warning: trimming empty <p>
BIC.html:34:1: Warning: inserting implicit <p>
BIC.html:34:1: Warning: trimming empty <p>
gmbn.html:52:1: Warning: inserting implicit <p>
gmbn.html:52:1: Warning: trimming empty <p>
gmdbn.html:40:1: Warning: inserting implicit <p>
gmdbn.html:40:1: Warning: trimming empty <p>
gmm.html:45:1: Warning: inserting implicit <p>
gmm.html:45:1: Warning: trimming empty <p>
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building ‘gmm_with_R.rnw’ using knitr
Warning in nlminb(P$t0, .obj1, x = x, w = w, ...) :
  NA/NaN function evaluation
Warning in nlminb(P$t0, .obj1, x = x, w = w, ...) :
  NA/NaN function evaluation
Warning: The provided gradv is not used when smooth=TRUE
Error: processing vignette ‘gmm_with_R.rnw’ failed with diagnostics:
Running ‘texi2dvi’ on ‘gmm_with_R.tex’ failed.
LaTeX errors:
! Argument of <c2> has an extra }.
<inserted text> 
                \par 
l.122 \section{Introduction}
                            
! Emergency stop.
<inserted text> 
                \par 
l.122 \section{Introduction}
                            
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘gmm_with_R.rnw’

SUMMARY: processing the following file failed:
  ‘gmm_with_R.rnw’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
Found the following HTML validation problems:
cond_moments.html:277:38: Warning: nested emphasis <code>
cond_moments.html:282:38: Warning: nested emphasis <code>
cond_moments.html:288:38: Warning: nested emphasis <code>
cond_moments.html:293:38: Warning: nested emphasis <code>
cond_moments.html:298:38: Warning: nested emphasis <code>
loglikelihood_int.html:292:38: Warning: nested emphasis <code>
loglikelihood_int.html:296:38: Warning: nested emphasis <code>
loglikelihood_int.html:301:38: Warning: nested emphasis <code>
loglikelihood_int.html:305:38: Warning: nested emphasis <code>
loglikelihood_int.html:310:38: Warning: nested emphasis <code>
loglikelihood_int.html:315:38: Warning: nested emphasis <code>
loglikelihood_int.html:321:38: Warning: nested emphasis <code>
loglikelihood_int.html:326:38: Warning: nested emphasis <code>
loglikelihood_int.html:331:38: Warning: nested emphasis <code>
loglikelihood_int.html:337:38: Warning: nested emphasis <code>
'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
Found the following math rendering problems:
flm_stat.Rd:51-54: Unexpected end of input in a macro argument, expected '}' in ...mathrm{tr}(\hat\mathbf{E}_q' \mathbf{...
flm_stat.Rd:57: Unexpected end of input in a macro argument, expected '}' in \hat\mathbf{E}_q
'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
Found the following HTML validation problems:
cr_run.html:115:1: Warning: trimming empty <dt>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
googlesheets4-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
googlesheets4-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
gosset.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
gosset.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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) rotations.Rd:103: Escaped LaTeX specials: \^
Package suggested but not available for checking: ‘gvcm.cat’
Unknown package ‘gvcm.cat’ in Rd xrefs
Found the following HTML validation problems:
exponential_anisotropic3D_alt.html:70:1: Warning: trimming empty <h3>
'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: \&
Running ‘testthat.R’ [148s/240s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(gppm)
  Loading required package: Rcpp
  > 
  > test_check("gppm")
  [ FAIL 1 | WARN 1 | SKIP 4 | PASS 1809 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (4)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-cv.R:21:3): Folds roughly same size ───────────────────────────
  unknown failure
  
  [ FAIL 1 | WARN 1 | SKIP 4 | PASS 1809 ]
  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
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
grainchanger-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
grainchanger-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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: \~
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
Found the following HTML validation problems:
summary_greek.html:58:1: Warning: trimming empty <dt>
'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.
Found the following HTML validation problems:
gridpattern-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
gridpattern-package.html:23:4: 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:
    News
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
sample_session_duration.Rd:30: Undefined control sequence: \k in ...lambda ~ Gamma(\k, \theta)
'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 math rendering problems:
fit_easylinear.Rd:39: Can't use function '$' in math mode in $b_{max}$
fit_easylinear.Rd:41: Can't use function '$' in math mode in $quota \cdot b_{...
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 HTML validation problems:
gsheet2tbl.html:31:5: Warning: trimming empty <p>
gsheet2tbl.html:31:1: Warning: trimming empty <li>
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Found the following HTML validation problems:
GSODR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
GSODR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
checkRd: (-1) fit.variogram.Rd:91: Escaped LaTeX specials: \&
checkRd: (-1) fit.variogram.gls.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) gstat.Rd:117: Escaped LaTeX specials: \&
checkRd: (-1) hscat.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) krige.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) krigeST.Rd:85: Escaped LaTeX specials: \&
checkRd: (-1) meuse.all.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) predict.gstat.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) variogram.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) variogramST.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) vgm.Rd:116: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) gsym.point.Rd:143: Escaped LaTeX specials: \&
Found the following HTML validation problems:
gtable-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
gtable-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
gt_plt_summary.html:62:1: Warning: <img> lacks "alt" attribute
gt_plt_winloss.html:99:1: Warning: <img> lacks "alt" attribute
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RRprof.out’
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
gutenberg_get_mirror.html:25:1: Warning: <a> illegal characters found in URI
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
Found the following HTML validation problems:
gwasrapidd-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
gwasrapidd-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) luzdat.Rd:21: Escaped LaTeX specials: \~
Found the following HTML validation problems:
gedit.html:139:6: Warning: trimming empty <p>
gedit.html:139:1: Warning: trimming empty <li>
'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
Found the following HTML validation problems:
gyrodemos.html:50:1: Warning: inserting implicit <p>
gyrodemos.html:50:1: Warning: trimming empty <p>
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    v.0.2.2
'LazyData' is specified without 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:
cf_key_meson_3pt.html:19:1: Warning: missing </h2> before <ul>
cf_key_meson_3pt.html:72:1: Warning: discarding unexpected </h2>
correlators_key_meson_3pt.html:19:1: Warning: missing </h2> before <ul>
correlators_key_meson_3pt.html:72:1: Warning: discarding unexpected </h2>
gevp.html:84:45: Warning: trimming empty <code>
gevp.html:85:17: Warning: trimming empty <code>
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: \&
'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.
Found the following HTML validation problems:
haven-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
haven-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
'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’:
  Cannot extract version info from the following section titles:
    TODO:
    "GW", "OLO"
    seriate(cophenetic(dend), method = "OLO", control = list(hclust = as.hclust(dend)))
    the downside in using cophenetic is that seriate has to go through running hclust all over again
    but we'll just have to accept it...
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgho’
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
HelpersMG-package.html:41:1: Warning: <img> attribute "," lacks value
HelpersMG-package.html:41:1: Warning: <img> attribute "align" not allowed for HTML5
HelpersMG-package.html:41:1: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘synbreed’
Found the following HTML validation problems:
IndivCtstmTrans.html:116:6: Warning: missing </span> before <p>
IndivCtstmTrans.html:116:93: Warning: inserting implicit <span>
IndivCtstmTrans.html:119:6: Warning: missing </span> before <p>
IndivCtstmTrans.html:119:90: Warning: inserting implicit <span>
IndivCtstmTrans.html:116:6: Warning: trimming empty <span>
IndivCtstmTrans.html:119:6: Warning: trimming empty <span>
'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
Found the following HTML validation problems:
get_breaks.html:78:1: Warning: trimming empty <dt>
'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
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following math rendering problems:
rCholCov.Rd:55: Can't use function '$' in math mode in ...au^{b}_j}^{(2)}$. Set $\hat{h}_...
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) trans.dens.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) Snow.Rd:118: Escaped LaTeX specials: \&
checkRd: (-1) Snow.Rd:142: Escaped LaTeX specials: \&
checkRd: (-1) Yeast.Rd:56: Escaped LaTeX specials: \&
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
Package suggested but not available for checking: ‘FGN’
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following math rendering problems:
rcorr.cens.Rd:14: Undefined control sequence: \var in \var{Dxy}=2(\var{c}...
rcspline.plot.Rd:44: Undefined control sequence: \var in 1 - \var{f}
rcspline.plot.Rd:45: Undefined control sequence: \var in \var{f} = \frac{10}...
rcspline.restate.Rd:32: Undefined control sequence: \var in \var{k}-1
rm.boot.Rd:122: Undefined control sequence: \var in \var{k} - 1
rm.boot.Rd:345: Undefined control sequence: \var in \var{m} > \var{n}
rm.boot.Rd:347: Undefined control sequence: \var in \var{m} < \var{n}
rm.boot.Rd:348-349: Undefined control sequence: \var in \var{n} -
    \var{m}
scat1d.Rd:19: Undefined control sequence: \var in \code{eps}*\var{w}
scat1d.Rd:22-23: Undefined control sequence: \var in ...\code{jitfrac}*\var{w},
    \code{ji...
scat1d.Rd:178: Undefined control sequence: \var in \max{(.1, 125/\var{n})}
scat1d.Rd:230-231: Undefined control sequence: \var in ...de{fill}*\min{(\var{u}-\var{d},\va...
scat1d.Rd:236-237: Undefined control sequence: \var in ...de{fill}*\min{(\var{u}-\var{d},\va...
scat1d.Rd:239: Undefined control sequence: \var in \min{(\var{u}-\var{d},\va...
scat1d.Rd:283: Undefined control sequence: \var in \var{l}<\var{d}<\va...
transace.Rd:87: Undefined control sequence: \var in \var{ginverse}(\var...
transace.Rd:101-102: Undefined control sequence: \var in \var{ginverse}(\var...
transace.Rd:250: Undefined control sequence: \var in \var{ginverse}(\var...
transcan.Rd:272: Undefined control sequence: \var in \var{n} < 30
transcan.Rd:273: Undefined control sequence: \var in 30 <= \var{n} < 100
transcan.Rd:274: Undefined control sequence: \var in \var{n} \ge 100
transcan.Rd:770-771: Undefined control sequence: \var in ...rac{1-\frac{(1-\var{R2})(\var{n}-1...
transcan.Rd:783: Undefined control sequence: \var in + \var{m}
transcan.Rd:788-789: Undefined control sequence: \var in 1-\frac{(1-\var{R2})(\var{n}-1...
transcan.Rd:797: Undefined control sequence: \var in \sqrt{\var{n}-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
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
Found the following HTML validation problems:
hms-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
hms-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
hmstimer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
hmstimer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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: \&
Found the following HTML validation problems:
hockeystick-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
hockeystick-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
'LazyData' is specified without 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: ‘CensRegMod’
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘germinar.Rmd’ using rmarkdown
Loading required package: magick
Linking to ImageMagick 6.9.11.60
Enabled features: fontconfig, freetype, fftw, heic, lcms, pango, webp, x11
Disabled features: cairo, ghostscript, raw, rsvg
Using 3 threads
Loading required package: cowplot
--- finished re-building ‘germinar.Rmd’

--- re-building ‘huito.Rmd’ using rmarkdown
Quitting from lines 29-31 (huito.Rmd) 
Error: processing vignette ‘huito.Rmd’ failed with diagnostics:
could not find function "gdoc2rmd"
--- failed re-building ‘huito.Rmd’

