'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
Running ‘testthat.R’ [13s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(adace)
  > 
  > test_check("adace")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 29 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-adace_func.R:98:3'): adace main function ─────────────────────
  message1$message (`actual`) not equal to "prediction from a rank-deficient fit may be misleading" (`expected`).
  
  actual vs expected
  - "prediction from rank-deficient fit; attr(*, \"non-estim\") has doubtful cases"
  + "prediction from a rank-deficient fit may be misleading"
  ── Failure ('test-adace_func.R:101:3'): adace main function ────────────────────
  message2$message (`actual`) not equal to "prediction from a rank-deficient fit may be misleading" (`expected`).
  
  actual vs expected
  - "prediction from rank-deficient fit; attr(*, \"non-estim\") has doubtful cases"
  + "prediction from a rank-deficient fit may be misleading"
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 29 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Unknown packages ‘HI’, ‘MHadaptive’ in Rd xrefs
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘table_AeRobiology’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Problems with news in ‘NEWS.md’:
No news entries found.
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
checkRd: (-1) BerryMielke.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) BlairLacy.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) Kvalseth.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) consensus.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) dsquared.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) l.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) lsquared.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) lsquared.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) var.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) adapt.Rd:41: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘RandomFields’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ call to ‘network’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
as.url:
  function(x, ...)
as.url.domain:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) deshrink.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) deshrink.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) plot.mat.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) plot.wa.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) predict.prcurve.Rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘BH-0.05-ListOfGenes.txt’ ‘BH-0.05-VM-ListOfGenes.txt’
  ‘CompleteListOfGenes.txt’ ‘GenesOutOfAnalysis.txt’
  ‘GenesOutOfAnalysis_NotEnoughObs.txt’
  ‘GenesOutOfAnalysis_NullVar.txt’ ‘VM-CompleteListOfGenes.txt’
  ‘bonferroni-0.05-ListOfGenes.txt’
  ‘bonferroni-0.05-VM-ListOfGenes.txt’
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
all.equal:
  function(target, current, ...)
all.equal.LayersR6:
  function(target, current)

all.equal:
  function(target, current, ...)
all.equal.RawR6:
  function(target, current)

all.equal:
  function(target, current, ...)
all.equal.AnnDataR6:
  function(target, current)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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: \_ \_
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following calls to attach():
File ‘apollo/R/apollo_attach.R’:
  attach(as.list(apollo_beta), warn.conflicts = FALSE)
  attach(database, warn.conflicts = FALSE)
  attach(draws, warn.conflicts = FALSE)
  attach(randcoeff, warn.conflicts = FALSE)
  attach(lcpars, warn.conflicts = FALSE)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘ARTP’
Found the following significant warnings:
  ARTP2_init.c:17:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ARTP2.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used C++ compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
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
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘asteRiskData’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
ihasNext:
  function(obj, ...)
ihasNext.default:
  function(obj)

ihasNext:
  function(obj, ...)
ihasNext.ihasNextOr:
  function(x)

ihasNext:
  function(obj, ...)
ihasNext.iteror:
  function(iter, ...)

compile:
  function(x, level, ...)
compile.coroutine:
  function(x, level)

as.promise:
  function(x)
as.promise.channel:
  function(ch, type)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
add_name_to_statistics:
  function(x, name)
add_name_to_statistics.data.frame:
  function(x, name, colname_for_variable)

add_name_to_tests:
  function(x, name)
add_name_to_tests.data.frame:
  function(x, name, colname_for_variable)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Unknown package ‘snpar’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  driver.c:114:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  driver.c:161:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  driver.c:199:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/audio.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
show_query:
  function(x, ...)
show_query.tbl_kusto_abstract:
  function(tbl)

slice_sample:
  function(.data, ..., n, prop, by, weight_by, replace)
slice_sample.tbl_kusto_abstract:
  function(x, n, ...)

semi_join:
  function(x, y, by, copy, ...)
semi_join.tbl_kusto_abstract:
  function(x, y, by, suffix, .strategy, .shufflekeys, .num_partitions,
           .remote, ...)

compute:
  function(x, ...)
compute.tbl_kusto:
  function(tbl, name, ...)

inner_join:
  function(x, y, by, copy, suffix, ..., keep)
inner_join.tbl_kusto_abstract:
  function(x, y, by, suffix, .strategy, .shufflekeys, .num_partitions,
           .remote, ...)

ungroup:
  function(x, ...)
ungroup.tbl_kusto_abstract:
  function(.data, ...)

left_join:
  function(x, y, by, copy, suffix, ..., keep)
left_join.tbl_kusto_abstract:
  function(x, y, by, suffix, .strategy, .shufflekeys, .num_partitions,
           .remote, ...)

full_join:
  function(x, y, by, copy, suffix, ..., keep)
full_join.tbl_kusto_abstract:
  function(x, y, by, suffix, .strategy, .shufflekeys, .num_partitions,
           .remote, ...)

anti_join:
  function(x, y, by, copy, ...)
anti_join.tbl_kusto_abstract:
  function(x, y, by, suffix, .strategy, .shufflekeys, .num_partitions,
           .remote, ...)

right_join:
  function(x, y, by, copy, suffix, ..., keep)
right_join.tbl_kusto_abstract:
  function(x, y, by, suffix, .strategy, .shufflekeys, .num_partitions,
           .remote, ...)

collect:
  function(x, ...)
collect.tbl_kusto:
  function(tbl, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘lixoftConnectors’
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
posterior_predict:
  function(object, ...)
posterior_predict.baggr:
  function(object, draws, newdata, transform, summary, message,
           interval)

pp_check:
  function(object, ...)
pp_check.baggr:
  function(x, type, nsamples)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘fdpbandsdata’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Quitting from lines 73-75 (Introduction.Rmd) 
Error: processing vignette ‘Introduction.Rmd’ failed with diagnostics:
undefined columns selected
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
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: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
Found the following significant warnings:
  bayesDccGarch.c:48:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  bayesDccGarch.c:110:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  bayesDccGarch.c:172:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bayesDccGarch.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
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.
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
rhat:
  function(x, ...)
rhat.bayesmanecfit:
  function(object, rhat_cutoff, ...)

rhat:
  function(x, ...)
rhat.bayesnecfit:
  function(object, rhat_cutoff, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
plot:
  function(x)
plot.posterior:
  function(x, add_prior, ...)

plot:
  function(x)
plot.posterior:
  function(x, add_prior, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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.
Specified C++11: please drop specification unless essential
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: \&
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
sql_translation:
  function(con)
sql_translation.wfsConnection:
  function(conn)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
autoplot:
  function(object, ...)
autoplot.plm:
  function(x, type, param, transformed, ...)

autoplot:
  function(object, ...)
autoplot.gplm:
  function(x, type, param, transformed, ...)

autoplot:
  function(object, ...)
autoplot.tournament:
  function(x, type, ...)

autoplot:
  function(object, ...)
autoplot.gplm0:
  function(x, type, param, transformed, ...)

autoplot:
  function(object, ...)
autoplot.plm0:
  function(x, type, param, transformed, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘dump.txt’
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  load.c:11:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./nanotime.h:6:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./nanotime.h:7:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  mark.c:75:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  mark.c:118:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  mark.c:119:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  nanotime.c:61:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  nanotime.c:71:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  process_memory.c:79:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bench.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘SoDA’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  rbimax.c:326:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/biclust.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘ffbase’
Package suggested but not available for checking: ‘INLA’
Found the following significant warnings:
  ./lib.h:6:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lib.c:3:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bigGP.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
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’.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘outputs’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ./binarizeBASCA.h:37:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  TASC.c:258:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  TASC_min.c:256:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  binarizeBASCA.c:358:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Binarize.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
'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: ‘msa’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘pointshape.dbf’ ‘pointshape.shp’ ‘pointshape.shx’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following significant warnings:
  ./binarizeBASCA.h:37:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  TASC.c:258:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  TASC_min.c:256:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  binarizeBASCA.c:358:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BiTrinA.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
extract:
  function(model, ...)
extract.bizicount:
  function(model, CI, id)

extract:
  function(model, ...)
extract.zicreg:
  function(model, CI, id)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.blob:
  function(x)

vec_ptype_full:
  function(x, ...)
vec_ptype_full.blob:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
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’
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ./include/register.h:46:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./include/register.h:75:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./include/register.h:76:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./include/register.h:82:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  globals.c:15:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  globals.c:33:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  test.counter.c:26:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  test.counter.c:35:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bnlearn.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
as.mcmc:
  function(x, ...)
as.mcmc.multNRMI:
  function(fitlist, thinning_to, ncores)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
Specified C++11: please drop specification unless essential
'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: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) R2txtJG.Rd:90: Escaped LaTeX specials: \#
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘cmdstanr’
Package suggested but not available for checking: ‘glmmADMB’
checkRd: (-1) brr-package.Rd:33: Escaped LaTeX specials: \&
Found the following significant warnings:
  BugsHelper.c:76:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  BugsHelper.c:87:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  BugsHelper.c:88:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BRugs.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gvcm.cat’
Specified C++11: please drop specification unless essential
Unknown package ‘gvcm.cat’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
as.data.table:
  function(x, keep.rownames, ...)
as.data.table.performance:
  function(x, type, format, keep.rownames, ...)

iid:
  function(x, ...)
iid.BuyseTTEM:
  function(x, treatment, strata, cause)

iid:
  function(x, ...)
iid.BuyseTestAuc:
  function(object, ...)

iid:
  function(x, ...)
iid.prodlim:
  function(object, add0, ...)

iid:
  function(x, ...)
iid.BuyseTestBrier:
  function(object, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
Found the following significant warnings:
  cairobem.c:50:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./Rapi.h:9:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./Rapi.h:11:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cairotalk.c:661:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cairotalk.c:1552:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cairotalk.c:1588:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  xlib-backend.c:156:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Cairo.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RxODE’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tmp.txt’
Found the following files/directories:
  ‘MDA231_tree.pdf’
checkRd: (-1) caic-class.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) caic-class.Rd:15: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
oob_pred:
  function(x, ...)
oob_pred.rfe:
  function(x, best, average)

oob_pred:
  function(x, ...)
oob_pred.train:
  function(x, best, average)

oob_pred:
  function(x, ...)
oob_pred.sbf:
  function(x, average)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GAMBoost’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
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: \&
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'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
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'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 files/directories:
  ‘hotcold.csv’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘CirceR’
Found the following files/directories:
  ‘out.png’ ‘out1.txt’ ‘out2.txt’
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
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
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘darts’
'LazyData' is specified without a 'data' directory
checkRd: (-1) hyptis.Rd:31: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘stepres00.txt’
Package suggested but not available for checking: ‘clusterCrit’
Unknown package ‘clusterCrit’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘countreg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘entab’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
resolved:
  function(x, ...)
resolved.CivisFuture:
  function(future, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
sql_translate_env:
  function(con)
sql_translate_env.src_ckan:
  function(x)
See section ‘Generic functions and methods’ 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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
checkRd: (-1) diagwl.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) diagwl.Rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
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’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) HINoV.Mod.rd:3: Escaped LaTeX specials: \&
checkRd: (-1) HINoV.Symbolic.rd:3: Escaped LaTeX specials: \&
checkRd: (-1) cluster.Gen.rd:14: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:18: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:29: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) cluster.Gen.rd:33: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:34: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:36: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:38: Escaped LaTeX specials: \_ \_
checkRd: (-1) cluster.Gen.rd:51: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:52: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:54: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:55: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:62: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) comparing.Partitions.rd:12: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.BC.rd:10: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.GDM.rd:33: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.SM.rd:10: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.C.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.G2.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.G3.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.H.rd:16: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.S.rd:12: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  optimal_assignment.c:47:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/clv.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:22: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tobit1’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘PopGenome’
autoplot:
  function(object, ...)
autoplot.bal.tab:
  function(x, stats, abs, agg.fun, var.order, drop.missing,
           drop.distance, thresholds, line, stars, grid, limits,
           colors, shapes, alpha, size, wrap, var.names, title,
           sample.names, labels, position, themes, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) drqssbc.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) qbsks.Rd:81: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
Package which this enhances but not available for checking: ‘rkward’
Package suggested but not available for checking: ‘userfriendlyscience’
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unexported object imported by a ‘:::’ call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘CAM’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following significant warnings:
  brentmin.c:237:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ContaminatedMixt.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'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
Specified C++11: please drop specification unless essential
checkRd: (-1) sgt.Rd:16: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) egde.Rd:26: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ggplot:
  function(data, mapping, ..., environment)
ggplot.cosinor.lm:
  function(object, x_str)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘covfefe_inauguration.txt’
'LazyData' is specified without a 'data' directory
merge_coverage:
  function(x)
merge_coverage.list:
  function(coverage_objs)

merge_coverage:
  function(x)
merge_coverage.character:
  function(files)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  bcplm.c:84:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/cplm.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Non-visible changes:
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
crps:
  function(y, ...)
crps.crch:
  function(object, newdata, average, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
Package suggested but not available for checking: ‘openVA’
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-crossva-and-openva.Rmd’ using rmarkdown
Quitting from lines 14-17 (using-crossva-and-openva.Rmd) 
Error: processing vignette ‘using-crossva-and-openva.Rmd’ failed with diagnostics:
there is no package called 'openVA'
--- failed re-building ‘using-crossva-and-openva.Rmd’

SUMMARY: processing the following file failed:
  ‘using-crossva-and-openva.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
autoplot:
  function(object, ...)
autoplot.NumericVariable:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.DatetimeVariable:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.CategoricalArrayVariable:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.CategoricalVariable:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.CrunchCubeCalculation:
  function(x, plot_type, ...)

autoplot:
  function(object, ...)
autoplot.tbl_crunch_cube:
  function(x, plot_type, measure)

autoplot:
  function(object, ...)
autoplot.CrunchCube:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.MultipleResponseVariable:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major features
    Minor features
checkRd: (-1) handmovement.Rd:9: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  init.c:11:47: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ctmcd.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used C++ compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
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’
slice_head:
  function(.data, ..., n, prop, by)
slice_head.cubble_df:
  function(data, ...)

slice_tail:
  function(.data, ..., n, prop, by)
slice_tail.cubble_df:
  function(data, ...)

summarise:
  function(.data, ..., .by, .groups)
summarise.cubble_df:
  function(data, ...)

ungroup:
  function(x, ...)
ungroup.cubble_df:
  function(data, ...)

slice_max:
  function(.data, order_by, ..., n, prop, by, with_ties, na_rm)
slice_max.cubble_df:
  function(data, ...)

group_by:
  function(.data, ..., .add, .drop)
group_by.cubble_df:
  function(data, ...)

slice_min:
  function(.data, order_by, ..., n, prop, by, with_ties, na_rm)
slice_min.cubble_df:
  function(data, ...)

vec_cast.data.frame:
  function(x, to, ...)
vec_cast.data.frame.cubble_df:
  function(x, y, ...)

tbl_sum:
  function(x)
tbl_sum.cubble_df:
  function(data)

slice_sample:
  function(.data, ..., n, prop, by, weight_by, replace)
slice_sample.cubble_df:
  function(data, ...)

vec_cast:
  function(x, to, ..., x_arg, to_arg, call)
vec_cast.cubble_df.data.frame:
  function(x, y, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘curephEM-vignette.Rmd’ using rmarkdown
Quitting from lines 41-42 (curephEM-vignette.Rmd) 
Error: processing vignette ‘curephEM-vignette.Rmd’ failed with diagnostics:
system is computationally singular: reciprocal condition number = 5.92971e-21
--- failed re-building ‘curephEM-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Package which this enhances but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'gurobi', 'rcbc'
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
survfit:
  function(formula, ...)
survfit.cyclopsFit:
  function(cyclopsFit, type)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dspg.Rd:29: Escaped LaTeX specials: \^ \^
checkRd: (-1) dspgd2015.Rd:31: Escaped LaTeX specials: \^ \^
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [39s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(dail)
  > 
  > test_check("dail")
  No internet connection or data source broken.
  Downloading 2015 dataset.
  trying URL 'https://dadosabertos-download.cgu.gov.br/FalaBR/Arquivos_FalaBR_Filtrado/Arquivos_csv_2015.zip'
  Content type 'application/x-zip-compressed' length 45626938 bytes (43.5 MB)
  ==================================================
  downloaded 43.5 MB
  
  ℹ Using "','" as decimal and "'.'" as grouping mark. Use `read_delim()` for more control.
  Downloading 2016 dataset.
  trying URL 'https://dadosabertos-download.cgu.gov.br/FalaBR/Arquivos_FalaBR_Filtrado/Arquivos_csv_2016.zip'
  Content type 'application/x-zip-compressed' length 52106684 bytes (49.7 MB)
  ==================================================
  downloaded 49.7 MB
  
  ℹ Using "','" as decimal and "'.'" as grouping mark. Use `read_delim()` for more control.
  Ended query.
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-appeals.R:61:5'): test the arguments agency, year, answer and search ──
  nrow(df10) (`actual`) not equal to 5 (`expected`).
  
  `actual` is NULL
  `expected` is a double vector (5)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: ‘pca3d’
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘my new data set.rds’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘stubthat’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Datastream DWE - now decommissioned by Refinitiv
    CRAN
Found the following significant warnings:
  init.c:29:43: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:30:45: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:31:46: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:33:51: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:34:52: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:36:43: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:37:43: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/datastructures.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used C++ compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("dataverse")
  > 
  > if (!requireNamespace("yaml", quietly = TRUE)) {
  +   warning("The 'yaml' package must be present to test the dataverse package.")
  + } else if (!requireNamespace("checkmate", quietly = TRUE)) {
  +   warning("The 'checkmate' package must be present to test the dataverse package.")
  + } else {
  +   server  <- Sys.getenv("DATAVERSE_SERVER")
  +   key     <- Sys.getenv("DATAVERSE_KEY")
  + 
  +   if (server == "" | key == "") {
  +     config  <- yaml::read_yaml(system.file("constants.yml", package = "dataverse"))
  +     # config  <- yaml::read_yaml("inst/constants.yml")
  + 
  +     Sys.setenv("DATAVERSE_SERVER" = config$server)
  +     Sys.setenv("DATAVERSE_KEY"    = config$api_token)
  + 
  +     # To better identify the source of problems, check if the token is expired.
  +     #   This check *should* be unnecessary on CRAN, since not CRAN tests should
  +     #   try to access any server.
  +     if (Sys.getenv("NOT_CRAN") %in% c("", "true")) {
  +       if (as.Date(config$api_token_expiration) < Sys.Date()) {
  +         stop(
  +           "The API token expired on `",
  +           config$api_token_expiration,
  +           "`, so the tests would probably fail.  ",
  +           "Please regenerate a new token and update `inst/constants.yml`"
  +         )
  +       }
  +     }
  +     rm(config)
  +   }
  +   rm(server, key)
  + 
  +   message("Using Dataverse server `", Sys.getenv("DATAVERSE_SERVER"), "`.")
  + 
  +   test_check("dataverse")
  + }
  Error: The API token expired on `2023-03-10`, so the tests would probably fail.  Please regenerate a new token and update `inst/constants.yml`
  Execution halted
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
sql_values_subquery:
  function(con, df, types, lvl, ...)
sql_values_subquery.PqConnection:
  function(con, df, types, lvl)

sql_values_subquery:
  function(con, df, types, lvl, ...)
sql_values_subquery.PostgreSQL:
  function(con, df, types, lvl)

sql_values_subquery:
  function(con, df, types, lvl, ...)
sql_values_subquery.Microsoft SQL Server:
  function(con, df, types, lvl)

db_write_table:
  function(con, table, types, values, temporary, ...)
db_write_table.PostgreSQLConnection:
  function(con, table, types, values, temporary, overwrite, ....)

sql_select:
  function(con, select, from, where, group_by, having, order_by, limit,
           distinct, ...)
sql_select.DBIConnection:
  function(con, select, from, where, group_by, having, window,
           order_by, limit, distinct, ..., subquery)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ./difeq.h:65:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  difeq.c:123:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./dopri.h:208:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dopri.c:245:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dde.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘smd_table.docx’
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
ggplot:
  function(data, mapping, ..., environment)
ggplot.ggdend:
  function(data, segments, labels, nodes, horiz, theme, offset_labels,
           na.rm, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Documentation.Rmd’ using rmarkdown
Quitting from lines 82-83 (Documentation.Rmd) 
Error: processing vignette ‘Documentation.Rmd’ failed with diagnostics:
Cannot load glue from the private library
--- failed re-building ‘Documentation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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’
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ./deque.h:73:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  constructor.c:43:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  deque.c:31:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dequer_native.c:9:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dequer.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
ggplot:
  function(data, mapping, ..., environment)
ggplot.ddplot:
  function(data, axis.location, ...)

ggplot:
  function(data, mapping, ..., environment)
ggplot.timeseries:
  function(data, edges, ...)

ggplot:
  function(data, mapping, ..., environment)
ggplot.histogram:
  function(data, spine, ...)

ggplot:
  function(data, mapping, ..., environment)
ggplot.barplot:
  function(data, spine, ...)

ggplot:
  function(data, mapping, ..., environment)
ggplot.parcoords:
  function(data, absoluteX, absoluteY, edges, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) geom_axis.Rd:10: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.N’ ‘.Nmiss’ ‘.Q1’ ‘.Q3’ ‘.factorN’ ‘.factorNmiss’ ‘.factorQ1’
  ‘.factorQ3’ ‘.factormax’ ‘.factormean’ ‘.factormedian’ ‘.factormin’
  ‘.factorsd’ ‘.max’ ‘.mean’ ‘.median’ ‘.min’ ‘.sd’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
Package which this enhances but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  void_dev.c:103:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  void_dev.c:182:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  void_dev.c:197:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/devoid.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) phihat.Rd:34: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # install.packages("testthat")
  > library(testthat)
  > # install.packages("forecast")
  > # library(forecast)
  > # install.packages("stats")
  > # library(stats)
  > # install.packages("future.apply")
  > # library(future.apply)
  > library(dhReg)
  Loading required package: forecast
  Loading required package: future.apply
  Loading required package: future
  > Data1 <- runif(runif(200,100,1000)) #To generate random number for example
  > Data_ts <- ts(Data1)
  > 
  > test_that("summary of Dynamic harmonic regression model", {
  +   M <- dhr(Data=Data_ts,XREG=NULL,Range=list(1:2,1),Frequency=c(24,168),Criteria="aicc")
  + })
  ── Error (???): summary of Dynamic harmonic regression model ───────────────────
  <defunctError/error/condition>
  Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
  Backtrace:
   1. dhReg::dhr(...)
   2. future::plan(future::multiprocess)
   3. future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
   4. future (local) warn_about_multiprocess(newStack)
   5. future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
   6. base (local) dfcn(msg = msg, package = .packageName)
  
  Error in reporter$stop_if_needed() : Test failed
  Calls: test_that -> <Anonymous>
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
colnames:
  function(x, do.NULL, prefix)
colnames.MultivariateAnalysis:
  function(x)

rownames:
  function(x, do.NULL, prefix)
rownames.MultivariateAnalysis:
  function(x)

colnames:
  function(x, do.NULL, prefix)
colnames.MultivariateAnalysis:
  function(x)

rownames:
  function(x, do.NULL, prefix)
rownames.MultivariateAnalysis:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
checkRd: (-1) sammy.Rd:51: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘discreteMTP’
Unknown package ‘discreteMTP’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) booter.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) ci.booted.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) pbooter.Rd:57: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
log_quantile:
  function(x, q, ...)
log_quantile.dist_na:
  function(x, p, ...)

log_quantile:
  function(x, q, ...)
log_quantile.distribution:
  function(x, p, ...)

log_quantile:
  function(x, q, ...)
log_quantile.dist_lognormal:
  function(x, p, ...)

log_quantile:
  function(x, q, ...)
log_quantile.dist_default:
  function(x, p, ...)

log_quantile:
  function(x, q, ...)
log_quantile.dist_normal:
  function(x, p, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./rfftw.h:34:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rfftw.c:149:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  util.c:231:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./zzz.h:10:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./zzz.h:44:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/diversitree.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used Fortran compiler: ‘GNU Fortran (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘Debian clang version 15.0.6’
Package suggested but not available for checking: ‘BOLTSSIRR’
'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
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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: \#
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) block.catlg.Rd:61: Escaped LaTeX specials: \^ \^
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
Found the following significant warnings:
  alive.c:200:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  alive.c:277:7: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/doRedis.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New features
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [187s/226s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("dplyr")
  [ FAIL 2 | WARN 270 | SKIP 305 | PASS 2764 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (305)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-filter.R:301:3'): hybrid function row_number does not trigger warning in filter (#3750) ──
  `out` is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-join-by.R:236:3'): nicely catches missing arguments when wrapped ──
  `fn(a)` did not throw the expected error.
  
  [ FAIL 2 | WARN 270 | SKIP 305 | PASS 2764 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
'LazyData' is specified without a 'data' directory
checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gompertz.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) hatvalues.drc.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) llogistic.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) modelFit.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) weibull1.Rd:67: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘dsBaseClient’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
dt_has_computation:
  function(x)
dt_has_computation.dtplyr_step:
  function(x, needs_copy)

count:
  function(x, ..., wt, sort, name)
count.dtplyr_step:
  function(.data, ..., wt, sort, name)

pull:
  function(.data, var, name, ...)
pull.dtplyr_step:
  function(.data, var, name)

show_query:
  function(x, ...)
show_query.dtplyr_step:
  function(x)

sample_n:
  function(tbl, size, replace, weight, .env, ...)
sample_n.dtplyr_step:
  function(tbl, size, replace, weight)

sample_frac:
  function(tbl, size, replace, weight, .env, ...)
sample_frac.dtplyr_step:
  function(tbl, size, replace, weight)

group_modify:
  function(.data, .f, ..., .keep)
group_modify.dtplyr_step:
  function(.tbl, .f, ..., keep)

add_count:
  function(x, ..., wt, sort, name, .drop)
add_count.dtplyr_step:
  function(.data, ..., wt, sort, name)

tally:
  function(x, wt, sort, name)
tally.dtplyr_step:
  function(.data, wt, sort, name)

ungroup:
  function(x, ...)
ungroup.dtplyr_step:
  function(.data, ...)

group_map:
  function(.data, .f, ..., .keep)
group_map.dtplyr_step:
  function(.tbl, .f, ..., keep)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lle’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  arms.c:105:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  arms.c:902:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dynsurv.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used C++ compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
'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
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.estimate:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘example_table1.csv’ ‘example_table1.txt’ ‘example_table2.csv’
  ‘example_table2.txt’ ‘example_table3.csv’ ‘example_table3.txt’
  ‘table1.csv’ ‘table2.csv’ ‘table2.txt’ ‘table3.txt’ ‘table4.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    breaking changes
    major changes
    minor changes
    Internal
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  include/ecos_bb.h:161:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ecos_bb/ecos_bb_preproc.c:298:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ecos/include/ecos_bb.h:161:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ECOSolveR.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.edbl_unit:
  function(x)

tbl_sum:
  function(x)
tbl_sum.edbl_table:
  function(.data)

vec_ptype_full:
  function(x, ...)
vec_ptype_full.edbl_unit:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
glm:
  function(formula, family, data, weights, subset, na.action, start,
           etastart, mustart, offset, control, model, method, x, y,
           singular.ok, contrasts, ...)
glm.sdf:
  function(formula, family, data, weightVar, relevels, varMethod,
           jrrIMax, omittedLevels, defaultConditions, recode,
           returnNumberOfPSU, returnVarEstInputs)

lm:
  function(formula, data, subset, weights, na.action, method, model, x,
           y, qr, singular.ok, contrasts, offset, ...)
lm.sdf:
  function(formula, data, weightVar, relevels, varMethod, jrrIMax,
           omittedLevels, defaultConditions, recode,
           returnVarEstInputs, returnNumberOfPSU,
           standardizeWithSamplingVar, verbose)

glm:
  function(formula, family, data, weights, subset, na.action, start,
           etastart, mustart, offset, control, model, method, x, y,
           singular.ok, contrasts, ...)
glm.sdf:
  function(formula, family, data, weightVar, relevels, varMethod,
           jrrIMax, omittedLevels, defaultConditions, recode,
           returnNumberOfPSU, returnVarEstInputs)

lm:
  function(formula, data, subset, weights, na.action, method, model, x,
           y, qr, singular.ok, contrasts, offset, ...)
lm.sdf:
  function(formula, data, weightVar, relevels, varMethod, jrrIMax,
           omittedLevels, defaultConditions, recode,
           returnVarEstInputs, returnNumberOfPSU,
           standardizeWithSamplingVar, verbose)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/eflm.Rcheck/00install.out’ for details.
'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’
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./eicm.h:70:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/eicm.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AuditErrors.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) compute.audit.errors.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) compute.stark.t.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) find.q.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) find.q.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) stark.test.Rd:50: Escaped LaTeX specials: \$
checkRd: (-1) stark.test.Rd:101: Escaped LaTeX specials: \$ \$
checkRd: (-1) tri.audit.sim.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) tri.calc.sample.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) tri.sample.Rd:34: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) weight.function.Rd:16: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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:
  emd-rubner.c:143:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  emd-rubner.c:153:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  emd-rubner.c:640:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/emdist.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘osmar’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ./utilities.h:7:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  utilities.c:14:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/emoa.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Math2:
  function(x, digits)
Math2.trackdata:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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
Package suggested but not available for checking: ‘RStoolbox’
Found the following files/directories:
  ‘Environmental variables.csv’ ‘Inf.txt’ ‘List of species.csv’ ‘Mean
  overlap among taxa.csv’ ‘Overlap among taxa.csv’ ‘Pointsize.dat’
  ‘Polar coordinates.csv’
'LazyData' is specified without a 'data' directory
checkRd: (-1) calibrate.Rd:151: Escaped LaTeX specials: \&
checkRd: (-1) cdfCompareCensored.Rd:299: Escaped LaTeX specials: \&
checkRd: (-1) detectionLimitCalibrate.Rd:149: Escaped LaTeX specials: \&
checkRd: (-1) ecdfPlotCensored.Rd:169: Escaped LaTeX specials: \&
checkRd: (-1) egammaAltCensored.Rd:344: Escaped LaTeX specials: \&
checkRd: (-1) egammaCensored.Rd:340: Escaped LaTeX specials: \&
checkRd: (-1) elnormAltCensored.Rd:694: Escaped LaTeX specials: \&
checkRd: (-1) elnormCensored.Rd:270: Escaped LaTeX specials: \&
checkRd: (-1) enormCensored.Rd:852: Escaped LaTeX specials: \&
checkRd: (-1) enparCensored.Rd:343: Escaped LaTeX specials: \&
checkRd: (-1) enparCensored.Rd:358: Escaped LaTeX specials: \&
checkRd: (-1) epoisCensored.Rd:354: Escaped LaTeX specials: \&
checkRd: (-1) ppointsCensored.Rd:406: Escaped LaTeX specials: \&
checkRd: (-1) predIntGammaSimultaneous.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) predIntGammaSimultaneous.Rd:171: Escaped LaTeX specials: \&
checkRd: (-1) predIntLnormSimultaneous.Rd:136: Escaped LaTeX specials: \&
checkRd: (-1) predIntLnormSimultaneous.Rd:137: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneous.Rd:204: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneous.Rd:205: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneousK.Rd:277: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneousK.Rd:278: Escaped LaTeX specials: \&
checkRd: (-1) qqPlotCensored.Rd:261: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTest.Rd:276: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTestCensored.Rd:324: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTestCensored.Rd:331: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
as.igraph:
  function(x, ...)
as.igraph.epicontacts:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘epidict’
Specified C++11: please drop specification unless essential
AaJ:
  function(Lx, ...)
AaJ.Lexis:
  function(Lx, formula, timeScale)

addCov:
  function(Lx, ...)
addCov.Lexis:
  function(Lx, clin, timescale, exnam, tfc)

addDrug:
  function(Lx, ...)
addDrug.Lexis:
  function(Lx, pdat, amt, dpt, apt, method, maxt, grace, tnam, prefix,
           sepfix, verbose)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘episcan_1geno_cc.txt’ ‘episcan_1geno_quant.txt’
  ‘episcan_2geno_cc.txt’ ‘episcan_2geno_quant.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) aic.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:64: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
Found the following significant warnings:
  Warning: replacing previous import ‘geiger::rescale’ by ‘phytools::rescale’ when loading ‘evobiR’
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/evobiR.Rcheck/00install.out’ for details.
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
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘ExactData’
checkRd: (-1) exams2sakai.Rd:152: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘iptools’ in Rd xrefs
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quanteda.textmodels’
Unknown package ‘quanteda.textmodels’ in Rd xrefs
Error(s) in re-building vignettes:
  ...
--- re-building ‘expp.Rmd’ using rmarkdown
Loading required package: expp
This is expp 1.2.5 For a tutorial type vignette("expp")

Attaching package: 'expp'

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

    as.data.frame

Quitting from lines 103-105 (expp.Rmd) 
Error: processing vignette ‘expp.Rmd’ failed with diagnostics:
unable to find an inherited method for function 'as.data.frame' for signature '"list"'
--- failed re-building ‘expp.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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’
autoplot_radf_distr:
  function(x, ...)
autoplot_radf_distr.sb_distr:
  function(object, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
tidy:
  function(x, ...)
tidy.VAR:
  function(x)

tidy:
  function(x, ...)
tidy.AR:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
ungroup:
  function(x, ...)
ungroup.fbl_ts:
  function(.data, ...)

ungroup:
  function(x, ...)
ungroup.grouped_fbl:
  function(.data, ...)

fortify:
  function(model, data, ...)
fortify.fbl_ts:
  function(object, level)

key_data:
  function(.data)
key_data.mdl_df:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'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
Package suggested but not available for checking: ‘hier.part’
Unknown package ‘hier.part’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
autoplot:
  function(object, ...)
autoplot.fairadapt:
  function(x, when, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  chli.c:5:48: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/fame.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
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’.
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./lu.h:44:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lu.c:828:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/fastclime.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Found the following files/directories:
  ‘default5.eps’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘clusterCrit’
Error(s) in re-building vignettes:
  ...
--- re-building ‘fasthplus.Rmd’ using rmarkdown
Quitting from lines 298-300 (fasthplus.Rmd) 
Error: processing vignette ‘fasthplus.Rmd’ failed with diagnostics:
there is no package called 'clusterCrit'
--- failed re-building ‘fasthplus.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘coxKM’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) Scent.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) Traffic.Rd:44: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘NNLM’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.Rprofile’
Specified C++11: please drop specification unless essential
Unexported objects imported by ‘:::’ calls:
  ‘fdapace:::GCVLwls1D1’ ‘fdapace:::GetSmoothedMeanCurve’
  ‘fdapace:::HandleNumericsAndNAN’ ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘vert.txt’
vec_arith:
  function(op, x, y, ...)
vec_arith.cf_lag:
  function(op, x, y)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘treesAll.txt’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New Stuff
'LazyData' is specified without a 'data' directory
checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./f2c.h:185:49: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:186:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:187:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:188:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:189:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:189:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:190:35: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:191:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:192:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:193:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:194:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:195:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/FGSG.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘MicrobeDS’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [6s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fiery)
  > 
  > test_check("fiery")
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 253 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-Fire.R:368:5'): futures can be added and called ────────────────
  <defunctError/error/condition>
  Error: Detected creation of a 'multiprocess' future, which are defunct in future (>= 1.32.0) [2023-03-06]. Instead, specify either 'multisession' (recommended) or 'multicore'.
  Backtrace:
      ▆
   1. └─app$async(...) at test-Fire.R:368:4
   2.   └─private$ASYNC$add(substitute(expr), then, substituted = TRUE)
   3.     └─private$make_future(expr, then, ...)
   4.       ├─base::do.call(private$catcher, list(expr = expr, lazy = private$lazy))
   5.       └─future::multiprocess(...)
   6.         └─future (local) dfcn(msg = msg, package = .packageName)
   7.           └─base::.Defunct(...)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 253 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘diveRsity’
Unknown package ‘diveRsity’ in Rd xrefs
Found the following files/directories:
  ‘AH_genepop.txt’ ‘AH_popname.txt’ ‘JSM_MS_freq.txt’
  ‘JSM_MS_genepop.txt’ ‘JSM_genepop_clipped_both.txt’
  ‘JSM_genepop_clipped_maf.txt’ ‘JSM_genepop_clipped_name.txt’
  ‘JSM_mtDNA_freq.txt’ ‘JSM_popname.txt’ ‘result_DJ.csv’
  ‘result_EBDJ.csv’ ‘result_EBFST.csv’ ‘result_EBFST_mtDNA.csv’
  ‘result_EBGstH.csv’ ‘result_GstH.csv’ ‘result_GstN.csv’
  ‘result_GstNC.csv’ ‘result_thetaWCpair.csv’
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'benchden', 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fk_regression.Rd:32: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'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: \&
Running ‘testthat.R’ [51s/87s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(flashr)
  > 
  > test_check("flashr")
  Please enter the number for a deck or 0 to exit: [ FAIL 1 | WARN 0 | SKIP 0 | PASS 44 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-utils.R:2:3'): connections to internet resources fail gracefully ──
  `fail_gracefully("http://httpbin.org/status/404")` did not throw the expected message.
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 44 ]
  Error: Test failures
  Execution halted
levelplot:
  function(x, data, ...)
levelplot.JPtest:
  function(JPobj, what, rotate, plot, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘FPCEnv’
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
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘flux.CH4.txt’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) pseudoOptim.Rd:27: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
Package suggested but not available for checking: ‘RandomFields’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) CatalogueAccessors.Rd:249: Escaped LaTeX specials: \^ \^
checkRd: (-1) FrF2.Rd:574: Escaped LaTeX specials: \^
checkRd: (-1) FrF2.Rd:629: Escaped LaTeX specials: \^ \^
checkRd: (-1) IAPlot.Rd:87: Escaped LaTeX specials: \$
checkRd: (-1) block.Rd:121: Escaped LaTeX specials: \^
checkRd: (-1) block.Rd:150: Escaped LaTeX specials: \^ \^
checkRd: (-1) blockpick.Rd:114: Escaped LaTeX specials: \^ \^
Packages suggested but not available for checking: 'dggrids', 'INLA'
Unknown package ‘frm’ in Rd xrefs
Unknown package ‘frm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
Found the following significant warnings:
  init.c:20:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/FSelectorRcpp.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used C++ compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Warning in formals(fun) : argument is not a function
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
semi_join:
  function(x, y, by, copy, ...)
semi_join.tbl_funnel:
  function(.data, ...)

anti_join:
  function(x, y, by, copy, ...)
anti_join.tbl_funnel:
  function(.data, ...)

inner_join:
  function(x, y, by, copy, suffix, ..., keep)
inner_join.tbl_funnel:
  function(.data, ...)

left_join:
  function(x, y, by, copy, suffix, ..., keep)
left_join.tbl_funnel:
  function(.data, ...)

right_join:
  function(x, y, by, copy, suffix, ..., keep)
right_join.tbl_funnel:
  function(.data, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘completeTrial_byArm_eventPriorRateC3=0.001_eventPriorRateT1=0_eventPriorRateT2=0_eventPriorWt=0.5.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.2.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.4.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.6.RData’
  ‘completeTrial_pooled_eventPriorRate=0.001_eventPriorWt=0.5.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.2.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.4.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.6.RData’
  ‘rcdf_byArm_arm=T1_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03.pdf’
  ‘rcdf_pooled_eventPriorRate=0.06.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  gamlr.c:87:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:12:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/gamlr.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LGAclaims.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:36: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) meyer.Rd:11: Escaped LaTeX specials: \&
Specified C++14: please drop specification unless essential
‘:::’ call which should be ‘::’: ‘graphics:::grid’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘checkdata.csv’ ‘gbmforest.sas’
Specified C++11: please drop specification unless essential
'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’
Package suggested but not available for checking: ‘paleofire’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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’.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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.
Specified C++11: please drop specification unless essential
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  arms.c:99:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  arms.c:900:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/genscore.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) getopt.Rd:60: Escaped LaTeX specials: \#
Package suggested but not available for checking: ‘argon2’
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ungroup:
  function(x, ...)
ungroup.tidy_dagitty:
  function(.data, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘ggESDA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Cardiological
> ### Title: Cardiological data example
> ### Aliases: Cardiological
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Cardiological)
> ggInterval_index(Cardiological, aes(x = Syst))
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'tbl_subset_col' not found
Calls: ggInterval_index ... as.data.frame -> [ -> [.symbolic_tbl -> getFromNamespace -> get
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggESDA.Rmd’ using rmarkdown
Quitting from lines 47-57 (ggESDA.Rmd) 
Error: processing vignette ‘ggESDA.Rmd’ failed with diagnostics:
object ‘tbl_subset_col’ not found
--- failed re-building ‘ggESDA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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
grid.draw:
  function(x, recording)
grid.draw.ggmultiplot:
  function(plot)
See section ‘Generic functions and methods’ 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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
makeContext:
  function(x)
makeContext.interactive_dotstack_grob:
  function(x, recording)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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: \&
‘:::’ call which should be ‘::’: ‘scales:::censor’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ‘:::’ call: ‘productplots:::bound’
  See the note in ?`:::` about the use of this operator.
'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
sample_frac:
  function(tbl, size, replace, weight, .env, ...)
sample_frac.periodic_df:
  function(tbl, size, replace, weight, .env)

fortify:
  function(model, data, ...)
fortify.periodic_df:
  function(data, ...)

sample_n:
  function(tbl, size, replace, weight, .env, ...)
sample_n.periodic_df:
  function(tbl, size, replace, weight, .env)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
makeContext:
  function(x)
makeContext.dotstackGrob:
  function(x, recording)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    History
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'nlmixr', 'lixoftConnectors'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    * Changes all data options to .data to decrease possibility of column naming overlap
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Unknown package ‘IC2’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mlr3proba’
'LazyData' is specified without a 'data' directory
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
VarCorr:
  function(x, sigma, ...)
VarCorr.lmertree:
  function(object, ...)

VarCorr:
  function(x, sigma, ...)
VarCorr.glmertree:
  function(object, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
isLMM:
  function(x, ...)
isLMM.glmmTMB:
  function(object)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++14: please drop specification unless essential
'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: \&
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unexported objects imported by ‘:::’ calls:
  ‘gargle:::secret_can_decrypt’ ‘gargle:::secret_read’
  See the note in ?`:::` about the use of this operator.
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.drive_id:
  function(x)
See section ‘Generic functions and methods’ 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
Specified C++14: please drop specification unless essential
sfNEmpty:
  function(sf)
sfNEmpty.sfc:
  function(sfc)

sfGeometryType:
  function(sf)
sfGeometryType.sfc:
  function(sfc)

sfEpsg:
  function(sf)
sfEpsg.sfc:
  function(sfc)

sfPrecision:
  function(sf)
sfPrecision.sfc:
  function(sfc)

sfProj:
  function(sf)
sfProj.sfc:
  function(sfc)

sfDimension:
  function(sf)
sfDimension.sfc:
  function(sfc)

sfGeometryAttributes:
  function(sf)
sfGeometryAttributes.sfc:
  function(sfc)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unexported objects imported by ‘:::’ calls:
  ‘gargle:::secret_can_decrypt’ ‘gargle:::secret_read’
  See the note in ?`:::` about the use of this operator.
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.sheets_id:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
.access_result:
  function(res, accessor)
.access_result.character:
  function(js, accessor)

.access_result:
  function(res, accessor)
.access_result.list:
  function(lst, accessor)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘gvcm.cat’
Specified C++11: please drop specification unless essential
Unknown package ‘gvcm.cat’ in Rd xrefs
Specified C++11: please drop specification unless essential
'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: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
Package suggested but not available for checking: ‘quanteda.textmodels’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) mlGraphicalVAR.Rd:79: Escaped LaTeX specials: \~
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
Found the following significant warnings:
  Offset.c:3:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:12:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  omp_diagnose.c:5:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  omp_diagnose.c:18:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/grattan.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Found the following significant warnings:
  init.c:11:46: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/gRc.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used C++ compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
pot:
  function(obj, ...)
pot.BlockGraph:
  function(newg, newd, ...)

h_edges:
  function(obj, ...)
h_edges.RootDepSet:
  function(obj, g)

createObj:
  function(obj, ...)
createObj.HRMBG:
  function(obj, data)

resetParams:
  function(obj, ...)
resetParams.MLE1params:
  function(obj, cnames)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
ungroup:
  function(x, ...)
ungroup.igrouped_df:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘p1_20up-vs-p2_25up_in_str1.txt’ ‘p1_20up-vs-p2_25up_in_str2.txt’
  ‘p2_25up-vs-p1_20up_in_str1.txt’ ‘p2_25up-vs-p1_20up_in_str2.txt’
  ‘s0_20up.txt’ ‘s0_30up.txt’ ‘s0_f2up.txt’ ‘strs.vec_01mx.txt’
  ‘strs.vec_02mx.txt’ ‘strs.vec_03mx.txt’ ‘strs.vec_04mx.txt’
  ‘strs.vec_05mx.txt’ ‘strs.vec_06mx.txt’ ‘strs.vec_30up.txt’
  ‘strs.vec_50up.txt’ ‘strs.vec_f2up.txt’ ‘uni_p1_20up-p2_25up.txt’
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
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  ‘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’
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Problems with news in ‘NEWS.md’:
No news entries found.
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  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.ga.breed’ ‘.ga.fitness’ ‘.ga.init’ ‘.ga.mutate’ ‘.ga.step’
  ‘.ga.weight’
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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Malformed Title field: should not end in a period.
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expand_state:
  function(x, ...)
expand_state.uneval_init:
  function(x, state_name, cycles)

expand_state:
  function(x, ...)
expand_state.uneval_state_list:
  function(x, state_name, cycles)

expand_state:
  function(x, ...)
expand_state.uneval_matrix:
  function(x, state_pos, state_name, cycles, n)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘synbreed’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
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‘:::’ 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
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘INLA’
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Package suggested but not available for checking: ‘colorfulVennPlot’
Specified C++11: please drop specification unless essential
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checkRd: (-1) Yeast.Rd:56: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘trackr’
Package which this enhances but not available for checking: ‘HadoopStreaming’
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pp_check:
  function(object, ...)
pp_check.hmcdm:
  function(object, plotfun, type)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.hms:
  function(x)

vec_ptype_full:
  function(x, ...)
vec_ptype_full.hms:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
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checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘ROI.plugin.mosek’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
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checkRd: (-1) get_reflectance.Rd:34: Escaped LaTeX specials: \&
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Found the following significant warnings:
  ./useful.h:6:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/hSDM.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
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Running ‘test-all.R’ [12s/14s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(htmltools)
  > 
  > test_check("htmltools")
  [ FAIL 2 | WARN 0 | SKIP 5 | PASS 2049 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Chinese locale not available (2)
  • On CRAN (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-tags.r:29:3'): Hanging commas don't break things ─────────────
  `as.character(div("one", , ))` threw an error with unexpected message.
  Expected match: "is empty"
  Actual message: "Argument 2 can't be empty."
  Backtrace:
      ▆
   1. ├─testthat::expect_error(as.character(div("one", , )), "is empty") at test-tags.r:29:2
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. ├─htmltools::div("one", , )
   7. │ └─rlang::dots_list(...)
   8. └─rlang::abort(message = message)
  ── Failure ('test-tags.r:31:3'): Hanging commas don't break things ─────────────
  `as.character(div(, "one", ))` threw an error with unexpected message.
  Expected match: "is empty"
  Actual message: "Argument 1 can't be empty."
  Backtrace:
      ▆
   1. ├─testthat::expect_error(as.character(div(, "one", )), "is empty") at test-tags.r:31:2
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. ├─htmltools::div(, "one", )
   7. │ └─rlang::dots_list(...)
   8. └─rlang::abort(message = message)
  
  [ FAIL 2 | WARN 0 | SKIP 5 | PASS 2049 ]
  Error: Test failures
  Execution halted
as.tags:
  function(x, ...)
as.tags.htmlwidget:
  function(x, standalone)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Running ‘testthat.R’ [17s/49s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(httr2)
  
  Attaching package: 'httr2'
  
  The following objects are masked from 'package:testthat':
  
      local_mock, with_mock
  
  > 
  > test_check("httr2")
  [ FAIL 1 | WARN 0 | SKIP 37 | PASS 299 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Can't find envvar HTTR2_KEY (2)
  • On CRAN (35)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-req-body.R:89:3'): can upload file with multipart ──────────────
  <httr2_http_504/httr2_http/rlang_error/error/condition>
  Error in `resp_abort(resp, error_body(req, resp))`: HTTP 504 Gateway Timeout.
  Backtrace:
      ▆
   1. ├─... %>% req_perform() at test-req-body.R:89:2
   2. └─httr2::req_perform(.)
   3.   └─httr2:::resp_abort(resp, error_body(req, resp))
   4.     └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 37 | PASS 299 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [4s/301s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("httr")
  Loading required package: httr
  [ FAIL 6 | WARN 0 | SKIP 7 | PASS 152 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Currently broken (1)
  • On CRAN (6)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-http-error.R:4:3'): http_error works with urls ───────────────
  http_error("http://httpbin.org/status/200") is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  ── Failure ('test-response.r:5:3'): status codes returned as expected ──────────
  GET("http://httpbin.org/status/320")$status_code not equal to 320.
  1/1 mismatches
  [1] 504 - 320 == 184
  ── Failure ('test-response.r:6:3'): status codes returned as expected ──────────
  GET("http://httpbin.org/status/404")$status_code not equal to 404.
  1/1 mismatches
  [1] 504 - 404 == 100
  ── Failure ('test-response.r:17:3'): POST posts ────────────────────────────────
  POST("http://httpbin.org/post")$status_code not equal to 200.
  1/1 mismatches
  [1] 504 - 200 == 304
  ── Failure ('test-response.r:21:3'): PATCH patches ─────────────────────────────
  GET("http://httpbin.org/patch")$status_code not equal to 405.
  1/1 mismatches
  [1] 504 - 405 == 99
  ── Error ('test-response.r:39:3'): headers returned as expected ────────────────
  Error in `names(headers) <- tolower(names(headers))`: attempt to set an attribute on NULL
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(round_trip(a = "a + b")$a, "a + b") at test-response.r:39:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─httr (local) round_trip(a = "a + b")
  
  [ FAIL 6 | WARN 0 | SKIP 7 | PASS 152 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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Package required but not available: ‘incidence2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
autoplot:
  function(object, ...)
autoplot.grid_search:
  function(x, type, ...)

autoplot:
  function(object, ...)
autoplot.stability_analysis:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.roc_curve:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.similarity_comparison:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
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’
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'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rggobi’
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Malformed Description field: should contain one or more complete sentences.
knit_print:
  function(x, ...)
knit_print.Iheatmap:
  function(x, options)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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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
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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.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/incidence2.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
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checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
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Found the following significant warnings:
  keyplayer-utils.c:24:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/influenceR.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Problems with news in ‘NEWS.md’:
No news entries found.
Package which this enhances but not available for checking: ‘gurobi’
Found the following files/directories:
  ‘c.txt’ ‘rho.txt’ ‘sta.txt’ ‘topo.txt’
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Package suggested but not available for checking: ‘INLA’
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
Malformed Title field: should not end in a period.
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Found the following files/directories:
  ‘Error_Estimation_Response_1.tiff’ ‘Error_Estimation_Response_2.tiff’
  ‘Error_Estimation_Response_3.tiff’
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'LazyData' is specified without a 'data' directory
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# NOTE - CRAN check detected: limiting maximum number of cores [2/32]

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
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Package suggested but not available for checking: ‘INLA’
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'LazyData' is specified without a 'data' directory
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) pine.Rd:20: Escaped LaTeX specials: \&
Found the following significant warnings:
  trace_islasso.c:39:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/islasso.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used Fortran compiler: ‘GNU Fortran (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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: \$
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
Found the following files/directories:
  ‘RMTplot.pdf’
'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'
influencePlot:
  function(model, ...)
influencePlot.ivreg:
  function(x, ...)

outlierTest:
  function(model, ...)
outlierTest.ivreg:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_500m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_1km:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_80km:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_10km:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_250m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_125m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_100m:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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'.
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’

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 nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘remMap’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_250m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_10km:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_80km:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_100m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_500m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_125m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_1km:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.json2:
  function(x)

vec_ptype_full:
  function(x, ...)
vec_ptype_full.json2:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'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)
Specified C++14: please drop specification unless essential
'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:
  ‘song.wav’ ‘song4karaoke.wav’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
r_to_py:
  function(x, convert)
r_to_py.keras_layer_wrapper:
  function(fn, convert)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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 ’
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
'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
calibrate:
  function(dsvord, ...)
calibrate.dsvord:
  function(dsvord, site, dims, family, gamma, keep.models)

varplot:
  function(pca, ...)
varplot.pca:
  function(x, dim)

loadings:
  function(pca, ...)
loadings.pca:
  function(x, dim, digits, cutoff)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: \&
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  init.c:19:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/largeList.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used C++ compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘example.llo’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘ergm.userterms’
checkRd: (-1) simulate.ergmm.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) simulate.ergmm.Rd:36: Escaped LaTeX specials: \$
Unknown package ‘ergm.userterms’ in Rd xrefs
GNU make is a SystemRequirements.
Found the following significant warnings:
  init.c:12:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:18:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:24:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:27:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:51:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/later.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used C++ compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'akmedoids', 'clusterCrit'
evaluate:
  function(...)
evaluate.lcMethod:
  function(object, classes, try, exclude, envir)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Unknown packages ‘clusterCrit’, ‘akmedoids’ in Rd xrefs
'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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘lazyData/R/requireData.R’:
  attach(NULL, pos = pos, name = searchDataName)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) goodnessfit.Rd:105: Escaped LaTeX specials: \&
checkRd: (-1) lba.Rd:252: Escaped LaTeX specials: \&
checkRd: (-1) pregnancy.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) pregnancy.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    lcars.0.3.1
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  lcopula-init.c:15:50: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/lcopula.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used C++ compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  lemna.c:98:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lemna.c:109:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lemna.c:120:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lemna.c:129:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lemna.c:138:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/lemna.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
File ‘libstableR/libs/libstableR.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘stable_integration.o’

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 nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:6:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/liGP.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LIMEcoli.Rd:125: Escaped LaTeX specials: \_
checkRd: (-1) Read.Rd:88: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:92: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:98: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:104: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:105: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:106: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:107: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:108: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:109: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:110: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:111: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:112: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:114: Escaped LaTeX specials: \# \#
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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: \_
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) SPSloess.Rd:71: Escaped LaTeX specials: \^ \^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: \$
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Running examples in ‘LogConcDEAD-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EMmixlcd
> ### Title: Estimate the mixture proportions and component densities using
> ###   EM algorithm
> ### Aliases: EMmixlcd
> ### Keywords: nonparametric multivariate EM classification
> 
> ### ** Examples
> 
> ##Simple bivariate normal data
>   set.seed( 1 )
>   n = 15
>   d = 2
>   props=c( 0.6, 0.4 )
>   shift=2
>   x <- matrix( rnorm( n*d ), ncol = d )
>   shiftvec <- ifelse( runif( n ) > props[ 1 ], 0, shift )
>   x[,1] <- x[,1] + shiftvec
>   EMmixlcd( x, k = 2, max.iter = 2)
*** buffer overflow detected ***: terminated
Aborted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LogConcDEAD.Rnw’ using Sweave
Loading required package: LogConcDEAD
Loading required package: mvtnorm
*** buffer overflow detected ***: terminated
Aborted
Found the following significant warnings:
  ./veclib.h:316:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/logistf.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
checkRd: (-1) butstrap.Rd:44: Escaped LaTeX specials: \&
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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: \&
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checkRd: (-1) sensspec.s.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Model_1.cm’ ‘dambacher.dot’ ‘levins.dot’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scio’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  LowRankQP.c:278:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  LowRankQP_init.c:29:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/LowRankQP.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
checkRd: (-1) lpepa.Rd:32: Escaped LaTeX specials: \&
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checkRd: (-1) lpepa.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:90: Escaped LaTeX specials: \&
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checkRd: (-1) lpridge.Rd:65: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘kerdiest’
checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) spectral.density.Rd:55: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test’
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘depth’
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
as_string:
  function(x, ...)
as_string.character:
  function(x, sep, conj)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++14: please drop specification unless essential
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: \_
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checkRd: (-1) write.magpie.Rd:39: Escaped LaTeX specials: \_
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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: \_
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Found the following significant warnings:
  Warning: replacing previous import ‘golem::pkg_version’ by ‘pkgload::pkg_version’ when loading ‘MainExistingDatasets’
  Warning: replacing previous import ‘golem::pkg_name’ by ‘pkgload::pkg_name’ when loading ‘MainExistingDatasets’
  Warning: replacing previous import ‘golem::pkg_path’ by ‘pkgload::pkg_path’ when loading ‘MainExistingDatasets’
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/MainExistingDatasets.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: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
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'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: \&
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Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    To do
Specified C++11: please drop specification unless essential
checkRd: (-1) sw_sfac.Rd:24: Escaped LaTeX specials: \_
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'LazyData' is specified without a 'data' directory
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autoplot:
  function(object, ...)
autoplot.bathy:
  function(x, geom, mapping, coast, ...)

fortify:
  function(model, data, ...)
fortify.bathy:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘flashier’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) size_t-class.Rd:6: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
File ‘Matrix/libs/Matrix.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘validity.o’

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 nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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: \&
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'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
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cplexAPI’
checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
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checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
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Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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) 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: \&
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checkRd: (-1) mctest.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:41: Escaped LaTeX specials: \&
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checkRd: (-1) omcdiag.Rd:41: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial version.
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
checkRd: (-1) glass.Rd:23: Escaped LaTeX specials: \_ \_ \_
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checkRd: (-1) glass.Rd:25: Escaped LaTeX specials: \_ \_ \_
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checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ./threat-safe-random.h:58:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./threat-safe-random.h:70:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mdgc.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used Fortran compiler: ‘GNU Fortran (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘Debian clang version 15.0.6’
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mriTest.Rd:9: Escaped LaTeX specials: \&
checkRd: (-1) riTest.Rd:9: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MethylCapSig’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mebootSpear.Rd:88: Escaped LaTeX specials: \_
checkRd: (-1) ullwan.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ullwan.Rd:8: Escaped LaTeX specials: \& \$
residualPlots:
  function(model, ...)
residualPlots.expData:
  function(object, ...)

residualPlots:
  function(model, ...)
residualPlots.neModel:
  function(object, ...)

residualPlot:
  function(model, ...)
residualPlot.neModel:
  function(object, ...)

residualPlot:
  function(model, ...)
residualPlot.expData:
  function(object, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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) 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
VarCorr:
  function(x, sigma, ...)
VarCorr.merModList:
  function(x, sigma, rdig)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘genuMet’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) dslp.Rd:11: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) cardiac.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) plvol.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) sbp.Rd:16: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
guide_train:
  function(guide, scale, aesthetic)
guide_train.vector:
  function(guide, scale, output)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package unavailable to check Rd xrefs: ‘DAPAR’
Specified C++11: please drop specification unless essential
checkRd: (-1) IPDNa.Rd:42: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./do_nothing.h:4:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  do_nothing.c:11:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:7:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  nanotimer.c:88:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/microbenchmark.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
‘:::’ call which should be ‘::’: ‘parallel:::detectCores’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘l1_similarity’
checkRd: (-1) AKMCS.Rd:215: Escaped LaTeX specials: \&
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checkRd: (-1) SubsetSimulation.Rd:152: Escaped LaTeX specials: \&
checkRd: (-1) oscillator_d6.Rd:14: Escaped LaTeX specials: \&
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Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
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: \&
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Package suggested but not available for checking: ‘mixRasch’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) ssize.propCI.Rd:38: Escaped LaTeX specials: \&
Found the following significant warnings:
  waveform.c:31:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  waveform.c:44:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mlbench.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
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
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
Found the following significant warnings:
  ./mlpack/core/data/save_impl.hpp:107:30: warning: 'quiet_save' is deprecated [-Wdeprecated-declarations]
  ./mlpack/core/data/save_impl.hpp:128:33: warning: 'quiet_save' is deprecated [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mlpack.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Debian clang version 15.0.6’
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as_learner:
  function(x, ...)
as_learner.PipeOp:
  function(x, clone)

as_learner:
  function(x, ...)
as_learner.Graph:
  function(x, clone)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
rd_info:
  function(obj, ...)
rd_info.Learner:
  function(obj)

rd_info:
  function(obj, ...)
rd_info.Task:
  function(obj, section)

rd_info:
  function(obj, ...)
rd_info.Measure:
  function(obj)
See section ‘Generic functions and methods’ 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
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.pdf’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Flury’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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', 'RandomFieldsUtils', 'MoBPSmaps'
Package suggested but not available for checking: ‘ArchR’
'LazyData' is specified without a 'data' directory
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
train:
  function(x, ...)
train.model_grid:
  function(mg, train_all, resample_seed)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
predictor_vars:
  function(model)
predictor_vars.default:
  function(model, data)

response_var:
  function(model)
response_var.default:
  function(model, data)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Could not detect any Conda Python Environments with `reticulate::conda_list()`. Conda is required for 'modeltime.gluonts'. Try using `reticulate::install_miniconda()`.

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    * efourier with default norm=TRUE now messages about how wrong it may be
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ordsampler.c:59:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:113:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:124:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:386:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:544:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:560:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:710:11: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:1102:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sampler.c:52:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sampler.c:149:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sampler.c:158:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sampler.c:729:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/monoreg.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘MortalityLaws’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
Error(s) in re-building vignettes:
  ...
--- re-building ‘movMF.Rnw’ using Sweave
Warning: unable to access index for repository https://datacube.wu.ac.at/src/contrib:
  cannot open URL ‘https://datacube.wu.ac.at/src/contrib/PACKAGES’
Warning: package 'corpus.useR.2008.abstracts' is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages

Error: processing vignette ‘movMF.Rnw’ failed with diagnostics:
 chunk 3 (label = corpus-package) 
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'corpus.useR.2008.abstracts'

--- failed re-building 'movMF.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) Context.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) psyfun.boot.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) psyfun.boot.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
checkRd: (-1) genotype_data.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) phenotype_data.Rd:15: Escaped LaTeX specials: \_
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'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: \$
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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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ms_sev.Rd:31: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Missing or unexported object: ‘rqPen::rq.lasso.fit’
MTElasso: no visible global function definition for ‘rq.lasso.fit’
Undefined global functions or variables:
  rq.lasso.fit
Running examples in ‘MTE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MTElasso
> ### Title: MTE-Lasso estimator
> ### Aliases: MTElasso
> 
> ### ** Examples
> 
> set.seed(2017)
> n=200; d=500
> X=matrix(rnorm(n*d), nrow=n, ncol=d)
> beta=c(rep(2,6), rep(0, d-6))
> y=X%*%beta+c(rnorm(150), rnorm(30,10,10), rnorm(20,0,100))
> output.MTELasso=MTElasso(X, y, p=2, t=0.05, method="MTE")
Error in rq.lasso.fit(x = X, y = as.vector(y), lambda = 0.1, intercept = intercept) : 
  could not find function "rq.lasso.fit"
Calls: MTElasso
Execution halted
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'LazyData' is specified without a 'data' directory
checkRd: (-1) mkjnw.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) mkjnw.Rd:6: Escaped LaTeX specials: \&
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'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) MultBiplotR-package.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) MultBiplotR-package.Rd:52: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) print.multcompLetters.Rd:20: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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pull:
  function(.data, var, name, ...)
pull.multidplyr_party_df:
  function(.data, var)

ungroup:
  function(x, ...)
ungroup.multidplyr_party_df:
  function(.data, ...)

collect:
  function(x, ...)
collect.multidplyr_party_df:
  function(.data, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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
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Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
Found the following significant warnings:
  namespace.c:4:11: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/namespace.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spatialClust’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.navigatr_nav_menu:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.navigatr_nav_input:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Package which this enhances but not available for checking: ‘openVA’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) netCoin-package.Rd:38: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
‘:::’ call which should be ‘::’: ‘lhs:::maximinLHS’
  See the note in ?`:::` about the use of this operator.
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map.png’ ‘maze.html’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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: \$
Package suggested but not available for checking: ‘DAISIE’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
# NOTE - CRAN check detected: limiting maximum number of cores [2/32]

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./veclib.h:302:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/nncc.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Found the following significant warnings:
  geodesic.c:57:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/nngeo.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Other ideas
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:16:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/norm.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used Fortran compiler: ‘GNU Fortran (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) prepareplot.Rd:64: Escaped LaTeX specials: \#
checkRd: (-1) prepareplot.Rd:68: Escaped LaTeX specials: \#
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
'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) Ardechedata.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) nsRFA-package.Rd:231: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'originr', 'parallelsugar'
Specified C++11: please drop specification unless essential
‘:::’ call which should be ‘::’: ‘DBItest:::get_default_context’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ‘:::’ call: ‘DBItest:::connect’
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  gutsRedIT.c:34:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  gutsRedIT.c:58:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  gutsRedSD.c:36:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  gutsRedSD.c:64:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  odeGUTS_init.c:5:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  odeGUTS_init.c:6:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/odeGUTS.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quanteda.textmodels’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘A_Brief_Introduction_to_openalexR.Rmd’ using rmarkdown
Quitting from lines 276-284 (A_Brief_Introduction_to_openalexR.Rmd) 
Error: processing vignette ‘A_Brief_Introduction_to_openalexR.Rmd’ failed with diagnostics:
Column 3 must be named.
Use `.name_repair` to specify repair.
Caused by error in `repaired_names()`:
! Names can't be empty.
✖ Empty name found at location 3.
--- failed re-building ‘A_Brief_Introduction_to_openalexR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘unary_ops’:
  ‘log10.ProcessNode’ ‘log10.ProcessGraphParameter’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘openNLPmodels.en’
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
Package suggested but not available for checking: ‘gurobi’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘result.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  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: \$
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘CorShrink’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
predictSurvProb:
  function(object, newdata, times, ...)
predictSurvProb.pamm:
  function(object, newdata, times)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) pan.bd.Rd:65: Escaped LaTeX specials: \$
rd_info:
  function(obj, ...)
rd_info.ParamSet:
  function(ps, descriptions, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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’
Specified C++11: please drop specification unless essential
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \# \# \#
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  PeakSegJoint_interface.c:113:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/PeakSegJoint.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘crrstep’
checkRd: (-1) pec.Rd:250: Escaped LaTeX specials: \&
checkRd: (-1) pec.Rd:251: Escaped LaTeX specials: \&
checkRd: (-1) pec.Rd:256: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘georob’
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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: \_ \_
Specified C++11: please drop specification unless essential
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  init.c:13:51: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Peptides.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used C++ compiler: ‘Debian clang version 15.0.6’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) chart.ECDF.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘DMwR’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dendextendRcpp’
'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.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRD.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRDUS.Rd:4: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.pdf’
'LazyData' is specified without a 'data' directory
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:29: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:31: Escaped LaTeX specials: \_ \_
checkRd: (-1) maxConnectedSet.Rd:35: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:37: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:39: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:41: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:45: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:47: Escaped LaTeX specials: \_ \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
S3 methods shown with full name in documentation object ‘log’:
  ‘log2.generic_spct’ ‘log10.generic_spct’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) phylo4d-methods.Rd:209: Escaped LaTeX specials: \$
'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: \&
Specified C++11: please drop specification unless essential
'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: \$ \$
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
vec_math:
  function(.fn, .x, ...)
vec_math.pillar_num:
  function(op, x, ...)
See section ‘Generic functions and methods’ 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
Specified C++11: please drop specification unless essential
'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’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sanitize_latex.Rd:49: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RStoolbox’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
Packages suggested but not available for checking:
  'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Packages suggested but not available for checking: 'USAboundaries', 'INLA'
Package unavailable to check Rd xrefs: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘pollimetrydata’
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘polyfreqs-mcmc.out’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘RClone’
Found the following significant warnings:
  init.c:24:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  omp_test.c:7:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/poppr.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
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: \$
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:146: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:148: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:126: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:219: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:221: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:225: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:229: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:231: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:233: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:235: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:237: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:301: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:303: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:305: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:307: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:309: Escaped LaTeX specials: \&
checkRd: (-1) med_pn.Rd:129: Escaped LaTeX specials: \&
Unknown package ‘advclust’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  sum.c:358:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  prod.c:27:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:28:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:29:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/PreciseSums.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting_started_with_prewas.Rmd’ using rmarkdown
Quitting from lines 136-141 (getting_started_with_prewas.Rmd) 
Error: processing vignette ‘getting_started_with_prewas.Rmd’ failed with diagnostics:
Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
--- failed re-building ‘getting_started_with_prewas.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  init.c:17:43: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:22:48: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  zhegv.c:232:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  zhegv.c:3715:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/PRIMME.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used C++ compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
show:
  function(object)
show.Data:
  function(x, ...)

show:
  function(object)
show.OptimizationProblem:
  function(x, ...)

show:
  function(object)
show.Portfolio:
  function(x, ...)

show:
  function(object)
show.Solution:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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
Package suggested but not available for checking: ‘ProFit’
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  pause.c:10:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/profvis.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cin’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rdt’
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  util.c:6:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/pscl.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
as.igraph:
  function(x, ...)
as.igraph.qgraph:
  function(object, attributes)
See section ‘Generic functions and methods’ 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.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘lambda.pdf’ ‘qqplot.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) GRI.Rd:3: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘quanteda.textmodels’
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
Quitting from lines 481-486 (quickstart.Rmd) 
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
object ‘data_corpus_irishbudget2010’ not found
--- failed re-building ‘quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘quanteda.textmodels’
Specified C++11: please drop specification unless essential
Unknown package ‘quanteda.textmodels’ in Rd xrefs
Running examples in ‘quanteda.textplots-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: textplot_scale1d
> ### Title: Plot a fitted scaling model
> ### Aliases: textplot_scale1d
> ### Keywords: textplot
> 
> ### ** Examples
> 
> library("quanteda")
Package version: 3.2.4
Unicode version: 15.0
ICU version: 72.1
Parallel computing: 4 of 32 threads used.
See https://quanteda.io for tutorials and examples.
> data(data_corpus_irishbudget2010, package = "quanteda.textmodels")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘quanteda.textmodels’
Calls: data -> find.package
Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = TRUE)
  > 
  > library("testthat")
  > library("quanteda")
  Package version: 3.2.4
  Unicode version: 15.0
  ICU version: 72.1
  Parallel computing: 4 of 32 threads used.
  See https://quanteda.io for tutorials and examples.
  > library("quanteda.textmodels")
  Error in library("quanteda.textmodels") : 
    there is no package called 'quanteda.textmodels'
  Execution halted
'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
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  glmBias.c:84:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/QuasiSeq.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fastshp', 'visualTest'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) qwraps2.Rd:73: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ../inst/include/sundials/sundials_nvector.h:163:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_nonlinearsolver.h:131:56: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_matrix.h:105:41: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_linearsolver.h:137:50: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lib/sundials/sundials_nonlinearsolver.c:26:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lib/sundials/sundials_matrix.c:29:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lib/sundials/sundials_nvector.c:28:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lib/sundials/sundials_linearsolver.c:28:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/r2sundials.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
as.tags:
  function(x, ...)
as.tags.data3js:
  function(x, standalone)
See section ‘Generic functions and methods’ 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
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quanteda.textmodels’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [42s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rainette)
  
  Attaching package: 'rainette'
  
  The following object is masked from 'package:stats':
  
      cutree
  
  > 
  > test_check("rainette")
  [ FAIL 1 | WARN 6 | SKIP 1 | PASS 183 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_rainette1.R:27:5'): order_docs ─────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'quanteda.textmodels'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_rainette1.R:27:4
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 6 | SKIP 1 | PASS 183 ]
  Deleting unused snapshots:
  • plots/base-rainette-plot-measure-docprop.svg
  • plots/base-rainette-plot-measure-frequency.svg
  • plots/base-rainette-plot-measure-lr.svg
  • plots/base-rainette-plot-with-free-scales.svg
  • plots/base-rainette-plot-with-k-and-without-negative.svg
  • plots/base-rainette-plot-with-k-n-terms-and-font-size.svg
  • plots/base-rainette-plot.svg
  • plots/base-rainette2-plot-measure-docprop.svg
  • plots/base-rainette2-plot-measure-frequency.svg
  • plots/base-rainette2-plot-measure-lr.svg
  • plots/base-rainette2-plot-with-complete-groups.svg
  • plots/base-rainette2-plot-with-free-scales.svg
  • plots/base-rainette2-plot-with-k-5.svg
  • plots/base-rainette2-plot-with-k-and-without-negative.svg
  • plots/base-rainette2-plot-with-k-n-terms-and-font-size.svg
  • plots/base-rainette2-plot.svg
  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 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
'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: ‘googlesheets’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  sketch.c:33:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sketch.c:38:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sketch.c:172:9: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sketch.c:206:6: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RaProR.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘rcanvec.cache’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.RData’
Found the following significant warnings:
  cddmp.c:23:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cddmp.c:63:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cddmp_f.c:24:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cddmp_f.c:64:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  nonred.c:99:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rcdd.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘data.csv’
Found the following significant warnings:
  RClickhouse_init.c:23:54: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  vendor/clickhouse-cpp/contrib/lz4/lz4.c:373:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  vendor/clickhouse-cpp/contrib/lz4/lz4.c:1474:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RClickhouse.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used C++ compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
sql_translate_env:
  function(con)
sql_translate_env.ClickhouseConnection:
  function(x)

db_desc:
  function(x)
db_desc.ClickhouseConnection:
  function(con)

db_analyze:
  function(con, table, ...)
db_analyze.ClickhouseConnection:
  function(con, sql, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'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.
as_tibble:
  function(x, ..., .rows, .name_repair, rownames)
as_tibble.CompadreDB:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘conics’
as.quadratic_constraint:
  function(x, ...)
as.quadratic_constraint.list:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘rredis’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dsTMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dgeMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.matrix:
  function(x, check.sym)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dsCMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.ddiMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dsyMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dpoMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dgTMatrix:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘PercentCodes’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rDEA_init.c:11:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rDEA.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘devAll’
'LazyData' is specified without a 'data' directory
as.integer64:
  function(x, ...)
as.integer64.SNOMEDconcept:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  dsdp/include/dsdp5.h:206:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../../include/dsdp5.h:206:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dsdpcops.c:20:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dsdpcops.c:28:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dsdpsetoptions.c:280:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sdpalloc.c:4:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sdpexit.c:4:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dsdperror.c:129:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rdsdp.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) re2_syntax.Rd:539: Escaped LaTeX specials: \_
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘Filled.RData’ ‘cleaned.RData’ ‘days’ ‘gridded’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘cur_plans’
rowwise:
  function(data, ...)
rowwise.redist_map:
  function(x, ...)

rowwise:
  function(data, ...)
rowwise.redist_plans:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  redland.c:771:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  redland.c:817:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  redland.c:1846:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/redland.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
roclet_process:
  function(x, blocks, env, base_path)
roclet_process.roclet_mergeNamespace:
  function(x, blocks, env, base_path, global_options)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
qq:
  function(x, data, ...)
qq.pffr:
  function(object, rep, level, s.rep, type, pch, rl.col, rep.col, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  init.c:9:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:13:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/reglogit.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
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: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'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
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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) ena.plot.group.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:46: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:38: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:42: Escaped LaTeX specials: \$
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PackageCites.bib’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
render:
  function(x)
render.pdf_image_stream:
  function(x, view)
See section ‘Generic functions and methods’ 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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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: \_ \_
Anova:
  function(mod, ...)
Anova.resi:
  function(object, alpha, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Burns.Rd:28: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) rec.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
'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) CardioRiskFactors.Rd:35: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  pcg_basic.c:69:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RGBM.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used C++ compiler: ‘Debian clang version 15.0.6’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Rglpk_read_file.c:17:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:42:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rglpk.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
checkRd: (-1) Rglpk_read_file.Rd:6: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) columbus.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) columbus.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) columbus.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) columbus.Rd:30: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
autoplot:
  function(object, ...)
autoplot.persistence_diagram:
  function(x, dimension, alpha, max_intervals, legend, greyblock, n,
           type, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'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
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ./convert.h:12:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  convert.c:79:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ring.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
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_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

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 nor [v]sprintf.
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
as.data.table:
  function(x, keep.rownames, ...)
as.data.table.ate:
  function(x, estimator, type, keep.rownames, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./init.h:19:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./init.h:26:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./init.h:30:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rjags.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used C++ compiler: ‘Debian clang version 15.0.6’
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 ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  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 nor [v]sprintf. 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.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
Specified C++14: please drop specification unless essential
Found the following significant warnings:
  RngWrap.c:12:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  RngWrap.c:23:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  RngWrap.c:304:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  RngWrap.c:328:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  zzz.c:11:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  zzz.c:13:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  zzz.c:17:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rlecuyer.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘USAboundaries’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Running examples in ‘RmdConcord-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: processConcordance
> ### Title: Get the concordance from the "datapos" values and record it in a
> ###   file.
> ### Aliases: processConcordance
> 
> ### ** Examples
> 
> # This example works on the file inst/sample/Sample.Rmd,
> # which should be a copy of the vignette Sample.Rmd.  This
> # is convenient because RStudio doesn't install vignettes by default.
> 
> # First, see the results without concordances:
> 
> library(RmdConcord)
> dir <- tempdir()
> infile <- system.file("sample/Sample.Rmd", package = "RmdConcord")
> outfile1 <- file.path(dir, "html_vignette.html")
> rmarkdown::render(infile,
+                   output_file = outfile1,
+                   quiet = TRUE)
Warning in file(con, "w") :
  cannot open file 'Sample.knit.md': Read-only file system
Error in file(con, "w") : cannot open the connection
Calls: <Anonymous> -> <Anonymous> -> write_utf8 -> writeLines -> file
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
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: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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.
Specified C++11: please drop specification unless essential
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: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
autoplot:
  function(object, ...)
autoplot.meteo_coverage:
  function(mateo_coverage, old_style)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following significant warnings:
  monitor.c:15:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/robustbase.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used Fortran compiler: ‘GNU Fortran (Debian 12.2.0-14) 12.2.0’
checkRd: (-1) aircraft.Rd:8: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RandomFields’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
File ‘RQuantLib/libs/RQuantLib.so’:
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
    Object: ‘utils.o’

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 nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.bpl’ ‘test.cr’ ‘test.ct’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘evolqg’
Unknown package ‘evolqg’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gdalUtils’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ./Stopwatch.h:13:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  Stopwatch.c:4:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rscimark.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘RSDA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: abalone
> ### Title: SODAS XML data file.
> ### Aliases: abalone
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(abalone)
> res <- sym.pca(abalone, 'centers')
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'tbl_subset_col' not found
Calls: sym.pca ... %in% -> [ -> [.symbolic_tbl -> getFromNamespace -> get
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 60-64 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
object ‘tbl_subset_col’ not found
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  tls.c:29:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rserve.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
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 ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  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 nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Vdgraph’
Unknown package ‘Vdgraph’ in Rd xrefs
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following significant warnings:
  ./rsyslog.h:15:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rsyslog.c:50:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rsyslog.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
Specified C++14: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘results’
checkRd: (-1) run.jags.study.Rd:67: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘glmmADMB’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gpuR’
Problems with news in ‘NEWS.md’:
No news entries found.
File ‘RVowpalWabbit/libs/RVowpalWabbit.so’:
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
    Object: ‘parse_args.o’

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 nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rWCVPdata’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) mapBubbles.Rd:62: Escaped LaTeX specials: \$
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++14: please drop specification unless essential
Specified C++14: please drop specification unless essential
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
ggplot:
  function(data, mapping, ..., environment)
ggplot.qqnorm.spss:
  function(x, plottype, line, l.col, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ./Gen_fun.h:17:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  Gen_fun.c:121:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./IFscratch.h:64:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  load_IFscratch.c:64:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  load_env.c:162:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/samon.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Found the following significant warnings:
  ./init.h:28:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./init.h:29:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SamplerCompare.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used Fortran compiler: ‘GNU Fortran (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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: \#
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘networkTomography’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
Specified C++11: please drop specification unless essential
checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
‘library’ or ‘require’ call to ‘progress’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./error.h:33:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/scclust.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘ssvd’
Unexported object imported by a ‘:::’ call: ‘simplifyEnrichment:::is_GO_id’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘untitled_consensus_cluster’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  linsys/cpu/direct/private.c:4:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/scs.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmGamPoi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'xbioc', 'MuSiC', 'seAMLessData'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quanteda.textmodels’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spgrass6’
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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) 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: \^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘copynumber’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
st_precision:
  function(x)
st_precision.sfnetwork:
  function(x, active, ...)

st_z_range:
  function(obj, ...)
st_z_range.sfnetwork:
  function(x, active, ...)

st_geometry:
  function(obj, ...)
st_geometry.sfnetwork:
  function(x, active, ...)

st_bbox:
  function(obj, ...)
st_bbox.sfnetwork:
  function(x, active, ...)

st_set_precision:
  function(x, precision)
st_set_precision.sfnetwork:
  function(x, value)

st_m_range:
  function(obj, ...)
st_m_range.sfnetwork:
  function(x, active, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) gPLS.Rd:72: Escaped LaTeX specials: \^
checkRd: (-1) gPLS.Rd:74: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:67: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:69: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:75: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:77: Escaped LaTeX specials: \^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Other ideas
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCOSA’
Package unavailable to check Rd xrefs: ‘rCOSA’
Package suggested but not available for checking: ‘hydromad’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
shinytest requires PhantomJS to record and run tests.
• To install it, run shinytest::installDependencies()
• If it is installed, please check it is available on the PATH

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./cairodev.h:86:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cairodev.c:11:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./outline.h:64:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./util.h:44:39: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./util.h:47:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  outline.c:169:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  register_routines.c:8:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  showtext.c:111:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  util.c:43:39: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  util.c:53:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/showtext.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘MM.csv’ ‘Simul.csv’ ‘catalytic.csv’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘copynumber’
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
Found the following files/directories:
  ‘simu.pheno’ ‘usedpars.txt’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [31s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(simpr)
  
  Attaching package: 'simpr'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("simpr")
  [ FAIL 1 | WARN 9 | SKIP 0 | PASS 50 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_calc_tidy.R:86:3'): Errors show up in tidied output. ─────────
  buggy_fit$.fit_error not equal to c(...).
  2/4 mismatches
  x[1]: "Error in eval(substitute(expr), data, enclos = parent.frame()): object 'y
  x[1]: ' not found\n"
  y[1]: "Error in t.test(y): object 'y' not found\n"
  
  x[2]: "Error in eval(substitute(expr), data, enclos = parent.frame()): object 'y
  x[2]: ' not found\n"
  y[2]: "Error in is.data.frame(x): object 'y' not found\n"
  
  [ FAIL 1 | WARN 9 | SKIP 0 | PASS 50 ]
  Error: Test failures
  Execution halted
Found the following files/directories:
  ‘SimRAD-exampleRefSeq-Fasta.fa’ ‘SimRAD-exampleRefSeq.fa’
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘fg_step_tab_pp’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
'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.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ex0723.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ex0915.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) ex1515.Rd:4: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Unknown package ‘InformationValue’ in Rd xrefs
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) hoods2dsmooth.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dmeitsjer.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dsmooth.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) smoothie-package.Rd:42: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘my_new_social_media_plot.png’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  SnowballC_init.c:7:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  stem.c:59:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SnowballC.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.solveEnv’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.som.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) som.Rd:128: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘NLMR’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
sample_n:
  function(tbl, size, replace, weight, .env, ...)
sample_n.tbl_spark:
  function(tbl, size, replace, weight, .env)

slice_:
  function(.data, ..., .dots)
slice_.tbl_spark:
  function(x, ...)

op_vars:
  function(op)
op_vars.tbl_spark:
  function(x)

sample_frac:
  function(tbl, size, replace, weight, .env, ...)
sample_frac.tbl_spark:
  function(tbl, size, replace, weight, .env)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Unknown package ‘sparsebn’ in Rd xrefs
Specified C++11: please drop specification unless essential
'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.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘RStoolbox’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
checkRd: (-1) sarorderedprobit.Rd:84: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', '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.explore', 'spatstat.model',
  '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.explore', 'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages suggested but not available for checking:
  'RandomFields', 'RandomFieldsUtils'

Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package unavailable to check Rd xrefs: ‘RandomFields’
Packages suggested but not available for checking:
  'RandomFields', 'RandomFieldsUtils'
Package unavailable to check Rd xrefs: ‘RandomFields’
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'spatstat.model', 'spatstat.linnet'
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: ‘spDataLarge’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.neig’
spFSR:
  function(x, ...)
spFSR.default:
  function(task, wrapper, scoring, perturb.amount, gain.min, gain.max,
           change.min, change.max, bb.bottom.threshold, mon.gain.A,
           mon.gain.a, mon.gain.alpha, hot.start.num.ft.factor,
           hot.start.max.auto.num.ft, use.hot.start, hot.start.range,
           rf.n.estimators, gain.type, num.features.selected,
           iters.max, stall.limit, n.samples.max, ft.weighting,
           encoding.type, is.debug, stall.tolerance, random.state,
           rounding, run.parallel, n.jobs, show.info, print.freq,
           num.cv.folds, num.cv.reps.eval, num.cv.reps.grad,
           num.grad.avg, perf.eval.method)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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’
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./spMC.h:44:11: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  spMC.c:303:11: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spMC.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Parallel computation will not perform. CPU cores in use: 1.