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

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

SUMMARY: processing the following file failed:
  ‘huito.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
Package suggested but not available for checking: ‘hurricaneexposuredata’
'LazyData' is specified without a 'data' directory
'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
Problems with news in ‘NEWS.md’:
No news entries found.
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 HTML validation problems:
cldr_currencies.html:91:70: Warning: inserting implicit <p>
cldr_currencies.html:91:70: Warning: trimming empty <p>
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’
'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: ‘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: \$
Packages suggested but not available for checking: 'glrt', 'MIICD'
Found the following math rendering problems:
loglogistic.Rd:31-42: Unknown column alignment: @ in ...\begin{array}{r@{\;=\;}ll}
    \m...
checkRd: (-1) dmahal.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
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
Found the following HTML validation problems:
idiogramFISH-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
idiogramFISH-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
idmodelr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
idmodelr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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 HTML validation problems:
igoR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
igoR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor fix
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
h.fn.exp.html:19:1: Warning: missing </h2> before <p>
h.fn.exp.html:22:109: Warning: discarding unexpected </h2>
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    BUG FIXES
Found the following HTML validation problems:
imagefluency-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
imagefluency-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without 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 math rendering problems:
USPSdigits.Rd:41: Undefined control sequence: \textsuperscript in 2\textsuperscript{nd}
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
immer_latent_regression.Rd:45: Unexpected end of input in a macro argument, expected '}' at end of input: \bold
'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
Package suggested but not available for checking: ‘gbm’
'LazyData' is specified without a 'data' directory
checkRd: (-1) tsAirgap.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) tsAirgapComplete.Rd:11: Escaped LaTeX specials: \&
Found the following HTML validation problems:
imputeTS-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
imputeTS-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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 HTML validation problems:
fit.infer.html:126:35: Warning: inserting implicit <p>
fit.infer.html:147:45: Warning: inserting implicit <p>
fit.infer.html:126:35: Warning: trimming empty <p>
fit.infer.html:147:45: Warning: trimming empty <p>
generate.html:112:35: Warning: inserting implicit <p>
generate.html:133:45: Warning: inserting implicit <p>
generate.html:112:35: Warning: trimming empty <p>
generate.html:133:45: Warning: trimming empty <p>
infer.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
infer.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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: \&
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 math rendering problems:
topo.Rd:20: Undefined control sequence: \textsuperscript in \textsuperscript{TM}
Found the following HTML validation problems:
DeepLift.html:93:6: Warning: missing </span> before <p>
DeepLift.html:93:105: Warning: inserting implicit <span>
DeepLift.html:93:6: Warning: trimming empty <span>
Gradient.html:64:6: Warning: missing </span> before <p>
Gradient.html:64:105: Warning: inserting implicit <span>
Gradient.html:67:6: Warning: missing </span> before <p>
Gradient.html:67:97: Warning: inserting implicit <span>
Gradient.html:70:6: Warning: missing </span> before <p>
Gradient.html:70:94: Warning: inserting implicit <span>
Gradient.html:64:6: Warning: trimming empty <span>
Gradient.html:67:6: Warning: trimming empty <span>
Gradient.html:70:6: Warning: trimming empty <span>
GradientBased.html:84:6: Warning: missing </span> before <p>
GradientBased.html:84:105: Warning: inserting implicit <span>
GradientBased.html:84:6: Warning: trimming empty <span>
LRP.html:89:6: Warning: missing </span> before <p>
LRP.html:89:105: Warning: inserting implicit <span>
LRP.html:89:6: Warning: trimming empty <span>
SmoothGrad.html:74:6: Warning: missing </span> before <p>
SmoothGrad.html:74:105: Warning: inserting implicit <span>
SmoothGrad.html:77:6: Warning: missing </span> before <p>
SmoothGrad.html:77:97: Warning: inserting implicit <span>
SmoothGrad.html:80:6: Warning: missing </span> before <p>
SmoothGrad.html:80:94: Warning: inserting implicit <span>
SmoothGrad.html:74:6: Warning: trimming empty <span>
SmoothGrad.html:77:6: Warning: trimming empty <span>
SmoothGrad.html:80:6: Warning: trimming empty <span>
'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: ‘gbm’
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: \_
Package required but not available: ‘gbm’

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 HTML validation problems:
invctr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
invctr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
aggregateData.html:94:372: Warning: inserting implicit <p>
aggregateData.html:94:372: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
iotables_read_tempdir.html:19:1: Warning: missing </h2> before <ul>
iotables_read_tempdir.html:63:1: Warning: discarding unexpected </h2>
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.
Found the following HTML validation problems:
ipaddress-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ipaddress-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘mpath’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘twang’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
aFiles.html:52:78: Warning: inserting implicit <p>
aFiles.html:52:78: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
checkRd: (-1) pine.Rd:20: Escaped LaTeX specials: \&
'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: \$
Package suggested but not available for checking: ‘RandomFields’
Unknown package ‘RandomFields’ in Rd xrefs
'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
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
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.
Found the following HTML validation problems:
JirAgileR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
JirAgileR-package.html:23:4: 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:
    joineR <1.1
Package which this enhances but not available for checking: ‘remMap’
Found the following HTML validation problems:
hc_rdslope_info.html:56:86: Warning: inserting implicit <p>
hc_rdslope_info.html:56:86: Warning: trimming empty <p>
hc_rdslope_interact.html:54:86: Warning: inserting implicit <p>
hc_rdslope_interact.html:54:86: Warning: trimming empty <p>
model_imp.html:402:100: Warning: inserting implicit <p>
model_imp.html:405:46: Warning: inserting implicit <p>
model_imp.html:437:39: Warning: inserting implicit <p>
model_imp.html:468:93: Warning: inserting implicit <p>
model_imp.html:479:83: Warning: inserting implicit <p>
model_imp.html:484:47: Warning: inserting implicit <p>
model_imp.html:518:73: Warning: inserting implicit <p>
model_imp.html:937:99: Warning: inserting implicit <p>
model_imp.html:942:118: Warning: inserting implicit <p>
model_imp.html:967:35: Warning: inserting implicit <p>
model_imp.html:974:38: Warning: inserting implicit <p>
model_imp.html:983:83: Warning: inserting implicit <p>
model_imp.html:989:59: Warning: inserting implicit <p>
model_imp.html:402:100: Warning: trimming empty <p>
model_imp.html:405:46: Warning: trimming empty <p>
model_imp.html:437:39: Warning: trimming empty <p>
model_imp.html:468:93: Warning: trimming empty <p>
model_imp.html:479:83: Warning: trimming empty <p>
model_imp.html:484:47: Warning: trimming empty <p>
model_imp.html:518:73: Warning: trimming empty <p>
model_imp.html:937:99: Warning: trimming empty <p>
model_imp.html:942:118: Warning: trimming empty <p>
model_imp.html:967:35: Warning: trimming empty <p>
model_imp.html:974:38: Warning: trimming empty <p>
model_imp.html:983:83: Warning: trimming empty <p>
model_imp.html:989:59: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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) 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
'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’
'LazyData' is specified without 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/c++/12/array:61:36: warning: array subscript 18446744073709551615 is above array bounds of ‘std::__array_traits<double, 1>::_Type’ {aka ‘const double [1]’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kdtools.Rcheck/00install.out’ for details.
'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
Found the following HTML validation problems:
MLP.html:77:6: Warning: missing </span> before <p>
MLP.html:77:90: Warning: inserting implicit <span>
MLP.html:77:6: Warning: trimming empty <span>
RBF.html:77:6: Warning: missing </span> before <p>
RBF.html:77:90: Warning: inserting implicit <span>
RBF.html:77:6: Warning: trimming empty <span>
'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
Found the following math rendering problems:
consensusmatrix.Rd:34-36: Undefined control sequence: \emph in\em...
'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’
Found the following HTML validation problems:
lactater-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
lactater-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
metab.kalman.Rd:51: Undefined control sequence: \do in ... + \beta_{t-1}*\do.obs_{t-1} + \e...
metab.mle.Rd:48: Undefined control sequence: \do in ... + \beta_{t-1}*\do.obs_{t-1} + \e...
Found the following HTML validation problems:
handle_event_error.html:36:89: Warning: inserting implicit <p>
handle_event_error.html:36:89: Warning: trimming empty <p>
html_response.html:24:45: Warning: inserting implicit <p>
html_response.html:24:45: Warning: trimming empty <p>
lambdr.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
lambdr.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
post_lambda_error.html:27:48: Warning: inserting implicit <p>
post_lambda_error.html:27:48: Warning: trimming empty <p>
Found the following HTML validation problems:
Gaussianize.html:136:38: Warning: nested emphasis <code>
Gaussianize.html:140:38: Warning: nested emphasis <code>
Gaussianize.html:145:38: Warning: nested emphasis <code>
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: \&
Problems with news in ‘NEWS.md’:
No news entries found.
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.
'LazyData' is specified without a 'data' directory
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'
checkRd: (-1) Col.Rd:17: Escaped LaTeX specials: \#
checkRd: (-1) regression-set.Rd:103: Escaped LaTeX specials: \$
Found the following HTML validation problems:
gini.index.html:82:1: Warning: nested emphasis <em>
'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
'LazyData' is specified without a 'data' directory
Running examples in ‘LCox-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LCox
> ### Title: Hypothesis Testing for longitudinal gene profiles and the
> ###   survival outcome.
> ### Aliases: LCox
> 
> ### ** Examples
> 
> data.list = simudata()
> data = data.list$data
> data.id = data.list$data.id
> res = LCox(data = data, data.id = data.id, geneID = 3:4)
> res = LCox(data = data, data.id = data.id, geneID = 3:4, varID = 4)
Error in `[.data.frame`(xx, "P(>|Chi|)") : undefined columns selected
Calls: LCox -> sapply -> lapply -> FUN -> [ -> [.data.frame
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
Package suggested but not available for checking: ‘gbm’
'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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
annotate_axis.html:91:1: Warning: trimming empty <h3>
'LazyData' is specified without 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) hydro.Rd:17: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
TariffTypeSingleEnum-class.html:19:1: Warning: missing </h2> before <dl>
TariffTypeSingleEnum-class.html:51:1: Warning: discarding unexpected </h2>
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', '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 required but not available: ‘gbm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following HTML validation problems:
lime-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
lime-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following math rendering problems:
WLindley.Rd:54: Undefined control sequence: \label in ...e^{-\theta x}  \label{density-weight...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
lmn_post.Rd:30-34: Undefined control sequence: \vspace in 
  \vspace{-1em}
  
lmn_prior.Rd:54-58: Undefined control sequence: \vspace in 
  \vspace{-1em}
Found the following math rendering problems:
Lcomoment.matrix.Rd:16-17: Undefined control sequence: \boldmath in  \mbox{\boldmath $\Lambda_k$} = ...
lmomgld.Rd:17-18: Undefined control sequence: \boldmath in \mbox{\boldmath $Y$} = 2\xi + \...
lmomgld.Rd:19-22: Undefined control sequence: \boldmath in ...mbda_3 = \mbox{\boldmath $Y$} + 6\alpha
  ...
lmomgld.Rd:25-27: Undefined control sequence: \boldmath in \mbox{\boldmath $Y$} = \frac{-3...
lmomgld.Rd:28-29: Undefined control sequence: \boldmath in \mbox{\boldmath $Z$} = \frac{20...
lmomgld.Rd:30-32: Undefined control sequence: \boldmath in ...mbda_4 = \mbox{\boldmath $Z$} -
          ...
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: \_
'LazyData' is specified without a 'data' directory
checkRd: (-1) hatr.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘twang’
'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: \^ \^
Found the following HTML validation problems:
UPSLTDdist.html:54:1: Warning: trimming empty <dt>
plot.LocalControlCR.html:63:1: Warning: trimming empty <dt>
plot.LocalControlCS.html:59:1: Warning: trimming empty <dt>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Package required but not available: ‘gbm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) logreg.myown.Rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:20: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:24: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:99: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:120: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:132: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:133: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:134: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:172: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:182: Escaped LaTeX specials: \_ \_
checkRd: (-1) logreg.myown.Rd:184: Escaped LaTeX specials: \_ \_
Found the following HTML validation problems:
dx.html:74:38: Warning: nested emphasis <code>
dx.html:81:38: Warning: nested emphasis <code>
dx.html:92:38: Warning: nested emphasis <code>
dx.html:100:38: Warning: nested emphasis <code>
dx.html:112:38: Warning: nested emphasis <code>
dx.html:148:38: Warning: nested emphasis <code>
dx.html:170:38: Warning: nested emphasis <code>
dx.html:229:38: Warning: nested emphasis <code>
dx.html:240:38: Warning: nested emphasis <code>
dx.html:251:38: Warning: nested emphasis <code>
dx.html:269:38: Warning: nested emphasis <code>
dx.html:282:38: Warning: nested emphasis <code>
plotGlm.html:219:38: Warning: nested emphasis <code>
plotGlm.html:225:38: Warning: nested emphasis <code>
plotGlm.html:233:38: Warning: nested emphasis <code>
plotGlm.html:240:38: Warning: nested emphasis <code>
plotGlm.html:248:38: Warning: nested emphasis <code>
plotGlm.html:271:38: Warning: nested emphasis <code>
plotGlm.html:279:38: Warning: nested emphasis <code>
plotGlm.html:286:38: Warning: nested emphasis <code>
'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:
set_log_name_path.html:19:1: Warning: missing </h2> before <ol>
set_log_name_path.html:31:1: Warning: discarding unexpected </h2>
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
events_long.html:19:1: Warning: missing </h2> before <ul>
events_long.html:35:1: Warning: discarding unexpected </h2>
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 HTML validation problems:
lookout-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
lookout-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
loon.ggplot-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
loon.ggplot-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
loon.shiny-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
loon.shiny-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
'LazyData' is specified without a 'data' directory
Checking should be performed on sources prepared by ‘R CMD build’.
'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
checkRd: (-1) lp.Rd:4: Escaped LaTeX specials: \_
checkRd: (-1) lp.Rd:53: Escaped LaTeX specials: \_
checkRd: (-1) lp.assign.Rd:4: Escaped LaTeX specials: \_
checkRd: (-1) lp.transport.Rd:4: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character ≤ (U+2264)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
Found the following files/directories:
  ‘lrstat-manual.tex’
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’
Found the following HTML validation problems:
evaluate.html:100:31: Warning: inserting implicit <p>
evaluate.html:100:31: Warning: trimming empty <p>
luz_callback.html:79:95: Warning: inserting implicit <p>
luz_callback.html:108:57: Warning: inserting implicit <p>
luz_callback.html:79:95: Warning: trimming empty <p>
luz_callback.html:108:57: Warning: trimming empty <p>
luz_metric.html:105:51: Warning: inserting implicit <p>
luz_metric.html:105:51: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘gbm’
Error(s) in re-building vignettes:
  ...
--- re-building ‘MLModels.Rmd’ using rmarkdown
--- finished re-building ‘MLModels.Rmd’