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
autoplot:
  function(object, ...)
autoplot.qts_sample:
  function(x, memberships, highlighted, with_animation, ...)

autoplot:
  function(object, ...)
autoplot.qts:
  function(x, highlighted_points, ...)

autoplot:
  function(object, ...)
autoplot.prcomp_qts:
  function(x, what, ...)

autoplot:
  function(object, ...)
autoplot.kma_qts:
  function(x, ...)
See section ‘Generic functions and methods’ 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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
estfun:
  function(x, ...)
estfun.ssym:
  function(object, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    To do
Package suggested but not available for checking: ‘starsdata’
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: ‘networksis’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
rowwise:
  function(data, ...)
rowwise.sticky_rowwise_df:
  function(.data, ..., .add)

rowwise:
  function(data, ...)
rowwise.sticky_grouped_df:
  function(.data, ..., .add)

rowwise:
  function(data, ...)
rowwise.sticky_tbl_df:
  function(.data, ..., .add)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘corrviz.html’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘myNewStrat.R’
Package suggested but not available for checking: ‘StrathE2E2examples’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Found the following significant warnings:
  ../inst/include/sundials/sundials_nvector.h:163:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_nonlinearsolver.h:131:56: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_matrix.h:106:41: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_linearsolver.h:137:50: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sundials/sundials/sundials_linearsolver.c:28:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sundials/sundials/sundials_matrix.c:29:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sundials/sundials/sundials_nonlinearsolver.c:26:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sundials/sundials/sundials_nvector.c:28:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/sundialr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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’
Specified C++11: please drop specification unless essential
autoplot:
  function(object, ...)
autoplot.pairwise:
  function(x, ...)

tbl_sum:
  function(x)
tbl_sum.pairwise_tbl:
  function(x, setup, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) estweights.Rd:42: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘INLA’
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘distr6’
Unknown package ‘distr6’ in Rd xrefs
Specified C++11: please drop specification unless essential
Unknown package ‘survJamda’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) diabetes.Rd:18: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘robets’
Unknown package ‘robets’ in Rd xrefs
Running examples in ‘sweep-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tidiers_robets
> ### Title: Tidying methods for robets (Robust Error, Trend, Seasonal)
> ###   exponential smoothing modeling of time series
> ### Aliases: tidiers_robets sw_tidy.robets sw_glance.robets
> ###   sw_augment.robets sw_tidy_decomp.robets
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(robets)
Error in library(robets) : there is no package called ‘robets’
Execution halted
Running ‘testthat.R’ [7s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sweep)
  > library(timetk)
  > library(forecast)
  > library(tidyverse)
  ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
  ✔ dplyr     1.1.0     ✔ readr     2.1.4
  ✔ forcats   1.0.0     ✔ stringr   1.5.0
  ✔ ggplot2   3.4.1     ✔ tibble    3.2.0
  ✔ lubridate 1.9.2     ✔ tidyr     1.3.0
  ✔ purrr     1.0.1     
  ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
  ✖ readr::edition_get()   masks testthat::edition_get()
  ✖ dplyr::filter()        masks stats::filter()
  ✖ purrr::is_null()       masks testthat::is_null()
  ✖ dplyr::lag()           masks stats::lag()
  ✖ readr::local_edition() masks testthat::local_edition()
  ✖ dplyr::matches()       masks tidyr::matches(), testthat::matches()
  ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
  > library(robets)
  Error in library(robets) : there is no package called 'robets'
  Execution halted
Package suggested but not available for checking: ‘swephRdata’
Specified C++11: please drop specification unless essential
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
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  syncrng.c:192:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  syncrng.c:231:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  syncrng.c:236:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  syncrng.c:241:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SyncRNG.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.csv’
'LazyData' is specified without a 'data' directory
bread:
  function(x, ...)
bread.systemfit:
  function(obj, ...)

estfun:
  function(x, ...)
estfun.systemfit:
  function(obj, residFit, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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’
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
'LazyData' is specified without a 'data' directory
is_valid:
  function(x, ...)
is_valid.Stacked_table:
  function(x)

is_valid:
  function(x, ...)
is_valid.Mashed_table:
  function(x)

is_valid:
  function(x, ...)
is_valid.TT_meta:
  function(dat)

is_valid:
  function(x, ...)
is_valid.Tatoo_report:
  function(x)

as.data.table:
  function(x, keep.rownames, ...)
as.data.table.Composite_table:
  function(x, multinames, sep, ...)

as.data.table:
  function(x, keep.rownames, ...)
as.data.table.Mashed_table:
  function(x, mash_method, insert_blank_row, id_vars, suffixes)
See section ‘Generic functions and methods’ 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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: \^
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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
Specified C++11: please drop specification unless essential
'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
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Unknown package ‘textreadr’ in Rd xrefs
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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) 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
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'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
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  common.c:36:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tiff.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
rowwise:
  function(data, ...)
rowwise.forest:
  function(.data, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
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
Package suggested but not available for checking: ‘robets’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'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.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pca3d’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘corpus.JSS.papers’
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘topicmodels.Rnw’ using Sweave
Warning: unable to access index for repository https://datacube.wu.ac.at/src/contrib:
  cannot open URL ‘https://datacube.wu.ac.at/src/contrib/PACKAGES’
Warning: package 'corpus.JSS.papers' is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages

Error: processing vignette ‘topicmodels.Rnw’ failed with diagnostics:
 chunk 6 
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'corpus.JSS.papers'

--- failed re-building 'topicmodels.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
qnormal:
  function(object, ...)
qnormal.toureg:
  function(object, nsim, level, envelope)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'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
anti_join:
  function(x, y, by, copy, ...)
anti_join.track:
  function(.data, ...)

sample_n:
  function(tbl, size, replace, weight, .env, ...)
sample_n.track:
  function(.data, ...)

ungroup:
  function(x, ...)
ungroup.track:
  function(.data, ...)

semi_join:
  function(x, y, by, copy, ...)
semi_join.track:
  function(.data, ...)

nest_join:
  function(x, y, by, copy, keep, name, ...)
nest_join.track:
  function(.data, ...)

rowwise:
  function(data, ...)
rowwise.track:
  function(.data, ...)

right_join:
  function(x, y, by, copy, suffix, ..., keep)
right_join.track:
  function(.data, ...)

inner_join:
  function(x, y, by, copy, suffix, ..., keep)
inner_join.track:
  function(.data, ...)

left_join:
  function(x, y, by, copy, suffix, ..., keep)
left_join.track:
  function(.data, ...)

full_join:
  function(x, y, by, copy, suffix, ..., keep)
full_join.track:
  function(.data, ...)

sample_frac:
  function(tbl, size, replace, weight, .env, ...)
sample_frac.track:
  function(.data, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Enhancements
    Other changes
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taxidata’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘TreeDistData’
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug fixes
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
'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
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
autoplot:
  function(object, ...)
autoplot.grnnForecast:
  function(forecast, highlight)
See section ‘Generic functions and methods’ 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
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
checkRd: (-1) lindner.Rd:44: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘sl3’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following significant warnings:
  interface.c:114:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ucminf.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used Fortran compiler: ‘GNU Fortran (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MortalityLaws’
Unknown package ‘MortalityLaws’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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: ‘USA.state.boundaries.data’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) arctic.oscillations.Rd:19: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) arctic.oscillations.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) babies.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:43: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) exec.pay.Rd:5: Escaped LaTeX specials: \$
checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) sp500.excess.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  rand.c:90:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rand.c:92:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rand.c:103:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rand.c:138:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/uuid.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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) 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
toMlm:
  function(x, ...)
toMlm.varest:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) irf.Rd:111: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  computeCox.c:15:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/vdra.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
sql_translation:
  function(con)
sql_translation.wfsConnection:
  function(conn)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    NEW FEATURES
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.csl_dates:
  function(x)

vec_proxy_order:
  function(x, ...)
vec_proxy_order.list_of_csl_names:
  function(x)

vec_proxy_order:
  function(x, ...)
vec_proxy_order.csl_dates:
  function(x)

knit_print:
  function(x, ...)
knit_print.vitae_brief:
  function(x, options)

knit_print:
  function(x, ...)
knit_print.vitae_detailed:
  function(x, options)

knit_print:
  function(x, ...)
knit_print.vitae_bibliography:
  function(x, options)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++14: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'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’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
plot_pop_vis:
  function(p_obj, ...)
plot_pop_vis.plotly:
  function(p_obj, tbl_pop, title_trace)

plot_pop_vis:
  function(p_obj, ...)
plot_pop_vis.ggplot:
  function(p_obj, tbl_pop, title_trace)

plot_prob_vis:
  function(p_obj, ...)
plot_prob_vis.plotly:
  function(p_obj, tbl_prob, distribution, title_main, title_x, title_y,
           title_trace)

plot_prob_vis:
  function(p_obj, ...)
plot_prob_vis.ggplot:
  function(p_obj, tbl_prob, distribution, title_main, title_x, title_y,
           title_trace)

plot_layout_vis:
  function(p_obj, ...)
plot_layout_vis.ggplot:
  function(p_obj, x, distribution, title_main, title_x, title_y)

plot_layout_vis:
  function(p_obj, ...)
plot_layout_vis.plotly:
  function(p_obj, x, distribution, title_main, title_x, title_y)

plot_conf_vis:
  function(p_obj, ...)
plot_conf_vis.ggplot:
  function(p_obj, tbl_p, title_trace)

plot_conf_vis:
  function(p_obj, ...)
plot_conf_vis.plotly:
  function(p_obj, tbl_p, title_trace)

plot_mod_vis:
  function(p_obj, ...)
plot_mod_vis.plotly:
  function(p_obj, tbl_pred, title_trace)

plot_mod_vis:
  function(p_obj, ...)
plot_mod_vis.ggplot:
  function(p_obj, tbl_pred, title_trace)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  init.c:11:39: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/WeightedCluster.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used C++ compiler: ‘Debian clang version 15.0.6’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘ATE’
Missing or unexported object: ‘MNP::predict.mnp’
Unknown package ‘ATE’ in Rd xrefs
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  random_wrap.c:9:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/wnominate.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used Fortran compiler: ‘GNU Fortran (Debian 12.2.0-14) 12.2.0’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RP2_data_1.txt’ ‘RP2_data_4.txt’ ‘RP2_qtl_1.txt’ ‘RP2_qtl_4.txt’
  ‘hp1_effect_qtl.txt’ ‘hp1_freq_mrk.txt’ ‘hp1_freq_qtl.txt’
  ‘hp1_genome.txt’ ‘hp1_last_hp_data.txt’ ‘hp1_lm_mrk.txt’
  ‘hp1_lm_qtl.txt’ ‘hp1_lm_qtl_mrk.txt’ ‘hp1_mrk.txt’ ‘hp1_qtl.txt’
  ‘hp2_effect_qtl.txt’ ‘hp2_freq_mrk.txt’ ‘hp2_freq_qtl.txt’
  ‘hp2_genome.txt’ ‘hp2_last_hp_data.txt’ ‘hp2_lm_mrk.txt’
  ‘hp2_lm_qtl.txt’ ‘hp2_lm_qtl_mrk.txt’ ‘hp2_mrk.txt’ ‘hp2_qtl.txt’
  ‘my_RP_data_1.txt’ ‘my_RP_data_4.txt’ ‘my_RP_mrk_1.txt’
  ‘my_RP_mrk_4.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xgb.txt’
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
predictdf:
  function(model, xseq, se, level)
predictdf.polr:
  function(model, xseq, se, level, data, method, formula, method.args,
           weight, n_boot)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:24:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:25:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:71:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:72:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/xml2.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 15.0.6’
* used C++ compiler: ‘Debian clang version 15.0.6’
'LazyData' is specified without 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: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
Found the following files/directories:
  ‘OPT.csv’ ‘testTecan_defaultLiquid.csv’ ‘testTecan_setLiquid.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘zdat’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    NEW DEPENDENCIES
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:74: Escaped LaTeX specials: \_
checkRd: (-1) zid.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
Package suggested but not available for checking: ‘SDMTools’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘abctools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mincrit
> ### Title: Summary statistics selection by minimizing a posterior sample
> ###   measure.
> ### Aliases: mincrit
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> # load example data:
> 
> data(coal)
> data(coalobs)
> 
> param<-coal[1:50000,2]
> simstats<-coal[1:50000,4:6]
> 
> # use matrix below just in case to preserve dimensions.
> 
> obsstats<-matrix(coalobs[1,4:6],nrow=1)
> obsparam<-matrix(coalobs[1,1])
> 
> # example of entropy minimization algorithm:
> 
> tmp <-mincrit(obsstats, param, simstats, tol=.01, method="rejection", 
+ do.crit=TRUE)
Warning in max(do.only) :
  no non-missing arguments to max; returning -Inf
doing statistics:  1    ( 1 / 7 )
Warning in (function (target, param, sumstat, tol, method, hcorr = TRUE,  :
  No parameter names are given, using P1, P2, ...
Warning in (function (target, param, sumstat, tol, method, hcorr = TRUE,  :
  No summary statistics names are given, using S1, S2, ...
doing criterion calculation...
Error in crit(valsi) : DLL requires the use of native symbols
Calls: mincrit -> crit
Execution halted
'LazyData' is specified without a 'data' directory
Running examples in ‘abmR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: energyVIZ
> ### Title: Creates a plot/table of energySIM() results
> ### Aliases: energyVIZ
> 
> ### ** Examples
> 
> 
> # 1. Define Population and Run energySIM()
> 
> pop1 <- as.species(x=-98.7, y=34.7)
> 
> EX1=energySIM(replicates=2,days=7,env_rast=ex_raster, search_radius=200,
+ sigma=.1, dest_x=-108.6, dest_y=26.2, mot_x=.9, mot_y=.9,
+ modeled_species=pop1,
+ optimum_lo=.8,optimum_hi=.9,init_energy=100,
+ direction="R",write_results=FALSE,single_rast=TRUE,mortality = TRUE)
Direction=R specified--Raster will be ignored
> 
> # 2. Run energyVIZ() on your result
> 
> energyVIZ(EX1,title="Visualizing EnergySIM results",type="plot", aspect_ratio=5/3,
+ label=TRUE)
Warning in geom_map(data = world, map = world, aes_string("long", "lat",  :
  Ignoring unknown aesthetics: x and y
> 
> energyVIZ(EX1,type="summary_table")
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: <Anonymous> ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
Running ‘testthat.R’ [9s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(adace)
  > 
  > test_check("adace")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 29 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-adace_func.R:98:3'): adace main function ─────────────────────
  message1$message (`actual`) not equal to "prediction from a rank-deficient fit may be misleading" (`expected`).
  
  actual vs expected
  - "prediction from rank-deficient fit; attr(*, \"non-estim\") has doubtful cases"
  + "prediction from a rank-deficient fit may be misleading"
  ── Failure ('test-adace_func.R:101:3'): adace main function ────────────────────
  message2$message (`actual`) not equal to "prediction from a rank-deficient fit may be misleading" (`expected`).
  
  actual vs expected
  - "prediction from rank-deficient fit; attr(*, \"non-estim\") has doubtful cases"
  + "prediction from a rank-deficient fit may be misleading"
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 29 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘adamethods-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: do_alphas_rss
> ### Title: Alphas and RSS of every set of archetypoids
> ### Aliases: do_alphas_rss
> 
> ### ** Examples
> 
> data(mtcars)
> data <- mtcars
> n <- nrow(data)
> m <- 10
> 
> k <- 3 
> numRep <- 2
> huge <- 200
> 
> suppressWarnings(RNGversion("3.5.0"))
> set.seed(1)
> rand_obs_si <- sample(1:n, size = m) 
> 
> si <- data[rand_obs_si,]
> ada_si <- do_ada(si, k, numRep, huge, FALSE) 
Error in get.knnx(data = train, query = test, k = k, algorithm) : 
  DLL requires the use of native symbols
Calls: do_ada -> archetypoids_norm_frob -> knn -> get.knnx
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Unknown packages ‘HI’, ‘MHadaptive’ in Rd xrefs
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘additive-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: additive
> ### Title: General Interface for Additive TidyModels
> ### Aliases: additive update.additive additive_fit
> 
> ### ** Examples
> 
> 
> additive()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: additive ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘BugReports.Rmd’ using rmarkdown
--- finished re-building ‘BugReports.Rmd’

--- re-building ‘GetStarted.Rmd’ using rmarkdown
Quitting from lines 49-55 (GetStarted.Rmd) 
Error: processing vignette ‘GetStarted.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘GetStarted.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘table_AeRobiology’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [2s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(africamonitor)
  africamonitor 0.2.3, see help(africamonitor)
  > 
  > test_check("africamonitor")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-accessdb.R:6:3'): reshaping works ──────────────────────────────
  Error in `alc(qDT_raw(X, row.names.col, keep.attr, if (length(class) || 
      keep.attr) class else c("data.table", "data.frame"), if (is.atomic(X) && 
      !is.matrix(X)) l1orlst(as.character(substitute(X))) else NULL))`: cannot take a writable DATAPTR of an ALTLIST [class: wrap_list, pkg: base]
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(data, am_pivot_wider(am_pivot_longer(data))) at test-accessdb.R:6:2
    2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─africamonitor::am_pivot_wider(am_pivot_longer(data))
    5. │ └─collapse::ftransformv(data, names_from, qF, sort = FALSE)
    6. └─africamonitor::am_pivot_longer(data)
    7.   ├─data.table::melt(...)
    8.   │ └─data.table::is.data.table(data)
    9.   └─collapse::qDT(data)
   10.     └─collapse:::alc(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Problems with news in ‘NEWS.md’:
No news entries found.
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
checkRd: (-1) BerryMielke.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) BlairLacy.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) Kvalseth.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) consensus.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) dsquared.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) l.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) lsquared.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) lsquared.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) var.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) adapt.Rd:41: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘RandomFields’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘AirMonitor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: monitor_toCSV
> ### Title: Convert monitor data as CSV
> ### Aliases: monitor_toCSV
> 
> ### ** Examples
> 
> library(AirMonitor)
> 
> monitor <-
+   Carmel_Valley %>%
+   monitor_filterDate(20160802, 20160803)
> 
> monitor_toCSV(monitor) %>% cat()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘alakazam-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sortGenes
> ### Title: Sort V(D)J genes
> ### Aliases: sortGenes
> 
> ### ** Examples
> 
> # Create a list of allele names
> genes <- c("IGHV1-69D*01","IGHV1-69*01","IGHV4-38-2*01","IGHV1-69-2*01",
+            "IGHV2-5*01","IGHV1-NL1*01", "IGHV1-2*01,IGHV1-2*05", 
+            "IGHV1-2", "IGHV1-2*02", "IGHV1-69*02")
> 
> # Sort genes by name
> sortGenes(genes)
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: sortGenes ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘AminoAcids-Vignette.Rmd’ using rmarkdown
--- finished re-building ‘AminoAcids-Vignette.Rmd’

--- re-building ‘Diversity-Vignette.Rmd’ using rmarkdown
--- finished re-building ‘Diversity-Vignette.Rmd’

--- re-building ‘Fastq-Vignette.Rmd’ using rmarkdown
--- finished re-building ‘Fastq-Vignette.Rmd’

--- re-building ‘Files-Vignette.Rmd’ using rmarkdown
--- finished re-building ‘Files-Vignette.Rmd’

--- re-building ‘GeneUsage-Vignette.Rmd’ using rmarkdown
Quitting from lines 85-101 (GeneUsage-Vignette.Rmd) 
Error: processing vignette ‘GeneUsage-Vignette.Rmd’ failed with diagnostics:
ℹ In argument: `gene = factor(gene, levels = sortGenes(unique(gene),
  method = "name"))`.
ℹ In group 1: `sample_id = "+7d"`.
Caused by error in `vectbl_assign()`:
! DLL requires the use of native symbols
--- failed re-building ‘GeneUsage-Vignette.Rmd’

--- re-building ‘Lineage-Vignette.Rmd’ using rmarkdown
--- finished re-building ‘Lineage-Vignette.Rmd’

--- re-building ‘Topology-Vignette.Rmd’ using rmarkdown
Quitting from lines 259-268 (Topology-Vignette.Rmd) 
Error: processing vignette ‘Topology-Vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Topology-Vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘GeneUsage-Vignette.Rmd’ ‘Topology-Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘alookr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compare_diag
> ### Title: Diagnosis of train set and test set of split_df object
> ### Aliases: compare_diag
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    combine

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

    filter, lag

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

    intersect, setdiff, setequal, union

> 
> # Credit Card Default Data
> head(ISLR::Default)
  default student   balance    income
1      No      No  729.5265 44361.625
2      No     Yes  817.1804 12106.135
3      No      No 1073.5492 31767.139
4      No      No  529.2506 35704.494
5      No      No  785.6559 38463.496
6      No     Yes  919.5885  7491.559
> 
> defaults <- ISLR::Default
> defaults$id <- seq(NROW(defaults))
> 
> set.seed(1)
> defaults[sample(seq(NROW(defaults)), 3), "student"] <- NA
> set.seed(2)
> defaults[sample(seq(NROW(defaults)), 10), "balance"] <- NA
> 
> sb <- defaults %>%
+   split_by(default)
> 
> sb %>%
+   compare_diag()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ call to ‘network’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘AMR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: antibiogram
> ### Title: Generate Antibiogram: Traditional, Combined, Syndromic, or
> ###   Weighted-Incidence Syndromic Combination (WISCA)
> ### Aliases: antibiogram plot.antibiogram autoplot.antibiogram
> ###   knit_print.antibiogram
> 
> ### ** Examples
> 
> # example_isolates is a data set available in the AMR package.
> # run ?example_isolates for more info.
> example_isolates
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: <Anonymous> ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running examples in ‘amt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bbox
> ### Title: Get bounding box of a track.
> ### Aliases: bbox bbox.track_xy bbox.steps_xy
> 
> ### ** Examples
> 
> data(deer)
> bbox(deer)
Geometry set for 1 feature 
Geometry type: POLYGON
Dimension:     XY
Bounding box:  xmin: 4309723 ymin: 3442716 xmax: 4318383 ymax: 3450713
Projected CRS: ETRS89 / LAEA Europe
POLYGON ((4309723 3442716, 4309723 3450713, 431...
> bbox(deer, spatial = FALSE)
   xmin    ymin    xmax    ymax 
4309723 3442716 4318383 3450713 
> bbox(deer, buffer = 100, spatial = FALSE)
   xmin    ymin    xmax    ymax 
4309623 3442616 4318483 3450813 
> 
> # For steps
> deer |> steps_by_burst() |> bbox(spatial = FALSE)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: bbox ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘p1_getting_started.Rmd’ using rmarkdown
Quitting from lines 237-243 (p1_getting_started.Rmd) 
Error: processing vignette ‘p1_getting_started.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘p1_getting_started.Rmd’

--- re-building ‘p2_hr.Rmd’ using rmarkdown
--- finished re-building ‘p2_hr.Rmd’

--- re-building ‘p3_rsf.Rmd’ using rmarkdown
--- finished re-building ‘p3_rsf.Rmd’

--- re-building ‘p4_SSF.Rmd’ using rmarkdown
Quitting from lines 58-59 (p4_SSF.Rmd) 
Error: processing vignette ‘p4_SSF.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘p4_SSF.Rmd’

--- re-building ‘p5_other_packages.Rmd’ using rmarkdown
--- finished re-building ‘p5_other_packages.Rmd’

--- re-building ‘p6_uhc_plots.Rmd’ using rmarkdown
--- finished re-building ‘p6_uhc_plots.Rmd’

SUMMARY: processing the following files failed:
  ‘p1_getting_started.Rmd’ ‘p4_SSF.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
as.url:
  function(x, ...)
as.url.domain:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) deshrink.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) deshrink.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) plot.mat.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) plot.wa.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) predict.prcurve.Rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Running examples in ‘AnanseSeurat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: import_seurat_scANANSE
> ### Title: import_seurat_scANANSE
> ### Aliases: import_seurat_scANANSE
> 
> ### ** Examples
> 
> sce_small <- readRDS(system.file("extdata","sce_small.Rds",package = 'AnanseSeurat'))
> infdir <- system.file("extdata","influence",package = 'AnanseSeurat')
> sce_small <- import_seurat_scANANSE(sce_small, anansnake_inf_dir = infdir)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: import_seurat_scANANSE ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
all.equal:
  function(target, current, ...)
all.equal.LayersR6:
  function(target, current)

all.equal:
  function(target, current, ...)
all.equal.RawR6:
  function(target, current)

all.equal:
  function(target, current, ...)
all.equal.AnnDataR6:
  function(target, current)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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: \_ \_
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [6s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(apa)
  > 
  > test_check("apa")
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 105 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-anova-apa.R:135:3'): Output for anova_apa: repeated-measures ANOVA ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─apa::anova_apa(...) at test-anova-apa.R:135:2
   2.   └─apa:::anova_apa_afex(...)
   3.     ├─tbl[tbl$effects %in% mauchlys, c("df_n", "df_d")] %<>% ...
   4.     ├─base::`[<-`(...)
   5.     └─tibble:::`[<-.tbl_df`(...)
   6.       └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   7.         └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   8.           ├─base::withCallingHandlers(...)
   9.           └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test-anova-apa.R:181:3'): Output for anova_apa: factorial repeated-measures ANOVA ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─apa::anova_apa(...) at test-anova-apa.R:181:2
   2.   └─apa:::anova_apa_afex(...)
   3.     ├─tbl[tbl$effects %in% mauchlys, c("df_n", "df_d")] %<>% ...
   4.     ├─base::`[<-`(...)
   5.     └─tibble:::`[<-.tbl_df`(...)
   6.       └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   7.         └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   8.           ├─base::withCallingHandlers(...)
   9.           └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 105 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following calls to attach():
File ‘apollo/R/apollo_attach.R’:
  attach(as.list(apollo_beta), warn.conflicts = FALSE)
  attach(database, warn.conflicts = FALSE)
  attach(draws, warn.conflicts = FALSE)
  attach(randcoeff, warn.conflicts = FALSE)
  attach(lcpars, warn.conflicts = FALSE)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘ARTP’
Found the following significant warnings:
  ARTP2_init.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ARTP2.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
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
Running ‘testthat.R’ [59s/92s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ashr)
  > context("ashr")
  > test_check("ashr")
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 122 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Rmosek cannot be loaded (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_myetruncnorm.R:24:3'): my_etruncnorm returns expected results ──
  Error in `truncnorm::etruncnorm(0, 99, -2, 3)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test_myetruncnorm.R:24:2
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─truncnorm::etruncnorm(0, 99, -2, 3)
  ── Error ('test_myetruncnorm.R:53:3'): my_vtruncnorm returns expected results ──
  Error in `truncnorm::vtruncnorm(-2, 3)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test_myetruncnorm.R:53:2
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─truncnorm::vtruncnorm(-2, 3)
  
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 122 ]
  Error: Test failures
  Execution halted
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
ihasNext:
  function(obj, ...)
ihasNext.default:
  function(obj)

ihasNext:
  function(obj, ...)
ihasNext.ihasNextOr:
  function(x)

ihasNext:
  function(obj, ...)
ihasNext.iteror:
  function(iter, ...)

compile:
  function(x, level, ...)
compile.coroutine:
  function(x, level)

as.promise:
  function(x)
as.promise.channel:
  function(ch, type)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
add_name_to_statistics:
  function(x, name)
add_name_to_statistics.data.frame:
  function(x, name, colname_for_variable)

add_name_to_tests:
  function(x, name)
add_name_to_tests.data.frame:
  function(x, name, colname_for_variable)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Unknown package ‘snpar’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  driver.c:114:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  driver.c:161:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  driver.c:199:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘autostats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_params
> ### Title: get params
> ### Aliases: get_params get_params.xgb.Booster get_params.workflow
> 
> ### ** Examples
> 
> 
> iris %>%
+   framecleaner::create_dummies() -> iris_dummies
1 column(s) have become 3 dummy columns
> 
> iris_dummies %>%
+   tidy_formula(target = Petal.Length) -> p_form
> 
> iris_dummies %>%
+   tidy_xgboost(p_form, mtry = .5, trees = 5L, loss_reduction = 2, sample_size = .7) -> xgb
Warning: `early_stop` was reduced to 4.
Warning: `early_stop` was reduced to 4.
accuracy tested on a validation set
# A tibble: 3 × 2
  .metric .estimate
  <chr>       <dbl>
1 ccc         0.849
2 rmse        0.887
3 rsq         0.915
> 
> ## reuse these parameters to find the cross validated error
> 
> rlang::exec(auto_model_accuracy, data = iris_dummies, formula = p_form, !!!get_params(xgb))
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: <Anonymous> ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘autostats.Rmd’ using rmarkdown
Quitting from lines 46-48 (autostats.Rmd) 
Error: processing vignette ‘autostats.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘autostats.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘autoTS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getBestModel
> ### Title: Determine best algorithm
> ### Aliases: getBestModel
> 
> ### ** Examples
> 
> library(autoTS)
> dates <- seq(lubridate::as_date("2005-01-01"),lubridate::as_date("2010-12-31"),"quarter")
> values <- 10+ 1:length(dates)/10 + rnorm(length(dates),mean = 0,sd = 10)
> ### Custom set of algorithm (including for bagged estimator)
> which.model <- getBestModel(dates,values,freq = "quarter",n_test = 4,
+                             algos = list("my.prophet","my.ets"),bagged = "custom")
n.changepoints greater than number of observations. Using 15
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: getBestModel ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘autoTS_vignette.Rmd’ using rmarkdown
Quitting from lines 102-108 (autoTS_vignette.Rmd) 
Error: processing vignette ‘autoTS_vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘autoTS_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘avidaR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_phenotype_id_from_genome_id
> ### Title: Get phenotype from genome
> ### Aliases: get_phenotype_id_from_genome_id
> 
> ### ** Examples
> 
> 
> # Create triplestore object
> triplestore <- triplestore_access$new()
> 
> # Set access options
> triplestore$set_access_options(
+   url = "https://graphdb.fortunalab.org",
+   user = "public_avida",
+   password = "public_avida",
+   repository = "avidaDB_test"
+ )
> 
> # Single genome
> get_phenotype_id_from_genome_id(genome_id = 1, triplestore = triplestore)
  genome_id phenotype_id
1  genome_1  phenotype_0
> 
> # More than one genome at seed_1
> get_phenotype_id_from_genome_id(
+   genome_id = c(1, 2, 3),
+   seed_id = 1,
+   triplestore = triplestore
+ )
  seed_id genome_id phenotype_id
1  seed_1  genome_1  phenotype_0
2  seed_1  genome_2  phenotype_0
3  seed_1  genome_3  phenotype_0
> 
> # More than one genome at more than one seed (e.g., seed_3 and seed_4)
> get_phenotype_id_from_genome_id(
+   genome_id = 1,
+   seed_id = c(3, 4),
+   phenotype_binary = TRUE,
+   triplestore = triplestore
+ )
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: get_phenotype_id_from_genome_id ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'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
show_query:
  function(x, ...)
show_query.tbl_kusto_abstract:
  function(tbl)

slice_sample:
  function(.data, ..., n, prop, by, weight_by, replace)
slice_sample.tbl_kusto_abstract:
  function(x, n, ...)

semi_join:
  function(x, y, by, copy, ...)
semi_join.tbl_kusto_abstract:
  function(x, y, by, suffix, .strategy, .shufflekeys, .num_partitions,
           .remote, ...)

compute:
  function(x, ...)
compute.tbl_kusto:
  function(tbl, name, ...)

inner_join:
  function(x, y, by, copy, suffix, ..., keep)
inner_join.tbl_kusto_abstract:
  function(x, y, by, suffix, .strategy, .shufflekeys, .num_partitions,
           .remote, ...)

ungroup:
  function(x, ...)
ungroup.tbl_kusto_abstract:
  function(.data, ...)

left_join:
  function(x, y, by, copy, suffix, ..., keep)
left_join.tbl_kusto_abstract:
  function(x, y, by, suffix, .strategy, .shufflekeys, .num_partitions,
           .remote, ...)

full_join:
  function(x, y, by, copy, suffix, ..., keep)
full_join.tbl_kusto_abstract:
  function(x, y, by, suffix, .strategy, .shufflekeys, .num_partitions,
           .remote, ...)

anti_join:
  function(x, y, by, copy, ...)
anti_join.tbl_kusto_abstract:
  function(x, y, by, suffix, .strategy, .shufflekeys, .num_partitions,
           .remote, ...)

right_join:
  function(x, y, by, copy, suffix, ..., keep)
right_join.tbl_kusto_abstract:
  function(x, y, by, suffix, .strategy, .shufflekeys, .num_partitions,
           .remote, ...)

collect:
  function(x, ...)
collect.tbl_kusto:
  function(tbl, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘lixoftConnectors’
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
posterior_predict:
  function(object, ...)
posterior_predict.baggr:
  function(object, draws, newdata, transform, summary, message,
           interval)

pp_check:
  function(object, ...)
pp_check.baggr:
  function(x, type, nsamples)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘fdpbandsdata’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘banter-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getBanterModel
> ### Title: Extract Random Forest Model
> ### Aliases: getBanterModel
> 
> ### ** Examples
> 
> data(train.data)
> # initialize BANTER model with event data
> bant.mdl <- initBanterModel(train.data$events)
> # add all detector models
> bant.mdl <- addBanterDetector(
+   bant.mdl, train.data$detectors, 
+   ntree = 50, sampsize = 1, num.cores = 1
+ )
> # run BANTER event model
> bant.mdl <- runBanterModel(bant.mdl, ntree = 1000, sampsize = 1)
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: runBanterModel ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘testthat.R’ [4s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(banter)
  Loading required package: magrittr
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  Welcome to banter v0.9.6
  See `banterGuide()` for a tutorial.
  > 
  > test_check("banter")
  [ FAIL 1 | WARN 10 | SKIP 0 | PASS 4 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-accessors.R:19:3'): getSampSize returns correct sample sizes ───
  Error in `vectbl_assign(x[[j]], cells[[j]], value)`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(runBanterModel(mdl, ntree = 50, sampsize = 1)) at test-accessors.R:19:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─banter::runBanterModel(mdl, ntree = 50, sampsize = 1)
    7. │ └─... %>% .meanVotes()
    8. └─banter:::.meanVotes(.)
    9.   └─base::replace(df, is.na(df), 0)
   10.     ├─base::`[<-`(`*tmp*`, list, value = `<dbl>`)
   11.     └─tibble:::`[<-.tbl_df`(`*tmp*`, list, value = `<dbl>`)
   12.       └─tibble:::tbl_subassign_matrix(x, j, value, j_arg, substitute(value))
   13.         ├─base::withCallingHandlers(...)
   14.         └─tibble:::vectbl_assign(x[[j]], cells[[j]], value)
  
  [ FAIL 1 | WARN 10 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
Running examples in ‘bapred-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bametric
> ### Title: Diverse metrics for quality of (adjusted) batch data
> ### Aliases: bametric
> 
> ### ** Examples
> 
> data(autism)
> 
> # Random subset of 150 variables:
> set.seed(1234)
> Xsub <- X[,sample(1:ncol(X), size=150)]
> 
> # In cases of batches with more than 20 observations
> # select 20 observations at random:
> subinds <- unlist(sapply(1:length(levels(batch)), function(x) {
+   indbatch <- which(batch==x)
+   if(length(indbatch) > 20)
+     indbatch <- sort(sample(indbatch, size=20))
+   indbatch
+ }))
> Xsub <- Xsub[subinds,]
> batchsub <- batch[subinds]
> ysub <- y[subinds]
> 
> 
> 
> 
> Xsubadj <- ba(x=Xsub, y=ysub, batch=batchsub, method = "combat")$xadj
> 
> 
> bametric(xba=Xsub, batch=batchsub, metric = "sep")
[1] 0.4241864
> bametric(xba=Xsubadj, batch=batchsub, metric = "sep")
[1] 0.06127109
> 
> bametric(xba=Xsub, batch=batchsub, metric = "avedist")
[1] 16.18661
> bametric(xba=Xsubadj, batch=batchsub, metric = "avedist")
[1] 15.13212
> 
> bametric(xba=Xsub, batch=batchsub, metric = "kldist")
Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols
Calls: bametric ... KL.divergence -> colMeans -> is.data.frame -> knnx.dist -> get.knnx
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Quitting from lines 73-75 (Introduction.Rmd) 
Error: processing vignette ‘Introduction.Rmd’ failed with diagnostics:
undefined columns selected
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘batchtma.Rmd’ using rmarkdown
Quitting from lines 116-120 (batchtma.Rmd) 
Error: processing vignette ‘batchtma.Rmd’ failed with diagnostics:
ℹ In index: 1.
Caused by error in `vectbl_assign()`:
! DLL requires the use of native symbols
--- failed re-building ‘batchtma.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++14: please drop specification unless essential
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: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
Found the following significant warnings:
  bayesDccGarch.c:48:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bayesDccGarch.c:110:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bayesDccGarch.c:172:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bayesDccGarch.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
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.
Specified C++11: please drop specification unless essential
'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
Running examples in ‘bayesian-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bayesian
> ### Title: General Interface for Bayesian TidyModels
> ### Aliases: bayesian update.bayesian bayesian_fit bayesian_formula
> ###   bayesian_terms bayesian_family bayesian_predict bayesian_write
> ###   bayesian_read
> 
> ### ** Examples
> 
> 
> bayesian()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: bayesian ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘BugReports.Rmd’ using rmarkdown
--- finished re-building ‘BugReports.Rmd’

--- re-building ‘GetStarted.Rmd’ using rmarkdown
Quitting from lines 51-56 (GetStarted.Rmd) 
Error: processing vignette ‘GetStarted.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘GetStarted.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
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.
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
rhat:
  function(x, ...)
rhat.bayesmanecfit:
  function(object, rhat_cutoff, ...)

rhat:
  function(x, ...)
rhat.bayesnecfit:
  function(object, rhat_cutoff, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘BayesNSGP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nsCrossdist3d
> ### Title: Calculate coordinate-specific cross-distance matrices, only for
> ###   nearest neighbors and store in an array
> ### Aliases: nsCrossdist3d
> 
> ### ** Examples
> 
> # Generate some coordinates and neighbors
> coords <- cbind(runif(100),runif(100))
> predCoords <- cbind(runif(200),runif(200))
> P_nID <- FNN::get.knnx(coords, predCoords, k = 10)$nn.index # Prediction NN
Error in FNN::get.knnx(coords, predCoords, k = 10) : 
  DLL requires the use of native symbols
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
plot:
  function(x)
plot.posterior:
  function(x, add_prior, ...)

plot:
  function(x)
plot.posterior:
  function(x, add_prior, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Running ‘testthat.R’ [186s/295s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bayesplot)
  This is bayesplot version 1.10.0
  - Online documentation and vignettes at mc-stan.org/bayesplot
  - bayesplot theme set to bayesplot::theme_default()
     * Does _not_ affect other ggplot2 plots
     * See ?bayesplot_theme_set for details on theme setting
  > 
  > Sys.unsetenv("R_TESTS")
  > test_check("bayesplot")
  [ FAIL 1 | WARN 20 | SKIP 73 | PASS 1014 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (73)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ppc-discrete.R:74:3'): ppc_bars_data includes all levels ───────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─bayesplot::ppc_bars_data(y_ord, yrep_ord2) at test-ppc-discrete.R:74:2
    2. │ └─bayesplot:::.ppc_bars_data(...)
    3. │   ├─... %>% select(!!!cols)
    4. │   ├─dplyr::full_join(yrep_summary, y_summary, by = c("group", "value"))
    5. │   └─dplyr:::full_join.data.frame(...)
    6. │     └─dplyr:::join_mutate(...)
    7. │       ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,2]>`)
    8. │       └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,2]>`)
    9. │         └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   10. │           └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   11. │             ├─base::withCallingHandlers(...)
   12. │             └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
   13. ├─dplyr::select(., !!!cols)
   14. ├─dplyr::arrange(., .data$x)
   15. └─dplyr::rename(., x = "value")
  
  [ FAIL 1 | WARN 20 | SKIP 73 | PASS 1014 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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.
Specified C++11: please drop specification unless essential
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: \&
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
sql_translation:
  function(con)
sql_translation.wfsConnection:
  function(conn)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
Specified C++11: please drop specification unless essential
Running examples in ‘bcTSNE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bctsne
> ### Title: Calculate BC t-SNE by orthogonal gradient descent
> ### Aliases: bctsne
> 
> ### ** Examples
> 
> ## Create small simulated dataset, A, with embeded batch effects
> set.seed(2731)
> kRid <- 20
> p    <- 100
> n    <- 200
> 
> W <- matrix(rnorm(p*kRid), kRid)
> S <- matrix(rnorm(n*kRid), n)
> z <- sample(1:3, rep = TRUE, size = n)
> Z <- model.matrix( ~ -1 + as.factor(z))
> l <- matrix(rnorm(kRid*NCOL(Z)), kRid)
> A <- (S - Z %*% t(l) ) %*% W
> 
> ## Scale A to give input, X 
> X <- scale(A)
> 
> resUnadj <- Rtsne::Rtsne(X)                 ## Standard t-SNE
> resAdj   <- bctsne(X = X, Z = Z, k = 10)    ## Batch-corrected t-SNE
Warning in type.convert.default(maxIter) :
  'as.is' should be specified by the caller; using TRUE
Error in bctsne(X = X, Z = Z, k = 10) : 
  DLL requires the use of native symbols
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
autoplot:
  function(object, ...)
autoplot.plm:
  function(x, type, param, transformed, ...)

autoplot:
  function(object, ...)
autoplot.gplm:
  function(x, type, param, transformed, ...)

autoplot:
  function(object, ...)
autoplot.tournament:
  function(x, type, ...)

autoplot:
  function(object, ...)
autoplot.gplm0:
  function(x, type, param, transformed, ...)

autoplot:
  function(object, ...)
autoplot.plm0:
  function(x, type, param, transformed, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘dump.txt’
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
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’
Running examples in ‘behaviorchange-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: abcd
> ### Title: Acyclic Behavior Change Diagram
> ### Aliases: abcd print.abcdiagram
> 
> ### ** Examples
> 
> ### Load one of the ABCD matrices supplied
> ### with the behaviorchange package
> data(abcd_specification_example_xtc);
> 
> ### Create ABCD matrix (using 'print' to allow pkgdown() to print properly).
> print(behaviorchange::abcd(abcd_specification_example_xtc));
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: print ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’ using rmarkdown
Quitting from lines 55-91 (abcd-laagdrempelige_nederlandse_uitleg.Rmd) 
Error: processing vignette ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’

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

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

--- re-building ‘determinant-selection-table.Rmd’ using rmarkdown
--- finished re-building ‘determinant-selection-table.Rmd’

--- re-building ‘determinant-selection-tutorial.Rmd’ using rmarkdown
--- finished re-building ‘determinant-selection-tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  load.c:11:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nanotime.h:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nanotime.h:7:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mark.c:75:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mark.c:118:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  mark.c:119:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nanotime.c:61:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nanotime.c:71:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  process_memory.c:79:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bench.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘benthos-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ambi
> ### Title: AZTI Marine Biotic Index (AMBI)
> ### Aliases: ambi ambi_ has_ambi has_ambi_
> 
> ### ** Examples
> 
>  ambi(
+      taxon = c("Euspira pulchella", "Nephtys cirrosa"), 
+      count = c(4, 6)
+  )
Warning: `filter_()` was deprecated in dplyr 0.7.0.
ℹ Please use `filter()` instead.
ℹ See vignette('programming') for more help
ℹ The deprecated feature was likely used in the benthos package.
  Please report the issue to the authors.
Warning: `select_()` was deprecated in dplyr 0.7.0.
ℹ Please use `select()` instead.
ℹ The deprecated feature was likely used in the benthos package.
  Please report the issue to the authors.
Warning: `summarise_()` was deprecated in dplyr 0.7.0.
ℹ Please use `summarise()` instead.
ℹ The deprecated feature was likely used in the benthos package.
  Please report the issue to the authors.
Warning: `mutate_()` was deprecated in dplyr 0.7.0.
ℹ Please use `mutate()` instead.
ℹ See vignette('programming') for more help
ℹ The deprecated feature was likely used in the benthos package.
  Please report the issue to the authors.
Warning: `arrange_()` was deprecated in dplyr 0.7.0.
ℹ Please use `arrange()` instead.
ℹ See vignette('programming') for more help
ℹ The deprecated feature was likely used in the benthos package.
  Please report the issue to the authors.
Warning: `group_by_()` was deprecated in dplyr 0.7.0.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
ℹ The deprecated feature was likely used in the benthos package.
  Please report the issue to the authors.
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: ambi ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘test-all.R’ [4s/7s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(benthos)
  > test_check("benthos")
  [ FAIL 1 | WARN 16 | SKIP 1 | PASS 146 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-indicators.R:201:5'): 'AMBI-index' has been correctly implemented ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-indicators.R:201:4
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─benthos::ambi(...)
    5. │ └─benthos::ambi_(.data, lazy(taxon), lazy(count), lazy(group))
    6. │   └─... %>% unlist(use.names = FALSE)
    7. ├─base::unlist(., use.names = FALSE)
    8. ├─dplyr::summarise_(., AMBI = ~1.5 * sum(0:4 * p))
    9. ├─dplyr::mutate_(., n = ~ifelse(is.na(n), 0, n), p = ~n/sum(n))
   10. ├─dplyr::arrange_(., ~GROUP)
   11. ├─dplyr::right_join(., tibble(GROUP = permissable_groups), by = "GROUP")
   12. └─dplyr:::right_join.data.frame(...)
   13.   └─dplyr:::join_mutate(...)
   14.     ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   15.     └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   16.       └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   17.         └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   18.           ├─base::withCallingHandlers(...)
   19.           └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 16 | SKIP 1 | PASS 146 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘SoDA’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘bibliometrix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rpys
> ### Title: Reference Publication Year Spectroscopy
> ### Aliases: rpys
> 
> ### ** Examples
> 
> 
> 
> data(scientometrics, package = "bibliometrixData")
> res <- rpys(scientometrics, sep=";", graph = TRUE)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: rpys ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  rbimax.c:326:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/biclust.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘ffbase’
Running examples in ‘bigdatadist-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: entropy
> ### Title: Entropy Computation
> ### Aliases: entropy
> ### Keywords: Entropy
> 
> ### ** Examples
> 
> require(MASS);
Loading required package: MASS
> data = mvrnorm(100,c(0,0),diag(2));
> entropy(data, alpha = 2, k.neighbor = 10, scale = FALSE)
Error in get.knn(data, k, algorithm) : 
  DLL requires the use of native symbols
Calls: entropy -> knn.dist -> get.knn
Execution halted
Package suggested but not available for checking: ‘INLA’
Found the following significant warnings:
  lib.h:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lib.c:3:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bigGP.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
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’.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘outputs’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  binarizeBASCA.h:37:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  TASC.c:258:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  TASC_min.c:256:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  binarizeBASCA.c:358:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Binarize.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
'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: ‘msa’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘pointshape.dbf’ ‘pointshape.shp’ ‘pointshape.shx’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
Running examples in ‘biospear-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predRes
> ### Title: Evaluation of the prediction accuracy of a prediction model
> ### Aliases: predRes plot.predRes
> ### Keywords: prediction
> 
> ### ** Examples
> 
> ########################################
> # Simulated data set
> ########################################
> 
> ## Low calculation time
>   set.seed(654321)
>   sdata <- simdata(
+     n = 500, p = 20, q.main = 3, q.inter = 0,
+     prob.tt = 0.5, alpha.tt = 0,
+     beta.main = -0.8,
+     b.corr = 0.6, b.corr.by = 4,
+     m0 = 5, wei.shape = 1, recr = 4, fu = 2,
+     timefactor = 1)
>   
>   newdata <- simdataV(
+     traindata = sdata,
+     Nvalid = 500
+   )
>    
>   resBM <- BMsel(
+     data = sdata, 
+     method = c("lasso", "lasso-pcvl"), 
+     inter = FALSE, 
+     folds = 5)

Computing selection with method: lasso

Computing selection with method: lasso-pcvl (lasso penalized extensions)
>   
>   predAcc <- predRes(
+     res = resBM,
+     traindata = sdata,
+     newdata = newdata,
+     time = 1:5)

Computing prediction criteria for: training set
Error in UnoC(Surv.rsp = surv.train, Surv.rsp.new = surv.new, lpnew = lp.new[,  : 
  DLL requires the use of native symbols
Calls: predRes ... lapply -> FUN -> matrix -> unlist -> lapply -> FUN -> UnoC
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following significant warnings:
  binarizeBASCA.h:37:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  TASC.c:258:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  TASC_min.c:256:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  binarizeBASCA.c:358:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BiTrinA.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
Running examples in ‘bitsqueezr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bits_as_string
> ### Title: Generate a text representation of the bits in a double
> ### Aliases: bits_as_string
> 
> ### ** Examples
> 
> # Output binary representation of pi
> bits_as_string(pi)
Error in bits_as_string(pi) : DLL requires the use of native symbols
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘BlanketStatsments-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculate_Uno_c
> ### Title: Calculate Uno's C for a given model.
> ### Aliases: calculate_Uno_c
> 
> ### ** Examples
> 
> data <- survival::lung
> cancer_mod <- survival::coxph(survival::Surv(time, status)~age, data = data)
> calculate_Uno_c(data, cancer_mod)
Error in survAUC::UnoC(Surv.rsp = Surv_model_old, Surv.rsp.new = Surv_model_new,  : 
  DLL requires the use of native symbols
Calls: calculate_Uno_c -> <Anonymous>
Execution halted
Running ‘testthat.R’ [5s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BlanketStatsments)
  > 
  > test_check("BlanketStatsments")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-Blanket_statsments.R:7:3'): Individual model functions ─────────
  Error in `survAUC::UnoC(Surv.rsp = Surv_model_old, Surv.rsp.new = Surv_model_new, 
      lpnew = pred_scores)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-Blanket_statsments.R:7:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─BlanketStatsments::calculate_Uno_c(data, mod)
   5.   └─survAUC::UnoC(...)
  ── Error ('test-Blanket_statsments.R:22:3'): Blanket stats /-ments ─────────────
  Error in `survAUC::UnoC(Surv.rsp = Surv_model_old, Surv.rsp.new = Surv_model_new, 
      lpnew = pred_scores)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-Blanket_statsments.R:22:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─BlanketStatsments::table_blanket_statsments(data, bl_stats)
   5.   └─BlanketStatsments::blanket_c_statistic(df, models, modality = "cox")
   6.     └─BlanketStatsments::calculate_Uno_c(...)
   7.       └─survAUC::UnoC(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
'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: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.blob:
  function(x)

vec_ptype_full:
  function(x, ...)
vec_ptype_full.blob:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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.
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
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’
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  include/register.h:46:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  include/register.h:75:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  include/register.h:76:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  include/register.h:82:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  globals.c:15:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  globals.c:33:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  test.counter.c:26:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  test.counter.c:35:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bnlearn.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
as.mcmc:
  function(x, ...)
as.mcmc.multNRMI:
  function(fitlist, thinning_to, ncores)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘bolasso-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bolasso
> ### Title: Bootsrap-enhanced Lasso
> ### Aliases: bolasso
> 
> ### ** Examples
> 
> mtcars[, c(2, 10:11)] <- lapply(mtcars[, c(2, 10:11)], as.factor)
> idx <- sample(nrow(mtcars), 22)
> mtcars_train <- mtcars[idx, ]
> mtcars_test <- mtcars[-idx, ]
> 
> ## Formula Interface
> 
> # Train model
> set.seed(123)
> bolasso_form <- bolasso(
+   form = mpg ~ .,
+   data = mtcars_train,
+   n.boot = 20,
+   nfolds = 5,
+   implement = "glmnet"
+ )
Loaded glmnet 4.1-6
> 
> # Extract selected variables
> selected_vars(bolasso_form, threshold = 0.9, select = "lambda.min")
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: selected_vars ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
Specified C++11: please drop specification unless essential
'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: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) R2txtJG.Rd:90: Escaped LaTeX specials: \#
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running examples in ‘bridger-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: suitSplit
> ### Title: suitSplit
> ### Aliases: suitSplit
> 
> ### ** Examples
> 
> suitSplit(missingCards = 6, cards_W = 13, cards_E = 8)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: suitSplit ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘cmdstanr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘tidy.Rmd’ using rmarkdown
Quitting from lines 296-322 (tidy.Rmd) 
Error: processing vignette ‘tidy.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘tidy.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘glmmADMB’
checkRd: (-1) brr-package.Rd:33: Escaped LaTeX specials: \&
Found the following significant warnings:
  BugsHelper.c:76:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  BugsHelper.c:87:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  BugsHelper.c:88:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BRugs.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gvcm.cat’
Specified C++11: please drop specification unless essential
Unknown package ‘gvcm.cat’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘adding-models-to-butcher.Rmd’ using rmarkdown
--- finished re-building ‘adding-models-to-butcher.Rmd’

--- re-building ‘available-axe-methods.Rmd’ using rmarkdown
Quitting from lines 22-45 (available-axe-methods.Rmd) 
Error: processing vignette ‘available-axe-methods.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘available-axe-methods.Rmd’

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

SUMMARY: processing the following file failed:
  ‘available-axe-methods.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
as.data.table:
  function(x, keep.rownames, ...)
as.data.table.performance:
  function(x, type, format, keep.rownames, ...)

iid:
  function(x, ...)
iid.BuyseTTEM:
  function(x, treatment, strata, cause)

iid:
  function(x, ...)
iid.BuyseTestAuc:
  function(object, ...)

iid:
  function(x, ...)
iid.prodlim:
  function(object, add0, ...)

iid:
  function(x, ...)
iid.BuyseTestBrier:
  function(object, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
Found the following significant warnings:
  cairobem.c:50:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Rapi.h:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Rapi.h:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cairotalk.c:661:23: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cairotalk.c:1552:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cairotalk.c:1588:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  xlib-backend.c:156:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Cairo.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RxODE’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tmp.txt’
Running examples in ‘Canek-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CorrectBatch
> ### Title: CorrectBatch
> ### Aliases: CorrectBatch
> 
> ### ** Examples
> 
> x <- SimBatches$batches[[1]]
> y <- SimBatches$batches[[2]]
> z <- CorrectBatch(x, y)
Error in get.knnx(data = t(queBatch), query = t(refBatch), k = kNN) : 
  DLL requires the use of native symbols
Calls: CorrectBatch -> GetMnnPairs -> get.knnx
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘toy_example.Rmd’ using rmarkdown
Quitting from lines 79-80 (toy_example.Rmd) 
Error: processing vignette ‘toy_example.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘toy_example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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
Running examples in ‘capm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PlotImmigrationFlow
> ### Title: Plot immigration flows
> ### Aliases: PlotImmigrationFlow
> 
> ### ** Examples
> 
> data(dogs)
> cls <- c("blue3", "orange", "skyblue", "darkgreen", "yellow3", "black")
> PlotImmigrationFlow(dogs, "acquisition_city", "Pinhais",
+                     cls = cls, agg.sources.suffix = " cities")
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: PlotImmigrationFlow ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'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
Specified C++11: please drop specification unless essential
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
Problems with news in ‘NEWS.md’:
No news entries found.
Error(s) in re-building vignettes:
  ...
--- re-building ‘circadian.Rmd’ using rmarkdown
Quitting from lines 56-100 (circadian.Rmd) 
Error: processing vignette ‘circadian.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘circadian.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
oob_pred:
  function(x, ...)
oob_pred.rfe:
  function(x, best, average)

oob_pred:
  function(x, ...)
oob_pred.train:
  function(x, best, average)

oob_pred:
  function(x, ...)
oob_pred.sbf:
  function(x, average)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘carpenter.Rmd’ using rmarkdown
Quitting from lines 121-137 (carpenter.Rmd) 
Error: processing vignette ‘carpenter.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘carpenter.Rmd’

SUMMARY: processing the following file failed:
  ‘carpenter.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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GAMBoost’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
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: \&
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘causact-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dag_diagrammer
> ### Title: Convert graph to Diagrammer object for visualization
> ### Aliases: dag_diagrammer
> 
> ### ** Examples
> 
> library("DiagrammeR")
> dag_create() %>%
+ dag_node("Get Card","y",
+          rhs = bernoulli(theta),
+          data = carModelDF$getCard) %>%
+   dag_diagrammer() %>%
+   render_graph(title = "DiagrammeR Version of causact_graph")
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Running examples in ‘causaloptim-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: interpret_bounds
> ### Title: Convert bounds string to a function
> ### Aliases: interpret_bounds
> 
> ### ** Examples
> 
> b <- graph_from_literal(X -+ Y, Ur -+ X, Ur -+ Y)
> V(b)$leftside <- c(0,0,0)
> V(b)$latent <- c(0,0,1)
> V(b)$nvals <- c(2,2,2)
> E(b)$rlconnect <- E(b)$edge.monotone <- c(0, 0, 0)
> obj <- analyze_graph(b, constraints = NULL, effectt = "p{Y(X = 1) = 1} - p{Y(X = 0) = 1}")
> bounds <- optimize_effect(obj)
*** buffer overflow detected ***: terminated
Aborted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(causaloptim)
  Loading required package: igraph
  
  Attaching package: 'igraph'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  The following objects are masked from 'package:stats':
  
      decompose, spectrum
  
  The following object is masked from 'package:base':
  
      union
  
  > 
  > test_check("causaloptim")
  *** buffer overflow detected ***: terminated
  Aborted
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running examples in ‘cccd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cccd
> ### Title: Class Cover Catch Digraph
> ### Aliases: cccd cccd.rw cccd.classify cccd.classifier cccd.classifier.rw
> ###   cccd.multiclass.classifier cccd.multiclass.classify plot.cccd
> ###   plot.cccdClassifier
> ### Keywords: graphs
> 
> ### ** Examples
> 
> set.seed(456330)
> z <- matrix(runif(1000),ncol=2)
> ind <- which(z[,1]<.5 & z[,2]<.5)
> x <- z[ind,]
> y <- z[-ind,]
> g <- cccd(x,y)
Error in get.knnx(y, x, k = 1, algorithm = algorithm) : 
  DLL requires the use of native symbols
Calls: cccd -> get.knnx
Execution halted
'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.
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘CirceR’
Found the following files/directories:
  ‘out.png’ ‘out1.txt’ ‘out2.txt’
Specified C++11: please drop specification unless essential
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
Running ‘testthat.R’ [15s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(celltrackR)
  > 
  > test_check("celltrackR")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 316 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('testClusterFunctions.R:57:3'): trackFeatureMap produces the right output ──
  Error in `FNN::get.knn(X, k)`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─testthat::expect_true(...) at testClusterFunctions.R:57:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. └─celltrackR::trackFeatureMap(TCells, c(speed), method = "UMAP")
    5.   └─uwot::umap(values, ...)
    6.     └─uwot:::uwot(...)
    7.       └─uwot:::data2set(...)
    8.         └─uwot:::x2set(...)
    9.           └─uwot:::x2nn(...)
   10.             └─uwot:::find_nn(...)
   11.               └─uwot:::FNN_nn(X, k = k, include_self = include_self)
   12.                 └─FNN::get.knn(X, k)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 316 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘QC.Rmd’ using rmarkdown
--- finished re-building ‘QC.Rmd’

--- re-building ‘ana-methods.Rmd’ using rmarkdown
--- finished re-building ‘ana-methods.Rmd’

--- re-building ‘clustering.Rmd’ using rmarkdown
Quitting from lines 163-167 (clustering.Rmd) 
Error: processing vignette ‘clustering.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘clustering.Rmd’

--- re-building ‘data-QC.Rmd’ using rmarkdown
--- finished re-building ‘data-QC.Rmd’

--- re-building ‘reading-converting-data.Rmd’ using rmarkdown
--- finished re-building ‘reading-converting-data.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
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
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘CGPfunctions-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chaid_table
> ### Title: Produce CHAID results tables from a partykit CHAID model
> ### Aliases: chaid_table
> 
> ### ** Examples
> 
> library(CGPfunctions)
> chaid_table(chaidUS)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: chaid_table ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using-Plot2WayANOVA.Rmd’ using rmarkdown
--- finished re-building ‘Using-Plot2WayANOVA.Rmd’

--- re-building ‘Using-PlotXTabs.Rmd’ using rmarkdown
--- finished re-building ‘Using-PlotXTabs.Rmd’

--- re-building ‘Using-PlotXTabs2.Rmd’ using rmarkdown
--- finished re-building ‘Using-PlotXTabs2.Rmd’

--- re-building ‘Using-chaid_table.Rmd’ using rmarkdown
Quitting from lines 88-94 (Using-chaid_table.Rmd) 
Error: processing vignette ‘Using-chaid_table.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Using-chaid_table.Rmd’

--- re-building ‘Using-newggslopegraph.Rmd’ using rmarkdown
--- finished re-building ‘Using-newggslopegraph.Rmd’

SUMMARY: processing the following file failed:
  ‘Using-chaid_table.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
Error(s) in re-building vignettes:
  ...
--- re-building ‘cheese.Rmd’ using rmarkdown
--- finished re-building ‘cheese.Rmd’

--- re-building ‘describe.Rmd’ using rmarkdown
Quitting from lines 213-218 (describe.Rmd) 
Error: processing vignette ‘describe.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘describe.Rmd’

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) hyptis.Rd:31: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘stepres00.txt’
Package suggested but not available for checking: ‘clusterCrit’
Unknown package ‘clusterCrit’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘countreg’
Running examples in ‘chillR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Empirical_daily_temperature_curve
> ### Title: Empirical daily temperature curve
> ### Aliases: Empirical_daily_temperature_curve
> ### Keywords: utility
> 
> ### ** Examples
> 
>  
> Empirical_daily_temperature_curve(Winters_hours_gaps)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: Empirical_daily_temperature_curve ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘chisquare-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chisquare
> ### Title: R function for chi-square and G-square test of independence,
> ###   measures of association, and standardized/moment-corrected
> ###   standardized/adjusted standardized residuals
> ### Aliases: chisquare
> ### Keywords: chiperm
> 
> ### ** Examples
> 
> #perform the test on the in-built 'diseases' dataset
> result <- chisquare(diseases, B=99)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: chisquare ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘entab’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
resolved:
  function(x, ...)
resolved.CivisFuture:
  function(future, ...)
See section ‘Generic functions and methods’ 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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Running examples in ‘climaemet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggclimat_walter_lieth
> ### Title: Walter and Lieth climatic diagram on 'ggplot2'
> ### Aliases: ggclimat_walter_lieth
> 
> ### ** Examples
> 
> 
> library(ggplot2)
> 
> wl <- ggclimat_walter_lieth(
+   climaemet::climaemet_9434_climatogram,
+   alt = "249",
+   per = "1981-2010",
+   est = "Zaragoza Airport"
+ )
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: ggclimat_walter_lieth ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
checkRd: (-1) diagwl.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) diagwl.Rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Running examples in ‘ClustAssess-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_feature_stability
> ### Title: Evaluate Feature Set Stability
> ### Aliases: get_feature_stability
> 
> ### ** Examples
> 
> set.seed(2021)
> # create an artificial expression matrix
> expr_matrix = matrix(c(runif(100*10), runif(100*10, min = 3, max = 4)), nrow = 200, byrow = TRUE)
> rownames(expr_matrix) = as.character(1:200)
> colnames(expr_matrix) = paste("feature", 1:10)
> 
> feature_stability_result = get_feature_stability(data_matrix = t(expr_matrix),
+    feature_set = colnames(expr_matrix),
+    feature_type = "feature_name",
+    steps = 5,
+    npcs = 2,
+    n_repetitions = 10,
+    algorithm = 1,
+    # the following parameters are used by the umap function and are not mandatory
+    n_neighbors = 3,
+    approx_pow = TRUE,
+    n_epochs = 0,
+    init = "random",
+    min_dist = 0.3)
Error in FNN::get.knn(X, k) : DLL requires the use of native symbols
Calls: get_feature_stability ... data2set -> x2set -> x2nn -> find_nn -> FNN_nn -> <Anonymous>
Execution halted
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’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) HINoV.Mod.rd:3: Escaped LaTeX specials: \&
checkRd: (-1) HINoV.Symbolic.rd:3: Escaped LaTeX specials: \&
checkRd: (-1) cluster.Gen.rd:14: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:18: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:29: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) cluster.Gen.rd:33: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:34: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:36: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:38: Escaped LaTeX specials: \_ \_
checkRd: (-1) cluster.Gen.rd:51: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:52: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:54: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:55: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:62: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) comparing.Partitions.rd:12: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.BC.rd:10: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.GDM.rd:33: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.SM.rd:10: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.C.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.G2.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.G3.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.H.rd:16: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.S.rd:12: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  optimal_assignment.c:47:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/clv.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:22: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tobit1’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘PopGenome’
autoplot:
  function(object, ...)
autoplot.bal.tab:
  function(x, stats, abs, agg.fun, var.order, drop.missing,
           drop.distance, thresholds, line, stars, grid, limits,
           colors, shapes, alpha, size, wrap, var.names, title,
           sample.names, labels, position, themes, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) drqssbc.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) qbsks.Rd:81: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
Package which this enhances but not available for checking: ‘rkward’
Package suggested but not available for checking: ‘userfriendlyscience’
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
Running ‘testthat.R’ [13s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(coder)
  > 
  > test_check("coder")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 119 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-classcodes.R:8:3'): classcodes ─────────────────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(...) at test-classcodes.R:8:2
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. ├─base::`[<-`(`*tmp*`, 1, 1, value = `<chr>`) at test-classcodes.R:8:17
   10. ├─coder:::`[<-.classcodes`(`*tmp*`, 1, 1, value = `<chr>`) at test-classcodes.R:8:17
   11. │ └─coder::as.classcodes(NextMethod(), .name = attr(x, "name", exact = TRUE))
   12. ├─base::NextMethod()
   13. └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, 1, value = `<chr>`)
   14.   └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   15.     └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   16.       ├─base::withCallingHandlers(...)
   17.       └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 119 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Running examples in ‘codified-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: table_nih_enrollment
> ### Title: Produce an NIH-compliant enrollment table.
> ### Aliases: table_nih_enrollment table_nih_enrollment_pretty
> 
> ### ** Examples
> 
> ds_1 <- tibble::tribble(
+   ~subject_id,   ~gender  , ~race                      ,   ~ethnicity                     ,
+            1L,   "Male"   , "Black or African American",  "Not Hispanic or Latino"        ,
+            2L,   "Male"   , "Black or African American",  "Not Hispanic or Latino"        ,
+            3L,   "Female" , "Black or African American",  "Unknown/Not Reported Ethnicity",
+            4L,   "Male"   , "White"                    ,  "Not Hispanic or Latino"        ,
+            5L,   "Male"   , "White"                    ,  "Not Hispanic or Latino"        ,
+            6L,   "Female" , "White"                    ,  "Not Hispanic or Latino"        ,
+            7L,   "Male"   , "White"                    ,  "Hispanic or Latino"            ,
+            8L,   "Male"   , "White"                    ,  "Hispanic or Latino"
+ )
> 
> table_nih_enrollment(ds_1)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: table_nih_enrollment ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘nih-enrollment-html.Rmd’ using rmarkdown
Quitting from lines 95-103 (nih-enrollment-html.Rmd) 
Error: processing vignette ‘nih-enrollment-html.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘nih-enrollment-html.Rmd’

SUMMARY: processing the following file failed:
  ‘nih-enrollment-html.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Running examples in ‘cogmapr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ConceptCentralityIndiv
> ### Title: Centrality of vertices by document
> ### Aliases: ConceptCentralityIndiv
> 
> ### ** Examples
> 
> project_name <- "a_new_project"
> main_path <- paste0(system.file("testdata", package = "cogmapr"), '/')
> my.project <- ProjectCMap(main_path, project_name)
> 
> ConceptCentralityIndiv(my.project)
Joining with `by = join_by(doc_id, name, num)`
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: ConceptCentralityIndiv ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
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
Unexported object imported by a ‘:::’ call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘CAM’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following significant warnings:
  brentmin.c:237:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ContaminatedMixt.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘convergEU-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: country_ranking
> ### Title: Ranking of EU countries by time
> ### Aliases: country_ranking
> 
> ### ** Examples
> 
> 
> # Example 1
> # Sorted dataframe in the format years by countries:
> require(tibble)
Loading required package: tibble
> myTB  <- tibble::tribble(
+ ~years, ~UK, ~DE, ~IT,
+ 1988,   1201, 868, 578,
+ 1989,   1150, 978, 682,
+ 1990,   998,  1250, 332,
+ 1991,  1600,  1350, 802
+ )
> 
> # Country ranking according to the indicator higher is the best:
> res <- country_ranking(myTB,timeName="years")
> 
> # Country ranking according to the indicator lower is the best:
> res1 <- country_ranking(myTB,timeName="years", typeInd="lowBest")
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: country_ranking ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PATTERNS-CONV.Rmd’ using rmarkdown
--- finished re-building ‘PATTERNS-CONV.Rmd’

--- re-building ‘measuring-convergence.Rmd’ using rmarkdown
Quitting from lines 233-236 (measuring-convergence.Rmd) 
Error: processing vignette ‘measuring-convergence.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘measuring-convergence.Rmd’

SUMMARY: processing the following file failed:
  ‘measuring-convergence.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
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘coranking.Rmd’ using rmarkdown
Quitting from lines 63-67 (coranking.Rmd) 
Error: processing vignette ‘coranking.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘coranking.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'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
Specified C++11: please drop specification unless essential
checkRd: (-1) sgt.Rd:16: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) egde.Rd:26: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘corrr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.cor_df
> ### Title: Create a correlation matrix from a cor_df object
> ### Aliases: autoplot.cor_df
> 
> ### ** Examples
> 
> x <- correlate(mtcars)
Correlation computed with
• Method: 'pearson'
• Missing treated using: 'pairwise.complete.obs'
> 
> autoplot(x)
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: autoplot ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘databases.Rmd’ using rmarkdown
--- finished re-building ‘databases.Rmd’

--- re-building ‘using-corrr.Rmd’ using rmarkdown
Quitting from lines 97-101 (using-corrr.Rmd) 
Error: processing vignette ‘using-corrr.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘using-corrr.Rmd’

SUMMARY: processing the following file failed:
  ‘using-corrr.Rmd’

Error: Vignette re-building failed.
Execution halted
ggplot:
  function(data, mapping, ..., environment)
ggplot.cosinor.lm:
  function(object, x_str)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘covfefe_inauguration.txt’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘correlation-utils.Rmd’ using rmarkdown
--- finished re-building ‘correlation-utils.Rmd’

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

--- re-building ‘external-data.Rmd’ using rmarkdown
Quitting from lines 94-100 (external-data.Rmd) 
Error: processing vignette ‘external-data.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘external-data.Rmd’

--- re-building ‘multi-signals.Rmd’ using rmarkdown
--- finished re-building ‘multi-signals.Rmd’

--- re-building ‘plotting-signals.Rmd’ using rmarkdown
--- finished re-building ‘plotting-signals.Rmd’

SUMMARY: processing the following file failed:
  ‘external-data.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘covidmx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: casos
> ### Title: Casos de COVID-19 en Mexico
> ### Aliases: casos
> 
> ### ** Examples
> 
> 
> # Para el ejemplo usaremos los datos precargados (datosabiertos) pero tu puedes
> # correr el ejemplo descargando informacion mas reciente:
> datos_covid <- datosabiertos
> 
> # Casos por entidad
> datos_covid <- datos_covid |> casos()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: casos ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
merge_coverage:
  function(x)
merge_coverage.list:
  function(coverage_objs)

merge_coverage:
  function(x)
merge_coverage.character:
  function(files)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘multicolor’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  bcplm.c:84:22: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cplm.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Non-visible changes:
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
crps:
  function(y, ...)
crps.crch:
  function(object, newdata, average, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Running examples in ‘crimeutils-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: make_desc_stats_table
> ### Title: Create a descriptive statistics table from numeric variables
> ### Aliases: make_desc_stats_table
> 
> ### ** Examples
> 
> make_desc_stats_table(mtcars, columns = c("mpg", "disp", "wt", "cyl"))
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: make_desc_stats_table ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
Running examples in ‘crmReg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cellwiseheatmap
> ### Title: Heatmap of cellwise outliers
> ### Aliases: cellwiseheatmap
> 
> ### ** Examples
> 
> library(crmReg)
> data(topgear)
> 
> # fit Cellwise Robust M-regression:
> crmfit <- crm(formula = MPG ~ ., data = topgear)
 - Center and scale the data...
 - Initial MM regression...
 - Apply SPADIMO to find outlying cells...
Error in get.knnx(data = as.matrix(data[wr == 1, -outlvars]), query = matrix(modifiedrow[-outlvars],  : 
  DLL requires the use of native symbols
Calls: crm ... ldply -> llply -> structure -> lapply -> FUN -> get.knnx
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
Error(s) in re-building vignettes:
  ...
--- re-building ‘crosstable-install.Rmd’ using rmarkdown
--- finished re-building ‘crosstable-install.Rmd’

--- re-building ‘crosstable-report.Rmd’ using rmarkdown
Quitting from lines 51-90 (crosstable-report.Rmd) 
Error: processing vignette ‘crosstable-report.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘crosstable-report.Rmd’

--- re-building ‘crosstable-selection.Rmd’ using rmarkdown
--- finished re-building ‘crosstable-selection.Rmd’

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

SUMMARY: processing the following file failed:
  ‘crosstable-report.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘openVA’
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-crossva-and-openva.Rmd’ using rmarkdown
Quitting from lines 14-17 (using-crossva-and-openva.Rmd) 
Error: processing vignette ‘using-crossva-and-openva.Rmd’ failed with diagnostics:
there is no package called 'openVA'
--- failed re-building ‘using-crossva-and-openva.Rmd’

SUMMARY: processing the following file failed:
  ‘using-crossva-and-openva.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
autoplot:
  function(object, ...)
autoplot.NumericVariable:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.DatetimeVariable:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.CategoricalArrayVariable:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.CategoricalVariable:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.CrunchCubeCalculation:
  function(x, plot_type, ...)

autoplot:
  function(object, ...)
autoplot.tbl_crunch_cube:
  function(x, plot_type, measure)

autoplot:
  function(object, ...)
autoplot.CrunchCube:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.MultipleResponseVariable:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(CruzPlot)
  > 
  > test_check("CruzPlot")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 12 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-tidy.R:30:3'): tidy flow ───────────────────────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─... %>% slice(0) at test-tidy.R:30:2
    2. ├─dplyr::slice(., 0)
    3. ├─dplyr::select(., !!names(starwars))
    4. ├─dplyr::filter(., between(height, 0, 50))
    5. ├─dplyr::arrange(., name)
    6. ├─dplyr::full_join(., df2, by = "homeworld")
    7. └─dplyr:::full_join.data.frame(., df2, by = "homeworld")
    8.   └─dplyr:::join_mutate(...)
    9.     ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   10.     └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   11.       └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   12.         └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   13.           ├─base::withCallingHandlers(...)
   14.           └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 12 ]
  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
Error(s) in re-building vignettes:
  ...
--- re-building ‘csdata.Rmd’ using rmarkdown
Quitting from lines 33-123 (csdata.Rmd) 
Error: processing vignette ‘csdata.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘csdata.Rmd’

--- re-building ‘locations_norway.Rmd’ using rmarkdown
Quitting from lines 29-43 (locations_norway.Rmd) 
Error: processing vignette ‘locations_norway.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘locations_norway.Rmd’

--- re-building ‘population_norway.Rmd’ using rmarkdown
Quitting from lines 43-83 (population_norway.Rmd) 
Error: processing vignette ‘population_norway.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘population_norway.Rmd’

SUMMARY: processing the following files failed:
  ‘csdata.Rmd’ ‘locations_norway.Rmd’ ‘population_norway.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘CSHShydRology-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ch_tidyhydat_ECDE_meta
> ### Title: Creates an ECDE-like dataframe of metadata from 'tidyhydat'
> ### Aliases: ch_tidyhydat_ECDE_meta
> 
> ### ** Examples
> 
> # This example uses the built-in test database, by setting the hydat_path parameter
> # You will want to use it with your actual HYDAT database
> library(tidyhydat)
> # check for existence of test database
> test_db <- hy_test_db()
> if (file.exists(test_db)) {
+   stations <- c("05AA008", "08MF005", "05HD008")
+   hy_set_default_db(test_db)
+   result <- ch_tidyhydat_ECDE_meta(stations)
+   metadata <- result[[1]]
+   version <- result[[2]]
+   hy_set_default_db(NULL)    # Reset HYDAT database
+ }
HYDAT version: 1.0 Date: 2022-07-21
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: ch_tidyhydat_ECDE_meta ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ctmcd.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
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’
slice_head:
  function(.data, ..., n, prop, by)
slice_head.cubble_df:
  function(data, ...)

slice_tail:
  function(.data, ..., n, prop, by)
slice_tail.cubble_df:
  function(data, ...)

summarise:
  function(.data, ..., .by, .groups)
summarise.cubble_df:
  function(data, ...)

ungroup:
  function(x, ...)
ungroup.cubble_df:
  function(data, ...)

slice_max:
  function(.data, order_by, ..., n, prop, by, with_ties, na_rm)
slice_max.cubble_df:
  function(data, ...)

group_by:
  function(.data, ..., .add, .drop)
group_by.cubble_df:
  function(data, ...)

slice_min:
  function(.data, order_by, ..., n, prop, by, with_ties, na_rm)
slice_min.cubble_df:
  function(data, ...)

vec_cast.data.frame:
  function(x, to, ...)
vec_cast.data.frame.cubble_df:
  function(x, y, ...)

tbl_sum:
  function(x)
tbl_sum.cubble_df:
  function(data)

slice_sample:
  function(.data, ..., n, prop, by, weight_by, replace)
slice_sample.cubble_df:
  function(data, ...)

vec_cast:
  function(x, to, ..., x_arg, to_arg, call)
vec_cast.cubble_df.data.frame:
  function(x, y, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'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’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
Error(s) in re-building vignettes:
  ...
--- re-building ‘Creating_a_confusion_matrix.Rmd’ using rmarkdown
Quitting from lines 109-113 (Creating_a_confusion_matrix.Rmd) 
Error: processing vignette ‘Creating_a_confusion_matrix.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Creating_a_confusion_matrix.Rmd’

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

--- re-building ‘cross_validating_custom_functions.Rmd’ using rmarkdown
Quitting from lines 245-259 (cross_validating_custom_functions.Rmd) 
Error: processing vignette ‘cross_validating_custom_functions.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘cross_validating_custom_functions.Rmd’

--- re-building ‘evaluate_by_id.Rmd’ using rmarkdown
Quitting from lines 110-115 (evaluate_by_id.Rmd) 
Error: processing vignette ‘evaluate_by_id.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘evaluate_by_id.Rmd’

--- re-building ‘picking_the_number_of_folds_for_cross-validation.Rmd’ using rmarkdown
Quitting from lines 76-137 (picking_the_number_of_folds_for_cross-validation.Rmd) 
Error: processing vignette ‘picking_the_number_of_folds_for_cross-validation.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘picking_the_number_of_folds_for_cross-validation.Rmd’

SUMMARY: processing the following files failed:
  ‘Creating_a_confusion_matrix.Rmd’
  ‘cross_validating_custom_functions.Rmd’ ‘evaluate_by_id.Rmd’
  ‘picking_the_number_of_folds_for_cross-validation.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'gurobi', 'rcbc'
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
survfit:
  function(formula, ...)
survfit.cyclopsFit:
  function(cyclopsFit, type)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dspg.Rd:29: Escaped LaTeX specials: \^ \^
checkRd: (-1) dspgd2015.Rd:31: Escaped LaTeX specials: \^ \^
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [28s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(dail)
  > 
  > test_check("dail")
  No internet connection or data source broken.
  Downloading 2015 dataset.
  trying URL 'https://dadosabertos-download.cgu.gov.br/FalaBR/Arquivos_FalaBR_Filtrado/Arquivos_csv_2015.zip'
  Content type 'application/x-zip-compressed' length 45626938 bytes (43.5 MB)
  ==================================================
  downloaded 43.5 MB
  
  ℹ Using "','" as decimal and "'.'" as grouping mark. Use `read_delim()` for more control.
  Downloading 2016 dataset.
  trying URL 'https://dadosabertos-download.cgu.gov.br/FalaBR/Arquivos_FalaBR_Filtrado/Arquivos_csv_2016.zip'
  Content type 'application/x-zip-compressed' length 52106684 bytes (49.7 MB)
  ==================================================
  downloaded 49.7 MB
  
  ℹ Using "','" as decimal and "'.'" as grouping mark. Use `read_delim()` for more control.
  Ended query.
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-appeals.R:61:5'): test the arguments agency, year, answer and search ──
  nrow(df10) (`actual`) not equal to 5 (`expected`).
  