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

Attaching package: 'MachineShop'

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

    ppr

Warning: Removed 70 rows containing missing values (geom_point).
Quitting from lines 237-247 (UserGuide.Rmd) 
Error: processing vignette ‘UserGuide.Rmd’ failed with diagnostics:
Call requires prior installation of package: gbm.
To address this issue, try running install.packages("gbm").
--- failed re-building ‘UserGuide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Found the following HTML validation problems:
mailmerge-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
mailmerge-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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 math rendering problems:
estimateD0.Rd:40: Undefined control sequence: \link in \link[base]{trigamma...
estimateD0Robust.Rd:80: Undefined control sequence: \link in \link[base]{trigamma...
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) china.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) china.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) japan.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) japan.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) nzHires.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) nzHires.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) rivers.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) rivers.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) world2Hires.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) world2Hires.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) worldHires.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) worldHires.Rd:52: Escaped LaTeX specials: \&
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
checkRd: (-1) mapproject.Rd:203: Escaped LaTeX specials: \_
checkRd: (-1) mapproject.Rd:204: Escaped LaTeX specials: \_
checkRd: (-1) mapproject.Rd:210: Escaped LaTeX specials: \&
'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
Found the following HTML validation problems:
mapSpain-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
mapSpain-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) county.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) county.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) france.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) france.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) italy.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) italy.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) match.map.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) nz.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) nz.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) state.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) state.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) state.carto.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) state.carto.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) state.vbm.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) state.vbm.Rd:45: Escaped LaTeX specials: \&
checkRd: (-1) usa.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) usa.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) world.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) world.Rd:45: Escaped LaTeX specials: \&
checkRd: (-1) world2.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) world2.Rd:54: Escaped LaTeX specials: \&
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
checkRd: (-1) GerberGreenImai.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) GerberGreenImai.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) GerberGreenImai.Rd:34: Escaped LaTeX specials: \#
checkRd: (-1) GerberGreenImai.Rd:35: Escaped LaTeX specials: \#
Packages suggested but not available for checking: 'gbm', 'gurobi'
'LazyData' is specified without a 'data' directory
checkRd: (-1) size_t-class.Rd:6: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
E.matrices.Rd:17-19: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
    {{{\...
H.matrices.Rd:16-18: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
    {{{\...
H.matrices.Rd:21-23: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
    {{{\...
T.matrices.Rd:19-22: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
  {{{\bf...
creation.matrix.Rd:18-25: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
  0&0&0&...
direct.prod.Rd:18-23: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
  {{x_{1...
direct.sum.Rd:20-23: Unknown column alignment: * in ...{\begin{array}{*{20}c}
     {\bf{...
entrywise.norm.Rd:16-18: Invalid size: '-' in ... \right.
   \kern-\nulldelimiters...
fibonacci.matrix.Rd:19-22: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
  {{f_{i...
frobenius.matrix.Rd:17-24: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}0&0& \c...
hadamard.prod.Rd:17-22: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
  {{x_{1...
hilbert.matrix.Rd:15-17: Invalid size: '-' in ... \right.
   \kern-\nulldelimiters...
s.Rd:20-23: Unknown column alignment: * in ...{\begin{array}{*{20}c}
     {\bf{...
spectral.norm.Rd:17-19: Unknown column alignment: * in ...{\begin{array}{*{20}c}
     {\lam...
stirling.matrix.Rd:20: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}i\\j\en...
stirling.matrix.Rd:27-33: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
  {S_0^0...
symmetric.pascal.matrix.Rd:16-18: Invalid size: '-' in ... \right.
   \kern-\nulldelimiters...
vandermonde.matrix.Rd:16-18: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
  {{\alp...
vandermonde.matrix.Rd:19-25: Unknown column alignment: * in ...{\begin{array}{*{20}{c}}
  1&{{\a...
'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) USCounties.Rd:26: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘utilities.R’
'LazyData' is specified without a 'data' directory
checkRd: (-1) maxControl.Rd:83: 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:
  ‘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
Package suggested but not available for checking: ‘gbm’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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
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: \&
Package required but not available: ‘symbolicDA’

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
checkRd: (-1) mebootSpear.Rd:88: Escaped LaTeX specials: \_
checkRd: (-1) ullwan.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ullwan.Rd:8: Escaped LaTeX specials: \& \$
checkRd: (-1) hydraulics_supplyfunctions.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) hydraulics_supplyfunctions.Rd:218: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
  'LazyDataCompression' is specified without a 'data' directory
Found the following HTML validation problems:
PlotMandala.html:82:4: Warning: <img> attribute "width" has invalid value "480px"
'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
checkRd: (-1) toLatexExtra.Rd:147: 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.
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.
Found the following HTML validation problems:
metabolic-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
metabolic-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
Package required but not available: ‘gbm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following math rendering problems:
rma.mv.Rd:76: Undefined control sequence: \vspace in ...t{struct="UN"} \vspace{1ex} \\ \left[...
rma.mv.Rd:86: Undefined control sequence: \vspace in ...{struct="CAR"} \vspace{1ex} \\ \left[...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
fat.Rd:52: Unexpected end of input in a macro argument, expected '}' in ...a_1\, \widehat \mathrm{SE}(\hat{b}_k)...
fat.Rd:56: Unexpected end of input in a macro argument, expected '}' in \widehat \mathrm{SE}(\hat{b}_k)
fat.Rd:60: Unexpected end of input in a macro argument, expected '}' in ...+ b\, \widehat \mathrm{SE}(\hat{\beta...
fat.Rd:72: Unexpected end of input in a macro argument, expected '}' in ...hi \; \widehat \mathrm{var}(\hat{\bet...
fat.Rd:74: Unexpected end of input in a macro argument, expected '}' in \widehat \mathrm{var}(\hat{b}_k...
fat.Rd:89: Unexpected end of input in a macro argument, expected '}' in ...hi \; \widehat \mathrm{var}(\hat{\bet...
fat.Rd:91: Unexpected end of input in a macro argument, expected '}' in \widehat \mathrm{var}(\hat{\bet...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following HTML validation problems:
metathis-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
metathis-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
checkRd: (-1) penman.Rd:48: Escaped LaTeX specials: \&
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: \&
Found the following HTML validation problems:
BA.est.html:149:32: Warning: trimming empty <code>
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Found the following HTML validation problems:
metR.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
metR.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
checkRd: (-1) gam.fit3.Rd:4: 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.
checkRd: (-1) mHMM.Rd:423: Escaped LaTeX specials: \&
'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’
Found the following math rendering problems:
ml_mcmc.Rd:210-211: Undefined control sequence: \boldmath in y=\boldmath{X}\boldmath{be...
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
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
checkRd: (-1) ees2010.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 HTML validation problems:
add_service.html:59:1: Warning: inserting implicit <p>
add_service.html:64:1: Warning: inserting implicit <p>
add_service.html:73:65: Warning: inserting implicit <p>
add_service.html:77:51: Warning: inserting implicit <p>
add_service.html:59:1: Warning: trimming empty <p>
add_service.html:64:1: Warning: trimming empty <p>
add_service.html:73:65: Warning: trimming empty <p>
add_service.html:77:51: Warning: trimming empty <p>
use_microservice.html:58:65: Warning: inserting implicit <p>
use_microservice.html:65:51: Warning: inserting implicit <p>
use_microservice.html:187:1: Warning: inserting implicit <p>
use_microservice.html:58:65: Warning: trimming empty <p>
use_microservice.html:65:51: Warning: trimming empty <p>
use_microservice.html:187:1: Warning: trimming empty <p>
Package required but not available: ‘gbm’

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
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.
Running ‘missing_data.frame.R’ [4s/6s]
  Running ‘missing_variable.R’ [3s/5s]
Running the tests in ‘tests/missing_variable.R’ failed.
Complete output:
  > stopifnot(require(mi))
  Loading required package: mi
  Loading required package: Matrix
  Loading required package: stats4
  mi (Version 1.1, packaged: 2022-06-05 05:31:15 UTC; ben)
  mi  Copyright (C) 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015 Trustees of Columbia University
  This program comes with ABSOLUTELY NO WARRANTY.
  This is free software, and you are welcome to redistribute it
  under the General Public License version 2 or later.
  Execute RShowDoc('COPYING') for details.
  > 
  > x <- rnorm(10)
  > x[1] <- NA
  > y <- missing_variable(x, type = "continuous")
  > 
  > y <- missing_variable(x, type = "irrelevant")
  > x <- rep(1, 10)
  > y <- missing_variable(x, type = "fixed")
  > x <- rep(1:5, each = 2)
  > y <- missing_variable(x, type = "group")
  > 
  > x[1] <- NA
  > y <- missing_variable(x, type = "unordered-categorical")
  > y <- missing_variable(x, type = "ordered-categorical")
  > y <- missing_variable(x, type = "interval")
  > 
  > x <- rbinom(10, size = 1, prob = 0.5)
  > x[1] <- NA
  > y <- missing_variable(x, type = "binary")
  Error in validObject(.Object) : 
    invalid class "binary" object: y : binary variables must have exactly two response categories
  Calls: missing_variable ... .local -> callNextMethod -> .nextMethod -> validObject
  Execution halted
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
Found the following math rendering problems:
test.cor.Rd:54: Undefined control sequence: \emph in \emph{E}(\textbf{z})...
test.cor.Rd:58: Undefined control sequence: \emph in \emph{E}(\textbf{z})...
'LazyData' is specified without a 'data' directory
Package required but not available: ‘relsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 HTML validation problems:
Bm.html:19:1: Warning: missing </h2> before <p>
Bm.html:22:1: Warning: discarding unexpected </h2>
Found the following math rendering problems:
NMixMCMC.Rd:133: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:134: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:138: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:139: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:142: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:143: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:155: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:156: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:177: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:178: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:197: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:224: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:229: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:234: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:239: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:252: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:256: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:271: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:276: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:281: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
NMixMCMC.Rd:287: Invalid size: '\textwidth' in \mbox{\hspace{\textwidth}}
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.
Found the following math rendering problems:
mixEMM.Rd:22: Unexpected end of input in a macro argument, expected '}' in \bar\mathbf{y}_{i}
mixEMM.Rd:53-54: Unexpected end of input in a macro argument, expected '}' in ...} - \gamma \bar\mathbf{y}_{i}
  \right)...
mixEMM.Rd:55: Unexpected end of input in a macro argument, expected '}' in \bar\mathbf{y}_{i}
mixEMM.Rd:63: Unexpected end of input in a macro argument, expected '}' in \bar\mathbf{y}_{i}
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) rm.oneway.test.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) rm.oneway.test.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) rm.oneway.test.Rd:48: 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: \&
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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
mlr3benchmark-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
mlr3benchmark-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
mlr3misc-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
mlr3misc-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Package suggested but not available for checking: ‘mlr3proba’
Found the following HTML validation problems:
DataBackendRaster.html:138:6: Warning: missing </span> before <p>
DataBackendRaster.html:138:90: Warning: inserting implicit <span>
DataBackendRaster.html:141:6: Warning: missing </span> before <p>
DataBackendRaster.html:141:89: Warning: inserting implicit <span>
DataBackendRaster.html:138:6: Warning: trimming empty <span>
DataBackendRaster.html:141:6: Warning: trimming empty <span>
DataBackendVector.html:102:6: Warning: missing </span> before <p>
DataBackendVector.html:102:90: Warning: inserting implicit <span>
DataBackendVector.html:105:6: Warning: missing </span> before <p>
DataBackendVector.html:105:89: Warning: inserting implicit <span>
DataBackendVector.html:102:6: Warning: trimming empty <span>
DataBackendVector.html:105:6: Warning: trimming empty <span>
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'bst', 'DiscriMiner', 'extraTrees', 'gbm', 'nodeHarvest', 'rknn',
  'rrlda'
Found the following HTML validation problems:
extractFDAFeatures.html:107:38: Warning: <code> is probably intended as </code>
extractFDAFeatures.html:107:73: Warning: discarding unexpected </code>
extractFDAFeatures.html:107:81: Warning: discarding unexpected </code>
impute.html:171:38: Warning: <code> is probably intended as </code>
impute.html:171:70: Warning: discarding unexpected </code>
impute.html:171:78: Warning: discarding unexpected </code>
mlr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
mlr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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’
Package required but not available: ‘mma’