  `actual` is NULL
  `expected` is a double vector (5)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: ‘pca3d’
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘my new data set.rds’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘stubthat’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Datastream DWE - now decommissioned by Refinitiv
    CRAN
Found the following significant warnings:
  init.c:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:30:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:36:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:37:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/datastructures.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Running examples in ‘data.tree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.Node
> ### Title: Plot a graph, or get a graphviz dot representation of the tree
> ### Aliases: plot.Node ToDiagrammeRGraph SetNodeStyle SetEdgeStyle
> ###   SetGraphStyle GetDefaultTooltip
> 
> ### ** Examples
> 
> data(acme)
> SetGraphStyle(acme, rankdir = "TB")
> SetEdgeStyle(acme, arrowhead = "vee", color = "blue", penwidth = 2)
> #per default, Node style attributes will be inherited:
> SetNodeStyle(acme, style = "filled,rounded", shape = "box", fillcolor = "GreenYellow", 
+              fontname = "helvetica", tooltip = GetDefaultTooltip)
> SetNodeStyle(acme$IT, fillcolor = "LightBlue", penwidth = "5px")
> #inheritance can be avoided:
> SetNodeStyle(acme$Accounting, inherit = FALSE, fillcolor = "Thistle", 
+              fontcolor = "Firebrick", tooltip = "This is the accounting department")
> SetEdgeStyle(acme$Research$`New Labs`, 
+              color = "red", 
+              label = "Focus!", 
+              penwidth = 3, 
+              fontcolor = "red")
> #use Do to set style on specific nodes:
> Do(acme$leaves, function(node) SetNodeStyle(node, shape = "egg"))
> plot(acme)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: plot ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("dataverse")
  > 
  > if (!requireNamespace("yaml", quietly = TRUE)) {
  +   warning("The 'yaml' package must be present to test the dataverse package.")
  + } else if (!requireNamespace("checkmate", quietly = TRUE)) {
  +   warning("The 'checkmate' package must be present to test the dataverse package.")
  + } else {
  +   server  <- Sys.getenv("DATAVERSE_SERVER")
  +   key     <- Sys.getenv("DATAVERSE_KEY")
  + 
  +   if (server == "" | key == "") {
  +     config  <- yaml::read_yaml(system.file("constants.yml", package = "dataverse"))
  +     # config  <- yaml::read_yaml("inst/constants.yml")
  + 
  +     Sys.setenv("DATAVERSE_SERVER" = config$server)
  +     Sys.setenv("DATAVERSE_KEY"    = config$api_token)
  + 
  +     # To better identify the source of problems, check if the token is expired.
  +     #   This check *should* be unnecessary on CRAN, since not CRAN tests should
  +     #   try to access any server.
  +     if (Sys.getenv("NOT_CRAN") %in% c("", "true")) {
  +       if (as.Date(config$api_token_expiration) < Sys.Date()) {
  +         stop(
  +           "The API token expired on `",
  +           config$api_token_expiration,
  +           "`, so the tests would probably fail.  ",
  +           "Please regenerate a new token and update `inst/constants.yml`"
  +         )
  +       }
  +     }
  +     rm(config)
  +   }
  +   rm(server, key)
  + 
  +   message("Using Dataverse server `", Sys.getenv("DATAVERSE_SERVER"), "`.")
  + 
  +   test_check("dataverse")
  + }
  Error: The API token expired on `2023-03-10`, so the tests would probably fail.  Please regenerate a new token and update `inst/constants.yml`
  Execution halted
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘data_preparation.Rmd’ using rmarkdown
Quitting from lines 365-366 (data_preparation.Rmd) 
Error: processing vignette ‘data_preparation.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘data_preparation.Rmd’

--- re-building ‘how-to.Rmd’ using rmarkdown
--- finished re-building ‘how-to.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘DBERlibR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: demo_group_diff
> ### Title: Demographic Group Differences
> ### Aliases: demo_group_diff
> 
> ### ** Examples
> 
> # Run the following codes directly in the console panel. The plots
> # generated through the link above may be displaced depending on the screen
> # resolution.
> demo_group_diff(score_csv_data =
+         system.file("extdata", "data_treat_pre.csv", package = "DBERlibR"),
+         group_csv_data =
+         system.file("extdata", "demographic_data.csv", package = "DBERlibR"),
+         m_cutoff = 0.15,
+         group_name = "grade")


Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: demo_group_diff ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dberlibr-vignette.Rmd’ using rmarkdown
Quitting from lines 75-114 (dberlibr-vignette.Rmd) 
Error: processing vignette ‘dberlibr-vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘dberlibr-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'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
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [53s/79s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dbparser)
  > 
  > test_check("dbparser")
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 72 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-drugbank-parser.R:327:5'): parse DrugBank DB - zim file ────────
  <XMLParserErrorList/simpleError/error/condition>
  Error: 1: Start tag expected, '<' not found
  
  Backtrace:
      ▆
   1. ├─purrr (local) q_parser(system.file("extdata", small_molecule, package = "dbparser")) at test-drugbank-parser.R:327:4
   2. │ ├─purrr:::capture_output(.f(...))
   3. │ │ └─base::withCallingHandlers(code, warning = wHandler, message = mHandler)
   4. │ └─dbparser (local) .f(...)
   5. │   └─dbparser:::read_drugbank_xml_db(db_path = db_path)
   6. │     └─XML::xmlParse(db_path)
   7. └─XML (local) `<fn>`(`<chr>`)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 72 ]
  Error: Test failures
  Execution halted
sql_values_subquery:
  function(con, df, types, lvl, ...)
sql_values_subquery.PqConnection:
  function(con, df, types, lvl)

sql_values_subquery:
  function(con, df, types, lvl, ...)
sql_values_subquery.PostgreSQL:
  function(con, df, types, lvl)

sql_values_subquery:
  function(con, df, types, lvl, ...)
sql_values_subquery.Microsoft SQL Server:
  function(con, df, types, lvl)

db_write_table:
  function(con, table, types, values, temporary, ...)
db_write_table.PostgreSQLConnection:
  function(con, table, types, values, temporary, overwrite, ....)

sql_select:
  function(con, select, from, where, group_by, having, order_by, limit,
           distinct, ...)
sql_select.DBIConnection:
  function(con, select, from, where, group_by, having, window,
           order_by, limit, distinct, ..., subquery)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘dca.Rmd’ using rmarkdown
Quitting from lines 48-51 (dca.Rmd) 
Error: processing vignette ‘dca.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘dca.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  difeq.h:65:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  difeq.c:123:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dopri.h:208:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dopri.c:245:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dde.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘algorithm.Rmd’ using rmarkdown
--- finished re-building ‘algorithm.Rmd’

--- re-building ‘extend.Rmd’ using rmarkdown
Quitting from lines 205-213 (extend.Rmd) 
Error: processing vignette ‘extend.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘extend.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Quitting from lines 133-151 (overview.Rmd) 
Error: processing vignette ‘overview.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘overview.Rmd’

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

SUMMARY: processing the following files failed:
  ‘extend.Rmd’ ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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
Error(s) in re-building vignettes:
  ...
--- re-building ‘coord.Rmd’ using rmarkdown
--- finished re-building ‘coord.Rmd’

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

--- re-building ‘ggarrange2.Rmd’ using rmarkdown
Quitting from lines 55-64 (ggarrange2.Rmd) 
Error: processing vignette ‘ggarrange2.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘ggarrange2.Rmd’

--- re-building ‘phylogenies.Rmd’ using rmarkdown
Quitting from lines 37-42 (phylogenies.Rmd) 
Error: processing vignette ‘phylogenies.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘phylogenies.Rmd’

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

SUMMARY: processing the following files failed:
  ‘ggarrange2.Rmd’ ‘phylogenies.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘smd_table.docx’
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
ggplot:
  function(data, mapping, ..., environment)
ggplot.ggdend:
  function(data, segments, labels, nodes, horiz, theme, offset_labels,
           na.rm, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
Running examples in ‘denovolyzeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: denovolyze
> ### Title: Evaluates burden of _de novo_ variation against expectation
> ### Aliases: denovolyze denovolyzeByClass denovolyzeByGene
> 
> ### ** Examples
> 
> 
> ### denovolyze
> 
> denovolyze(genes=autismDeNovos$gene,
+            classes=autismDeNovos$class,
+            nsamples=1078)
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: denovolyze ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Documentation.Rmd’ using rmarkdown
Quitting from lines 82-83 (Documentation.Rmd) 
Error: processing vignette ‘Documentation.Rmd’ failed with diagnostics:
cannot open the connection to ‘https://raw.githubusercontent.com/mvankessel-EMC/DependencyReviewerWhitelists/main/dependencies.csv’
--- failed re-building ‘Documentation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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’
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  deque.h:73:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  constructor.c:43:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  deque.c:31:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dequer_native.c:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dequer.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
ggplot:
  function(data, mapping, ..., environment)
ggplot.ddplot:
  function(data, axis.location, ...)

ggplot:
  function(data, mapping, ..., environment)
ggplot.timeseries:
  function(data, edges, ...)

ggplot:
  function(data, mapping, ..., environment)
ggplot.histogram:
  function(data, spine, ...)

ggplot:
  function(data, mapping, ..., environment)
ggplot.barplot:
  function(data, spine, ...)

ggplot:
  function(data, mapping, ..., environment)
ggplot.parcoords:
  function(data, absoluteX, absoluteY, edges, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) geom_axis.Rd:10: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.N’ ‘.Nmiss’ ‘.Q1’ ‘.Q3’ ‘.factorN’ ‘.factorNmiss’ ‘.factorQ1’
  ‘.factorQ3’ ‘.factormax’ ‘.factormean’ ‘.factormedian’ ‘.factormin’
  ‘.factorsd’ ‘.max’ ‘.mean’ ‘.median’ ‘.min’ ‘.sd’
Error(s) in re-building vignettes:
  ...
--- re-building ‘a_usage_guide.Rmd’ using rmarkdown
Quitting from lines 71-72 (a_usage_guide.Rmd) 
Error: processing vignette ‘a_usage_guide.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘a_usage_guide.Rmd’

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

--- re-building ‘c_other_software_comparison.Rmd’ using rmarkdown
Quitting from lines 48-54 (c_other_software_comparison.Rmd) 
Error: processing vignette ‘c_other_software_comparison.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘c_other_software_comparison.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘a_usage_guide.Rmd’ ‘c_other_software_comparison.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘descstat.Rmd’ using rmarkdown
Quitting from lines 680-681 (descstat.Rmd) 
Error: processing vignette ‘descstat.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘descstat.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
Package which this enhances but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  void_dev.c:103:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  void_dev.c:182:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  void_dev.c:197:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/devoid.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘dextergui.Rmd’ using rmarkdown
Quitting from lines 157-159 (dextergui.Rmd) 
Error: processing vignette ‘dextergui.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘dextergui.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Running examples in ‘dexterMST-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_mst_test
> ### Title: Define a new multi stage test
> ### Aliases: create_mst_test
> 
> ### ** Examples
> 
> # extended example
> # we: 
> # 1) define an mst design
> # 2) simulate mst data
> # 3) create a project, enter scoring rules and define the MST test
> # 4) do an analysis
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> 
> items = data.frame(item_id=sprintf("item%02i",1:70), item_score=1, delta=sort(runif(70,-1,1)))
> 
> design = data.frame(item_id=sprintf("item%02i",1:70),
+                     module_id=rep(c('M4','M2','M5','M1','M6','M3', 'M7'),each=10))
> 
> routing_rules = routing_rules = mst_rules(
+  `124` = M1[0:5] --+ M2[0:10] --+ M4, 
+  `125` = M1[0:5] --+ M2[11:15] --+ M5,
+  `136` = M1[6:10] --+ M3[6:15] --+ M6,
+  `137` = M1[6:10] --+ M3[16:20] --+ M7)
> 
> theta = rnorm(3000)
> 
> dat = sim_mst(items, theta, design, routing_rules,'all')
> dat$test_id='sim_test'
> dat$response=dat$item_score
> 
> 
> scoring_rules = data.frame(
+   item_id = rep(items$item_id,2), 
+   item_score= rep(0:1,each=nrow(items)),
+   response= rep(0:1,each=nrow(items))) # dummy respons
>   
> 
> db = create_mst_project(":memory:")
> add_scoring_rules_mst(db, scoring_rules)
Added 140 scoring rules
> 
> create_mst_test(db,
+                 test_design = design,
+                 routing_rules = routing_rules,
+                 test_id = 'sim_test',
+                 routing = "all")
> 
> add_response_data_mst(db, dat)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: add_response_data_mst ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘multistage_fundamentals.Rmd’ using rmarkdown
Quitting from lines 263-266 (multistage_fundamentals.Rmd) 
Error: processing vignette ‘multistage_fundamentals.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘multistage_fundamentals.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Running examples in ‘dexter-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DIF
> ### Title: Exploratory test for Differential Item Functioning
> ### Aliases: DIF
> 
> ### ** Examples
> 
> db = start_new_project(verbAggrRules, ":memory:", person_properties=list(gender='unknown'))
> add_booklet(db, verbAggrData, "agg")
no column `person_id` provided, automatically generating unique person id's
$items
 [1] "S1DoCurse"   "S1DoScold"   "S1DoShout"   "S1WantCurse" "S1WantScold"
 [6] "S1WantShout" "S2DoCurse"   "S2DoScold"   "S2DoShout"   "S2WantCurse"
[11] "S2WantScold" "S2WantShout" "S3DoCurse"   "S3DoScold"   "S3DoShout"  
[16] "S3WantCurse" "S3WantScold" "S3WantShout" "S4DoCurse"   "S4DoScold"  
[21] "S4DoShout"   "S4WantCurse" "S4WantScold" "S4WantShout"

$person_properties
[1] "gender"

$columns_ignored
[1] "anger"

> dd = DIF(db,person_property="gender")
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: DIF ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DIF_vignette.Rmd’ using rmarkdown
Quitting from lines 42-44 (DIF_vignette.Rmd) 
Error: processing vignette ‘DIF_vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘DIF_vignette.Rmd’

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

--- re-building ‘Plausible_Values.Rmd’ using rmarkdown
Quitting from lines 90-93 (Plausible_Values.Rmd) 
Error: processing vignette ‘Plausible_Values.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Plausible_Values.Rmd’

--- re-building ‘Test_Individual_differences.Rmd’ using rmarkdown
Quitting from lines 62-66 (Test_Individual_differences.Rmd) 
Error: processing vignette ‘Test_Individual_differences.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Test_Individual_differences.Rmd’

--- re-building ‘dexter.Rmd’ using rmarkdown
Quitting from lines 143-145 (dexter.Rmd) 
Error: processing vignette ‘dexter.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘dexter.Rmd’

--- re-building ‘profile-plots.Rmd’ using rmarkdown
Quitting from lines 52-58 (profile-plots.Rmd) 
Error: processing vignette ‘profile-plots.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘profile-plots.Rmd’

SUMMARY: processing the following files failed:
  ‘DIF_vignette.Rmd’ ‘Plausible_Values.Rmd’
  ‘Test_Individual_differences.Rmd’ ‘dexter.Rmd’ ‘profile-plots.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘dfoliatR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: outbreak
> ### Title: Composite defoliation series to determine outbreak events
> ### Aliases: outbreak
> 
> ### ** Examples
> 
> data("dmj_defol")
> head(outbreak(dmj_defol))
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: head ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘testthat.R’ [8s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dfoliatR)
  > 
  > test_check("dfoliatR")
  [ FAIL 1 | WARN 7 | SKIP 3 | PASS 8 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-outbreak.R:6:1'): (code run outside of `test_that()`) ──────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─dfoliatR::outbreak(efk_defol) at test-outbreak.R:6:0
   2.   ├─base::`[<-`(...)
   3.   └─tibble:::`[<-.tbl_df`(...)
   4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   5.       └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   6.         ├─base::withCallingHandlers(...)
   7.         └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 7 | SKIP 3 | PASS 8 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) phihat.Rd:34: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [3s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # install.packages("testthat")
  > library(testthat)
  > # install.packages("forecast")
  > # library(forecast)
  > # install.packages("stats")
  > # library(stats)
  > # install.packages("future.apply")
  > # library(future.apply)
  > library(dhReg)
  Loading required package: forecast
  Loading required package: future.apply
  Loading required package: future
  > Data1 <- runif(runif(200,100,1000)) #To generate random number for example
  > Data_ts <- ts(Data1)
  > 
  > test_that("summary of Dynamic harmonic regression model", {
  +   M <- dhr(Data=Data_ts,XREG=NULL,Range=list(1:2,1),Frequency=c(24,168),Criteria="aicc")
  + })
  ── Error (???): summary of Dynamic harmonic regression model ───────────────────
  <defunctError/error/condition>
  Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
  Backtrace:
   1. dhReg::dhr(...)
   2. future::plan(future::multiprocess)
   3. future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
   4. future (local) warn_about_multiprocess(newStack)
   5. future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
   6. base (local) dfcn(msg = msg, package = .packageName)
  
  Error in reporter$stop_if_needed() : Test failed
  Calls: test_that -> <Anonymous>
  Execution halted
Running examples in ‘DiagrammeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_global_graph_attrs
> ### Title: Add one or more global graph attributes
> ### Aliases: add_global_graph_attrs
> 
> ### ** Examples
> 
> # Create a new graph with no
> # global graph attributes and
> # add a global graph attribute
> graph <-
+   create_graph(
+     attr_theme = NULL) %>%
+   add_global_graph_attrs(
+     attr = "overlap",
+     value = "true",
+     attr_type = "graph")
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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 ‘diffdf-basic.Rmd’ using rmarkdown
Quitting from lines 79-82 (diffdf-basic.Rmd) 
Error: processing vignette ‘diffdf-basic.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘diffdf-basic.Rmd’

SUMMARY: processing the following file failed:
  ‘diffdf-basic.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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
colnames:
  function(x, do.NULL, prefix)
colnames.MultivariateAnalysis:
  function(x)

rownames:
  function(x, do.NULL, prefix)
rownames.MultivariateAnalysis:
  function(x)

colnames:
  function(x, do.NULL, prefix)
colnames.MultivariateAnalysis:
  function(x)

rownames:
  function(x, do.NULL, prefix)
rownames.MultivariateAnalysis:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘dimRed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FruchtermanReingold-class
> ### Title: Fruchterman Reingold Graph Layout
> ### Aliases: FruchtermanReingold-class FruchtermanReingold
> 
> ### ** Examples
> 
> if(requireNamespace(c("igraph", "coRanking"), quietly = TRUE)) {
+ 
+ dat <- loadDataSet("Swiss Roll", n = 100)
+ emb <- embed(dat, "FruchtermanReingold")
+ plot(emb, type = "2vars")
+ 
+ }
Error in rankmatrix_C(dX) : DLL requires the use of native symbols
Calls: embed ... em_graph_layout -> construct_knn_graph -> <Anonymous> -> rankmatrix_C
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘INLA’
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building ‘disbayes.Rmd’ using rmarkdown
Quitting from lines 254-259 (disbayes.Rmd) 
Error: processing vignette ‘disbayes.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘disbayes.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Quitting from lines 139-156 (my-vignette.Rmd) 
Error: processing vignette ‘my-vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) sammy.Rd:51: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘discreteMTP’
Unknown package ‘discreteMTP’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) booter.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) ci.booted.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) pbooter.Rd:57: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
log_quantile:
  function(x, q, ...)
log_quantile.dist_na:
  function(x, p, ...)

log_quantile:
  function(x, q, ...)
log_quantile.distribution:
  function(x, p, ...)

log_quantile:
  function(x, q, ...)
log_quantile.dist_lognormal:
  function(x, p, ...)

log_quantile:
  function(x, q, ...)
log_quantile.dist_default:
  function(x, p, ...)

log_quantile:
  function(x, q, ...)
log_quantile.dist_normal:
  function(x, p, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rfftw.h:34:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rfftw.c:149:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  util.c:231:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.h:10:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/diversitree.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used Fortran compiler: ‘GNU Fortran (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Package suggested but not available for checking: ‘BOLTSSIRR’
'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
Specified C++11: please drop specification unless essential
Running examples in ‘dm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dm_add_fk
> ### Title: Add foreign keys
> ### Aliases: dm_add_fk
> 
> ### ** Examples
> 
> ## Don't show: 
> if (rlang::is_installed("nycflights13") && rlang::is_installed("DiagrammeR")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ nycflights_dm <- dm(
+   planes = nycflights13::planes,
+   flights = nycflights13::flights,
+   weather = nycflights13::weather
+ )
+ 
+ nycflights_dm %>%
+   dm_draw()
+ 
+ # Create foreign keys:
+ nycflights_dm %>%
+   dm_add_pk(planes, tailnum) %>%
+   dm_add_fk(flights, tailnum, planes) %>%
+   dm_add_pk(weather, c(origin, time_hour)) %>%
+   dm_add_fk(flights, c(origin, time_hour), weather) %>%
+   dm_draw()
+ 
+ # Keys can be checked during creation:
+ try(
+   nycflights_dm %>%
+     dm_add_pk(planes, tailnum) %>%
+     dm_add_fk(flights, tailnum, planes, check = TRUE)
+ )
+ ## Don't show: 
+ }) # examplesIf
> nycflights_dm <- dm(planes = nycflights13::planes, flights = nycflights13::flights, 
+     weather = nycflights13::weather)
> nycflights_dm %>% dm_draw()
> nycflights_dm %>% dm_add_pk(planes, tailnum) %>% dm_add_fk(flights, tailnum, 
+     planes) %>% dm_add_pk(weather, c(origin, time_hour)) %>% dm_add_fk(flights, c(origin, 
+     time_hour), weather) %>% dm_draw()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: <Anonymous> ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘DMwR2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: centralImputation
> ### Title: Fill in NA values with central statistics
> ### Aliases: centralImputation
> ### Keywords: models
> 
> ### ** Examples
> 
> data(algae,package="DMwR2")
> cleanAlgae <- centralImputation(algae)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: centralImputation ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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: \#
Error(s) in re-building vignettes:
  ...
--- re-building ‘dobin.Rmd’ using rmarkdown
Quitting from lines 209-212 (dobin.Rmd) 
Error: processing vignette ‘dobin.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘dobin.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) block.catlg.Rd:61: Escaped LaTeX specials: \^ \^
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
Found the following significant warnings:
  alive.c:200:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  alive.c:277:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/doRedis.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New features
Specified C++11: please drop specification unless essential
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
Running examples in ‘dotwhisker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dwplot
> ### Title: Dot-and-Whisker Plots of Regression Results
> ### Aliases: dwplot dw_plot
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> # Plot regression coefficients from a single model object
> data(mtcars)
> m1 <- lm(mpg ~ wt + cyl + disp, data = mtcars)
> dwplot(m1, vline = geom_vline(xintercept = 0, colour = "grey50", linetype = 2)) +
+     xlab("Coefficient")
> # using 99% confidence interval
> dwplot(m1, ci = .99)
> # Plot regression coefficients from multiple models
> m2 <- update(m1, . ~ . - disp)
> dwplot(list(full = m1, nodisp = m2))
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: dwplot ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dotwhisker-vignette.Rmd’ using rmarkdown
Quitting from lines 62-66 (dotwhisker-vignette.Rmd) 
Error: processing vignette ‘dotwhisker-vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘dotwhisker-vignette.Rmd’

--- re-building ‘kl2007_examples.Rmd’ using rmarkdown
--- finished re-building ‘kl2007_examples.Rmd’

SUMMARY: processing the following file failed:
  ‘dotwhisker-vignette.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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘dowser-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getTrees
> ### Title: Estimate lineage tree topologies, branch lengths, and internal
> ###   node states if desired
> ### Aliases: getTrees
> 
> ### ** Examples
> 
> data(ExampleClones)
> 
> trees <- getTrees(ExampleClones[10,])
> plotTrees(trees)[[1]]
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: plotTrees ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Building-Trees-Vignette.Rmd’ using rmarkdown
--- finished re-building ‘Building-Trees-Vignette.Rmd’

--- re-building ‘Discrete-Trait-Vignette.Rmd’ using rmarkdown
Quitting from lines 118-122 (Discrete-Trait-Vignette.Rmd) 
Error: processing vignette ‘Discrete-Trait-Vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Discrete-Trait-Vignette.Rmd’

--- re-building ‘Germlines-Vignette.Rmd’ using rmarkdown
--- finished re-building ‘Germlines-Vignette.Rmd’

--- re-building ‘Measurable-Evolution.Rmd’ using rmarkdown
Quitting from lines 129-135 (Measurable-Evolution.Rmd) 
Error: processing vignette ‘Measurable-Evolution.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Measurable-Evolution.Rmd’

--- re-building ‘Plotting-Trees-Vignette.Rmd’ using rmarkdown
Quitting from lines 40-53 (Plotting-Trees-Vignette.Rmd) 
Error: processing vignette ‘Plotting-Trees-Vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Plotting-Trees-Vignette.Rmd’

--- re-building ‘Quickstart-Vignette.Rmd’ using rmarkdown
Quitting from lines 34-56 (Quickstart-Vignette.Rmd) 
Error: processing vignette ‘Quickstart-Vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Quickstart-Vignette.Rmd’

--- re-building ‘Sequences-Vignette.Rmd’ using rmarkdown
Quitting from lines 38-54 (Sequences-Vignette.Rmd) 
Error: processing vignette ‘Sequences-Vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Sequences-Vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘Discrete-Trait-Vignette.Rmd’ ‘Measurable-Evolution.Rmd’
  ‘Plotting-Trees-Vignette.Rmd’ ‘Quickstart-Vignette.Rmd’
  ‘Sequences-Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘base.Rmd’ using rmarkdown
--- finished re-building ‘base.Rmd’

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

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

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

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

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

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

--- re-building ‘two-table.Rmd’ using rmarkdown
Quitting from lines 112-114 (two-table.Rmd) 
Error: processing vignette ‘two-table.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘two-table.Rmd’

--- re-building ‘window-functions.Rmd’ using rmarkdown
--- finished re-building ‘window-functions.Rmd’

SUMMARY: processing the following file failed:
  ‘two-table.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
'LazyData' is specified without a 'data' directory
checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gompertz.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) hatvalues.drc.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) llogistic.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) modelFit.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) weibull1.Rd:67: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
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 ‘i_end’ with type ‘arma::uvec’ {aka ‘arma::Col<unsigned int>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dsfa.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘dsBaseClient’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘DSWE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: KnnPCFit
> ### Title: KNN : Fit
> ### Aliases: KnnPCFit
> 
> ### ** Examples
> 
> 
> data = data1[c(1:100),]
> xCol = 2
> yCol = 7
> subsetSelection = FALSE
> 
> knn_model = KnnPCFit(data, xCol, yCol, subsetSelection)
Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols
Calls: KnnPCFit -> computeBestK -> knnx.index -> get.knnx
Execution halted
Running examples in ‘DTAT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: de.bioRxiv.240846
> ### Title: Simulated '3+3/PC' dose-titration study from bioRxiv paper no.
> ###   240846
> ### Aliases: de.bioRxiv.240846
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(de.bioRxiv.240846)
> # Demonstrate that the new S4 3+3/PC implementation reproduces the
> # simulated trial from the paper:
> set.seed(2017)
> CV <- 0.7; mean_mtd <- 1.0
> shape <- CV^-2; scale <- mean_mtd/shape
> trial <- new("DE", doses=0.25 * 1.4^(0:6),
+              MTDi=rgamma(24, shape=shape, scale=scale),
+              units="mg")
> trial <- titration(trial, periods=10)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: titration ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Designing-33PC.Rmd’ using rmarkdown
Quitting from lines 154-161 (Designing-33PC.Rmd) 
Error: processing vignette ‘Designing-33PC.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Designing-33PC.Rmd’

SUMMARY: processing the following file failed:
  ‘Designing-33PC.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
dt_has_computation:
  function(x)
dt_has_computation.dtplyr_step:
  function(x, needs_copy)

count:
  function(x, ..., wt, sort, name)
count.dtplyr_step:
  function(.data, ..., wt, sort, name)

pull:
  function(.data, var, name, ...)
pull.dtplyr_step:
  function(.data, var, name)

show_query:
  function(x, ...)
show_query.dtplyr_step:
  function(x)

sample_n:
  function(tbl, size, replace, weight, .env, ...)
sample_n.dtplyr_step:
  function(tbl, size, replace, weight)

sample_frac:
  function(tbl, size, replace, weight, .env, ...)
sample_frac.dtplyr_step:
  function(tbl, size, replace, weight)

group_modify:
  function(.data, .f, ..., .keep)
group_modify.dtplyr_step:
  function(.tbl, .f, ..., keep)

add_count:
  function(x, ..., wt, sort, name, .drop)
add_count.dtplyr_step:
  function(.data, ..., wt, sort, name)

tally:
  function(x, wt, sort, name)
tally.dtplyr_step:
  function(.data, wt, sort, name)

ungroup:
  function(x, ...)
ungroup.dtplyr_step:
  function(.data, ...)

group_map:
  function(.data, .f, ..., .keep)
group_map.dtplyr_step:
  function(.tbl, .f, ..., keep)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Running examples in ‘dvmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clean_glm
> ### Title: Create a Clean Summary Table from a glm Object
> ### Aliases: clean_glm
> 
> ### ** Examples
> 
> fit <- glm(mpg ~ wt + as.factor(cyl) + hp, data = mtcars)
> clean_glm(fit)
Waiting for profiling to be done...
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: clean_glm ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lle’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [146s/245s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dynfeature)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(purrr)
  
  Attaching package: 'purrr'
  
  The following object is masked from 'package:testthat':
  
      is_null
  
  > 
  > test_check("dynfeature")
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 17 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-calculate_feature_importance.R:159:3'): Testing calculate_cell_feature_importance ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─dynfeature::calculate_cell_feature_importance(trajectory) at test-calculate_feature_importance.R:159:2
    2. │ ├─... %>% select(-.data$waypoint_id)
    3. │ ├─dplyr::full_join(...)
    4. │ └─dplyr:::full_join.data.frame(...)
    5. │   └─dplyr:::join_mutate(...)
    6. │     ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    7. │     └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    8. │       └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9. │         └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   10. │           ├─base::withCallingHandlers(...)
   11. │           └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
   12. └─dplyr::select(., -.data$waypoint_id)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 17 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  arms.c:105:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  arms.c:902:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dynsurv.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Running ‘testthat.R’ [115s/173s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dynwrap)
  > 
  > test_check("dynwrap")
  [ FAIL 1 | WARN 50 | SKIP 3 | PASS 519 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  • dyndimre2d cannot be loaded (1)
  • empty test (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-milestone_convertors.R:74:3'): Testing convert_progressions_to_milestone_percentages ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─... %>% ... at test-milestone_convertors.R:74:2
    2. ├─dplyr::mutate(...)
    3. ├─dplyr::full_join(...)
    4. └─dplyr:::full_join.data.frame(...)
    5.   └─dplyr:::join_mutate(...)
    6.     ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,2]>`)
    7.     └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,2]>`)
    8.       └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9.         └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   10.           ├─base::withCallingHandlers(...)
   11.           └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 50 | SKIP 3 | PASS 519 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
'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
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.estimate:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'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
Running examples in ‘ebmc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sbag
> ### Title: Implementation of SMOTEBagging
> ### Aliases: sbag
> 
> ### ** Examples
> 
> data("iris")
> iris <- iris[1:70, ]
> iris$Species <- factor(iris$Species, levels = c("setosa", "versicolor"), labels = c("0", "1"))
> model1 <- sbag(Species ~ ., data = iris, size = 10, alg = "c50")
Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols
Calls: sbag -> <Anonymous> -> knearest -> <Anonymous> -> get.knnx
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Running examples in ‘eCAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: par.eCAR.Leroux
> ### Title: R wrapper that accesses C code to fit parametric Leroux CAR
> ###   spatial regression model that accounts for spatial confounding
> ### Aliases: par.eCAR.Leroux
> 
> ### ** Examples
> 
> 
> # Our R-package
> library(eCAR)
> 
> data(lipcancer)
> 
> 
> W <- lipcancer$neighborhood.Matrix
> M <- diag(apply(W,1,sum))
> R <- M-W
> e.dec <- eigen(R)
> e.val <- e.dec$values
> D.eigval = diag(e.val)
> 
> 
> Y <- lipcancer$data$observed
> X <- lipcancer$data$pcaff
> E <- lipcancer$data$expected
> 
> set.seed(101)
> fit1 <- par.eCAR.Leroux(y=Y, x=X, W=W, E=E, C=NULL, model="Poisson",
+                          draws=10000, burn=5000, thin=1, verbose=FALSE,
+                          joint_prior_lamx_lamz=FALSE, m=0, s2=4)
A Poisson model is being fit 
Error in par.eCAR.Leroux(y = Y, x = X, W = W, E = E, C = NULL, model = "Poisson",  : 
  DLL requires the use of native symbols
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [5s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(echarty)
  > 
  > test_check("echarty")
  
   series: 1 coords: 3 
  Reading layer `nc' from data source 
    `/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sf/shape/nc.shp' 
    using driver `ESRI Shapefile'
  Simple feature collection with 100 features and 14 fields
  Geometry type: MULTIPOLYGON
  Dimension:     XY
  Bounding box:  xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
  Geodetic CRS:  NAD27
  
   series: 108 coords: 2529 
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 110 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-other.R:106:3'): ec.data for treePC ────────────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─base::`[<-`(`*tmp*`, nrow(df) + 1, , value = `<list>`) at test-other.R:106:2
   2. └─tibble:::`[<-.tbl_df`(`*tmp*`, nrow(df) + 1, , value = `<list>`) at test-other.R:106:2
   3.   └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   4.     └─tibble:::tbl_subassign_row(xo, i, value, i_arg, value_arg, call)
   5.       ├─base::withCallingHandlers(...)
   6.       └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 110 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘ecocomDP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_taxa_shared_sites
> ### Title: Plot number of unique taxa shared across sites
> ### Aliases: plot_taxa_shared_sites
> 
> ### ** Examples
> 
> ## Not run: 
> ##D # Read a dataset of interest
> ##D dataset <- read_data("edi.193.5")
> ##D 
> ##D # Plot the dataset
> ##D plot_taxa_shared_sites(dataset)
> ##D 
> ##D # Flatten the dataset, manipulate, then plot
> ##D dataset %>% 
> ##D   flatten_data() %>% 
> ##D   dplyr::filter(lubridate::as_date(datetime) > "2003-07-01") %>%
> ##D   dplyr::filter(as.numeric(location_id) > 4) %>%
> ##D   plot_taxa_shared_sites()
> ##D   
> ##D # Plot from the observation table directly
> ##D plot_taxa_shared_sites(dataset$tables$observation)
> ## End(Not run)
> 
> # Plot the example dataset
> plot_taxa_shared_sites(ants_L1)
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: plot_taxa_shared_sites ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘convert.Rmd’ using rmarkdown
--- finished re-building ‘convert.Rmd’

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

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

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

--- re-building ‘use.Rmd’ using rmarkdown
Quitting from lines 226-250 (use.Rmd) 
Error: processing vignette ‘use.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘use.Rmd’