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 required but not available: ‘gbm’

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
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 math rendering problems:
MNIW.Rd:40-48: Undefined control sequence: \arraycolsep in 
  \arraycolsep=1.4pt
  \begin{a...
MNIW.Rd:49-53: Undefined control sequence: \vspace in 
  \vspace{-1em}
  
mniw-package.Rd:13-21: Undefined control sequence: \arraycolsep in 
  \arraycolsep=1.4pt
  \begin{a...
mniw-package.Rd:22-26: Undefined control sequence: \vspace in 
  \vspace{-1em}
  
rRxNorm.Rd:25-33: Undefined control sequence: \arraycolsep in 
  \arraycolsep=1.4pt
  \begin{a...
rRxNorm.Rd:34-38: Undefined control sequence: \vspace in 
  \vspace{-2em}
'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
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No news entries found.
Package suggested but not available for checking: ‘alstructure’

Packages which this enhances but not available for checking:
  'miraculix', 'MoBPSmaps'
Package required but not available: ‘gbm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following math rendering problems:
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residuals.moc.Rd:26-28: Invalid delimiter type 'ordgroup' in ...um_{i=1}^n\Bigl{(}\frac{d\hat{F}(...
residuals.moc.Rd:89-92: Invalid delimiter type 'ordgroup' in ...eviance = \Bigl{\lbrace}2\cdot wt\cdot
  ...
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Running examples in ‘modelbased-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estimate_slopes
> ### Title: Estimate Marginal Effects
> ### Aliases: estimate_slopes
> 
> ### ** Examples
> 
> if (require("emmeans")) {
+   # Get an idea of the data
+   if (require("ggplot2")) {
+     ggplot(iris, aes(x = Petal.Length, y = Sepal.Width)) +
+       geom_point(aes(color = Species)) +
+       geom_smooth(color = "black", se = FALSE) +
+       geom_smooth(aes(color = Species), linetype = "dotted", se = FALSE) +
+       geom_smooth(aes(color = Species), method = "lm", se = FALSE)
+   }
+ 
+   # Model it
+   model <- lm(Sepal.Width ~ Species * Petal.Length, data = iris)
+   # Compute the marginal effect of Petal.Length at each level of Species
+   slopes <- estimate_slopes(model, trend = "Petal.Length", at = "Species")
+   slopes
+   if (require("see")) {
+     plot(slopes)
+   }
+   standardize(slopes)
+ 
+   if (require("mgcv") && require("see")) {
+     model <- mgcv::gam(Sepal.Width ~ s(Petal.Length), data = iris)
+     slopes <- estimate_slopes(model, at = "Petal.Length", length = 50)
+     summary(slopes)
+     plot(slopes)
+ 
+     model <- mgcv::gam(Sepal.Width ~ s(Petal.Length, by = Species), data = iris)
+     slopes <- estimate_slopes(model,
+       trend = "Petal.Length",
+       at = c("Petal.Length", "Species"), length = 20
+     )
+     summary(slopes)
+     plot(slopes)
+   }
+ }
Loading required package: emmeans
Loading required package: ggplot2
Loading required package: see
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-40. For overview type 'help("mgcv-package")'.
No numeric variable was specified for slope estimation. Selecting `trend = "Petal.Length"`.
Error in emmeans::emtrends(model, specs = args$emmeans_specs, var = args$trend,  : 
  Variable 'Petal.Length' is not in the dataset
Calls: estimate_slopes -> get_emtrends -> <Anonymous>
Execution halted
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ames.html:35:83: Warning: inserting implicit <p>
ames.html:35:83: Warning: trimming empty <p>
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modeldb-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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Found the following files/directories:
  ‘BIO_TCandNLCD_NLCD.jpg’ ‘BIO_TCandNLCD_TCB.jpg’
  ‘BIO_TCandNLCD_TCG.jpg’ ‘BIO_TCandNLCD_TCW.jpg’
  ‘BIO_TCandNLCD_corrplot.jpg’ ‘BIO_TCandNLCD_mask_all_predictors.jpg’
  ‘BIO_TCandNLCD_projections.txt’ ‘RF_BIO_TCandNLCD_01.img’
  ‘RF_BIO_TCandNLCD_01.img.aux.xml’
  ‘RF_BIO_TCandNLCD_01_mapmake_arguments.txt’
  ‘RF_BIO_TCandNLCD_01_projections.txt’ ‘RF_BIO_TCandNLCD_OOB.csv’
  ‘RF_BIO_TCandNLCD_OOB_corrplot.jpg’
  ‘RF_BIO_TCandNLCD_OOB_corrplot.pdf’ ‘RF_BIO_TCandNLCD_OOB_error.jpg’
  ‘RF_BIO_TCandNLCD_OOB_error.pdf’
  ‘RF_BIO_TCandNLCD_OOB_importance.jpg’
  ‘RF_BIO_TCandNLCD_OOB_importance.pdf’
  ‘RF_BIO_TCandNLCD_OOB_scatterplot.jpg’
  ‘RF_BIO_TCandNLCD_OOB_scatterplot.pdf’
  ‘RF_BIO_TCandNLCD_model_building_arguments.txt’
  ‘RF_Bio_TC_model_building_arguments.txt’ ‘example.test.csv’
  ‘example.train.csv’
Found the following HTML validation problems:
modelr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
modelr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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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
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Found the following HTML validation problems:
moodleR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
moodleR-package.html:27:4: Warning: <img> attribute "align" not allowed for HTML5
moodleR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
moodleR-package.html:27:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
Package required but not available: ‘bst’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Context.Rd:27: Escaped LaTeX specials: \&
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atleast.one.endpoint.Rd:29: Can't use function '$' in math mode in $k\in\{1,\ldots,...
mpe.t.test.Rd:22: Can't use function '$' in math mode in $\mu_{Tk}-\mu_{C...
mpe.t.test.Rd:23: Can't use function '$' in math mode in $k\in\{1,\ldots,...
mpe.z.test.Rd:23: Can't use function '$' in math mode in $\mu_{Tk}-\mu_{C...
mpe.z.test.Rd:24: Can't use function '$' in math mode in $k\in\{1,\ldots,...
power.known.var.Rd:29: Can't use function '$' in math mode in $\mu_{Tk}-\mu_{C...
power.known.var.Rd:30: Can't use function '$' in math mode in $k\in\{1,\ldots,...
power.unknown.var.Rd:33: Can't use function '$' in math mode in $\mu_{Tk}-\mu_{C...
power.unknown.var.Rd:34: Can't use function '$' in math mode in $k\in\{1,\ldots,...
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: \_
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GNU make is a SystemRequirements.
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detfct.fit.html:132:1: Warning: trimming empty <li>
detfct.fit.opt.html:133:1: Warning: trimming empty <li>
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FindMaxHomoOptimalPartitions.html:102:38: Warning: nested emphasis <code>
FindMaxHomoOptimalPartitions.html:108:38: Warning: nested emphasis <code>
FindMaxHomoOptimalPartitions.html:114:38: Warning: nested emphasis <code>
linearModelTraining.html:80:38: Warning: nested emphasis <code>
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  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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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
checkRd: (-1) MultBiplotR-package.Rd:50: Escaped LaTeX specials: \&
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checkRd: (-1) print.multcompLetters.Rd:20: Escaped LaTeX specials: \$
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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multilinguer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
multilinguer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following HTML validation problems:
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multinomineq-package.html:24:4: Warning: <img> attribute "align" not allowed for HTML5
multinomineq-package.html:24:4: Warning: <img> attribute "align" not allowed for HTML5
multinomineq-package.html:24:4: Warning: <img> attribute "hspace" not allowed for HTML5
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std.coef.Rd:61: Undefined control sequence: \var in ...^{*}=s_{X_{i}} \var{VIF}(X_i)^{-0....
'LazyData' is specified without a 'data' directory
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Package required but not available: ‘gbm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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    PREVIOUS (Incomplete below)
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namedropR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
namedropR-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Malformed Description field: should contain one or more complete sentences.
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    Minor changes
Found the following HTML validation problems:
nasapower-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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Problems with news in ‘NEWS.md’:
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    Version (2018-01-22)
    Version  (2017-08-22)
    Version
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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’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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    Slightly modified tests
'LazyData' is specified without a 'data' directory
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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.
Problems with news in ‘NEWS.md’:
No news entries found.
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GNU make is a SystemRequirements.
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nBartlett.Rd:45-50: Undefined control sequence: \raise in ... }
      \over {{\raise0.7ex\hbox{$1$}...
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m_ng.html:129:38: Warning: nested emphasis <code>
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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pm.Rd:47: Undefined control sequence: \emph in \emph{e}
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'LazyData' is specified without a 'data' directory
checkRd: (-1) euc.dist.Rd:50: Escaped LaTeX specials: \&
Found the following math rendering problems:
funsW345values.Rd:28-29: Undefined control sequence: \boldmath in ...ymbol \delta^t \boldmath A(\theta)) \bol...
funsW345values.Rd:30: Undefined control sequence: \boldmath in \boldmath A(\theta) = (a_...
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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    norgeo (development version)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
cub_spline_est.rd:40: Can't use function '$' in math mode in ...^T \alpha\leq 0$, $j=0,1,\ldots...
checkRd: (-1) prepareplot.Rd:64: Escaped LaTeX specials: \#
checkRd: (-1) prepareplot.Rd:68: Escaped LaTeX specials: \#
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
Error(s) in re-building vignettes:
  ...
--- re-building ‘entropy_np.Rnw’ using Sweave
Nonparametric Kernel Methods for Mixed Datatypes (version 0.60-11)
[vignette("np_faq",package="np") provides answers to frequently asked questions]
[vignette("np",package="np") an overview]
[vignette("entropy_np",package="np") an overview of entropy-based methods]
Error: processing vignette ‘entropy_np.Rnw’ failed with diagnostics:
Running ‘texi2dvi’ on ‘entropy_np.tex’ failed.
LaTeX errors:
! Argument of <c2> has an extra }.
<inserted text> 
                \par 
l.57 \begin{document}
                     
! Emergency stop.
<inserted text> 
                \par 
l.57 \begin{document}
                     
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘entropy_np.Rnw’

--- re-building ‘np.Rnw’ using Sweave
Warning in Ops.factor(dfemale + dmarried + educ + exper + tenure, female) :
  ‘|’ not meaningful for factors
Error: processing vignette ‘np.Rnw’ failed with diagnostics:
Running ‘texi2dvi’ on ‘np.tex’ failed.
LaTeX errors:
! Argument of <c2> has an extra }.
<inserted text> 
                \par 
l.77 \begin{document}
                     
! Emergency stop.
<inserted text> 
                \par 
l.77 \begin{document}
                     
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘np.Rnw’

--- re-building ‘np_faq.Rnw’ using Sweave
--- finished re-building ‘np_faq.Rnw’