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

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building ‘EcoEnsemble.Rmd’ using rmarkdown
Quitting from lines 580-627 (EcoEnsemble.Rmd) 
Error: processing vignette ‘EcoEnsemble.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘EcoEnsemble.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  include/ecos_bb.h:161:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ecos_bb/ecos_bb_preproc.c:298:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ecos/include/ecos_bb.h:161:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ECOSolveR.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.edbl_unit:
  function(x)

tbl_sum:
  function(x)
tbl_sum.edbl_table:
  function(.data)

vec_ptype_full:
  function(x, ...)
vec_ptype_full.edbl_unit:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
glm:
  function(formula, family, data, weights, subset, na.action, start,
           etastart, mustart, offset, control, model, method, x, y,
           singular.ok, contrasts, ...)
glm.sdf:
  function(formula, family, data, weightVar, relevels, varMethod,
           jrrIMax, omittedLevels, defaultConditions, recode,
           returnNumberOfPSU, returnVarEstInputs)

lm:
  function(formula, data, subset, weights, na.action, method, model, x,
           y, qr, singular.ok, contrasts, offset, ...)
lm.sdf:
  function(formula, data, weightVar, relevels, varMethod, jrrIMax,
           omittedLevels, defaultConditions, recode,
           returnVarEstInputs, returnNumberOfPSU,
           standardizeWithSamplingVar, verbose)

glm:
  function(formula, family, data, weights, subset, na.action, start,
           etastart, mustart, offset, control, model, method, x, y,
           singular.ok, contrasts, ...)
glm.sdf:
  function(formula, family, data, weightVar, relevels, varMethod,
           jrrIMax, omittedLevels, defaultConditions, recode,
           returnNumberOfPSU, returnVarEstInputs)

lm:
  function(formula, data, subset, weights, na.action, method, model, x,
           y, qr, singular.ok, contrasts, offset, ...)
lm.sdf:
  function(formula, data, weightVar, relevels, varMethod, jrrIMax,
           omittedLevels, defaultConditions, recode,
           returnVarEstInputs, returnNumberOfPSU,
           standardizeWithSamplingVar, verbose)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [34s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(effectsize)
  > 
  > test_check("effectsize")
  [ FAIL 1 | WARN 0 | SKIP 12 | PASS 692 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (12)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-print.R:48:3'): print | effectsize table ───────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─testthat::expect_s3_class(print_html(d), "gt_tbl") at test-print.R:48:2
    2. │ └─testthat::quasi_label(enquo(object), arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─insight::print_html(d)
    5. └─effectsize:::print_html.effectsize_table(d)
    6.   └─insight::export_table(x_fmt, format = "html", ...)
    7.     └─insight:::.export_table(...)
    8.       └─insight:::.format_html_table(...)
    9.         └─gt::gt(final, groupname_col = group_by_columns)
   10.           └─gt::cols_align(data = data, align = "auto")
   11.             └─gt:::dt_boxhead_edit(data = data, var = column_names[i], column_align = align[i])
   12.               ├─base::`[[<-`(...)
   13.               └─tibble:::`[[<-.tbl_df`(...)
   14.                 └─tibble:::tbl_subassign(...)
   15.                   └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   16.                     ├─base::withCallingHandlers(...)
   17.                     └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 0 | SKIP 12 | PASS 692 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/eflm.Rcheck/00install.out’ for details.
'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’
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Running examples in ‘eHDPrep-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: assess_quality
> ### Title: Assess quality of a dataset
> ### Aliases: assess_quality
> 
> ### ** Examples
> 
> # general example
> data(example_data)
> res <- assess_quality(example_data, patient_id)
> 
> # example of internal consistency checks on more simple dataset
> # describing bean counts
> require(tibble)
Loading required package: tibble
> 
> # creating `data`:
> beans <- tibble::tibble(red_beans = 1:15,
+ blue_beans = 1:15,
+ total_beans = 1:15*2,
+ red_bean_summary = c(rep("few_beans",9), rep("many_beans",6)))
> 
> # creating `consis_tbl`
> bean_rules <- tibble::tribble(~varA, ~varB, ~lgl_test, ~varA_boundaries, ~varB_boundaries,
+ "red_beans", "blue_beans", "==", NA, NA,
+ "red_beans", "total_beans", "<=", NA,NA,
+ "red_beans", "red_bean_summary", NA, "1:9", "few_beans",
+ "red_beans", "red_bean_summary", NA, "10:15", "many_beans")
> 
> # add some inconsistencies
> beans[1, "red_bean_summary"] <- "many_beans"
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: [<- ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_eHDPrep.Rmd’ using rmarkdown
Quitting from lines 324-328 (Introduction_to_eHDPrep.Rmd) 
Error: processing vignette ‘Introduction_to_eHDPrep.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Introduction_to_eHDPrep.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  eicm.h:70:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/eicm.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Running examples in ‘ei.Datasets-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: merge_small_options
> ### Title: Merge small parties and/or candidates
> ### Aliases: merge_small_options
> 
> ### ** Examples
> 
> collapsed.tibble <- merge_small_options(x = ei_NZ_2020, min.party = 3, min.candidate = 5)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: merge_small_options ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Running examples in ‘eks-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tidyst_kde_local_test
> ### Title: Tidy and geospatial kernel density based local two-sample
> ###   comparison tests
> ### Aliases: tidy_kde_local_test st_kde_local_test
> ### Keywords: smooth
> 
> ### ** Examples
> 
> ## tidy local test between unsuccessful and successful grafts
> data(hsct, package="ks")
> hsct <- dplyr::as_tibble(hsct)
> hsct <- dplyr::filter(hsct, PE.Ly65Mac1 >0 & APC.CD45.2>0)
> hsct6 <- dplyr::filter(hsct, subject==6)   ## unsuccessful graft 
> hsct6 <- dplyr::select(hsct6, PE.Ly65Mac1, APC.CD45.2)
> hsct12 <- dplyr::filter(hsct, subject==12) ## successful graft 
> hsct12 <- dplyr::select(hsct12, PE.Ly65Mac1, APC.CD45.2)
> t1 <- tidy_kde_local_test(data1=hsct6, data2=hsct12)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: tidy_kde_local_test ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
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) 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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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:
  emd-rubner.c:143:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  emd-rubner.c:153:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  emd-rubner.c:640:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  emd-rubner.c:810:20: warning: ‘minI’ is used uninitialized [-Wuninitialized]
  emd-rubner.c:810:26: warning: ‘minJ’ is used uninitialized [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/emdist.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘osmar’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  utilities.h:7:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  utilities.c:14:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/emoa.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Math2:
  function(x, digits)
Math2.trackdata:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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)’
Error(s) in re-building vignettes:
  ...
--- re-building ‘ClassificationEg.Rmd’ using rmarkdown
Quitting from lines 100-197 (ClassificationEg.Rmd) 
Error: processing vignette ‘ClassificationEg.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘ClassificationEg.Rmd’

--- re-building ‘RegressionEg.Rmd’ using rmarkdown
Quitting from lines 82-142 (RegressionEg.Rmd) 
Error: processing vignette ‘RegressionEg.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘RegressionEg.Rmd’

SUMMARY: processing the following files failed:
  ‘ClassificationEg.Rmd’ ‘RegressionEg.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RStoolbox’
Found the following files/directories:
  ‘Environmental variables.csv’ ‘Inf.txt’ ‘List of species.csv’ ‘Mean
  overlap among taxa.csv’ ‘Overlap among taxa.csv’ ‘Pointsize.dat’
  ‘Polar coordinates.csv’
'LazyData' is specified without a 'data' directory
checkRd: (-1) calibrate.Rd:151: Escaped LaTeX specials: \&
checkRd: (-1) cdfCompareCensored.Rd:299: Escaped LaTeX specials: \&
checkRd: (-1) detectionLimitCalibrate.Rd:149: Escaped LaTeX specials: \&
checkRd: (-1) ecdfPlotCensored.Rd:169: Escaped LaTeX specials: \&
checkRd: (-1) egammaAltCensored.Rd:344: Escaped LaTeX specials: \&
checkRd: (-1) egammaCensored.Rd:340: Escaped LaTeX specials: \&
checkRd: (-1) elnormAltCensored.Rd:694: Escaped LaTeX specials: \&
checkRd: (-1) elnormCensored.Rd:270: Escaped LaTeX specials: \&
checkRd: (-1) enormCensored.Rd:852: Escaped LaTeX specials: \&
checkRd: (-1) enparCensored.Rd:343: Escaped LaTeX specials: \&
checkRd: (-1) enparCensored.Rd:358: Escaped LaTeX specials: \&
checkRd: (-1) epoisCensored.Rd:354: Escaped LaTeX specials: \&
checkRd: (-1) ppointsCensored.Rd:406: Escaped LaTeX specials: \&
checkRd: (-1) predIntGammaSimultaneous.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) predIntGammaSimultaneous.Rd:171: Escaped LaTeX specials: \&
checkRd: (-1) predIntLnormSimultaneous.Rd:136: Escaped LaTeX specials: \&
checkRd: (-1) predIntLnormSimultaneous.Rd:137: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneous.Rd:204: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneous.Rd:205: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneousK.Rd:277: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneousK.Rd:278: Escaped LaTeX specials: \&
checkRd: (-1) qqPlotCensored.Rd:261: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTest.Rd:276: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTestCensored.Rd:324: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTestCensored.Rd:331: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
Running examples in ‘eph-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculate_errors
> ### Title: Calculo del desvío estándar y el coeficiente de variación
> ### Aliases: calculate_errors
> 
> ### ** Examples
> 
> 
> tabla <- eph::toybase_individual_2016_03 %>%
+   eph::organize_labels() %>%
+   dplyr::filter(AGLOMERADO == 32) %>%
+   calculate_tabulates(x = "CH03",
+                          weights = "PONDERA",
+                          add.totals = "row")
Warning in set_val_lab.default(data[[curr_name]], curr_lab) :
  You are trying to put value labels on factor. It can lead to unexpected results. Factor will be converted to character.
Warning in set_val_lab.default(data[[curr_name]], curr_lab) :
  You are trying to put value labels on factor. It can lead to unexpected results. Factor will be converted to character.
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘testthat.R’ [4s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(eph)
  > 
  > test_check("eph")
  [ FAIL 1 | WARN 2 | SKIP 5 | PASS 11 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (5)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-calculate_tabulates.R:11:3'): totales por fila ─────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─... %>% as.data.frame(.) at test-calculate_tabulates.R:11:2
    2. ├─base::as.data.frame(.)
    3. ├─eph::calculate_tabulates(...)
    4. │ └─tabulado %>% janitor::adorn_totals("row")
    5. └─janitor::adorn_totals(., "row")
    6.   ├─base::`[<-`(`*tmp*`, 1, 1, value = `<chr>`)
    7.   └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, 1, value = `<chr>`)
    8.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9.       └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   10.         ├─base::withCallingHandlers(...)
   11.         └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 2 | SKIP 5 | PASS 11 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘eph.Rmd’ using rmarkdown
Quitting from lines 109-115 (eph.Rmd) 
Error: processing vignette ‘eph.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘eph.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
as.igraph:
  function(x, ...)
as.igraph.epicontacts:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘epicontacts-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_clusters
> ### Title: Assign cluster IDs to epicontacts data
> ### Aliases: get_clusters
> 
> ### ** Examples
> 
> if (require(outbreaks)) {
+ ## build data
+ x <- make_epicontacts(ebola_sim$linelist, ebola_sim$contacts,
+                        id = "case_id",
+                        to = "case_id",
+                        from = "infector",
+                        directed = TRUE)
+ 
+ 
+ ## add cluster membership and sizes to epicontacts 'linelist'
+ y <- get_clusters(x, output = "epicontacts")
+ y
+ 
+ ## return a data.frame with linelist member ids and cluster memberships as
+ ## factors
+ z <- get_clusters(x, output = "data.frame")
+ head(z)
+ 
+ }
Loading required package: outbreaks
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: get_clusters ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epicontacts.Rmd’ using rmarkdown
Quitting from lines 228-242 (epicontacts.Rmd) 
Error: processing vignette ‘epicontacts.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘epicontacts.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘epidict’
Specified C++11: please drop specification unless essential
AaJ:
  function(Lx, ...)
AaJ.Lexis:
  function(Lx, formula, timeScale)

addCov:
  function(Lx, ...)
addCov.Lexis:
  function(Lx, clin, timescale, exnam, tfc)

addDrug:
  function(Lx, ...)
addDrug.Lexis:
  function(Lx, pdat, amt, dpt, apt, method, maxt, grace, tnam, prefix,
           sepfix, verbose)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘addLexis.rnw’ using Sweave

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


Error: processing vignette ‘addLexis.rnw’ failed with diagnostics:
 chunk 16 
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols

--- failed re-building ‘addLexis.rnw’

--- re-building ‘crisk.rnw’ using Sweave
--- finished re-building ‘crisk.rnw’

--- re-building ‘flup.rnw’ using Sweave

Attaching package: ‘survival’

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

    Surv

--- finished re-building ‘flup.rnw’

--- re-building ‘simLexis.rnw’ using Sweave
--- finished re-building ‘simLexis.rnw’

--- re-building ‘yll.rnw’ using Sweave
Warning in d * offset :
  longer object length is not a multiple of shorter object length
Warning in d * offset :
  longer object length is not a multiple of shorter object length
Warning in d * offset :
  longer object length is not a multiple of shorter object length
--- finished re-building ‘yll.rnw’

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

Error: Vignette re-building failed.
Execution halted
'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
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘colors.Rmd’ using rmarkdown
--- finished re-building ‘colors.Rmd’

--- re-building ‘forecast-arima.Rmd’ using rmarkdown
Quitting from lines 44-45 (forecast-arima.Rmd) 
Error: processing vignette ‘forecast-arima.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘forecast-arima.Rmd’

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

--- re-building ‘lme4-lmer.Rmd’ using rmarkdown
--- finished re-building ‘lme4-lmer.Rmd’

--- re-building ‘plotting-integration.Rmd’ using rmarkdown
--- finished re-building ‘plotting-integration.Rmd’

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

--- re-building ‘usage-shiny.Rmd’ using rmarkdown
--- finished re-building ‘usage-shiny.Rmd’

SUMMARY: processing the following file failed:
  ‘forecast-arima.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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘eSDM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: overlay_sdm
> ### Title: Overlay SDM predictions onto base geometry
> ### Aliases: overlay_sdm
> 
> ### ** Examples
> 
> pol1.geom <- sf::st_sfc(
+   sf::st_polygon(list(rbind(c(1,1), c(3,1), c(3,3), c(1,3), c(1,1)))),
+   crs = 4326
+ )
> pol2.geom <- sf::st_sfc(
+   sf::st_polygon(list(rbind(c(0,0), c(2,0), c(2,2), c(0,2), c(0,0)))),
+   crs = 4326
+ )
> pol2.sf <- sf::st_sf(data.frame(Dens = 0.5), geometry = pol2.geom, crs = 4326)
> 
> overlay_sdm(pol1.geom, pol2.sf, 1, 25)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: overlay_sdm ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘testthat.R’ [3s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(eSDM)
  > 
  > test_check("eSDM")
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 38 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-overlay_sdm.R:25:3'): simple overlay ───────────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(overlay_sdm(sfc2, sf1, 1, 100), sf2) at test-overlay_sdm.R:25:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. └─eSDM::overlay_sdm(sfc2, sf1, 1, 100)
    5.   ├─base::`[<-`(...)
    6.   └─tibble:::`[<-.tbl_df`(...)
    7.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    8.       └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
    9.         ├─base::withCallingHandlers(...)
   10.         └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 38 ]
  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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) aic.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:64: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘evclass-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EkNNfit
> ### Title: Training of the EkNN classifier
> ### Aliases: EkNNfit
> 
> ### ** Examples
> 
> ## Iris dataset
> data(iris)
> x<-iris[,1:4]
> y<-iris[,5]
> fit<-EkNNfit(x,y,K=5)
Error in get.knn(x, k = K) : DLL requires the use of native symbols
Calls: EkNNfit -> get.knn
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Quitting from lines 45-49 (Introduction.Rmd) 
Error: processing vignette ‘Introduction.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘evclust_vignette.Rnw’ using Sweave

Error: processing vignette ‘evclust_vignette.Rnw’ failed with diagnostics:
 chunk 25 (label = EK-NNclus_S2) 
Error in get.knn(x, K) : DLL requires the use of native symbols

--- failed re-building 'evclust_vignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
Found the following significant warnings:
  Warning: replacing previous import ‘geiger::rescale’ by ‘phytools::rescale’ when loading ‘evobiR’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/evobiR.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘sample .nwk’
'LazyData' is specified without a 'data' directory
Running examples in ‘EvoPhylo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_treerates_sgn
> ### Title: Plot Bayesian evolutionary tree with rate thresholds for
> ###   selection mode
> ### Aliases: plot_treerates_sgn
> 
> ### ** Examples
> 
> # See vignette("rates-selection") for how to use this
> # function as part of an analysis pipeline
> 
> ## MrBayes example
> # Load example tree and posterior
> data("tree3p")
> data("posterior3p")
> 
> plot_treerates_sgn(
+   type = "MrBayes",
+   tree3p, posterior3p,          #MrBayes tree file with data for all partitions
+   trans = "none",
+   summary = "mean",             #MrBayes specific argument
+   drop.dummyextant = TRUE,      #MrBayes specific argument
+   clock = 1,                           #Show rates for clock partition 1
+   threshold = c("1 SD", "3 SD"),       #sets background rate threshold for selection mode
+   branch_size = 1.5, tip_size = 3,                          #sets size for tree elements
+   xlim = c(-450, -260), nbreaks = 8, geo_size = list(3, 3)) #sets limits and breaks for geoscale
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: plot_treerates_sgn ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘ExactData’
checkRd: (-1) exams2sakai.Rd:152: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Running examples in ‘exceldata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: importExcelData
> ### Title: Import Excel Data based on the specifications in a data
> ###   dictionary
> ### Aliases: importExcelData
> 
> ### ** Examples
> 
> exampleDataFile <- system.file("extdata", "exampleData.xlsx", package = "exceldata")
> import <- importExcelData(exampleDataFile,
+ dictionarySheet = 'DataDictionary',dataSheet = 'DataEntry')
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: importExcelData ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘iptools’ in Rd xrefs
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘ExNRuleEnsemble-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ExNRule
> ### Title: The Extended Neighbourhood Rule for k Nearest Neibour Ensemble
> ### Aliases: ExNRule
> ### Keywords: ExNRule Bootstraping Ensemble Classification
> 
> ### ** Examples
> 
> data(ILPD)
> 
> X <- ILPD[,-11]
> Y <- as.factor(ILPD[,11])
> 
> n <- nrow(ILPD)
> train <- sample(1:n, 0.7*n, replace = FALSE)
> 
> xtrain <- X[train,]
> xtest <- X[-train,]
> 
> ytrain <- Y[train]
> ytest <- Y[-train]
> 
> mymod <- ExNRule(xtrain, xtest, ytrain, k=3, r=500, p=round(sqrt(ncol(xtrain))))
Error in get.knnx(xtrain, xtest, k = 1) : 
  DLL requires the use of native symbols
Calls: ExNRule ... replicate -> sapply -> lapply -> FUN -> mod -> EKNN -> get.knnx
Execution halted
'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
GNU make is a SystemRequirements.
Running examples in ‘explore-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: data_dict_md
> ### Title: Create a data dictionary Markdown file
> ### Aliases: data_dict_md
> 
> ### ** Examples
> 
> # Data dictionary of a dataframe
> data_dict_md(iris,
+              title = "iris flower data set",
+              output_dir = tempdir())
> 
> # Data dictionary of a dataframe with additional description of variables
> description <- data.frame(
+                  variable = c("Species"),
+                  description = c("Species of Iris flower"))
> data_dict_md(iris,
+              title = "iris flower data set",
+              description = description,
+              output_dir = tempdir())
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: data_dict_md ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quanteda.textmodels’
Unknown package ‘quanteda.textmodels’ in Rd xrefs
Error(s) in re-building vignettes:
  ...
--- re-building ‘expp.Rmd’ using rmarkdown
Loading required package: expp
This is expp 1.2.5 For a tutorial type vignette("expp")

Attaching package: 'expp'

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

    as.data.frame

Quitting from lines 103-105 (expp.Rmd) 
Error: processing vignette ‘expp.Rmd’ failed with diagnostics:
unable to find an inherited method for function 'as.data.frame' for signature '"list"'
--- failed re-building ‘expp.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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’
autoplot_radf_distr:
  function(x, ...)
autoplot_radf_distr.sb_distr:
  function(object, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘exuber-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: datestamp
> ### Title: Date-stamping periods of mildly explosive behavior
> ### Aliases: datestamp datestamp.radf_obj
> 
> ### ** Examples
> 
> 
> rsim_data <- radf(sim_data)
> 
> ds_data <- datestamp(rsim_data)
Using `radf_crit` for `cv`.
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: datestamp ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(exuber)
  > 
  > test_check("exuber")
  Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
    DLL requires the use of native symbols
  Calls: test_check ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘exuber.Rmd’ using rmarkdown
Quitting from lines 55-60 (exuber.Rmd) 
Error: processing vignette ‘exuber.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘exuber.Rmd’

--- re-building ‘plotting.Rmd’ using rmarkdown
Quitting from lines 58-59 (plotting.Rmd) 
Error: processing vignette ‘plotting.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘plotting.Rmd’

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

SUMMARY: processing the following files failed:
  ‘exuber.Rmd’ ‘plotting.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘eyelinker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: %In%
> ### Title: Find if value belongs to a set of intervals
> ### Aliases: %In% %within%
> 
> ### ** Examples
> 
> start <- c(0, 1, 2)
> end <- c(.5, 1.3, 3)
> intv <- cbind(start, end) # The first interval is 0-0.5, second is 1-1.3, etc.
> c(0, .6, 1.5, 3) %In% intv
Error in .local(from, to, ...) : DLL requires the use of native symbols
Calls: %In% ... .local -> which_nearest -> which_nearest -> .local -> .Call
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basics.Rmd’ using rmarkdown
Quitting from lines 66-74 (basics.Rmd) 
Error: processing vignette ‘basics.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘basics.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
tidy:
  function(x, ...)
tidy.VAR:
  function(x)

tidy:
  function(x, ...)
tidy.AR:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
ungroup:
  function(x, ...)
ungroup.fbl_ts:
  function(.data, ...)

ungroup:
  function(x, ...)
ungroup.grouped_fbl:
  function(.data, ...)

fortify:
  function(model, data, ...)
fortify.fbl_ts:
  function(object, level)

key_data:
  function(.data)
key_data.mdl_df:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'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
Package suggested but not available for checking: ‘hier.part’
Unknown package ‘hier.part’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
autoplot:
  function(object, ...)
autoplot.fairadapt:
  function(x, when, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  chli.c:5:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fame.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
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’.
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  lu.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lu.c:828:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fastclime.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Found the following files/directories:
  ‘default5.eps’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘clusterCrit’
Error(s) in re-building vignettes:
  ...
--- re-building ‘fasthplus.Rmd’ using rmarkdown
Quitting from lines 298-300 (fasthplus.Rmd) 
Error: processing vignette ‘fasthplus.Rmd’ failed with diagnostics:
there is no package called 'clusterCrit'
--- failed re-building ‘fasthplus.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘coxKM’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) Scent.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) Traffic.Rd:44: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
Running examples in ‘fastrep-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: freq_tbl
> ### Title: freq_tbl
> ### Aliases: freq_tbl
> 
> ### ** Examples
> 
> iris %>%
+   fastrep::freq_tbl(Species) %>%
+   fastrep::tbl("You can combine this function too!")
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘testthat.R’ [3s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fastrep)
  
  Attaching package: 'fastrep'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > 
  > test_check("fastrep")
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 11 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-frequency.R:4:3'): sum total ───────────────────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-frequency.R:4:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─(function(x) x[4, 2])(iris %>% fastrep::freq_tbl(Species))
    5. ├─iris %>% fastrep::freq_tbl(Species) at test-frequency.R:5:35
    6. ├─fastrep::freq_tbl(., Species)
    7. │ └─dplyr::tibble(...)
    8. │   └─tibble:::tibble_quos(xs, .rows, .name_repair)
    9. │     └─rlang::eval_tidy(xs[[j]], mask)
   10. └─janitor::adorn_totals(dplyr::arrange(non_order, Species), "row")
   11.   ├─base::`[<-`(`*tmp*`, 1, 1, value = `<chr>`)
   12.   └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, 1, value = `<chr>`)
   13.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   14.       └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   15.         ├─base::withCallingHandlers(...)
   16.         └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 11 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Quitting from lines 55-57 (my-vignette.Rmd) 
Error: processing vignette ‘my-vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Rconnection.cc:282:52: warning: format ‘%p’ expects argument of type ‘void*’, but argument 3 has type ‘Rexp*’ [-Wformat=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘NNLM’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Running ‘testthat.R’ [37s/60s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fastTopics)
  > test_check("fastTopics")
  [ FAIL 1 | WARN 2 | SKIP 7 | PASS 233 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • NNLM cannot be loaded (1)
  • on_cran is TRUE (6)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_plots.R:79:3'): Test that other plotting functions work ────────
  Error in `FNN::get.knn(X, k)`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_plots.R:79:2
    2. │ └─base::withVisible(...elt(i))
    3. └─fastTopics::umap_plot(fit1, fill = "loading", verbose = FALSE)
    4.   └─fastTopics::umap_from_topics(fit, dims = 2, ...)
    5.     └─uwot::umap(...)
    6.       └─uwot:::uwot(...)
    7.         └─uwot:::data2set(...)
    8.           └─uwot:::x2set(...)
    9.             └─uwot:::x2nn(...)
   10.               └─uwot:::find_nn(...)
   11.                 └─uwot:::FNN_nn(X, k = k, include_self = include_self)
   12.                   └─FNN::get.knn(X, k)
  
  [ FAIL 1 | WARN 2 | SKIP 7 | PASS 233 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.Rprofile’
Specified C++11: please drop specification unless essential
Unexported objects imported by ‘:::’ calls:
  ‘fdapace:::GCVLwls1D1’ ‘fdapace:::GetSmoothedMeanCurve’
  ‘fdapace:::HandleNumericsAndNAN’ ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘vert.txt’
vec_arith:
  function(op, x, y, ...)
vec_arith.cf_lag:
  function(op, x, y)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘treesAll.txt’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New Stuff
'LazyData' is specified without a 'data' directory
checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘FFTrees_accuracy_statistics.Rmd’ using rmarkdown
--- finished re-building ‘FFTrees_accuracy_statistics.Rmd’

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

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

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

--- re-building ‘FFTrees_mytree.Rmd’ using rmarkdown
Quitting from lines 340-350 (FFTrees_mytree.Rmd) 
Error: processing vignette ‘FFTrees_mytree.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘FFTrees_mytree.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  f2c.h:185:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:186:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:187:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:188:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:189:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:190:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:191:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:192:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:193:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:194:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  f2c.h:195:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FGSG.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘MicrobeDS’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘finalfit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ff_permute
> ### Title: Permuate explanatory variables to produce multiple output tables
> ###   for common regression models
> ### Aliases: ff_permute finalfit_permute
> 
> ### ** Examples
> 
> explanatory_base = c("age.factor", "sex.factor")
> explanatory_permute = c("obstruct.factor", "perfor.factor", "node4.factor")
> 
> # Linear regression
> colon_s %>%
+   finalfit_permute("nodes", explanatory_base, explanatory_permute)
Note: dependent includes missing data. These are dropped.
Note: dependent includes missing data. These are dropped.
Note: dependent includes missing data. These are dropped.
Note: dependent includes missing data. These are dropped.
Note: dependent includes missing data. These are dropped.
Note: dependent includes missing data. These are dropped.
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘all_plots_examples.Rmd’ using rmarkdown
--- finished re-building ‘all_plots_examples.Rmd’

--- re-building ‘all_tables_examples.Rmd’ using rmarkdown
Quitting from lines 1376-1386 (all_tables_examples.Rmd) 
Error: processing vignette ‘all_tables_examples.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘all_tables_examples.Rmd’

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

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: ‘diveRsity’
Unknown package ‘diveRsity’ in Rd xrefs
Found the following files/directories:
  ‘AH_genepop.txt’ ‘AH_popname.txt’ ‘JSM_MS_freq.txt’
  ‘JSM_MS_genepop.txt’ ‘JSM_genepop_clipped_both.txt’
  ‘JSM_genepop_clipped_maf.txt’ ‘JSM_genepop_clipped_name.txt’
  ‘JSM_mtDNA_freq.txt’ ‘JSM_popname.txt’ ‘result_DJ.csv’
  ‘result_EBDJ.csv’ ‘result_EBFST.csv’ ‘result_EBFST_mtDNA.csv’
  ‘result_EBGstH.csv’ ‘result_GstH.csv’ ‘result_GstN.csv’
  ‘result_GstNC.csv’ ‘result_thetaWCpair.csv’
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'benchden', 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fk_regression.Rd:32: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'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: \&
levelplot:
  function(x, data, ...)
levelplot.JPtest:
  function(JPobj, what, rotate, plot, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘FPCEnv’
GNU make is a SystemRequirements.
Running ‘test_base.R’ [54s/88s]
Running the tests in ‘tests/test_base.R’ failed.
Complete output:
  > test_partial <- TRUE
  > 
  > if (test_partial)
  +   options(
  +     warnPartialMatchArgs = TRUE,
  +     warnPartialMatchAttr = TRUE,
  +     warnPartialMatchDollar = TRUE
  +   )
  > 
  > if (require("testthat")){
  +     test_check("flexsurv")
  + }
  Loading required package: testthat
  Loading required package: flexsurv
  Loading required package: survival
  [ FAIL 1 | WARN 66 | SKIP 0 | PASS 581 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_fmsm.R:34:3'): simfinal_fmsm ───────────────────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─flexsurv::simfinal_fmsm(weim) at test_fmsm.R:34:2
    2. │ └─flexsurv:::simfinal_fmsm_noci(...)
    3. │   └─... %>% ...
    4. ├─dplyr::full_join(., probsu, by = c("state", "quantity", "val"))
    5. ├─dplyr::full_join(., means, by = c("state", "quantity", "val"))
    6. └─dplyr:::full_join.data.frame(...)
    7.   └─dplyr:::join_mutate(...)
    8.     ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,3]>`)
    9.     └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,3]>`)
   10.       └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   11.         └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   12.           ├─base::withCallingHandlers(...)
   13.           └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 66 | SKIP 0 | PASS 581 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘standsurv.Rmd’ using rmarkdown
--- finished re-building ‘standsurv.Rmd’

--- re-building ‘flexsurv.Rnw’ using knitr
--- finished re-building ‘flexsurv.Rnw’

--- re-building ‘multistate.Rnw’ using knitr
Quitting from lines 584-586 (multistate.Rnw) 
Error: processing vignette ‘multistate.Rnw’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘multistate.Rnw’

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

--- re-building ‘flexsurv-examples.Rnw’ using Sweave
Loading required package: survival
Forming integrated rmst function...
Forming integrated mean function...
Loading required package: TH.data
Loading required package: MASS

Attaching package: ‘TH.data’

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

    geyser

--- finished re-building ‘flexsurv-examples.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Running examples in ‘flightplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arrange_path
> ### Title: Helper function to reorder the values in the input flight
> ###   dataframe.
> ### Aliases: arrange_path
> 
> ### ** Examples
> 
> arrange_path(sample_trips)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: arrange_path ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘flowTraceR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert_all_levels
> ### Title: Conversion of software specific levels
> ### Aliases: convert_all_levels
> 
> ### ** Examples
> 
> # Load libraries
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(stringr)
> library(tidyr)
> library(comprehenr)
> library(tibble)
> 
> # MaxQuant example data
> evidence <- tibble::tibble(
+   "Modified sequence" = c("_AACLLPK_",
+    "_ALTDM(Oxidation (M))PQM(Oxidation (M))R_",
+    "ALTDM(Dummy_Modification)PQMK"),
+   Charge = c(2,2,3),
+   "Protein group IDs" = c("26", "86;17", "86;17")
+ )
> 
> proteingroups <- tibble::tibble(
+ "Protein IDs" = c("A0A075B6P5;P01615;A0A087WW87;P01614;A0A075B6S6", "P02671", "P02672"),
+ id = c(26, 86, 17)
+ )
> 
> # Conversion
> convert_all_levels(
+  input_df = evidence,
+  input_MQ_pg = proteingroups,
+  software = "MaxQuant"
+ )
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: convert_all_levels ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Example_RT_distribution.Rmd’ using rmarkdown
--- finished re-building ‘Example_RT_distribution.Rmd’

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

--- re-building ‘Workflow.Rmd’ using rmarkdown
Quitting from lines 75-79 (Workflow.Rmd) 
Error: processing vignette ‘Workflow.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘flux.CH4.txt’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) pseudoOptim.Rd:27: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘FNN-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: KL.dist
> ### Title: Kullback-Leibler Divergence
> ### Aliases: KL.dist KLx.dist
> ### Keywords: manip
> 
> ### ** Examples
> 
>     set.seed(1000)
>     X<- rexp(10000, rate=0.2)
>     Y<- rexp(10000, rate=0.4)
>     
>     KL.dist(X, Y, k=5)                 
Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols
Calls: KL.dist ... KL.divergence -> colMeans -> is.data.frame -> knnx.dist -> get.knnx
Execution halted
'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
Running examples in ‘foqat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dm8n_np
> ### Title: Calculate daily maximum-8-hour ozone without printing plot
> ### Aliases: dm8n_np
> 
> ### ** Examples
> 
> dm8n_np(aqi,colio=6)
Joining with `by = join_by(temp_datetime)`
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: dm8n_np ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Air_Quality.Rmd’ using rmarkdown
Quitting from lines 46-48 (Air_Quality.Rmd) 
Error: processing vignette ‘Air_Quality.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Air_Quality.Rmd’

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

--- re-building ‘Basic_Functions.Rmd’ using rmarkdown
Quitting from lines 46-48 (Basic_Functions.Rmd) 
Error: processing vignette ‘Basic_Functions.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Basic_Functions.Rmd’

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

--- re-building ‘Plot_Functions.Rmd’ using rmarkdown
Quitting from lines 34-44 (Plot_Functions.Rmd) 
Error: processing vignette ‘Plot_Functions.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Plot_Functions.Rmd’

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

SUMMARY: processing the following files failed:
  ‘Air_Quality.Rmd’ ‘Basic_Functions.Rmd’ ‘Plot_Functions.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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
Package suggested but not available for checking: ‘RandomFields’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘freqparcoord-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: freqparcoord
> ### Title: Frequency-based parallel coordinates.
> ### Aliases: freqparcoord
> 
> ### ** Examples
> 
> # baseball player data courtesy of UCLA Stat. Dept., www.socr.ucla.edu
> data(mlb)
> 
> # plot baseball data, broken down by position category (infield,
> # outfield, etc.); plot the 5 higest-density values in each group
> freqparcoord(mlb,5,4:6,7,method="maxdens")
Error in get.knn(data, k = k) : DLL requires the use of native symbols
Calls: freqparcoord -> smoothz -> sf -> get.knn
Execution halted
Running examples in ‘freqtables-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: freq_format
> ### Title: Format freq_table Output for Publication and Dissemination
> ### Aliases: freq_format
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(freqtables)
> 
> data(mtcars)
> 
> # One-way frequency tables with defaults
> 
> mtcars %>%
+   freq_table(am) %>%
+   freq_format(
+     recipe = "percent (lcl - ucl)",
+     name = "percent_95",
+     digits = 2
+   ) %>%
+   select(var, cat, percent_95)
  var cat            percent_95
1  am   0 59.38 (40.94 - 75.50)
2  am   1 40.62 (24.50 - 59.06)
> #> # A tibble: 2 x 3
> #>   var   cat   percent_95
> #>   <chr> <chr> <chr>
> #> 1 am    0     59.38 (40.94 - 75.50)
> #> 2 am    1     40.62 (24.50 - 59.06)
> 
> # Two-way frequency tables with defaults
> 
> mtcars %>%
+   freq_table(am, cyl) %>%
+     freq_format(
+     recipe = "percent_row (lcl_row - ucl_row)",
+     name = "percent_95",
+     digits = 2
+   ) %>%
+   select(1:4, percent_95)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘testthat.R’ [6s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(freqtables)
  > 
  > test_check("freqtables")
  [ FAIL 1 | WARN 11 | SKIP 0 | PASS 74 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-freq_format.R:59:1'): (code run outside of `test_that()`) ──────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─mtcars %>% freq_table(am, vs) %>% ... at test-freq_format.R:59:0
   2. └─freqtables::freq_format(...)
   3.   ├─base::`[<-`(`*tmp*`, i, name, value = `<chr>`)
   4.   └─tibble:::`[<-.tbl_df`(`*tmp*`, i, name, value = `<chr>`)
   5.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   6.       └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   7.         ├─base::withCallingHandlers(...)
   8.         └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 11 | SKIP 0 | PASS 74 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) CatalogueAccessors.Rd:249: Escaped LaTeX specials: \^ \^
checkRd: (-1) FrF2.Rd:574: Escaped LaTeX specials: \^
checkRd: (-1) FrF2.Rd:629: Escaped LaTeX specials: \^ \^
checkRd: (-1) IAPlot.Rd:87: Escaped LaTeX specials: \$
checkRd: (-1) block.Rd:121: Escaped LaTeX specials: \^
checkRd: (-1) block.Rd:150: Escaped LaTeX specials: \^ \^
checkRd: (-1) blockpick.Rd:114: Escaped LaTeX specials: \^ \^
Packages suggested but not available for checking: 'dggrids', 'INLA'
Unknown package ‘frm’ in Rd xrefs
Unknown package ‘frm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
Found the following significant warnings:
  init.c:20:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FSelectorRcpp.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Warning in formals(fun) : argument is not a function
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘format_columns.Rmd’ using rmarkdown
Quitting from lines 170-178 (format_columns.Rmd) 
Error: processing vignette ‘format_columns.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘format_columns.Rmd’

--- re-building ‘group-rows.Rmd’ using rmarkdown
--- finished re-building ‘group-rows.Rmd’

--- re-building ‘transform-headers.Rmd’ using rmarkdown
--- finished re-building ‘transform-headers.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'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
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
semi_join:
  function(x, y, by, copy, ...)
semi_join.tbl_funnel:
  function(.data, ...)

anti_join:
  function(x, y, by, copy, ...)
anti_join.tbl_funnel:
  function(.data, ...)

inner_join:
  function(x, y, by, copy, suffix, ..., keep)
inner_join.tbl_funnel:
  function(.data, ...)

left_join:
  function(x, y, by, copy, suffix, ..., keep)
left_join.tbl_funnel:
  function(.data, ...)

right_join:
  function(x, y, by, copy, suffix, ..., keep)
right_join.tbl_funnel:
  function(.data, ...)
See section ‘Generic functions and methods’ 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
Running examples in ‘fusen-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: inflate
> ### Title: Inflate Rmd to package
> ### Aliases: inflate
> 
> ### ** Examples
> 
> # Create a new project
> dummypackage <- tempfile("dummypackage")
> dir.create(dummypackage)
> 
> # {fusen} steps
> dev_file <- add_flat_template(template = "full", pkg = dummypackage, overwrite = TRUE)
Created file .here in /home/hornik/tmp/scratch/RtmpV8OLmm/dummypackage2e108b1c0b4f78 . Please start a new R session in the new project directory.
> flat_file <- dev_file[grepl("flat", dev_file)]
> fill_description(pkg = dummypackage, fields = list(Title = "Dummy Package"))
[1] "/home/hornik/tmp/scratch/RtmpV8OLmm/dummypackage2e108b1c0b4f78/DESCRIPTION"
> inflate(
+   pkg = dummypackage, flat_file = flat_file,
+   vignette_name = "Exploration of my Data", check = FALSE
+ )
✔ Setting active project to '/home/hornik/tmp/scratch/RtmpV8OLmm/dummypackage2e108b1c0b4f78'
ℹ Loading dummypackage2e108b1c0b4f78
Writing 'NAMESPACE'
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: inflate ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
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 files/directories:
  ‘completeTrial_byArm_eventPriorRateC3=0.001_eventPriorRateT1=0_eventPriorRateT2=0_eventPriorWt=0.5.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.2.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.4.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.6.RData’
  ‘completeTrial_pooled_eventPriorRate=0.001_eventPriorWt=0.5.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.2.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.4.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.6.RData’
  ‘rcdf_byArm_arm=T1_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03.pdf’
  ‘rcdf_pooled_eventPriorRate=0.06.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘fuzzyjoin-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genome_join
> ### Title: Join two tables based on overlapping genomic intervals: both a
> ### Aliases: genome_join genome_inner_join genome_left_join
> ###   genome_right_join genome_full_join genome_semi_join genome_anti_join
> 
> ### ** Examples
> 
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> 
> x1 <- tibble(id1 = 1:4,
+              chromosome = c("chr1", "chr1", "chr2", "chr2"),
+              start = c(100, 200, 300, 400),
+              end = c(150, 250, 350, 450))
> 
> x2 <- tibble(id2 = 1:4,
+              chromosome = c("chr1", "chr2", "chr2", "chr1"),
+              start = c(140, 210, 400, 300),
+              end = c(160, 240, 415, 320))
> 
> if (requireNamespace("IRanges", quietly = TRUE)) {
+   # note that the the third and fourth items don't join (even though
+   # 300-350 and 300-320 overlap) since the chromosomes are different:
+   genome_inner_join(x1, x2, by = c("chromosome", "start", "end"))
+ 
+   # other functions:
+   genome_full_join(x1, x2, by = c("chromosome", "start", "end"))
+   genome_left_join(x1, x2, by = c("chromosome", "start", "end"))
+   genome_right_join(x1, x2, by = c("chromosome", "start", "end"))
+   genome_semi_join(x1, x2, by = c("chromosome", "start", "end"))
+   genome_anti_join(x1, x2, by = c("chromosome", "start", "end"))
+ }
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: genome_full_join ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  gamlr.c:87:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gamlr.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LGAclaims.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:36: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) meyer.Rd:11: Escaped LaTeX specials: \&
Specified C++14: please drop specification unless essential
‘:::’ call which should be ‘::’: ‘graphics:::grid’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘checkdata.csv’ ‘gbmforest.sas’
Specified C++11: please drop specification unless essential
'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’
Package suggested but not available for checking: ‘paleofire’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘analyze.Rmd’ using rmarkdown
--- finished re-building ‘analyze.Rmd’

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

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

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

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

--- re-building ‘noise.Rmd’ using rmarkdown
Quitting from lines 88-120 (noise.Rmd) 
Error: processing vignette ‘noise.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘noise.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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’.
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [243s/365s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(GDPuc)
  > 
  > test_check("GDPuc")
  [ FAIL 2 | WARN 5 | SKIP 0 | PASS 5260 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-replace_NAs.R:21:3'): convertGDP replace missing conversion factors ──
  Error in `vectbl_assign(x[[j]], cells[[j]], value)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─GDPuc::convertGDP(...) at test-replace_NAs.R:21:2
   2.   ├─base::`[<-`(`*tmp*`, is.na(x), value = `<dbl>`)
   3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, is.na(x), value = `<dbl>`)
   4.     └─tibble:::tbl_subassign_matrix(x, j, value, j_arg, substitute(value))
   5.       ├─base::withCallingHandlers(...)
   6.       └─tibble:::vectbl_assign(x[[j]], cells[[j]], value)
  ── Error ('test-replace_NAs.R:143:3'): convertGDP replace_NAs = c('linear', 'no_conversion') ──
  Error in `vectbl_assign(x[[j]], cells[[j]], value)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─GDPuc::convertGDP(...) at test-replace_NAs.R:143:2
   2.   ├─base::`[<-`(`*tmp*`, is.na(x), value = `<dbl>`)
   3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, is.na(x), value = `<dbl>`)
   4.     └─tibble:::tbl_subassign_matrix(x, j, value, j_arg, substitute(value))
   5.       ├─base::withCallingHandlers(...)
   6.       └─tibble:::vectbl_assign(x[[j]], cells[[j]], value)
  