SUMMARY: processing the following files failed:
  ‘entropy_np.Rnw’ ‘np.Rnw’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) frfast.Rd:172: Escaped LaTeX specials: \~
checkRd: (-1) globaltest.Rd:114: Escaped LaTeX specials: \~
checkRd: (-1) localtest.Rd:139: Escaped LaTeX specials: \~
Found the following math rendering problems:
globaltest.Rd:97-98: Undefined control sequence: \emph in ...m{some}
   \quad \emph{i}, \emph{j} \...
localtest.Rd:115-116: Undefined control sequence: \emph in ...{some}} \quad 
  \emph{i}, \emph{j} \...
'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
checkRd: (-1) Ardechedata.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) nsRFA-package.Rd:231: 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
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) dataca20.Rd:23: Escaped LaTeX specials: \~
checkRd: (-1) dataca20.Rd:23: 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 math rendering problems:
Overbeck2.Rd:52: Can't use function '$' in math mode in $K$
Overbeck2.Rd:53: Can't use function '$' in math mode in $X_{i}$
Overbeck2.Rd:55: Can't use function '$' in math mode in $X$
Found the following HTML validation problems:
soi.html:37:100: Warning: inserting implicit <p>
soi.html:37:100: Warning: trimming empty <p>
Found the following HTML validation problems:
swTFreeze.html:114:1: Warning: trimming empty <li>
Found the following math rendering problems:
swSpecificHeat.Rd:35: Got group of unknown type: 'internal'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘morse’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp500_1950_2018.Rd:6: Escaped LaTeX specials: \&
Found the following HTML validation problems:
openintro-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
openintro-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: There's no line here to end.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...
Found the following files/directories:
  ‘OpenML-manual.tex’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Older changes
    trunk
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘openNLPmodels.en’
Package suggested but not available for checking: ‘gbm’
Error(s) in re-building vignettes:
  ...
--- re-building ‘opera-vignette.Rmd’ using rmarkdown
Loading required package: nlme
This is mgcv 1.8-40. For overview type 'help("mgcv-package")'.
Loading required package: ggplot2
Loading required package: lattice
Quitting from lines 118-121 (./../inst/rmd/example.Rmd) 
Quitting from lines 15-18 (./../inst/rmd/example.Rmd) 
Error: processing vignette ‘opera-vignette.Rmd’ failed with diagnostics:
Required packages are missing: gbm
--- failed re-building ‘opera-vignette.Rmd’

--- re-building ‘regional_forecasting.Rmd’ using rmarkdown
Warning in par(def.par, new = FALSE) :
  argument 1 does not name a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  argument 1 does not name a graphical parameter
--- finished re-building ‘regional_forecasting.Rmd’

SUMMARY: processing the following file failed:
  ‘opera-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘gurobi’
checkRd: (-1) problem.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) problem.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) problem.Rd:45: Escaped LaTeX specials: \$
'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
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: ‘rrelaxiv’
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
Package suggested but not available for checking: ‘twang’
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.
'LazyData' is specified without a 'data' directory
'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’
checkRd: (-1) compartmentalModel.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) multilinearReferenceTissueModel.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) simplifiedReferenceTissueModel.Rd:60: Escaped LaTeX specials: \&
Found the following math rendering problems:
chebyshev.c.inner.products.Rd:18-22: Unknown column alignment: * in ...{\begin{array}{*{20}c}
     {4\,\...
chebyshev.t.inner.products.Rd:18-23: Unknown column alignment: * in ...{\begin{array}{*{20}c}
     {\fra...
gegenbauer.inner.products.Rd:19-25: Unknown column alignment: * in ...{\begin{array}{*{20}c}
     {\fra...
schebyshev.t.inner.products.Rd:18-23: Unknown column alignment: * in ...{\begin{array}{*{20}c}
     {\fra...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
    development version
Found the following HTML validation problems:
macos_keychain.html:220:35: Warning: inserting implicit <p>
macos_keychain.html:225:88: Warning: inserting implicit <p>
macos_keychain.html:234:79: Warning: inserting implicit <p>
macos_keychain.html:240:109: Warning: inserting implicit <p>
macos_keychain.html:250:95: Warning: inserting implicit <p>
macos_keychain.html:265:62: Warning: inserting implicit <p>
macos_keychain.html:445:104: Warning: inserting implicit <p>
macos_keychain.html:462:98: Warning: inserting implicit <p>
macos_keychain.html:474:58: Warning: inserting implicit <p>
macos_keychain.html:220:35: Warning: trimming empty <p>
macos_keychain.html:225:88: Warning: trimming empty <p>
macos_keychain.html:234:79: Warning: trimming empty <p>
macos_keychain.html:240:109: Warning: trimming empty <p>
macos_keychain.html:250:95: Warning: trimming empty <p>
macos_keychain.html:265:62: Warning: trimming empty <p>
macos_keychain.html:445:104: Warning: trimming empty <p>
macos_keychain.html:462:98: Warning: trimming empty <p>
macos_keychain.html:474:58: Warning: trimming empty <p>
windows_credentials.html:172:33: Warning: inserting implicit <p>
windows_credentials.html:183:62: Warning: inserting implicit <p>
windows_credentials.html:196:69: Warning: inserting implicit <p>
windows_credentials.html:204:102: Warning: inserting implicit <p>
windows_credentials.html:212:71: Warning: inserting implicit <p>
windows_credentials.html:220:50: Warning: inserting implicit <p>
windows_credentials.html:172:33: Warning: trimming empty <p>
windows_credentials.html:183:62: Warning: trimming empty <p>
windows_credentials.html:196:69: Warning: trimming empty <p>
windows_credentials.html:204:102: Warning: trimming empty <p>
windows_credentials.html:212:71: Warning: trimming empty <p>
windows_credentials.html:220:50: Warning: trimming empty <p>
Found the following HTML validation problems:
osmextract-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
osmextract-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following math rendering problems:
plot.osmose.Rd:501: Can't use function '$' in math mode in freq = 1/x$model$start
plot.osmose.config.Rd:141: Can't use function '$' in math mode in freq = 1/x$model$start
'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.
Running ‘testthat.R’ [40s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(outerbase)
  > 
  > test_check("outerbase")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 63 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-obombasic.R:72:3): basic test ─────────────────────────────────
  base mat agreement (`actual`) not equal to 0 (`expected`).
  
    `actual`: 2
  `expected`: 0
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 63 ]
  Error: Test failures
  Execution halted
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
Package required but not available: ‘twang’