  [ FAIL 2 | WARN 5 | SKIP 0 | PASS 5260 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘handle_NAs.Rmd’ using rmarkdown
Quitting from lines 66-82 (handle_NAs.Rmd) 
Error: processing vignette ‘handle_NAs.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘handle_NAs.Rmd’

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) plot_summary.Rd:14: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Running examples in ‘genBaRcode-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotClusterGgTree
> ### Title: Plotting a Cluster ggTree
> ### Aliases: plotClusterGgTree
> 
> ### ** Examples
> 
> data(BC_dat)
> plotClusterGgTree(BC_dat, tree_est = "UPGMA", type = "circular")
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: plotClusterGgTree ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘genBaRcode_GUI_Vignette.Rmd’ using rmarkdown
--- finished re-building ‘genBaRcode_GUI_Vignette.Rmd’

--- re-building ‘genBaRcode_Vignette.Rmd’ using rmarkdown
Quitting from lines 692-696 (genBaRcode_Vignette.Rmd) 
Error: processing vignette ‘genBaRcode_Vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘genBaRcode_Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Specified C++11: please drop specification unless essential
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  arms.c:99:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  arms.c:900:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/genscore.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘geofi_datasets.Rmd’ using rmarkdown
--- finished re-building ‘geofi_datasets.Rmd’

--- re-building ‘geofi_joining_attribute_data.Rmd’ using rmarkdown
Quitting from lines 105-113 (geofi_joining_attribute_data.Rmd) 
Error: processing vignette ‘geofi_joining_attribute_data.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘geofi_joining_attribute_data.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Running examples in ‘geomander-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: suggest_component_connection
> ### Title: Suggest Connections for Disconnected Groups
> ### Aliases: suggest_component_connection
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> data(checkerboard)
> checkerboard <- checkerboard %>% filter(i != 1, j != 1)
> adj <- adjacency(checkerboard)
Warning: Planarizing skipped. `x` missing CRS.
> suggest_component_connection(checkerboard, adj)
Warning: Planarizing skipped. `x` missing CRS.
Warning: Planarizing skipped. `x` missing CRS.
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: suggest_component_connection ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) getopt.Rd:60: Escaped LaTeX specials: \#
Package suggested but not available for checking: ‘argon2’
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggalignment.Rmd’ using rmarkdown
Quitting from lines 27-33 (ggalignment.Rmd) 
Error: processing vignette ‘ggalignment.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘ggalignment.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [312s/495s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > if (requireNamespace('testthat', quietly = TRUE)) {
  +   library(testthat)
  +   library(GGally)
  + 
  +   test_check("GGally")
  + }
  Loading required package: ggplot2
  Registered S3 method overwritten by 'GGally':
    method from   
    +.gg   ggplot2
  # weights:  24 (14 variable)
  initial  value 50552.644463 
  iter  10 value 45030.930814
  iter  20 value 43102.145726
  final  value 43101.422966 
  converged
  [ FAIL 1 | WARN 1347 | SKIP 3 | PASS 626 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ggparcoord.R:218:3'): missing ──────────────────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─base::`[<-`(`*tmp*`, 3, 1, value = `<lgl>`) at test-ggparcoord.R:218:2
   2. └─tibble:::`[<-.tbl_df`(`*tmp*`, 3, 1, value = `<lgl>`) at test-ggparcoord.R:218:2
   3.   └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   4.     └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   5.       ├─base::withCallingHandlers(...)
   6.       └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 1347 | SKIP 3 | PASS 626 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggasym-corrr.Rmd’ using rmarkdown
Quitting from lines 55-67 (ggasym-corrr.Rmd) 
Error: processing vignette ‘ggasym-corrr.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘ggasym-corrr.Rmd’

--- re-building ‘ggasym-stats.Rmd’ using rmarkdown
--- finished re-building ‘ggasym-stats.Rmd’

SUMMARY: processing the following file failed:
  ‘ggasym-corrr.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ungroup:
  function(x, ...)
ungroup.tidy_dagitty:
  function(.data, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘ggdag-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Pathways
> ### Title: Find Open Paths Between Variables
> ### Aliases: Pathways dag_paths ggdag_paths ggdag_paths_fan
> 
> ### ** Examples
> 
> confounder_triangle(x_y_associated = TRUE) %>%
+   dag_paths(from = "x", to = "y")
Error in `map()`:
ℹ In index: 1.
Caused by error in `vectbl_assign()`:
! DLL requires the use of native symbols
Backtrace:
     ▆
  1. ├─confounder_triangle(x_y_associated = TRUE) %>% ...
  2. ├─ggdag::dag_paths(., from = "x", to = "y")
  3. │ └─pathways %>% ...
  4. ├─purrr::map_df(...)
  5. │ └─purrr::map(.x, .f, ...)
  6. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  7. │     ├─purrr:::with_indexed_errors(...)
  8. │     │ └─base::withCallingHandlers(...)
  9. │     ├─purrr:::call_with_cleanup(...)
 10. │     └─ggdag (local) .f(.x[[i]], ...)
 11. │       ├─base::`[<-`(`*tmp*`, path_df$name == vars[[2]], "path", value = `<chr>`)
 12. │       └─tibble:::`[<-.tbl_df`(...)
 13. │         └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 14. │           └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
 15. │             ├─base::withCallingHandlers(...)
 16. │             └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
 17. └─base::.handleSimpleError(...)
 18.   └─purrr (local) h(simpleError(msg, call))
 19.     └─cli::cli_abort(...)
 20.       └─rlang::abort(...)
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bias-structures.Rmd’ using rmarkdown
--- finished re-building ‘bias-structures.Rmd’

--- re-building ‘intro-to-dags.Rmd’ using rmarkdown
Quitting from lines 119-120 (intro-to-dags.Rmd) 
Error: processing vignette ‘intro-to-dags.Rmd’ failed with diagnostics:
ℹ In index: 1.
Caused by error in `vectbl_assign()`:
! DLL requires the use of native symbols
--- failed re-building ‘intro-to-dags.Rmd’

--- re-building ‘intro-to-ggdag.Rmd’ using rmarkdown
Quitting from lines 84-92 (intro-to-ggdag.Rmd) 
Error: processing vignette ‘intro-to-ggdag.Rmd’ failed with diagnostics:
ℹ In index: 1.
Caused by error in `vectbl_assign()`:
! DLL requires the use of native symbols
--- failed re-building ‘intro-to-ggdag.Rmd’

SUMMARY: processing the following files failed:
  ‘intro-to-dags.Rmd’ ‘intro-to-ggdag.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘ggESDA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Cardiological
> ### Title: Cardiological data example
> ### Aliases: Cardiological
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Cardiological)
> ggInterval_index(Cardiological, aes(x = Syst))
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'tbl_subset_col' not found
Calls: ggInterval_index ... as.data.frame -> [ -> [.symbolic_tbl -> getFromNamespace -> get
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggESDA.Rmd’ using rmarkdown
Quitting from lines 47-57 (ggESDA.Rmd) 
Error: processing vignette ‘ggESDA.Rmd’ failed with diagnostics:
object ‘tbl_subset_col’ not found
--- failed re-building ‘ggESDA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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
grid.draw:
  function(x, recording)
grid.draw.ggmultiplot:
  function(plot)
See section ‘Generic functions and methods’ 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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
makeContext:
  function(x)
makeContext.interactive_dotstack_grob:
  function(x, recording)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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: \&
‘:::’ call which should be ‘::’: ‘scales:::censor’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ‘:::’ call: ‘productplots:::bound’
  See the note in ?`:::` about the use of this operator.
Running examples in ‘ggmotif-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: motifLocation
> ### Title: Extract and Visualize Motif Information from MEME Software
> ### Aliases: motifLocation
> 
> ### ** Examples
> 
> # without phylogenetic tree
> filepath <- system.file("examples", "meme.xml", package = "ggmotif")
> motif_extract <- getMotifFromMEME(data = filepath, format="xml")
> motif_plot <- motifLocation(data = motif_extract)
> 
> # with phylogenetic tree
> filepath <- system.file("examples", "meme.xml", package = "ggmotif")
> treepath <- system.file("examples", "ara.nwk", package="ggmotif")
> motif_extract <- getMotifFromMEME(data = filepath, format="xml")
> motif_plot <- motifLocation(data = motif_extract, tree = treepath)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: motifLocation ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggmotif.Rmd’ using rmarkdown
Quitting from lines 133-141 (ggmotif.Rmd) 
Error: processing vignette ‘ggmotif.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘ggmotif.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'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
sample_frac:
  function(tbl, size, replace, weight, .env, ...)
sample_frac.periodic_df:
  function(tbl, size, replace, weight, .env)

fortify:
  function(model, data, ...)
fortify.periodic_df:
  function(data, ...)

sample_n:
  function(tbl, size, replace, weight, .env, ...)
sample_n.periodic_df:
  function(tbl, size, replace, weight, .env)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
makeContext:
  function(x)
makeContext.dotstackGrob:
  function(x, recording)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    History
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'nlmixr', 'lixoftConnectors'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Running examples in ‘ggsurvfit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_quantile
> ### Title: Add Quantile Annotation
> ### Aliases: add_quantile
> 
> ### ** Examples
> 
> survfit2(Surv(time, status) ~ sex, data = df_lung) %>%
+   ggsurvfit() +
+   add_quantile(linetype = 2) +
+   scale_ggsurvfit()
> 
> survfit2(Surv(time, status) ~ 1, data = df_lung) %>%
+   ggsurvfit() +
+   add_quantile(linetype = 2) +
+   add_quantile(y_value = 0.9, linetype = 3) +
+   scale_ggsurvfit()
> 
> survfit2(Surv(time, status) ~ sex, data = df_lung) %>%
+   ggsurvfit() +
+   add_quantile(linetype = 2, y_value = NULL, x_value = 10) +
+   scale_ggsurvfit()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: +.gg ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘themes.Rmd’ using rmarkdown
Quitting from lines 62-68 (themes.Rmd) 
Error: processing vignette ‘themes.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘themes.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Unknown package ‘IC2’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘gitdown-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nest_commits_by_pattern
> ### Title: Nest all commits by each pattern found in the commit messages
> ### Aliases: nest_commits_by_pattern
> 
> ### ** Examples
> 
> repo <- fake_repo()
> nest_commits_by_pattern(repo)
# A tibble: 6 × 6
  pattern.type pattern.content   pattern.title     pattern_nu…¹ link_…² data    
  <chr>        <chr>             <chr>                    <dbl> <chr>   <list>  
1 Issues       #1                #1                           1 issues… <tibble>
2 Issues       #2                #2                           2 issues… <tibble>
3 Issues       #12               #12                         12 issues… <tibble>
4 Issues       #32               #32                         32 issues… <tibble>
5 Issues       #145              #145                       145 issues… <tibble>
6 Issues       No related issues No related issues           NA issues… <tibble>
# … with abbreviated variable names ¹​pattern_numeric, ²​link_pattern
> 
> # With table of correspondence
> pattern.table <- data.frame(
+   number = c("#2", "#1", "#1000"),
+   title = c("#2 A second issue to illustrate a blog post",
+             "#1 An example of issue",
+             "#1000 issue with no commit"))
>  nest_commits_by_pattern(
+   repo,
+   pattern.table = pattern.table,
+   pattern = c("Tickets" = "ticket[[:digit:]]+", "Issues" = "#[[:digit:]]+"))
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: nest_commits_by_pattern ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mlr3proba’
'LazyData' is specified without a 'data' directory
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
VarCorr:
  function(x, sigma, ...)
VarCorr.lmertree:
  function(object, ...)

VarCorr:
  function(x, sigma, ...)
VarCorr.glmertree:
  function(object, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
isLMM:
  function(x, ...)
isLMM.glmmTMB:
  function(object)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++14: please drop specification unless essential
'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: \&
Running examples in ‘globalKinhom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Kglobal
> ### Title: (cross) K functions with a global intensity reweighting
> ### Aliases: Kglobal Kcross.global
> 
> ### ** Examples
> 
> rho <- funxy(function(x,y) 80*(1+x), owin())
> X <- rpoispp(rho)
> K <- Kglobal(X)
Error in rhorho(u, v, hx * r, hy * r, X, sigma = sigma, cutoff = cutoff,  : 
  DLL requires the use of native symbols
Calls: Kglobal -> expectedPairs_iso_kernloo -> rhorho
Execution halted
Running ‘tests.R’ [3s/4s]
Running the tests in ‘tests/tests.R’ failed.
Complete output:
  > require(globalKinhom)
  Loading required package: globalKinhom
  Loading required package: spatstat.random
  Loading required package: spatstat.data
  Loading required package: spatstat.geom
  spatstat.geom 3.1-0
  spatstat.random 3.1-4
  Loading required package: spatstat.explore
  Loading required package: nlme
  spatstat.explore 3.1-0
  > 
  > set.seed(49)
  > 
  > lambda <- funxy(function(x,y) 200*(.5*exp(-((x-.5)^2 + (y-.5)^2)*2) + .5), owin())
  > 
  > X <- rpoispp(lambda)
  > Y <- rpoispp(lambda)
  >  
  > g.truef <- pcfglobal(X,lambda=lambda)
  > c.truef <- pcfcross.global(X, Y,lambdaX=lambda, lambdaY=lambda)
  > K.truef <- Kglobal(X,lambda=lambda)
  > Kcross.truef <- Kcross.global(X, Y,lambdaX=lambda, lambdaY=lambda)
  > print("done with estimates using true gamma")
  [1] "done with estimates using true gamma"
  > 
  > g <- pcfglobal(X, interpolate=TRUE)
  Error in rhorho(u, v, hx * r, hy * r, X, sigma = sigma, cutoff = cutoff,  : 
    DLL requires the use of native symbols
  Calls: pcfglobal -> expectedPairs_iso_kernloo -> rhorho
  Execution halted
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘GraphicalMultiplicity.Rmd’ using rmarkdown
Quitting from lines 193-206 (GraphicalMultiplicity.Rmd) 
Error: processing vignette ‘GraphicalMultiplicity.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘GraphicalMultiplicity.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Running examples in ‘gmGeostats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ana
> ### Title: Flow anamorphosis transform Compute a transformation that
> ###   gaussianizes a certain data set
> ### Aliases: ana
> 
> ### ** Examples
> 
> library(compositions)
Welcome to compositions, a package for compositional data analysis.
Find an intro with "? compositions"


Attaching package: ‘compositions’

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

    logratioVariogram

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

    anova, cor, cov, dist, var

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

    %*%, norm, scale, scale.default

> data("jura", package="gstat")
> Y = acomp(jura.pred[,c(10,12,13)])
> plot(Y)
> anafun = ana(Y)
> class(anafun)
[1] "function"
> z = anafun(Y)
Error in anaForward(x, Y, sigma0 = sigma0, sigma1 = sigma1, sphere = sphere,  : 
  DLL requires the use of native symbols
Calls: anafun -> anaForward
Execution halted
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Running examples in ‘GNE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GNE.nseq
> ### Title: Non smooth equation reformulation of the GNE problem.
> ### Aliases: GNE.nseq
> ### Keywords: nonlinear optimize
> 
> ### ** Examples
> 
> 
> 
> #-------------------------------------------------------------------------------
> # (1) Example 5 of von Facchinei et al. (2007)
> #-------------------------------------------------------------------------------
> 
> dimx <- c(1, 1)
> #Gr_x_j O_i(x)
> grobj <- function(x, i, j)
+ {
+ 	if(i == 1)
+ 		res <- c(2*(x[1]-1), 0)
+ 	if(i == 2)
+ 		res <- c(0, 2*(x[2]-1/2))
+ 	res[j]	
+ }
> #Gr_x_k Gr_x_j O_i(x)
> heobj <- function(x, i, j, k)
+ 	2 * (i == j && j == k)
> 
> dimlam <- c(1, 1)
> #constraint function g_i(x)
> g <- function(x, i)
+ 	sum(x[1:2]) - 1
> #Gr_x_j g_i(x)
> grg <- function(x, i, j)
+ 	1
> #Gr_x_k Gr_x_j g_i(x)
> heg <- function(x, i, j, k)
+ 	0
> 
> 
> 
> #true value is (3/4, 1/4, 1/2, 1/2)
> 
> z0 <- rep(0, sum(dimx)+sum(dimlam))
> 
> funSSR(z0, dimx, dimlam, grobj=grobj, constr=g, grconstr=grg, compl=phiFB, echo=FALSE)
Error in funSSR(z0, dimx, dimlam, grobj = grobj, constr = g, grconstr = grg,  : 
  DLL requires the use of native symbols
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GNE-howto.Rnw’ using Sweave
Loading required package: alabama
Loading required package: numDeriv
Loading required package: nleqslv
Loading required package: BB
Loading required package: SQUAREM

Error: processing vignette ‘GNE-howto.Rnw’ failed with diagnostics:
 chunk 6 (label = singjac) 
Error in jacSSR(z0, dimx, dimlam, heobj = heobj, myarg, constr = g, grconstr = grg,  : 
  DLL requires the use of native symbols

--- failed re-building ‘GNE-howto.Rnw’

SUMMARY: processing the following file failed:
  ‘GNE-howto.Rnw’

Error: Vignette re-building failed.
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
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unexported objects imported by ‘:::’ calls:
  ‘gargle:::secret_can_decrypt’ ‘gargle:::secret_read’
  See the note in ?`:::` about the use of this operator.
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.drive_id:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [10s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(googledrive)
  > 
  > test_check("googledrive")
  Test file naming scheme:
  • foo-TEST-drive_something
  • foo-TEST-drive_something-hornik-64ec6cd8
  [ FAIL 1 | WARN 0 | SKIP 122 | PASS 254 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • No Drive token (81)
  • On CRAN (41)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-compat-dplyr.R:231:3'): right_join() restores to the type of first input ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─googledrive:::expect_bare_tibble(dplyr::right_join(y, x, by = "id")) at test-compat-dplyr.R:231:2
    2. │ └─testthat::expect_s3_class(...) at tests/testthat/helper.R:53:3
    3. │   └─testthat::quasi_label(enquo(object), arg = "object")
    4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
    5. ├─dplyr::right_join(y, x, by = "id")
    6. └─dplyr:::right_join.data.frame(y, x, by = "id")
    7.   └─dplyr:::join_mutate(...)
    8.     ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    9.     └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   10.       └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   11.         └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   12.           ├─base::withCallingHandlers(...)
   13.           └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 0 | SKIP 122 | PASS 254 ]
  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
Specified C++14: please drop specification unless essential
sfNEmpty:
  function(sf)
sfNEmpty.sfc:
  function(sfc)

sfGeometryType:
  function(sf)
sfGeometryType.sfc:
  function(sfc)

sfEpsg:
  function(sf)
sfEpsg.sfc:
  function(sfc)

sfPrecision:
  function(sf)
sfPrecision.sfc:
  function(sfc)

sfProj:
  function(sf)
sfProj.sfc:
  function(sfc)

sfDimension:
  function(sf)
sfDimension.sfc:
  function(sfc)

sfGeometryAttributes:
  function(sf)
sfGeometryAttributes.sfc:
  function(sfc)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unexported objects imported by ‘:::’ calls:
  ‘gargle:::secret_can_decrypt’ ‘gargle:::secret_read’
  See the note in ?`:::` about the use of this operator.
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.sheets_id:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
.access_result:
  function(res, accessor)
.access_result.character:
  function(js, accessor)

.access_result:
  function(res, accessor)
.access_result.list:
  function(lst, accessor)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘gvcm.cat’
Specified C++11: please drop specification unless essential
Unknown package ‘gvcm.cat’ in Rd xrefs
Specified C++11: please drop specification unless essential
Running examples in ‘GpGp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: L_mult
> ### Title: Multiply approximate Cholesky by a vector
> ### Aliases: L_mult
> 
> ### ** Examples
> 
> n <- 2000
> locs <- matrix( runif(2*n), n, 2 )
> covparms <- c(2, 0.2, 0.75, 0.1)
> ord <- order_maxmin(locs)
Error in FNN::get.knn(locs, k = m) : 
  DLL requires the use of native symbols
Calls: order_maxmin -> <Anonymous>
Execution halted
'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: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘GPvecchia-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculate_posterior_VL
> ### Title: Vecchia Laplace extension of GPVecchia for non-Gaussian data
> ### Aliases: calculate_posterior_VL
> 
> ### ** Examples
> 
> z=rnorm(10); locs=matrix(1:10,ncol=1); vecchia.approx=vecchia_specify(locs,m=5)
Error in FNN::get.knnx(locs[data_inds, , drop = FALSE], locs[query_inds,  : 
  DLL requires the use of native symbols
Calls: vecchia_specify -> findOrderedNN_kdtree2 -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GPvecchia_vignette.Rmd’ using rmarkdown
Quitting from lines 85-86 (GPvecchia_vignette.Rmd) 
Error: processing vignette ‘GPvecchia_vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘GPvecchia_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘GPvecchia_vignette.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
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quanteda.textmodels’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) mlGraphicalVAR.Rd:79: Escaped LaTeX specials: \~
Specified C++11: please drop specification unless essential
Running examples in ‘graphlayouts-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: layout_umap
> ### Title: UMAP graph layouts
> ### Aliases: layout_umap layout_with_umap layout_igraph_umap
> 
> ### ** Examples
> 
> library(igraph)

Attaching package: ‘igraph’

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

    decompose, spectrum

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

    union

> 
> g <- sample_islands(10,20,0.6,10)
> xy <- layout_with_umap(g,min_dist = 0.5)
Error in FNN::get.knn(X, k) : DLL requires the use of native symbols
Calls: layout_with_umap ... data2set -> x2set -> x2nn -> find_nn -> FNN_nn -> <Anonymous>
Execution halted
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
Found the following significant warnings:
  Offset.c:3:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  omp_diagnose.c:5:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  omp_diagnose.c:18:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/grattan.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Found the following significant warnings:
  init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gRc.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
pot:
  function(obj, ...)
pot.BlockGraph:
  function(newg, newd, ...)

h_edges:
  function(obj, ...)
h_edges.RootDepSet:
  function(obj, g)

createObj:
  function(obj, ...)
createObj.HRMBG:
  function(obj, data)

resetParams:
  function(obj, ...)
resetParams.MLE1params:
  function(obj, cnames)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘grobblR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alter_column_names
> ### Title: Alter column names of a grob matrix
> ### Aliases: alter_column_names
> 
> ### ** Examples
> 
> 
> data.frame(var1 = c(5, 14, 6, 10), var2 = c(3, 30, 17, 7)) %>%
+   grob_matrix() %>% 
+   alter_column_names(c('COLUMN NAME')) %>%
+   view_grob()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘grob_layout.Rmd’ using rmarkdown
--- finished re-building ‘grob_layout.Rmd’

--- re-building ‘grob_matrix.Rmd’ using rmarkdown
Quitting from lines 191-200 (grob_matrix.Rmd) 
Error: processing vignette ‘grob_matrix.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘grob_matrix.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
ungroup:
  function(x, ...)
ungroup.igrouped_df:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘GroupTest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AYP
> ### Title: AYP of California, 2013
> ### Aliases: AYP
> ### Keywords: AYP
> 
> ### ** Examples
> 
> data(AYP)
> 
> AYP.result <- GT.wrapper( AYP, alpha=0.1, eta=alpha, pi1.ini=0.5,
+ pi2.1.ini=0.05, L=2, muL.ini=c(3,-2), sigmaL.ini=c(1,1),
+ cL.ini=c(0.5,0.5), DELTA=0.0001, sigma.KNOWN=TRUE )
[1] 0.6613213
[1] 0.119436
[1] 0.1516792
[1] 0.1151573
[1] 0.08519608
[1] 0.06364048
[1] 0.04822856
[1] 0.03708593
[1] 0.02891132
[1] 0.02282343
[1] 0.01822341
[1] 0.01530005
[1] 0.01354042
[1] 0.01194355
[1] 0.01050693
[1] 0.009223337
[1] 0.008082644
[1] 0.007073244
[1] 0.006183023
[1] 0.0054
[1] 0.004712724
[1] 0.004110512
[1] 0.003583553
[1] 0.003122947
[1] 0.002720695
[1] 0.002369656
[1] 0.002063486
[1] 0.001796576
[1] 0.00156398
[1] 0.001361349
[1] 0.001184867
[1] 0.001031192
[1] 0.0008973965
[1] 0.0007809259
[1] 0.0006795473
[1] 0.0005913127
[1] 0.0005145234
[1] 0.0004476984
[1] 0.0003895473
[1] 0.000338946
[1] 0.0002949155
[1] 0.0002566033
[1] 0.0002232674
[1] 0.0001942617
[1] 0.000169024
[1] 0.000147065
[1] 0.0001279588
[1] 0.0001113348
[1] 9.687066e-05
Error in dnorm(TestStatistic[[g]]$X) : 
  Non-numeric argument to mathematical function
Calls: GT.wrapper -> GT.localfdr -> dnorm
Execution halted
Malformed Description field: should contain one or more complete sentences.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘p1_20up-vs-p2_25up_in_str1.txt’ ‘p1_20up-vs-p2_25up_in_str2.txt’
  ‘p2_25up-vs-p1_20up_in_str1.txt’ ‘p2_25up-vs-p1_20up_in_str2.txt’
  ‘s0_20up.txt’ ‘s0_30up.txt’ ‘s0_f2up.txt’ ‘strs.vec_01mx.txt’
  ‘strs.vec_02mx.txt’ ‘strs.vec_03mx.txt’ ‘strs.vec_04mx.txt’
  ‘strs.vec_05mx.txt’ ‘strs.vec_06mx.txt’ ‘strs.vec_30up.txt’
  ‘strs.vec_50up.txt’ ‘strs.vec_f2up.txt’ ‘uni_p1_20up-p2_25up.txt’
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘FMD mag discontinuities_disc.png’ ‘FMD mag
  discontinuities_disc1.res’ ‘FMD mag discontinuities_disc2.res’
  ‘IDYLLWILD_bvmed.png’ ‘IDYLLWILD_fig.png’ ‘Schuster's
  diagram_schu.png’ ‘hour.res’
Error(s) in re-building vignettes:
  ...
--- re-building ‘GraphicalMultiplicity.Rmd’ using rmarkdown
--- finished re-building ‘GraphicalMultiplicity.Rmd’

--- re-building ‘PoissonMixtureModel.Rmd’ using rmarkdown
Quitting from lines 322-352 (PoissonMixtureModel.Rmd) 
Error: processing vignette ‘PoissonMixtureModel.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘PoissonMixtureModel.Rmd’

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

--- re-building ‘VaccineEfficacy.Rmd’ using rmarkdown
Quitting from lines 142-157 (VaccineEfficacy.Rmd) 
Error: processing vignette ‘VaccineEfficacy.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘VaccineEfficacy.Rmd’

--- re-building ‘gsSurvBasicExamples.Rmd’ using rmarkdown
Quitting from lines 206-215 (gsSurvBasicExamples.Rmd) 
Error: processing vignette ‘gsSurvBasicExamples.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘gsSurvBasicExamples.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘PoissonMixtureModel.Rmd’ ‘VaccineEfficacy.Rmd’
  ‘gsSurvBasicExamples.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) gsym.point.Rd:143: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Running examples in ‘gtExtras-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_text_img
> ### Title: Add text and an image to the left or right of it
> ### Aliases: add_text_img
> 
> ### ** Examples
> 
> library(gt)
> title_car <- mtcars %>%
+   head() %>%
+   gt() %>%
+   gt::tab_header(
+     title = add_text_img(
+       "A table about cars made with",
+       url = "https://www.r-project.org/logo/Rlogo.png"
+     )
+   )
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
Running examples in ‘gto-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: body_add_gt
> ### Title: Add 'gt' table into a Word document
> ### Aliases: body_add_gt
> 
> ### ** Examples
> 
> 
>  library(officer)
>  library(gt)
> 
>  gt_tbl <- gt(head(exibble))
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: gt ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running examples in ‘gt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as_word
> ### Title: Output a *gt* object as Word
> ### Aliases: as_word
> 
> ### ** Examples
> 
> # Use `gtcars` to create a gt table;
> # add a header and then export as
> # OOXML code for Word
> tab_rtf <-
+   gtcars %>%
+   dplyr::select(mfr, model) %>%
+   dplyr::slice(1:2) %>%
+   gt() %>%
+   tab_header(
+     title = md("Data listing from **gtcars**"),
+     subtitle = md("`gtcars` is an R dataset")
+   ) %>%
+   as_word()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running examples in ‘gtreg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tbl_listing
> ### Title: Data Listing Table
> ### Aliases: tbl_listing
> 
> ### ** Examples
> 
> library(dplyr, warn.conflicts = FALSE)
> 
> tbl_listing_ex1 <-
+   head(df_adverse_events, n = 10) %>%
+   select(system_organ_class, adverse_event, grade, drug_attribution, patient_id) %>%
+   arrange(adverse_event, desc(grade)) %>%
+   tbl_listing(group_by = system_organ_class) %>%
+   bold_labels()
> 
> set.seed(11234)
> tbl_listing_ex2 <-
+ df_patient_characteristics %>%
+   dplyr::slice_sample(n = 10) %>%
+   select(patient_id, status, discontinued, off_trt_ae) %>%
+   tbl_listing() %>%
+   as_gt() %>%
+   gt::opt_row_striping()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running examples in ‘gtsummary-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as_gt
> ### Title: Convert gtsummary object to a gt object
> ### Aliases: as_gt
> 
> ### ** Examples
> 
> # Example 1 ----------------------------------
> as_gt_ex1 <-
+   trial[c("trt", "age", "response", "grade")] %>%
+   tbl_summary(by = trt) %>%
+   as_gt()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gallery.Rmd’ using rmarkdown
--- finished re-building ‘gallery.Rmd’

--- re-building ‘gtsummary_definition.Rmd’ using rmarkdown
Quitting from lines 69-92 (gtsummary_definition.Rmd) 
Error: processing vignette ‘gtsummary_definition.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘gtsummary_definition.Rmd’

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

--- re-building ‘rmarkdown.Rmd’ using rmarkdown
Quitting from lines 31-171 (rmarkdown.Rmd) 
Error: processing vignette ‘rmarkdown.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘rmarkdown.Rmd’

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

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

--- re-building ‘themes.Rmd’ using rmarkdown
Quitting from lines 48-56 (themes.Rmd) 
Error: processing vignette ‘themes.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘themes.Rmd’

SUMMARY: processing the following files failed:
  ‘gtsummary_definition.Rmd’ ‘rmarkdown.Rmd’ ‘themes.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RRprof.out’
checkRd: (-1) GUTS-package.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) GUTS.Rd:201: Escaped LaTeX specials: \&
checkRd: (-1) GUTS.Rd:209: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) luzdat.Rd:21: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘hacksaw-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: shift_row_values
> ### Title: Shift row values left or right
> ### Aliases: shift_row_values
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> df <- tibble(
+     s = c(NA, 1, NA, NA),
+     t = c(NA, NA, 1, NA),
+     u = c(NA, NA, 2, 5),
+     v = c(5, 1, 9, 2),
+     x = c(1, 5, 6, 7),
+     y = c(NA, NA, 8, NA),
+     z = 1:4
+ )
> df %>% shift_row_values()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hacksaw)
  > 
  > test_check("hacksaw")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-shift_row_values.R:23:3'): Can shift tibble row values ─────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─hacksaw::shift_row_values(dftbl) at test-shift_row_values.R:23:2
   2.   ├─base::`[<-`(`*tmp*`, at, , value = `<df[,7]>`)
   3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, at, , value = `<df[,7]>`)
   4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   5.       └─tibble:::tbl_subassign_row(xo, i, value, i_arg, value_arg, call)
   6.         ├─base::withCallingHandlers(...)
   7.         └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]
  Error: Test failures
  Execution halted
Running examples in ‘hacksig-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hack_estimate
> ### Title: Hack the ESTIMATE scores
> ### Aliases: hack_estimate
> 
> ### ** Examples
> 
> hack_estimate(test_expr)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: hack_estimate ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hacksig.Rmd’ using rmarkdown
Quitting from lines 165-166 (hacksig.Rmd) 
Error: processing vignette ‘hacksig.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘hacksig.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.ga.breed’ ‘.ga.fitness’ ‘.ga.init’ ‘.ga.mutate’ ‘.ga.step’
  ‘.ga.weight’
Specified C++11: please drop specification unless essential
'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: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Running examples in ‘HDCurves-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: emp_deriv
> ### Title: Estimate of empirical derivative based on sequence of quotient
> ###   differences.
> ### Aliases: emp_deriv
> 
> ### ** Examples
> 
> 
>   # Our R-package
>   library(HDCurves)
> 
>   data(growth)
> 
>   y <- growth$hgtm[,1]
>   t <- growth$age
> 
>   fprime <- emp_deriv(y=y, t=t, D=10, u=1, ztype=0)
Error in emp_deriv(y = y, t = t, D = 10, u = 1, ztype = 0) : 
  DLL requires the use of native symbols
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Getting-Started.Rmd’ using rmarkdown
Quitting from lines 90-93 (Getting-Started.Rmd) 
Error: processing vignette ‘Getting-Started.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Getting-Started.Rmd’

SUMMARY: processing the following file failed:
  ‘Getting-Started.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Running examples in ‘HDoutliers-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HDoutliers
> ### Title: Leland Wilkinson's _hdoutliers_ Algorithm for Outlier Detection
> ### Aliases: HDoutliers
> ### Keywords: cluster
> 
> ### ** Examples
> 
> 
> data(dots)
> out.W <- HDoutliers(dots$W)
Error in get.knn(data, k, algorithm) : 
  DLL requires the use of native symbols
Calls: HDoutliers -> getHDoutliers -> knn.dist -> get.knn
Execution halted
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [30s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(HDStIM)
  > 
  > test_check("HDStIM")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('testHDStIM.R:16:5'): Whether HDStIM maps the same number of cells. ──
  Error in `FNN::get.knn(X, k)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─HDStIM::HDStIM(...) at testHDStIM.R:16:4
   2.   └─uwot::umap(...)
   3.     └─uwot:::uwot(...)
   4.       └─uwot:::data2set(...)
   5.         └─uwot:::x2set(...)
   6.           └─uwot:::x2nn(...)
   7.             └─uwot:::find_nn(...)
   8.               └─uwot:::FNN_nn(X, k = k, include_self = include_self)
   9.                 └─FNN::get.knn(X, k)
  ── Error ('testPlots.R:12:3'): If plot_umap returns 0. ─────────────────────────
  Error in `FNN::get.knn(X, k)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─HDStIM::HDStIM(...) at testPlots.R:12:2
   2.   └─uwot::umap(...)
   3.     └─uwot:::uwot(...)
   4.       └─uwot:::data2set(...)
   5.         └─uwot:::x2set(...)
   6.           └─uwot:::x2nn(...)
   7.             └─uwot:::find_nn(...)
   8.               └─uwot:::FNN_nn(X, k = k, include_self = include_self)
   9.                 └─FNN::get.knn(X, k)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘HDStIM.Rmd’ using rmarkdown
Quitting from lines 36-47 (HDStIM.Rmd) 
Error: processing vignette ‘HDStIM.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘HDStIM.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘auto-kmeans.Rmd’ using rmarkdown
--- finished re-building ‘auto-kmeans.Rmd’

--- re-building ‘getting-started.Rmd’ using rmarkdown
--- finished re-building ‘getting-started.Rmd’

--- re-building ‘kmeans-umap.Rmd’ using rmarkdown
Quitting from lines 147-148 (kmeans-umap.Rmd) 
Error: processing vignette ‘kmeans-umap.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘kmeans-umap.Rmd’

SUMMARY: processing the following file failed:
  ‘kmeans-umap.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘healthyR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: umap_list
> ### Title: UMAP Projection
> ### Aliases: umap_list
> 
> ### ** Examples
> 
> library(healthyR.data)

== Welcome to healthyR.data ===========================================================================
If you find this package useful, please leave a star: 
   https://github.com/spsanderson/healthyR.data'

If you encounter a bug or want to request an enhancement please file an issue at:
   https://github.com/spsanderson/healthyR.data/issues

Thank you for using healthyR.data
> library(healthyR)
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(broom)
> 
> data_tbl <- healthyR_data %>%
+     filter(ip_op_flag == "I") %>%
+     filter(payer_grouping != "Medicare B") %>%
+     filter(payer_grouping != "?") %>%
+     select(service_line, payer_grouping) %>%
+     mutate(record = 1) %>%
+     as_tibble()
> 
> uit_tbl <- kmeans_user_item_tbl(
+    .data           = data_tbl
+    , .row_input    = service_line
+    , .col_input    =  payer_grouping
+    , .record_input = record
+  )
> 
> kmm_tbl <- kmeans_mapped_tbl(uit_tbl)
> 
> umap_list(.data = uit_tbl, kmm_tbl, 3)
Error in FNN::get.knn(X, k) : DLL requires the use of native symbols
Calls: umap_list ... data2set -> x2set -> x2nn -> find_nn -> FNN_nn -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
--- finished re-building ‘getting-started.Rmd’

--- re-building ‘kmeans-umap.Rmd’ using rmarkdown
Quitting from lines 150-151 (kmeans-umap.Rmd) 
Error: processing vignette ‘kmeans-umap.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘kmeans-umap.Rmd’

SUMMARY: processing the following file failed:
  ‘kmeans-umap.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘healthyR.ts-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ts_model_spec_tune_template
> ### Title: Time Series Model Spec Template
> ### Aliases: ts_model_spec_tune_template
> 
> ### ** Examples
> 
> ts_model_spec_tune_template("ets")
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: ts_model_spec_tune_template ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘heatwaveR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: category
> ### Title: Calculate the categories of events.
> ### Aliases: category
> 
> ### ** Examples
> 
> res_WA <- detect_event(ts2clm(sst_WA,
+                        climatologyPeriod = c("1983-01-01", "2012-12-31")))
> # Note that the name argument expects a character vector
> cat_WA <- category(res_WA, name = "WA")
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: category ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MHW_to_nc.Rmd’ using rmarkdown
--- finished re-building ‘MHW_to_nc.Rmd’

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

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

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

--- re-building ‘event_categories.Rmd’ using rmarkdown
Quitting from lines 38-51 (event_categories.Rmd) 
Error: processing vignette ‘event_categories.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘event_categories.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
expand_state:
  function(x, ...)
expand_state.uneval_init:
  function(x, state_name, cycles)

expand_state:
  function(x, ...)
expand_state.uneval_state_list:
  function(x, state_name, cycles)

expand_state:
  function(x, ...)
expand_state.uneval_matrix:
  function(x, state_pos, state_name, cycles, n)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘synbreed’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘heuristicsmineR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.petrinet
> ### Title: Converts the object to a Petrinet
> ### Aliases: as.petrinet
> 
> ### ** Examples
> 
> data(L_heur_1)
> cn <- causal_net(L_heur_1, threshold = .8)
> pn <- as.petrinet(cn)
> petrinetR::render_PN(pn)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: <Anonymous> ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
checkRd: (-1) erode.hexbin.Rd:43: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘hextri-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hexclass
> ### Title: Hexagonal binning with classes
> ### Aliases: hextri hextri.default hextri.formula
> ### Keywords: hplot
> 
> ### ** Examples
> 
> xx<-rnorm(1000)
> yy<-rnorm(1000)
> cc<-cut(xx*yy,c(-Inf,-.4,0,.4,Inf))
> 
> plot(xx,yy,col=(1:4)[cc])
> hextri(xx,yy,cc,1:4,nbins=20,border=TRUE,style="size")
> 
> ##formula method
> data(NHANES, package="hexbin")
> hextri(Weight~Age, class=Smoke, col=c("red","orange","green","grey40"),
+    data=NHANES, style="size",nbins=20, main="Smoking")
> legend("topright",fill=c("red","orange","green","grey40"),
+    legend=c("Current","Past","Never","unknown"),bty="n")
> 
> ## minimum sizes
> 
> data(NHANES, package="hexbin")
> hextri(Weight~Age, class=Smoke, col=c("red","orange","green","grey40"),
+    data=NHANES, style="size",nbins=20, main="Smoking",minfrac=.2)
> legend("topright",fill=c("red","orange","green","grey40"),
+    legend=c("Current","Past","Never","unknown"),bty="n")
> 
> 
> ## using the return value of hextri
> rval<-hextri(xx,yy,cc,1:4,nbins=20,border=TRUE,style="alpha")
> plot(y~x,data=rval,type="n")
> with(rval, polygon(x,y,col=col,border=NA))
> 
> ## diffusion
> xx<-runif(10000)
> yy<-runif(10000)
> cc<-rep(1:3,c(4750,4750,500))
> hextri(xx,yy,cc,2:4,border=TRUE,diffuse=FALSE,style="size")
> hextri(xx,yy,cc,2:4,border=TRUE,diffuse=TRUE,sorted=TRUE, style="size")
Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols
Calls: hextri ... hexclass_diffuse -> diffuse -> <Anonymous> -> get.knnx
Execution halted
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
‘:::’ 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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘colorfulVennPlot’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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 ‘Supersonic_Routes.Rmd’ using rmarkdown
Quitting from lines 229-243 (Supersonic_Routes.Rmd) 
Error: processing vignette ‘Supersonic_Routes.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Supersonic_Routes.Rmd’