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 HTML validation problems:
eff.html:65:38: Warning: nested emphasis <code>
eff.html:71:38: Warning: nested emphasis <code>
'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: \$
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pad_int
'LazyData' is specified without 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) eseq.Rd:36: Escaped LaTeX specials: \_
checkRd: (-1) eseq.Rd:38: Escaped LaTeX specials: \_
Found the following math rendering problems:
specialg.Rd:62: Can't use function '$' in math mode in a_i \leq b_i$,$i=1, \ldots, ...
Found the following HTML validation problems:
pairwise-package.html:64:184: Warning: <a> illegal characters found in URI
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
handle_package_not_found.html:49:102: Warning: inserting implicit <p>
handle_package_not_found.html:49:102: Warning: trimming empty <p>
pak_package_sources.html:32:39: Warning: inserting implicit <p>
pak_package_sources.html:55:39: Warning: inserting implicit <p>
pak_package_sources.html:98:61: Warning: inserting implicit <p>
pak_package_sources.html:104:35: Warning: inserting implicit <p>
pak_package_sources.html:32:39: Warning: trimming empty <p>
pak_package_sources.html:55:39: Warning: trimming empty <p>
pak_package_sources.html:98:61: Warning: trimming empty <p>
pak_package_sources.html:104:35: Warning: trimming empty <p>
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
Found the following HTML validation problems:
timePaleoPhy.html:262:4: Warning: nested emphasis <em>
Found the following HTML validation problems:
paletteer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
paletteer-package.html:30:4: Warning: <img> attribute "align" not allowed for HTML5
paletteer-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
paletteer-package.html:30:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
palmerpenguins-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
palmerpenguins-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
document.html:43:1: Warning: trimming empty <dt>
document.html:45:1: Warning: trimming empty <dt>
document.html:46:1: Warning: trimming empty <dt>
document.html:56:1: Warning: trimming empty <dt>
document.html:58:1: Warning: trimming empty <dt>
document.html:59:1: Warning: trimming empty <dt>
document.html:62:1: Warning: trimming empty <dt>
document.html:64:1: Warning: trimming empty <dt>
document.html:65:1: Warning: trimming empty <dt>
document.html:68:1: Warning: trimming empty <dt>
document.html:69:1: Warning: trimming empty <dt>
document.html:72:1: Warning: trimming empty <dt>
document.html:73:1: Warning: trimming empty <dt>
document.html:76:1: Warning: trimming empty <dt>
document.html:78:1: Warning: trimming empty <dt>
document.html:79:1: Warning: trimming empty <dt>
document.html:89:1: Warning: trimming empty <dt>
document.html:91:1: Warning: trimming empty <dt>
document.html:92:1: Warning: trimming empty <dt>
document.html:95:1: Warning: trimming empty <dt>
document.html:97:1: Warning: trimming empty <dt>
document.html:98:1: Warning: trimming empty <dt>
document.html:107:1: Warning: trimming empty <dt>
document.html:114:1: Warning: trimming empty <dt>
document.html:121:1: Warning: trimming empty <dt>
document.html:128:1: Warning: trimming empty <dt>
document.html:135:1: Warning: trimming empty <dt>
document.html:142:1: Warning: trimming empty <dt>
document.html:149:1: Warning: trimming empty <dt>
document.html:156:1: Warning: trimming empty <dt>
document.html:163:1: Warning: trimming empty <dt>
document.html:170:1: Warning: trimming empty <dt>
document.html:177:1: Warning: trimming empty <dt>
document.html:184:1: Warning: trimming empty <dt>
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: \_
Found the following HTML validation problems:
pvargmm.html:141:1: Warning: <center> element removed from HTML5
'LazyData' is specified without a 'data' directory
checkRd: (-1) pan.bd.Rd:65: Escaped LaTeX specials: \$
Found the following HTML validation problems:
apa_barplot.html:83:1: Warning: trimming empty <dt>
apa_beeplot.html:84:1: Warning: trimming empty <dt>
apa_interval.html:96:1: Warning: trimming empty <dt>
apa_lineplot.html:84:1: Warning: trimming empty <dt>
apa_print.emmGrid.html:77:1: Warning: trimming empty <dt>
apa_print.glm.html:107:1: Warning: trimming empty <dt>
apa_print.htest.html:90:1: Warning: trimming empty <dt>
apa_print.papaja_wsci.html:50:1: Warning: trimming empty <dt>
revision_letter_pdf.html:48:1: Warning: trimming empty <dt>
Found the following HTML validation problems:
param6-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
param6-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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 math rendering problems:
parfm.Rd:112-113: Undefined control sequence: \slash in ...exp \left( - u \slash \theta \right)}...
Found the following files/directories:
  ‘NUL’
Found the following files/directories:
  ‘parsnip-manual.tex’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
particles-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
particles-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Found the following HTML validation problems:
patchwork-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
patchwork-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Packages required but not available: 'gbm', 'twang'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following HTML validation problems:
pathviewr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
pathviewr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Checking should be performed on sources prepared by ‘R CMD build’.
GNU make is a SystemRequirements.
checkRd: (-1) plot-methods.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) plot-methods.Rd:125: Escaped LaTeX specials: \_
Found the following math rendering problems:
find_astar.Rd:5: Can't use function '$' in math mode in $\alpha^*$
find_astar.Rd:18: Can't use function '$' in math mode in $\alpha^*$
find_astar.Rd:14: Can't use function '$' in math mode in $\alpha^*$
find_astar.Rd:22: Can't use function '$' in math mode in $\alpha$
summary.colspace.Rd:42: Can't use function '$' in math mode in $\alpha$
summary.colspace.Rd:73: Can't use function '$' in math mode in $\alpha$
tcsplot.Rd:81: Can't use function '$' in math mode in $\alpha^*$
vol.Rd:28: Can't use function '$' in math mode in $\alpha^*$
vol.Rd:77: Can't use function '$' in math mode in $\alpha$
voloverlap.Rd:34: Can't use function '$' in math mode in $\alpha^*$
voloverlap.Rd:127: Can't use function '$' in math mode in $\alpha$
checkRd: (-1) glue_search_tables.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) mq_update_broker.Rd:28: Escaped LaTeX specials: \#
Found the following HTML validation problems:
swf_register_activity_type.html:154:8: Warning: nested emphasis <em>
checkRd: (-1) ec2_create_key_pair.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:27: Escaped LaTeX specials: \#
Found the following files/directories:
  ‘paws.compute-manual.tex’
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: \#
'LazyData' is specified without 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 math rendering problems:
calcArea.Rd:33: Undefined control sequence: \emph in -186 + 6\emph{i}^\circ < x \...
convUL.Rd:28-29: Undefined control sequence: \emph in -186 + 6\emph{i}^\circ < x \...
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
Package suggested but not available for checking: ‘PythonInR’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gbm’
'LazyData' is specified without 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
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 in Depends field not imported from: ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  ‘A.txt’ ‘Ainv.txt’
'LazyData' is specified without a 'data' directory
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
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: \&
Found the following HTML validation problems:
Return.Geltner.html:58:32: Warning: trimming empty <code>
centeredmoments.html:24:32: Warning: trimming empty <code>
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
Found the following HTML validation problems:
personalr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
personalr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Found the following math rendering problems:
fingerprint.regression.Rd:87: Can't use function '$' in math mode in $\lambda$
fingerprint.regression.Rd:88: Can't use function '$' in math mode in $\delta$
fingerprint.regression.Rd:88: Can't use function '$' in math mode in $\kappa$
pez.evenness.Rd:47: Can't use function '$' in math mode in $\lambda$
pez.evenness.Rd:47: Can't use function '$' in math mode in $\delta$
pez.evenness.Rd:48: Can't use function '$' in math mode in $\kappa$
phy.signal.Rd:13: Can't use function '$' in math mode in $\lambda$
phy.signal.Rd:13: Can't use function '$' in math mode in $\delta$
phy.signal.Rd:14: Can't use function '$' in math mode in $\kappa$
sim.meta.Rd:43: Can't use function '$' in math mode in $\lambda$
sim.meta.Rd:47: Can't use function '$' in math mode in $\lambda$
sim.meta.Rd:51: Can't use function '$' in math mode in $\lambda$
sim.phy.Rd:94-96: Can't use function '$' in math mode in $p(speciate)_i =...
sim.phy.Rd:96-98: Can't use function '$' in math mode in $p(extinct)_i = ...
sim.phy.Rd:98: Can't use function '$' in math mode in $i$
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Misplaced \cr.
<argument> ...|t-1}+y_{t}\right )-\log y_{t}!-\cr 
                                                  \log \Gamma \left (a_{t|t-...
l.1245 ...\right)\log \left(1+b_{t|t-1}\right)}}{}
Found the following math rendering problems:
pgam.likelihood.Rd:20-21: Undefined control sequence: \cr in ...t)-\log y_{t}!-\cr
  \log \Gamma\lef...
Found the following files/directories:
  ‘pgam-manual.tex’
'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
'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
SIR.html:67:1: Warning: <center> element removed from HTML5
competition.html:72:1: Warning: <center> element removed from HTML5
example1.html:62:1: Warning: <center> element removed from HTML5
example10.html:62:1: Warning: <center> element removed from HTML5
example11.html:62:1: Warning: <center> element removed from HTML5
example12.html:62:1: Warning: <center> element removed from HTML5
example13.html:62:1: Warning: <center> element removed from HTML5
example14.html:62:1: Warning: <center> element removed from HTML5
example15.html:62:1: Warning: <center> element removed from HTML5
example2.html:62:1: Warning: <center> element removed from HTML5
example3.html:62:1: Warning: <center> element removed from HTML5
example4.html:62:1: Warning: <center> element removed from HTML5
example5.html:62:1: Warning: <center> element removed from HTML5
example6.html:62:1: Warning: <center> element removed from HTML5
example7.html:62:1: Warning: <center> element removed from HTML5
example8.html:62:1: Warning: <center> element removed from HTML5
example9.html:62:1: Warning: <center> element removed from HTML5
exponential.html:65:1: Warning: <center> element removed from HTML5
lindemannMechanism.html:65:1: Warning: <center> element removed from HTML5
logistic.html:67:1: Warning: <center> element removed from HTML5
lotkaVolterra.html:69:1: Warning: <center> element removed from HTML5
monomolecular.html:67:1: Warning: <center> element removed from HTML5
morrisLecar.html:67:1: Warning: <center> element removed from HTML5
morrisLecar.html:70:1: Warning: <center> element removed from HTML5
simplePendulum.html:65:1: Warning: <center> element removed from HTML5
toggle.html:68:1: Warning: <center> element removed from HTML5
vanDerPol.html:65:1: Warning: <center> element removed from HTML5
vonBertalanffy.html:67:1: Warning: <center> element removed from HTML5
Found the following files/directories:
  ‘test.pdf’
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
phenology-package.html:28:1: Warning: <img> attribute "," lacks value
phenology-package.html:28:1: Warning: <img> attribute "align" not allowed for HTML5
phenology-package.html:28:1: Warning: <img> attribute "align" not allowed for HTML5
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 HTML validation problems:
estimate.probability.html:33:1: Warning: trimming empty <li>
estimate.probability.html:35:1: Warning: trimming empty <li>
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
Found the following HTML validation problems:
photobiologyInOut-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
photobiologyInOut-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
photobiologyLamps-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
photobiologyLamps-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
photobiologyLEDs-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
photobiologyLEDs-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
photobiologyWavebands-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
photobiologyWavebands-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) 11_d.EMControl.Rd:52: Escaped LaTeX specials: \_
checkRd: (-1) plotdots.Rd:33: Escaped LaTeX specials: \#
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: \&
Package suggested but not available for checking: ‘gbm’
'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
Found the following HTML validation problems:
piecepackr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
piecepackr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
board_rsconnect.html:128:59: Warning: inserting implicit <p>
board_rsconnect.html:134:92: Warning: inserting implicit <p>
board_rsconnect.html:128:59: Warning: trimming empty <p>
board_rsconnect.html:134:92: Warning: trimming empty <p>
pins-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
pins-package.html:23:4: 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’:
No news entries found.
Package suggested but not available for checking: ‘ggsubplot’
'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
checkRd: (-1) sanitize_latex.Rd:49: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
pkgcache-package.html:38:78: Warning: inserting implicit <p>
pkgcache-package.html:51:62: Warning: inserting implicit <p>
pkgcache-package.html:93:146: Warning: inserting implicit <p>
pkgcache-package.html:38:78: Warning: trimming empty <p>
pkgcache-package.html:51:62: Warning: trimming empty <p>
pkgcache-package.html:93:146: Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following HTML validation problems:
pkglite-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
pkglite-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
DependencyReporter.html:35:1: Warning: trimming empty <dt>
FunctionReporter.html:101:1: Warning: trimming empty <dt>
InheritanceReporter.html:79:1: Warning: trimming empty <dt>
PackageReporters.html:34:1: Warning: trimming empty <dt>
SummaryReporter.html:33:1: Warning: trimming empty <dt>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
PL94171-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
PL94171-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Running ‘testthat.R’ [158s/245s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PlackettLuce)
  > 
  > test_check("PlackettLuce")
  Loading required package: prefmod
  Loading required package: gnm
  Loading required package: colorspace
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 293 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-anova.R:26:9): PLADMM anova matches rank ordered logit model [salad] ──
  anova1$`Pr(>Chi)` not equal to anova2$`P(>|Chi|)`.
  Types not compatible: double is not NULL
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 293 ]
  Error: Test failures
  Execution halted
'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’
Found the following HTML validation problems:
mus_b_trans.html:19:1: Warning: missing </h2> before <dl>
mus_b_trans.html:34:1: Warning: discarding unexpected </h2>
vdj_length_prob.html:19:1: Warning: missing </h2> before <dl>
vdj_length_prob.html:36:1: Warning: discarding unexpected </h2>
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
palettes.html:90:1: Warning: trimming empty <li>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘gbm’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
plsim.MAVE.Rd:35: Undefined control sequence: \boldmath in \boldmath{\alpha}_0
plsim.MAVE.Rd:36: Undefined control sequence: \boldmath in \boldmath{\beta}_0
plsim.MAVE.Rd:55: Undefined control sequence: \boldmath in \hat{\eta}(Z^T\boldmath{\hat{\alpha} }...
plsim.MAVE.Rd:64: Undefined control sequence: \boldmath in Z^T\boldmath{\hat{\alpha}}
plsim.bw.Rd:50: Undefined control sequence: \boldmath in \boldmath{\alpha}_0
plsim.bw.Rd:51: Undefined control sequence: \boldmath in \boldmath{\beta}_0
plsim.est.Rd:33: Undefined control sequence: \boldmath in \boldmath{\alpha}_0
plsim.est.Rd:34: Undefined control sequence: \boldmath in \boldmath{\beta}_0
plsim.est.Rd:49: Undefined control sequence: \boldmath in \hat{\eta}(Z^T\boldmath{\hat{\alpha} }...
plsim.est.Rd:57: Undefined control sequence: \boldmath in Z^T\boldmath{\hat{\alpha}}
plsim.ini.Rd:34: Undefined control sequence: \boldmath in \boldmath{\alpha}_0
plsim.ini.Rd:35: Undefined control sequence: \boldmath in \boldmath{\beta}_0
plsim.lam.Rd:32: Undefined control sequence: \boldmath in \boldmath{\alpha}_0
plsim.lam.Rd:33: Undefined control sequence: \boldmath in \boldmath{\beta}_0
plsim.vs.hard.Rd:39: Undefined control sequence: \boldmath in \boldmath{\alpha}_0
plsim.vs.hard.Rd:40: Undefined control sequence: \boldmath in \boldmath{\beta}_0
plsim.vs.soft.Rd:34: Undefined control sequence: \boldmath in \boldmath{\alpha}_0
plsim.vs.soft.Rd:35: Undefined control sequence: \boldmath in \boldmath{\beta}_0
plsim.vs.soft.Rd:57: Undefined control sequence: \boldmath in \hat{\eta}(Z^T\boldmath{\hat{\alpha} }...
plsim.vs.soft.Rd:66: Undefined control sequence: \boldmath in Z^T\boldmath{\hat{\alpha}}
Found the following HTML validation problems:
plsmod-package.html:37:98: Warning: inserting implicit <p>
plsmod-package.html:50:99: Warning: inserting implicit <p>
plsmod-package.html:55:71: Warning: inserting implicit <p>
plsmod-package.html:62:47: Warning: inserting implicit <p>
plsmod-package.html:37:98: Warning: trimming empty <p>
plsmod-package.html:50:99: Warning: trimming empty <p>
plsmod-package.html:55:71: Warning: trimming empty <p>
plsmod-package.html:62:47: Warning: trimming empty <p>
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
Found the following HTML validation problems:
plu-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
plu-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gbm’
'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 math rendering problems:
1dpoilog.Rd:31: Undefined control sequence: \emph in \code{nu}\,\emph{y}
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
poissonreg-package.html:38:90: Warning: inserting implicit <p>
poissonreg-package.html:74:31: Warning: inserting implicit <p>
poissonreg-package.html:38:90: Warning: trimming empty <p>
poissonreg-package.html:74:31: Warning: trimming empty <p>
'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’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Documentation
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘polyfreqs-mcmc.out’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
Package required but not available: ‘gbm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
poorman.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
poorman.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘relsurv’
Running ‘testthat.R’ [53s/84s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("popEpi")
  > library("data.table")
  > 
  > using_r_devel <- grepl(pattern = "devel", x = R.version$status)
  > if (using_r_devel) {
  +   ## memory leak problem in data.table 1.11.2 in R-devel (3.6.0 atm)
  +   requireNamespace("data.table")
  +   data.table::setDTthreads(threads = 1L)
  + }
  > 
  > test_check("popEpi")
  NOTE: entry.status has been set to "DM" for all.
     first.bad.surv.int last.bad.surv.int surv.obs
  1:                 61               120      NaN
     first.bad.surv.int last.bad.surv.int surv.obs
  1:                 61               120      NaN
     agegr first.bad.surv.int last.bad.surv.int surv.obs
  1:     3                 61               120      NaN
     agegr first.bad.surv.int last.bad.surv.int surv.obs
  1:     3                 61               120      NaN
  [ FAIL 2 | WARN 0 | SKIP 41 | PASS 267 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (41)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_survtab_relative.R:7:3): relative survivals about the same as relsurv's ──
  <packageNotFoundError/error/condition>
  Error in `library(relsurv)`: there is no package called 'relsurv'
  Backtrace:
      ▆
   1. └─base::library(relsurv) at test_survtab_relative.R:7:2
  ── Error (test_survtab_relative.R:130:3): Ederer I expected survival curve agrees with survival::survexp ──
  <packageNotFoundError/error/condition>
  Error in `library(relsurv)`: there is no package called 'relsurv'
  Backtrace:
      ▆
   1. └─base::library(relsurv) at test_survtab_relative.R:130:2
  
  [ FAIL 2 | WARN 0 | SKIP 41 | PASS 267 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking:
  'BASIX', 'WhopGenome', 'BlockFeST'
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’
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
Package suggested but not available for checking: ‘gbm’
'LazyData' is specified without 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 math rendering problems:
cachet.Rd:126-127: Undefined control sequence: \textbackslash in ...a_{idx} \cup X \textbackslash
    A_a)
calct.Rd:64-65: Undefined control sequence: \textbackslash in t(y \cup X \textbackslash
    A_a)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character − (U+2212)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
Found the following files/directories:
  ‘powerHaDeX-manual.tex’
Found the following HTML validation problems:
powerjoin-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
powerjoin-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    [1.7.3]
    [1.7.2]
    [1.7.1]
    [1.7.0]
    [1.6.1]
    [1.6.0]
    [1.5.2]
    [1.5.1]
    [1.5.0]
    [1.4.0]
    [1.3.0]
    [1.2.0]
    [1.1.1]
    [1.1.0]
    [1.0.0]
    [0.2.0]
    [0.1.1]
    [0.1.0]
Found the following HTML validation problems:
plot.Method.html:107:1: Warning: inserting implicit <p>
plot.Method.html:112:1: Warning: inserting implicit <p>
plot.Method.html:118:1: Warning: inserting implicit <p>
plot.Method.html:104:1: Warning: trimming empty <p>
plot.Method.html:107:1: Warning: trimming empty <p>
plot.Method.html:109:1: Warning: trimming empty <p>
plot.Method.html:112:1: Warning: trimming empty <p>
plot.Method.html:114:1: Warning: trimming empty <p>
plot.Method.html:118:1: Warning: trimming empty <p>
plot.StepOne.html:86:1: Warning: inserting implicit <p>
plot.StepOne.html:86:1: Warning: trimming empty <p>
plot.StepThree.html:86:1: Warning: inserting implicit <p>
plot.StepThree.html:86:1: Warning: trimming empty <p>
plot.StepTwo.html:86:1: Warning: inserting implicit <p>
plot.StepTwo.html:86:1: Warning: trimming empty <p>
plot.Validation.html:92:1: Warning: inserting implicit <p>
plot.Validation.html:92:1: Warning: trimming empty <p>
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
Found the following HTML validation problems:
leukemia.html:19:1: Warning: missing </h2> before <ul>
leukemia.html:29:1: Warning: discarding unexpected </h2>
'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
Package suggested but not available for checking: ‘PerfMeas’
'LazyData' is specified without a 'data' directory
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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PReMiuM.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:
preregr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
preregr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following HTML validation problems:
presize-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
presize-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
new_app.html:119:43: Warning: inserting implicit <p>
new_app.html:205:35: Warning: inserting implicit <p>
new_app.html:237:40: Warning: inserting implicit <p>
new_app.html:329:21: Warning: inserting implicit <p>
new_app.html:344:82: Warning: inserting implicit <p>
new_app.html:352:65: Warning: inserting implicit <p>
new_app.html:395:72: Warning: inserting implicit <p>
new_app.html:119:43: Warning: trimming empty <p>
new_app.html:205:35: Warning: trimming empty <p>
new_app.html:237:40: Warning: trimming empty <p>
new_app.html:329:21: Warning: trimming empty <p>
new_app.html:344:82: Warning: trimming empty <p>
new_app.html:352:65: Warning: trimming empty <p>
new_app.html:395:72: Warning: trimming empty <p>
new_app_process.html:75:88: Warning: inserting implicit <p>
new_app_process.html:75:88: Warning: trimming empty <p>
'LazyData' is specified without 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
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:
  'RandomFields', 'gurobi', 'rcbc', 'cplexAPI'
Unknown package ‘RandomFields’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
prismatic-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
prismatic-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
proceduralnames-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
proceduralnames-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
prodigenr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
prodigenr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProFit’
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
handlers.html:80:4: Warning: nested emphasis <em>
with_progress.html:102:4: Warning: nested emphasis <em>
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
refmodel-init-get.html:313:36: Warning: inserting implicit <p>
refmodel-init-get.html:313:36: Warning: trimming empty <p>
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’
Package suggested but not available for checking: ‘cin’
Found the following HTML validation problems:
prospectr-package.html:25:1: Warning: <img> attribute "align" not allowed for HTML5
prospectr-package.html:25:1: Warning: <img> attribute "align" not allowed for HTML5
Package suggested but not available for checking: ‘rdt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
Package in Depends field not imported from: ‘rpart’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'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: ‘WebPower’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘gbm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Missing delimiter (. inserted).
<to be read again> 
                   \let 
l.750 ...}\right)+b_{0_{1}}-b_{0_{2}}\right} dX}{}
                                                  ,
! Missing } inserted.
<inserted text> 
                }
l.750 ...}\right)+b_{0_{1}}-b_{0_{2}}\right} dX}{}
                                                  ,
! Missing delimiter (. inserted).
<to be read again> 
                   }
l.750 ...}\right)+b_{0_{1}}-b_{0_{2}}\right} dX}{}
                                                  ,
! Extra \right.
<to be read again> 
                   }
l.750 ...}\right)+b_{0_{1}}-b_{0_{2}}\right} dX}{}
                                                  ,
! Extra }, or forgotten $.
<recently read> }
                 
l.750 ...}\right)+b_{0_{1}}-b_{0_{2}}\right} dX}{}
                                                  ,
Found the following math rendering problems:
dot-integrate_dmod.Rd:53: Undefined control sequence: \link in ...p f_{2}(X)\left\link[=X\left(b_{1_{...
Found the following files/directories:
  ‘psychmeta-manual.tex’
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: \&
checkRd: (-1) cor.plot.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) mediate.Rd:94: Escaped LaTeX specials: \&
checkRd: (-1) multilevel.reliability.Rd:120: Escaped LaTeX specials: \&
checkRd: (-1) testRetest.Rd:47: Escaped LaTeX specials: \&
Found the following HTML validation problems:
psymonitor-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
psymonitor-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ptvapi.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ptvapi.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
CVDictionarySingleton.html:64:6: Warning: missing </span> before <p>
CVDictionarySingleton.html:64:91: Warning: inserting implicit <span>
CVDictionarySingleton.html:64:6: Warning: trimming empty <span>
QCMetaFilenames.html:64:6: Warning: missing </span> before <p>
QCMetaFilenames.html:64:91: Warning: inserting implicit <span>
QCMetaFilenames.html:64:6: Warning: trimming empty <span>
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
Found the following HTML validation problems:
purrr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
purrr-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
reduce.html:108:68: Warning: inserting implicit <p>
reduce.html:108:68: Warning: trimming empty <p>
'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 files/directories:
  ‘lambda.pdf’ ‘qqplot.pdf’
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
qrandommaxint.Rd:6: Can't use function '$' in math mode in U(-.Machine$integer.max,.Ma...
qrandommaxint.Rd:14: Can't use function '$' in math mode in U(-.Machine$integer.max,.Ma...
qrandommaxint.Rd:27: Can't use function '$' in math mode in U(-.Machine$integer.max,.Ma...
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
GEV.Rd:37-41: Undefined control sequence: \cases in F(x) = \cases{
      \exp(-(1-...
GPD.Rd:49-53: Undefined control sequence: \cases in F(x) = \cases{
      1-(1+\xi ...
risk_measures.Rd:85: Can't use function '$' in math mode in $t$
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 HTML validation problems:
quadmesh-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
quadmesh-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
bounded.reg.html:204:33: Warning: unescaped & or unknown entity "&beta"
bounded.reg.html:213:1: Warning: inserting implicit <p>
bounded.reg.html:213:1: Warning: trimming empty <p>
bounded.reg.html:201:34: Warning: <center> element removed from HTML5
elastic.net.html:210:33: Warning: unescaped & or unknown entity "&beta"
elastic.net.html:219:1: Warning: inserting implicit <p>
elastic.net.html:219:1: Warning: trimming empty <p>
elastic.net.html:207:48: Warning: <center> element removed from HTML5
quadrupen-package.html:57:33: Warning: unescaped & or unknown entity "&beta"
quadrupen-package.html:67:1: Warning: inserting implicit <p>
quadrupen-package.html:67:1: Warning: trimming empty <p>
quadrupen-package.html:55:2: Warning: <center> element removed from HTML5
'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
'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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘fastshp’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following math rendering problems:
frame_fn_obs.Rd:24: Can't use function '$' in math mode in ...=r[\tau-I(r<0)]$ for $\tau \in ...
frame_fn_path.Rd:24: Can't use function '$' in math mode in ...=r[\tau-I(r<0)]$ for $\tau \in ...
'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
Found the following HTML validation problems:
prioritize.html:71:98: Warning: inserting implicit <p>
prioritize.html:107:71: Warning: inserting implicit <p>
prioritize.html:71:98: Warning: trimming empty <p>
prioritize.html:107:71: Warning: trimming empty <p>
'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
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
NullObject.html:47:1: Warning: inserting implicit <p>
NullObject.html:51:1: Warning: inserting implicit <p>
NullObject.html:56:1: Warning: inserting implicit <p>
NullObject.html:47:1: Warning: trimming empty <p>
NullObject.html:51:1: Warning: trimming empty <p>
NullObject.html:56:1: Warning: trimming empty <p>
Singleton.html:86:1: Warning: inserting implicit <p>
Singleton.html:92:1: Warning: inserting implicit <p>
Singleton.html:86:1: Warning: trimming empty <p>
Singleton.html:92:1: Warning: trimming empty <p>
ValueObject.html:61:1: Warning: inserting implicit <p>
ValueObject.html:98:73: Warning: inserting implicit <p>
ValueObject.html:110:37: Warning: inserting implicit <p>
ValueObject.html:115:34: Warning: inserting implicit <p>
ValueObject.html:182:78: Warning: inserting implicit <p>
ValueObject.html:270:1: Warning: inserting implicit <p>
ValueObject.html:61:1: Warning: trimming empty <p>
ValueObject.html:98:73: Warning: trimming empty <p>
ValueObject.html:110:37: Warning: trimming empty <p>
ValueObject.html:115:34: Warning: trimming empty <p>
ValueObject.html:182:78: Warning: trimming empty <p>
ValueObject.html:270:1: Warning: trimming empty <p>
'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
Found the following HTML validation problems:
ragg-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ragg-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) fdepth.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) fdepth.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
'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
'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.
checkRd: (-1) pseudoRNG.Rd:74: Escaped LaTeX specials: \_
Found the following math rendering problems:
colltest.Rd:34-38: Got group of unknown type: 'internal'
colltest.Rd:39: Got group of unknown type: 'internal'
colltestsparse.Rd:31-35: Got group of unknown type: 'internal'
colltestsparse.Rd:36: Got group of unknown type: 'internal'
Found the following HTML validation problems:
rangeMapper.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rangeMapper.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Packages suggested but not available for checking:
  'biomod2', '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
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 HTML validation problems:
rasterly-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rasterly-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following math rendering problems:
RPT.Rd:47: Can't use function '$' in math mode in \sigma^2(P)$ when $X_1,\dot...
'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 HTML validation problems:
yc_get.html:38:1: Warning: trimming empty <li>
Found the following HTML validation problems:
getblock.html:58:1: Warning: trimming empty <h3>
getrawtransaction.html:57:1: Warning: trimming empty <h3>
'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’:
  Cannot extract version info from the following section titles:
    names consisting of just one part, family, were missing processing of escaped
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘fts’
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
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
Running ‘run-all.R’ [4s/7s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > library(mlr)
  Loading required package: ParamHelpers
  Warning message: 'mlr' is in 'maintenance-only' mode since July 2019.
  Future development will only happen in 'mlr3'
  (<https://mlr3.mlr-org.com>). Due to the focus on 'mlr3' there might be
  uncaught bugs meanwhile in {mlr} - please consider switching.
  > 
  > test_check("RBPcurve")
  Loading required package: RBPcurve
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_add.R:18:9): add_functions ──────────────────────────────────────
  Error in `rect(y1, x1, y2, x2, ...)`: invalid graphics state
  Backtrace:
      ▆
   1. └─RBPcurve (local) checkAdd(fun = k, obj = obj, plot.values = i, show.info = j) at test_add.R:18:8
   2.   ├─base::do.call(fun, fun.arg) at test_add.R:9:2
   3.   └─RBPcurve::addWellCalib(obj = `<RBPObj>`, plot.values = TRUE)
   4.     ├─TeachingDemos::subplot(...)
   5.     ├─base::do.call(...)
   6.     ├─graphics::barplot(...)
   7.     └─graphics::barplot.default(...)
   8.       └─graphics (local) xyrect(...)
   9.         └─graphics::rect(y1, x1, y2, x2, ...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
getblock.html:58:1: Warning: trimming empty <h3>
getrawtransaction.html:57:1: Warning: trimming empty <h3>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RCALI.Rcheck/00install.out’ for details.
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’
'LazyData' is specified without 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:
rchie-package.html:23:4: Warning: <img> attribute "width" has invalid value "120px"
rchie-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rchie-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following files/directories:
  ‘data.csv’
'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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘conics’
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following HTML validation problems:
colorMaps.html:79:1: Warning: inserting implicit <p>
colorMaps.html:79:1: Warning: trimming empty <p>
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.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Todo
Found the following HTML validation problems:
cal_knee_point.html:81:62: Warning: nested emphasis <em>
cal_knee_point.html:81:89: Warning: nested emphasis <em>
estimate_dataset_bmr.html:82:62: Warning: nested emphasis <em>
estimate_dataset_bmr.html:82:89: Warning: nested emphasis <em>
'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) nonlinear_MVE.Rd:73: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
Rdistance-package.html:19:1: Warning: missing </h2> before <ul>
Rdistance-package.html:68:1: Warning: discarding unexpected </h2>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.pdf’
'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
'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
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
readthat-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
readthat-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
readxl-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
readxl-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Found the following HTML validation problems:
GeneratedPipeline.html:85:6: Warning: missing </span> before <p>
GeneratedPipeline.html:85:88: Warning: inserting implicit <span>
GeneratedPipeline.html:85:6: Warning: trimming empty <span>
GeneratedTransformation.html:89:6: Warning: missing </span> before <p>
GeneratedTransformation.html:89:94: Warning: inserting implicit <span>
GeneratedTransformation.html:89:6: Warning: trimming empty <span>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 files/directories:
  ‘Filled.RData’ ‘cleaned.RData’ ‘days’ ‘gridded’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Package required but not available: ‘gbm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 required but not available: ‘gbm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) rcpp_grad_ram.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) rcpp_grad_ram.Rd:48: Escaped LaTeX specials: \&
'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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/relsurv.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: ‘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’:
  Cannot extract version info from the following section titles:
    DEPRECATED AND DEFUNCT
Found the following HTML validation problems:
copulaCorrection.html:85:1: Warning: inserting implicit <p>
copulaCorrection.html:96:1: Warning: inserting implicit <p>
copulaCorrection.html:85:1: Warning: trimming empty <p>
copulaCorrection.html:96:1: Warning: trimming empty <p>
hetErrorsIV.html:66:1: Warning: inserting implicit <p>
hetErrorsIV.html:66:1: Warning: trimming empty <p>
higherMomentsIV.html:62:1: Warning: inserting implicit <p>
higherMomentsIV.html:62:1: Warning: trimming empty <p>
latentIV.html:75:1: Warning: inserting implicit <p>
latentIV.html:92:1: Warning: inserting implicit <p>
latentIV.html:75:1: Warning: trimming empty <p>
latentIV.html:92:1: Warning: trimming empty <p>
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
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 HTML validation problems:
replaceVals.html:84:31: Warning: <em> is probably intended as </em>
replaceVals.html:84:69: Warning: discarding unexpected </em>
replaceVals.html:84:93: Warning: discarding unexpected </em>
'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:
Dbf4myc.html:68:20: Warning: <a> illegal characters found in URI
Dbf4myc.html:69:12: Warning: <a> illegal characters found in URI
MFAseq.html:68:38: Warning: <a> illegal characters found in URI
MFAseq.html:69:29: Warning: <a> illegal characters found in URI
W303.html:66:20: Warning: <a> illegal characters found in URI
W303.html:67:12: Warning: <a> illegal characters found in URI
W303_G2.html:58:4: Warning: <a> illegal characters found in URI
W303_S.html:58:4: Warning: <a> illegal characters found in URI
W303norm.html:68:20: Warning: <a> illegal characters found in URI
W303norm.html:69:12: Warning: <a> illegal characters found in URI
sortSeq.html:77:28: Warning: <a> illegal characters found in URI
sortSeq.html:78:20: Warning: <a> illegal characters found in URI
sortSeq.html:79:16: Warning: <a> illegal characters found in URI
sortSeq.html:80:17: Warning: <a> illegal characters found in URI
Found the following files/directories:
  ‘PackageCites.bib’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
.find_regression_estimate: no visible global function definition for
  ‘data_findcols’
report_table.MixMod: no visible global function definition for
  ‘data_findcols’
report_table.anova: no visible global function definition for
  ‘data_findcols’
report_table.aov: no visible global function definition for
  ‘data_findcols’
report_table.aovlist: no visible global function definition for
  ‘data_findcols’
report_table.brmsfit: no visible global function definition for
  ‘data_findcols’
report_table.glm: no visible global function definition for
  ‘data_findcols’
report_table.glmmTMB: no visible global function definition for
  ‘data_findcols’
report_table.ivreg: no visible global function definition for
  ‘data_findcols’
report_table.lavaan: no visible global function definition for
  ‘data_findcols’
report_table.lm: no visible global function definition for
  ‘data_findcols’
report_table.lme: no visible global function definition for
  ‘data_findcols’
report_table.merMod: no visible global function definition for
  ‘data_findcols’
report_table.stanreg: no visible global function definition for
  ‘data_findcols’
report_table.survreg: no visible global function definition for
  ‘data_findcols’
report_table.zeroinfl: no visible global function definition for
  ‘data_findcols’
Undefined global functions or variables:
  data_findcols
Running examples in ‘report-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: report.default
> ### Title: Template to add report support for new objects
> ### Aliases: report.default report_effectsize.default report_table.default
> ###   report_statistics.default report_parameters.default
> ###   report_intercept.default report_model.default report_random.default
> ###   report_priors.default report_performance.default report_info.default
> ###   report_text.default
> 
> ### ** Examples
> 
> library(report)
> 
> # Add a reproducible example instead of the following
> model <- lm(Sepal.Length ~ Petal.Length * Species, data = iris)
> r <- report(model)
Error in data_findcols(table, candidates) : 
  could not find function "data_findcols"
Calls: report ... report_statistics -> report_statistics.lm -> .find_regression_estimate
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cite_packages.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 ‘cite_packages.Rmd’

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

--- re-building ‘report.Rmd’ using rmarkdown
Warning: Following variable(s) were not found: n_Obs
Warning: Following variable(s) were not found: n_Obs
Warning: Following variable(s) were not found: n_Obs
Warning in .effectsize_t.test(model, type = type, verbose = verbose, ...) :
  Unable to retrieve data from htest object. Using t_to_d() approximation.
Quitting from lines 105-108 (report.Rmd) 
Error: processing vignette ‘report.Rmd’ failed with diagnostics:
could not find function "data_findcols"
--- failed re-building ‘report.Rmd’

SUMMARY: processing the following file failed:
  ‘report.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 HTML validation problems:
reprex-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
reprex-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
checkRd: (-1) KitchenhamEtAl.CorrelationsAmongParticipants.Madeyski10.Rd:7: Escaped LaTeX specials: \&
checkRd: (-1) KitchenhamEtAl.CorrelationsAmongParticipants.Madeyski10.Rd:56: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘gdalUtils’
'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:
    reqres (development version)
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
reqres-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
reqres-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
Found the following HTML validation problems:
resemble-package.html:26:4: Warning: <img> attribute "align" not allowed for HTML5
resemble-package.html:26:4: Warning: <img> attribute "align" not allowed for HTML5
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.
Found the following HTML validation problems:
RestRserve-package.html:91:34: Warning: inserting implicit <p>
RestRserve-package.html:105:62: Warning: inserting implicit <p>
RestRserve-package.html:137:71: Warning: inserting implicit <p>
RestRserve-package.html:157:74: Warning: inserting implicit <p>
RestRserve-package.html:196:79: Warning: inserting implicit <p>
RestRserve-package.html:205:65: Warning: inserting implicit <p>
RestRserve-package.html:118:1: Warning: <img> lacks "alt" attribute
RestRserve-package.html:91:34: Warning: trimming empty <p>
RestRserve-package.html:105:62: Warning: trimming empty <p>
RestRserve-package.html:137:71: Warning: trimming empty <p>
RestRserve-package.html:157:74: Warning: trimming empty <p>
RestRserve-package.html:196:79: Warning: trimming empty <p>
RestRserve-package.html:205:65: Warning: trimming empty <p>
RestRserve-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
RestRserve-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following HTML validation problems:
py_iterator.html:56:154: Warning: inserting implicit <p>
py_iterator.html:65:87: Warning: inserting implicit <p>
py_iterator.html:82:35: Warning: inserting implicit <p>
py_iterator.html:56:154: Warning: trimming empty <p>
py_iterator.html:65:87: Warning: trimming empty <p>
py_iterator.html:82:35: Warning: trimming empty <p>
Packages suggested but not available for checking:
  'gWidgets2RGtk2', 'cairoDevice', 'RGtk2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘evdbayes’
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
Found the following HTML validation problems:
read_facts.html:70:56: Warning: inserting implicit <p>
read_facts.html:79:63: Warning: inserting implicit <p>
read_facts.html:70:56: Warning: trimming empty <p>
read_facts.html:79:63: Warning: trimming empty <p>
write_facts.html:90:56: Warning: inserting implicit <p>
write_facts.html:100:62: Warning: inserting implicit <p>
write_facts.html:90:56: Warning: trimming empty <p>
write_facts.html:100:62: Warning: trimming empty <p>
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
Found the following HTML validation problems:
RfEmpImp-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
RfEmpImp-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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
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
checkRd: (-1) Rglpk_read_file.Rd:6: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
rgoogleads-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rgoogleads-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Extra }, or forgotten \endgroup.
l.3   \item param}
                  }
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.3   \item param}}
                   
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.5   \item return}
                   }
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.5   \item return}}
                    
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
Found the following files/directories:
  ‘RGoogleAnalytics-manual.tex’
'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
Found the following HTML validation problems:
rgraph6-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rgraph6-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
rgugik-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rgugik-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
build_js.html:51:53: Warning: inserting implicit <p>
build_js.html:54:76: Warning: inserting implicit <p>
build_js.html:57:78: Warning: inserting implicit <p>
build_js.html:60:85: Warning: inserting implicit <p>
build_js.html:51:53: Warning: trimming empty <p>
build_js.html:54:76: Warning: trimming empty <p>
build_js.html:57:78: Warning: trimming empty <p>
build_js.html:60:85: Warning: trimming empty <p>
lint_js.html:54:106: Warning: inserting implicit <p>
lint_js.html:54:106: Warning: trimming empty <p>
'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
Found the following HTML validation problems:
rhub-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
rhub-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'LazyData' is specified without a 'data' directory
Package required but not available: ‘twang’

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
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
'LazyData' is specified without a 'data' directory
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 HTML validation problems:
ringostat-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
ringostat-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
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
Package required but not available: ‘relsurv’

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: ‘gbm’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    References
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 math rendering problems:
FitCbmRoc.Rd:49: Undefined control sequence: \eqn in N(\eqn{mu},1)
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
RKorAPClient-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
RKorAPClient-package.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
'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: \$
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! 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.
! 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.
Found the following files/directories:
  ‘rlang-manual.tex’
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
theta.html:19:1: Warning: missing </h2> before <p>
theta.html:22:1: Warning: discarding unexpected </h2>
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