--- re-building ‘Supersonic_Routes_in_depth.Rmd’ using rmarkdown
Quitting from lines 52-91 (Supersonic_Routes_in_depth.Rmd) 
Error: processing vignette ‘Supersonic_Routes_in_depth.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Supersonic_Routes_in_depth.Rmd’

SUMMARY: processing the following files failed:
  ‘Supersonic_Routes.Rmd’ ‘Supersonic_Routes_in_depth.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) Snow.Rd:118: Escaped LaTeX specials: \&
checkRd: (-1) Snow.Rd:142: Escaped LaTeX specials: \&
checkRd: (-1) Yeast.Rd:56: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘trackr’
Package which this enhances but not available for checking: ‘HadoopStreaming’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
pp_check:
  function(object, ...)
pp_check.hmcdm:
  function(object, plotfun, type)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: \&
Running examples in ‘Hmsc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: constructKnots
> ### Title: constructKnots
> ### Aliases: constructKnots
> 
> ### ** Examples
> 
> #Creating knots for some 2 dimensional spatial data
> n = 100
> xycoords = matrix(runif(2*n),ncol=2)
> xyKnots = constructKnots(xycoords,knotDist = 0.2, minKnotDist = 0.5)
Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols
Calls: constructKnots -> knnx.dist -> get.knnx
Execution halted
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.hms:
  function(x)

vec_ptype_full:
  function(x, ...)
vec_ptype_full.hms:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘ROI.plugin.mosek’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Specified C++11: please drop specification unless essential
checkRd: (-1) attributes_speclib.Rd:73: Escaped LaTeX specials: \$
checkRd: (-1) get_reflectance.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  useful.h:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hSDM.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘test-all.R’ [9s/13s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(htmltools)
  > 
  > test_check("htmltools")
  [ FAIL 2 | WARN 0 | SKIP 5 | PASS 2049 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Chinese locale not available (2)
  • On CRAN (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-tags.r:29:3'): Hanging commas don't break things ─────────────
  `as.character(div("one", , ))` threw an error with unexpected message.
  Expected match: "is empty"
  Actual message: "Argument 2 can't be empty."
  Backtrace:
      ▆
   1. ├─testthat::expect_error(as.character(div("one", , )), "is empty") at test-tags.r:29:2
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. ├─htmltools::div("one", , )
   7. │ └─rlang::dots_list(...)
   8. └─rlang::abort(message = message)
  ── Failure ('test-tags.r:31:3'): Hanging commas don't break things ─────────────
  `as.character(div(, "one", ))` threw an error with unexpected message.
  Expected match: "is empty"
  Actual message: "Argument 1 can't be empty."
  Backtrace:
      ▆
   1. ├─testthat::expect_error(as.character(div(, "one", )), "is empty") at test-tags.r:31:2
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. ├─htmltools::div(, "one", )
   7. │ └─rlang::dots_list(...)
   8. └─rlang::abort(message = message)
  
  [ FAIL 2 | WARN 0 | SKIP 5 | PASS 2049 ]
  Error: Test failures
  Execution halted
as.tags:
  function(x, ...)
as.tags.htmlwidget:
  function(x, standalone)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  htree.c:126:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:135:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:324:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:362:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:408:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:517:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:693:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:711:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:813:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1476:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1494:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1528:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1679:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1754:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1839:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1869:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:1909:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:2906:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  htree.c:3696:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/htree.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Trancura9414001.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) Trancura9414001.Rd:28: Escaped LaTeX specials: \_
checkRd: (-1) hydroPSO.Rd:390: Escaped LaTeX specials: \&
checkRd: (-1) hydroPSO.Rd:408: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:7: Escaped LaTeX specials: \&
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘switchr’
Running ‘testthat.R’ [3s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(magrittr)
  > library(testthat)
  
  Attaching package: 'testthat'
  
  The following objects are masked from 'package:magrittr':
  
      equals, is_less_than, not
  
  > library(i2dash)
  
  Attaching package: 'i2dash'
  
  The following object is masked from 'package:graphics':
  
      title
  
  The following object is masked from 'package:base':
  
      source
  
  > 
  > test_check("i2dash")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 50 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-add-content.R:98:5'): adding components to a dashboard is correct ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─gt::gt(mtcars) at test-add-content.R:98:4
   2.   └─gt::cols_align(data = data, align = "auto")
   3.     └─gt:::dt_boxhead_edit(data = data, var = column_names[i], column_align = align[i])
   4.       ├─base::`[[<-`(...)
   5.       └─tibble:::`[[<-.tbl_df`(...)
   6.         └─tibble:::tbl_subassign(...)
   7.           └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   8.             ├─base::withCallingHandlers(...)
   9.             └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 50 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘incidence2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
autoplot:
  function(object, ...)
autoplot.grid_search:
  function(x, type, ...)

autoplot:
  function(object, ...)
autoplot.stability_analysis:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.roc_curve:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.similarity_comparison:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘IAPWS95-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BT
> ### Title: Second Virial Coefficient (B), Function of Temperature
> ### Aliases: BT
> 
> ### ** Examples
> 
> Temp <- 500.
> B_T <- BT(Temp)
Error in BT(Temp) : DLL requires the use of native symbols
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘IAPWS95.Rmd’ using rmarkdown
Quitting from lines 34-47 (IAPWS95.Rmd) 
Error: processing vignette ‘IAPWS95.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘IAPWS95.Rmd’

SUMMARY: processing the following file failed:
  ‘IAPWS95.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
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’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) pulmonary.Rd:13: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rggobi’
Running examples in ‘ider-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gendata
> ### Title: Data generator for intrinsic dimension estimation.
> ### Aliases: gendata
> 
> ### ** Examples
> 
> ## global intrinsic dimension estimate
> x <- gendata(DataName='SwissRoll')
> estmle <- lbmle(x=x,k1=3,k2=5)
Error in FNN::get.knn(x, k = k) : DLL requires the use of native symbols
Calls: lbmle -> TkX -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘IDSL.IPA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IPA_targeted_xlsxAnalyzer
> ### Title: IPA Targeted xlsxAnalyzer
> ### Aliases: IPA_targeted_xlsxAnalyzer
> 
> ### ** Examples
> 
> ## To generate the IPA spreadsheet parameters
> s_path <- system.file("extdata", package = "IDSL.IPA")
> SSh1 <- paste0(s_path,"/IPA_parameters.xlsx")
> spreadsheet <- readxl::read_xlsx(SSh1, sheet = 'IPA_targeted')
> temp_wd <- tempdir()
> temp_wd_zip <- paste0(temp_wd,"/idsl_ipa_test_files.zip")
> download.file(paste0("https://github.com/idslme/IDSL.IPA/blob/main/",
+ "IPA_educational_files/idsl_ipa_test_files.zip?raw=true"),
+ destfile = temp_wd_zip, mode = "wb")
trying URL 'https://github.com/idslme/IDSL.IPA/blob/main/IPA_educational_files/idsl_ipa_test_files.zip?raw=true'
Content type 'application/zip' length 5500957 bytes (5.2 MB)
==================================================
downloaded 5.2 MB

> unzip(temp_wd_zip, exdir = temp_wd)
> spreadsheet[3, 4] <- temp_wd
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: [<- ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Package suggested but not available for checking: ‘IFCdata’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
knit_print:
  function(x, ...)
knit_print.Iheatmap:
  function(x, options)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘imbalance-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: neater
> ### Title: Fitering of oversampled data based on non-cooperative game
> ###   theory
> ### Aliases: neater
> 
> ### ** Examples
> 
> data(iris0)
> 
> newSamples <- smotefamily::SMOTE(iris0[,-5], iris0[,5])$syn_data
Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols
Calls: <Anonymous> -> knearest -> <Anonymous> -> get.knnx
Execution halted
Running ‘testthat.R’ [25s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(imbalance)
  > 
  > test_check("imbalance")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 75 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('testNEATER.R:31:1'): (code run outside of `test_that()`) ────────────
  Error in `get.knnx(data, query, k, algorithm)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─imbalance (local) neaterTestOutput("glass0") at testNEATER.R:31:0
   2.   └─smotefamily::SMOTE(dataset[, -minIndex], dataset[, minIndex]) at testNEATER.R:20:2
   3.     └─smotefamily::knearest(P_set, P_set, K)
   4.       └─FNN::knnx.index(D, P, k = (n_clust + 1), algo = "kd_tree")
   5.         └─FNN::get.knnx(data, query, k, algorithm)
  ── Error ('testwrappers.R:28:1'): (code run outside of `test_that()`) ──────────
  Error in `get.knnx(data, query, k, algorithm)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─imbalance (local) wrapperTestOutputRatio("SMOTE") at testwrappers.R:28:0
   2.   └─imbalance::oversample(glass0, ratio = ratio, method = method) at testwrappers.R:18:2
   3.     └─smotefamily (local) selectedMethod(...)
   4.       └─smotefamily::knearest(P_set, P_set, K)
   5.         └─FNN::knnx.index(D, P, k = (n_clust + 1), algo = "kd_tree")
   6.           └─FNN::get.knnx(data, query, k, algorithm)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 75 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘imbalance.Rmd’ using rmarkdown
Quitting from lines 236-242 (imbalance.Rmd) 
Error: processing vignette ‘imbalance.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘imbalance.Rmd’

SUMMARY: processing the following file failed:
  ‘imbalance.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
Running examples in ‘immunarch-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geneUsage
> ### Title: Main function for estimation of V-gene and J-gene statistics
> ### Aliases: geneUsage get_aliases get_genes
> 
> ### ** Examples
> 
> data(immdata)
> gu <- geneUsage(immdata$data)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: geneUsage ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/incidence2.Rcheck/00install.out’ for details.
Running examples in ‘IndepTest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: KLentropy
> ### Title: KLentropy
> ### Aliases: KLentropy
> 
> ### ** Examples
> 
> n=1000; x=rnorm(n); KLentropy(x,30,stderror=TRUE)   # The true value is 0.5*log(2*pi*exp(1)) = 1.42.
Error in get.knn(data, k, algorithm) : 
  DLL requires the use of native symbols
Calls: KLentropy -> knn.dist -> get.knn
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Found the following significant warnings:
  keyplayer-utils.c:24:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/influenceR.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Problems with news in ‘NEWS.md’:
No news entries found.
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
Running examples in ‘InjurySeverityScore-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: injury_score
> ### Title: Calculate injury severity score from ICD-9
> ### Aliases: injury_score
> 
> ### ** Examples
> 
> pat_id <- c(2,2,2,2,2,1,2,1,2,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1)
> icd9 <- c('874.2', '874.8', '900.81', '900.82', '900.89', '805.06', 
+           'E966', '805.07', 'V14.0', '807.02', 'V70.4', '821.01', '823.20', 
+           '860.0', '861.01', '861.21', '861.22', '863.84', '864.04', '865.04', 
+           '865.09', '866.02', '868.04', '958.4')
> sample_data <- data.frame(subj = pat_id, code = icd9, stringsAsFactors = FALSE)
> injury_score(sample_data, subj, code)
Warning: There was 1 warning in `dplyr::summarise()`.
ℹ In argument: `max_w_9 = max(severity)`.
Caused by warning in `max()`:
! no non-missing arguments to max; returning -Inf
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: injury_score ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running examples in ‘injurytools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: injprev
> ### Title: Calculate injury prevalence
> ### Aliases: injprev
> 
> ### ** Examples
> 
> 
> injprev(injd, by = "monthly", var_type_injury = "injury_type")
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: injprev ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘estimate-epi-measures.Rmd’ using rmarkdown
Quitting from lines 244-246 (estimate-epi-measures.Rmd) 
Error: processing vignette ‘estimate-epi-measures.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘estimate-epi-measures.Rmd’

--- re-building ‘prepare-injury-data.Rmd’ using rmarkdown
--- finished re-building ‘prepare-injury-data.Rmd’

--- re-building ‘visualize-injury-data.Rmd’ using rmarkdown
Quitting from lines 496-509 (visualize-injury-data.Rmd) 
Error: processing vignette ‘visualize-injury-data.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘visualize-injury-data.Rmd’

SUMMARY: processing the following files failed:
  ‘estimate-epi-measures.Rmd’ ‘visualize-injury-data.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘dataManip.Rmd’ using rmarkdown
Quitting from lines 127-138 (dataManip.Rmd) 
Error: processing vignette ‘dataManip.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘dataManip.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘display.Rmd’ using rmarkdown
Quitting from lines 131-132 (display.Rmd) 
Error: processing vignette ‘display.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘display.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
Malformed Title field: should not end in a period.
Running examples in ‘insurancerating-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.restricted
> ### Title: Automatically create a ggplot for objects obtained from
> ###   restrict_coef()
> ### Aliases: autoplot.restricted
> 
> ### ** Examples
> 
> freq <- glm(nclaims ~ bm + zip, weights = power, family = poisson(),
+  data = MTPL)
> zip_df <- data.frame(zip = c(0,1,2,3), zip_rst = c(0.8, 0.9, 1, 1.2))
> freq %>%
+   restrict_coef(., zip_df) %>%
+   autoplot()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
# NOTE - CRAN check detected: limiting maximum number of cores [2/32]

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Intervals-class.Rd:109: Escaped LaTeX specials: \_
checkRd: (-1) Intervals-class.Rd:110: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:68: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:76: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:77: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:78: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:79: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:81: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:88: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:89: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) sgd.Rd:12: Escaped LaTeX specials: \_
Running examples in ‘intervals-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clusters
> ### Title: Identify clusters in a collection of positions or intervals
> ### Aliases: clusters clusters,numeric-method
> ###   clusters,Intervals_virtual-method
> 
> ### ** Examples
> 
> # Numeric method
> w <- 20
> x <- sample( 1000, 100 )
> c1 <- clusters( x, w )
Error in .local(x, ...) : DLL requires the use of native symbols
Calls: clusters ... clusters -> .local -> reduce -> reduce -> .local -> .Call
Execution halted
Running ‘intervals_test_code.R’ [1s/1s]
Running the tests in ‘tests/intervals_test_code.R’ failed.
Complete output:
  > library( "intervals" )
  > 
  > ######## NAs and empty intervals
  > 
  > u <- Intervals_full( as.numeric(NA), type = "Z" )
  > u <- c( u, u )
  > v <- Intervals_full( c(1,3,1,Inf), type = "Z" )
  > x <- Intervals( 1, closed = FALSE, type = "Z" ) # empty
  > w <- c( x, u, v )
  Warning message:
  Coercion to 'Intervals_full' required. 
  > rownames(w) <- letters[ 1:nrow(w) ]
  > 
  > x
  Object of class Intervals
  1 interval over Z:
  (1, 1)
  > u
  Object of class Intervals_full
  2 intervals over Z:
  [NA, NA]
  [NA, NA]
  > v
  Object of class Intervals_full
  2 intervals over Z:
  [1, 1]
  [3, Inf]
  > w
  Object of class Intervals_full
  5 intervals over Z:
  a (1, 1)
  b [NA, NA]
  c [NA, NA]
  d [1, 1]
  e [3, Inf]
  > 
  > is.na(w)
      a     b     c     d     e 
  FALSE  TRUE  TRUE FALSE FALSE 
  > empty(w)
  [1]  TRUE    NA    NA FALSE FALSE
  > 
  > distance_to_nearest( u, v )
  Error in .local(from, to, ...) : DLL requires the use of native symbols
  Calls: distance_to_nearest ... .local -> which_nearest -> which_nearest -> .local -> .Call
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intervals_overview.Rnw’ using Sweave

Error: processing vignette ‘intervals_overview.Rnw’ failed with diagnostics:
 chunk 5 (label = plotting) 
Error in plot.Intervals_full(x, ...) : 
  DLL requires the use of native symbols

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

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Running examples in ‘intRinsic-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compute_mus
> ### Title: Compute the ratio statistics needed for the intrinsic dimension
> ###   estimation
> ### Aliases: compute_mus print.mus plot.mus
> 
> ### ** Examples
> 
> X           <- replicate(2,rnorm(1000))
> mu          <- compute_mus(X, n1 = 1, n2 = 2)
Error in FNN::get.knn(X, k = n2) : DLL requires the use of native symbols
Calls: compute_mus -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
'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: ‘surveyspec’
Running ‘testthat.R’ [25s/57s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(iNZightTools)
  
  Attaching package: 'iNZightTools'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("iNZightTools")
  Loading required package: survey
  Loading required package: grid
  Loading required package: Matrix
  Loading required package: survival
  
  Attaching package: 'survey'
  
  The following object is masked from 'package:graphics':
  
      dotchart
  
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  Loading required namespace: styler
  [ FAIL 1 | WARN 6 | SKIP 4 | PASS 362 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (2)
  • packageVersion("survey") < package_version("4.2") is TRUE (1)
  • surveyspec cannot be loaded (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (???): Full join works ────────────────────────────────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─d1 %>% ...
    2. ├─dplyr::full_join(...)
    3. └─dplyr:::full_join.data.frame(...)
    4.   └─dplyr:::join_mutate(...)
    5.     ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,2]>`)
    6.     └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,2]>`)
    7.       └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    8.         └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
    9.           ├─base::withCallingHandlers(...)
   10.           └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 6 | SKIP 4 | PASS 362 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘iotables-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: equation_solve
> ### Title: Solve a basic (matrix) equation
> ### Aliases: equation_solve
> 
> ### ** Examples
> 
> Im = data.frame (
+ a = c("row1", "row2"), 
+ b = c(1,1), 
+ c = c(2,0))
> LHS = data.frame (
+ a = "lhs", 
+ b = 1, 
+ c = 0.5)
> equation_solve (Im = Im, LHS = LHS)
The technology columns are not matching.
Error in equation_solve(Im = Im, LHS = LHS) : 
  Error: no result is returned.
Execution halted
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [23s/38s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(iotables)
  > 
  > test_check("iotables")
  [ FAIL 2 | WARN 14 | SKIP 0 | PASS 84 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-multiplier_create.R:18:1'): (code run outside of `test_that()`) ──
  Error in `equation_solve(LHS = input_vector, Im = Im)`: Error: no result is returned.
  Backtrace:
      ▆
   1. └─iotables::multiplier_create(...) at test-multiplier_create.R:18:0
   2.   └─iotables::equation_solve(LHS = input_vector, Im = Im)
  ── Error ('test-total_tax_add.R:1:1'): (code run outside of `test_that()`) ─────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. └─iotables::total_tax_add(...) at test-total_tax_add.R:1:0
    2.   ├─dplyr::full_join(...)
    3.   └─dplyr:::full_join.data.frame(...)
    4.     └─dplyr:::join_mutate(...)
    5.       ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,14]>`)
    6.       └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,14]>`)
    7.         └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    8.           └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
    9.             ├─base::withCallingHandlers(...)
   10.             └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 2 | WARN 14 | SKIP 0 | PASS 84 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘environmental_impact.Rmd’ using rmarkdown
Quitting from lines 52-58 (environmental_impact.Rmd) 
Error: processing vignette ‘environmental_impact.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘environmental_impact.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 236-248 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
Error: no result is returned.
--- failed re-building ‘intro.Rmd’

--- re-building ‘united_kingdom_2010.Rmd’ using rmarkdown
Quitting from lines 54-62 (united_kingdom_2010.Rmd) 
Error: processing vignette ‘united_kingdom_2010.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘united_kingdom_2010.Rmd’

--- re-building ‘working_with_eurostat.Rmd’ using rmarkdown
Quitting from lines 124-133 (working_with_eurostat.Rmd) 
Error: processing vignette ‘working_with_eurostat.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘working_with_eurostat.Rmd’

SUMMARY: processing the following files failed:
  ‘environmental_impact.Rmd’ ‘intro.Rmd’ ‘united_kingdom_2010.Rmd’
  ‘working_with_eurostat.Rmd’

Error: Vignette re-building failed.
Execution halted
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.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘IPEDS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: admission_reqs
> ### Title: Function for Admission Requirements for an Institution
> ### Aliases: admission_reqs
> 
> ### ** Examples
> 
> admission_reqs(167835)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: admission_reqs ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘IPEDS-vignette.Rmd’ using rmarkdown
Quitting from lines 114-115 (IPEDS-vignette.Rmd) 
Error: processing vignette ‘IPEDS-vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘IPEDS-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Running examples in ‘ipft-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ipfProbabilistic
> ### Title: This function implements a probabilistic algorithm
> ### Aliases: ipfProbabilistic
> 
> ### ** Examples
> 
> 
>     groups <- ipfGroup(ipftrain, X, Y)
>     model <- ipfProbabilistic(ipftrain[, 1:168], ipftrain[, 169:170], groups = groups)
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: ipfProbabilistic ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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: \&
Running examples in ‘ir-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ir_remove_missing
> ### Title: Removes empty data values in an object of class 'ir'
> ### Aliases: ir_remove_missing
> 
> ### ** Examples
> 
> # create sample data with some missing rows and one entire missing spectra
> x <-
+    ir::ir_sample_data
> x$spectra[[1]] <- x$spectra[[1]][0, ]
> x$spectra[[2]][1:100, "y"] <- NA_real_
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: [<- ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) pine.Rd:20: Escaped LaTeX specials: \&
Found the following significant warnings:
  trace_islasso.c:39:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/islasso.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used Fortran compiler: ‘GNU Fortran (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘ISO11784Tools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert_to_all
> ### Title: Convert a list of codes to all other formats
> ### Aliases: convert_to_all
> 
> ### ** Examples
> 
> convert_to_all(c('3DD.ABC4567890'))
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: convert_to_all ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ISO11784Tools.Rmd’ using rmarkdown
Quitting from lines 67-68 (ISO11784Tools.Rmd) 
Error: processing vignette ‘ISO11784Tools.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘ISO11784Tools.Rmd’

SUMMARY: processing the following file failed:
  ‘ISO11784Tools.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘quick_start.Rmd’ using rmarkdown
Quitting from lines 48-62 (quick_start.Rmd) 
Error: processing vignette ‘quick_start.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘quick_start.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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: \$
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Running examples in ‘isotracer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_covariates
> ### Title: Add fixed effects of one or several covariates to some
> ###   parameters.
> ### Aliases: add_covariates
> 
> ### ** Examples
> 
> # Using a subset of the topology from the Trinidad case study
> m <- new_networkModel() %>%
+   set_topo("NH4, NO3 -> epi, FBOM", "epi -> petro, pseph")
Using default distribution family for proportions ("gamma_cv").
  (eta is the coefficient of variation of gamma distributions.)
Using default distribution family for sizes ("normal_cv").
  (zeta is the coefficient of variation of normal distributions.)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++14: please drop specification unless essential
Found the following files/directories:
  ‘RMTplot.pdf’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Get_Start.Rmd’ using rmarkdown
Quitting from lines 27-89 (Get_Start.Rmd) 
Error: processing vignette ‘Get_Start.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Get_Start.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'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'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘IxPopDyMod-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vary_many_params
> ### Title: Generate copies of a 'config' with all combinations of modified
> ###   parameters
> ### Aliases: vary_many_params
> 
> ### ** Examples
> 
> 
> # create new configs with different values for the parameter determining
> # mortality of eggs (which is found in row 2) and that determining
> # mortality of larvae (which is found in row 4)
> cfgs <- vary_many_params(config_ex_1,
+                         param_rows = c(2, 4),
+                         values_list = list(c(0, 0.1), c(.99, .98)))
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: vary_many_params ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running examples in ‘janitor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adorn_ns
> ### Title: Add underlying Ns to a tabyl displaying percentages.
> ### Aliases: adorn_ns
> 
> ### ** Examples
> 
> 
> mtcars %>%
+   tabyl(am, cyl) %>%
+   adorn_percentages("col") %>%
+   adorn_pct_formatting() %>%
+   adorn_ns(position = "front")
 am         4         6          8
  0 3 (27.3%) 4 (57.1%) 12 (85.7%)
  1 8 (72.7%) 3 (42.9%)  2 (14.3%)
>   
> # Format the Ns with a custom format_func:
> set.seed(1)
> bigger_dat <- data.frame(sex = rep(c("m", "f"), 3000),
+                          age = round(runif(3000, 1, 102), 0))
> bigger_dat$age_group = cut(bigger_dat$age, quantile(bigger_dat$age, c(0, 1/3, 2/3, 1)))
> 
> bigger_dat %>%
+   tabyl(age_group, sex, show_missing_levels = FALSE) %>%
+   adorn_totals(c("row", "col")) %>%
+   adorn_percentages("col") %>%
+   adorn_pct_formatting(digits = 1) %>% 
+   adorn_ns(format_func = function(x) format(x, big.mark = ".", decimal.mark = ","))
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘janitor.Rmd’ using rmarkdown
--- finished re-building ‘janitor.Rmd’

--- re-building ‘tabyls.Rmd’ using rmarkdown
Quitting from lines 69-72 (tabyls.Rmd) 
Error: processing vignette ‘tabyls.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘tabyls.Rmd’

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

Error: Vignette re-building failed.
Execution halted
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_500m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_1km:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_80km:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_10km:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_250m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_125m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_100m:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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'.
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’

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 nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘remMap’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_250m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_10km:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_80km:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_100m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_500m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_125m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_1km:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘jrt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: info.plot
> ### Title: Plot the information function for a judge or for the entire set
> ###   of judges.
> ### Aliases: info.plot
> 
> ### ** Examples
> 
> 
> # Load dataset
> data <- jrt::ratings
> 
> # Fit model
> fit <- jrt(data, irt.model = "PCM")
The possible responses detected are: 1-2-3-4-5

 -== General Summary ==-
- 6 Judges
- 300 Products
- 5 response categories (1-2-3-4-5)
- Mean judgment = 2.977 | SD = 0.862

-== IRT Summary ==-
- Model: Partial Credit Model (Masters, 1982) | doi: 10.1007/BF02296272
- Estimation package: mirt (Chalmers, 2012) | doi: 10.18637/jss.v048.i06
- Estimation algorithm: Expectation-Maximization (EM; Bock & Atkin, 1981) | doi: 10.1007/BF02293801
- Method of factor scoring: Expected A Posteriori (EAP)
- AIC = 4022.956 | AICc =  | BIC = 4115.551 | SABIC = 4115.551

-== Model-based reliability ==-
- Empirical reliability | Average in the sample: .889
- Expected reliability | Assumes a Normal(0,1) prior density: .759

Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: jrt ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Quitting from lines 81-82 (my-vignette.Rmd) 
Error: processing vignette ‘my-vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.json2:
  function(x)

vec_ptype_full:
  function(x, ...)
vec_ptype_full.json2:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘got_chars.Rmd’ using rmarkdown
--- finished re-building ‘got_chars.Rmd’

--- re-building ‘reading-writing-json.Rmd’ using rmarkdown
Quitting from lines 87-95 (reading-writing-json.Rmd) 
Error: processing vignette ‘reading-writing-json.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘reading-writing-json.Rmd’

SUMMARY: processing the following file failed:
  ‘reading-writing-json.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Running examples in ‘jtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: export_summs
> ### Title: Export regression summaries to tables
> ### Aliases: export_summs
> 
> ### ** Examples
> 
> states <- as.data.frame(state.x77)
> fit1 <- lm(Income ~ Frost, data = states)
> fit2 <- lm(Income ~ Frost + Illiteracy, data = states)
> fit3 <- lm(Income ~ Frost + Illiteracy + Murder, data = states)
> 
> if (requireNamespace("huxtable")) {
+   # Export all 3 regressions with "Model #" labels,
+   # standardized coefficients, and robust standard errors
+   export_summs(fit1, fit2, fit3,
+                model.names = c("Model 1","Model 2","Model 3"),
+                coefs = c("Frost Days" = "Frost",
+                          "% Illiterate" = "Illiteracy",
+                          "Murder Rate" = "Murder"),
+                scale = TRUE, robust = TRUE)
+ }
Loading required namespace: huxtable
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: export_summs ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
'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)
Specified C++14: please drop specification unless essential
Running examples in ‘justifier-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apply_graph_theme
> ### Title: Apply multiple DiagrammeR global graph attributes
> ### Aliases: apply_graph_theme
> 
> ### ** Examples
> 
> exampleJustifier <- '
+ ---
+ assertion:
+   -
+     id: assertion_id
+     label: "An assertion"
+ decision:
+   -
+     id: decision_id
+     label: "A decision"
+     justification:
+       -
+         id: justification_id
+         label: "A justification"
+         assertion:
+           -
+             id: assertion_id
+             description: "A description of an assertion"
+             source:
+               -
+                 id: source1_id
+                 label: "First source"
+               -
+                 id: source2_id
+                 label: "second source"
+ ---
+ ';
> justifications <-
+   justifier::load_justifications(text=exampleJustifier);
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: <Anonymous> ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘general-introduction-to-justifier.Rmd’ using rmarkdown
--- finished re-building ‘general-introduction-to-justifier.Rmd’

--- re-building ‘justifier-in-intervention-development.Rmd’ using rmarkdown
Quitting from lines 370-376 (justifier-in-intervention-development.Rmd) 
Error: processing vignette ‘justifier-in-intervention-development.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘justifier-in-intervention-development.Rmd’

--- re-building ‘justifier-in-study-design.Rmd’ using rmarkdown
Quitting from lines 251-257 (justifier-in-study-design.Rmd) 
Error: processing vignette ‘justifier-in-study-design.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘justifier-in-study-design.Rmd’

SUMMARY: processing the following files failed:
  ‘justifier-in-intervention-development.Rmd’
  ‘justifier-in-study-design.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 files/directories:
  ‘song.wav’ ‘song4karaoke.wav’
Running examples in ‘karel-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: acciones
> ### Title: Acciones que Karel puede realizar
> ### Aliases: acciones avanzar girar_izquierda poner_coso juntar_coso
> ###   girar_derecha darse_vuelta
> 
> ### ** Examples
> 
> generar_mundo("mundo001")
> avanzar()
> juntar_coso()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: juntar_coso ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘testthat.R’ [5s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(karel)
  > 
  > test_check("karel")
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 70 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-actions.R:9:3'): Karel's actions perform as expected ───────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─karel::juntar_coso() at test-actions.R:9:2
   2.   ├─base::`[<-`(`*tmp*`, 1, , value = `<list>`)
   3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, , value = `<list>`)
   4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   5.       └─tibble:::tbl_subassign_row(xo, i, value, i_arg, value_arg, call)
   6.         ├─base::withCallingHandlers(...)
   7.         └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test-english_wrapers.R:27:3'): Karel's actions and superpowers perform as expected in English ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─karel::pick_beeper() at test-english_wrapers.R:27:2
   2.   └─karel::juntar_coso()
   3.     ├─base::`[<-`(`*tmp*`, 1, , value = `<list>`)
   4.     └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, , value = `<list>`)
   5.       └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   6.         └─tibble:::tbl_subassign_row(xo, i, value, i_arg, value_arg, call)
   7.           ├─base::withCallingHandlers(...)
   8.           └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 70 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
r_to_py:
  function(x, convert)
r_to_py.keras_layer_wrapper:
  function(fn, convert)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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 ’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [3s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(knn.covertree)
  > 
  > test_check('knn.covertree')
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-knn.r:10:2'): knn works the same as FNN ────────────────────────
  Error in `FNN::get.knn(e, 5L)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─FNN::get.knn(e, 5L) at test-knn.r:10:8
  ── Error ('test-knn.r:24:2'): knnx works the same as to FNN ────────────────────
  Error in `FNN::get.knnx(e[am == "manual", ], e[am == "automatic", ], 5L)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─FNN::get.knnx(e[am == "manual", ], e[am == "automatic", ], 5L) at test-knn.r:24:8
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
Running examples in ‘ks-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kms
> ### Title: Kernel mean shift clustering
> ### Aliases: kms summary.kms plot.kms
> ### Keywords: cluster
> 
> ### ** Examples
> 
> library(MASS)
> data(crabs)
> kms.crabs <- kms(x=crabs[,c("FL","CW")])
Error in FNN::get.knnx(ms.temp$mode, ms.temp$mode, k = 2) : 
  DLL requires the use of native symbols
Calls: kms -> ms.merge.num -> <Anonymous>
Execution halted
'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
calibrate:
  function(dsvord, ...)
calibrate.dsvord:
  function(dsvord, site, dims, family, gamma, keep.models)

varplot:
  function(pca, ...)
varplot.pca:
  function(x, dim)

loadings:
  function(pca, ...)
loadings.pca:
  function(x, dim, digits, cutoff)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: \&
Specified C++11: please drop specification unless essential
Running examples in ‘lares-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: freqs_plot
> ### Title: Combinated Frequencies Plot for Categorical Features
> ### Aliases: freqs_plot
> 
> ### ** Examples
> 
> Sys.unsetenv("LARES_FONT") # Temporal
> data(dft) # Titanic dataset
> 
> df <- freqs_plot(dft, Pclass, Survived)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: freqs_plot ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Found the following significant warnings:
  init.c:19:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/largeList.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘example.llo’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘ergm.userterms’
checkRd: (-1) simulate.ergmm.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) simulate.ergmm.Rd:36: Escaped LaTeX specials: \$
Unknown package ‘ergm.userterms’ in Rd xrefs
GNU make is a SystemRequirements.
Found the following significant warnings:
  init.c:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:18:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:24:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:27:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:51:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/later.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'akmedoids', 'clusterCrit'
evaluate:
  function(...)
evaluate.lcMethod:
  function(object, classes, try, exclude, envir)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Unknown packages ‘clusterCrit’, ‘akmedoids’ in Rd xrefs
'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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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
Running examples in ‘lazytrade-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check_if_optimize
> ### Title: Function check_if_optimize.
> ### Aliases: check_if_optimize
> 
> ### ** Examples
> 
> 
> library(lazytrade)
> library(magrittr)
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(readr)
> library(lubridate)

Attaching package: ‘lubridate’

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

    date, intersect, setdiff, union

> 
> path_data <- normalizePath(tempdir(),winslash = "/")
> 
> file.copy(from = system.file("extdata", "Setup.csv", package = "lazytrade"),
+           to = file.path(path_data, "Setup.csv"), overwrite = TRUE)
[1] TRUE
> 
> system_list <- read_csv(file.path(path_data, "Setup.csv"))
Rows: 39 Columns: 3
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (2): Pair, Period
dbl (1): Magic

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
> 
> data(profit_factorDF)
> 
> 
> # without writing to the file
> check_if_optimize(x = profit_factorDF,
+                   system_list = system_list,
+                   path_data,
+                   num_trades_to_consider = 3,
+                   profit_factor_limit = 0.8,
+                   write_mode = TRUE)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: check_if_optimize ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘testthat.R’ [5s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lazytrade)
  > 
  > test_check("lazytrade")
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 25 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-check_if_optimize.R:27:3'): data trnasformation ────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─... %>% ... at test-check_if_optimize.R:27:2
    2. ├─dplyr::inner_join(., y = system_list, by = c(MagicNumber = "Magic"))
    3. ├─dplyr::mutate(., ToOptimize = 1)
    4. ├─dplyr::select(., MagicNumber, PrFact)
    5. ├─dplyr::filter(., PrFact < profit_factor_limit)
    6. ├─dplyr::ungroup(.)
    7. ├─lazytrade::get_profit_factorDF(., num_trades_to_consider)
    8. │ └─DF_P %>% dplyr::full_join(DF_L, by = "MagicNumber")
    9. ├─dplyr::full_join(., DF_L, by = "MagicNumber")
   10. └─dplyr:::full_join.data.frame(., DF_L, by = "MagicNumber")
   11.   └─dplyr:::join_mutate(...)
   12.     ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   13.     └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   14.       └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   15.         └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   16.           ├─base::withCallingHandlers(...)
   17.           └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 25 ]
  Error: Test failures
  Execution halted
checkRd: (-1) goodnessfit.Rd:105: Escaped LaTeX specials: \&
checkRd: (-1) lba.Rd:252: Escaped LaTeX specials: \&
checkRd: (-1) pregnancy.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) pregnancy.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    lcars.0.3.1
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  lcopula-init.c:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lcopula.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
Running examples in ‘lcsm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: extract_param
> ### Title: Extract labelled parameters of lavaan objects
> ### Aliases: extract_param
> 
> ### ** Examples
> 
> # First create a lavaan object
> bi_lcsm_01 <- fit_bi_lcsm(data = data_bi_lcsm, 
+                           var_x = names(data_bi_lcsm)[2:4], 
+                           var_y = names(data_bi_lcsm)[12:14],
+                           model_x = list(alpha_constant = TRUE, 
+                                          beta = TRUE, 
+                                          phi = FALSE),
+                           model_y = list(alpha_constant = TRUE, 
+                                          beta = TRUE, 
+                                          phi = TRUE),
+                           coupling = list(delta_lag_xy = TRUE, 
+                                           xi_lag_yx = TRUE)
+                                           )
Warning in lav_model_vcov(lavmodel = lavmodel, lavsamplestats = lavsamplestats,  :
  lavaan WARNING:
    The variance-covariance matrix of the estimated parameters (vcov)
    does not appear to be positive definite! The smallest eigenvalue
    (= 5.782312e-16) is close to zero. This may be a symptom that the
    model is not identified.
> 
> # Now extract parameter estimates              
> extract_param(bi_lcsm_01)
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: extract_param ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘testthat.R’ [7s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lcsm)
  This is lcsm 0.3.2
  Please report any issues or ideas at:
  https://github.com/milanwiedemann/lcsm/issues
  
  > 
  > test_check("lcsm")
  Parameter estimates for the data simulation are taken from the argument 'model_param'.
  All parameter estimates for the LCSM have been specified in the argument 'model_param'.
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 28 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-extract_param.R:10:1'): (code run outside of `test_that()`) ────
  Error in `vectbl_assign(x[[j]], cells[[j]], value)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─lcsm::extract_param(model_test) at test-extract_param.R:10:0
   2.   ├─base::`[<-`(`*tmp*`, table == "", value = `<lgl>`)
   3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, table == "", value = `<lgl>`)
   4.     └─tibble:::tbl_subassign_matrix(x, j, value, j_arg, substitute(value))
   5.       ├─base::withCallingHandlers(...)
   6.       └─tibble:::vectbl_assign(x[[j]], cells[[j]], value)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 28 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lcsm-parameters.Rmd’ using rmarkdown
--- finished re-building ‘lcsm-parameters.Rmd’

--- re-building ‘v0-longitudinal-plots.Rmd’ using rmarkdown
--- finished re-building ‘v0-longitudinal-plots.Rmd’

--- re-building ‘v1-lavaan-syntax.Rmd’ using rmarkdown
--- finished re-building ‘v1-lavaan-syntax.Rmd’

--- re-building ‘v2-path-diagrams.Rmd’ using rmarkdown
--- finished re-building ‘v2-path-diagrams.Rmd’

--- re-building ‘v3-extract-tutorial.Rmd’ using rmarkdown
Quitting from lines 74-82 (v3-extract-tutorial.Rmd) 
Error: processing vignette ‘v3-extract-tutorial.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘v3-extract-tutorial.Rmd’

--- re-building ‘v4-simulate-data.Rmd’ using rmarkdown
--- finished re-building ‘v4-simulate-data.Rmd’

SUMMARY: processing the following file failed:
  ‘v3-extract-tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  lemna.c:98:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lemna.c:109:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lemna.c:120:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lemna.c:129:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lemna.c:138:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lemna.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘less-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CoverTree
> ### Title: CoverTree - Nearest Neighbor Search
> ### Aliases: CoverTree
> 
> ### ** Examples
> 
> 
> ## ------------------------------------------------
> ## Method `CoverTree$new`
> ## ------------------------------------------------
> 
> data(abalone)
> ct <- CoverTree$new(abalone[1:100,])
> 
> ## ------------------------------------------------
> ## Method `CoverTree$query`
> ## ------------------------------------------------
> 
> res <- ct$query(abalone[1:3,], k=2)
Error in FNN::get.knnx(data = private$X, query = query, k = k, algorithm = "cover_tree") : 
  DLL requires the use of native symbols
Calls: <Anonymous> -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/liGP.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LIMEcoli.Rd:125: Escaped LaTeX specials: \_
checkRd: (-1) Read.Rd:88: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:92: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:98: Escaped LaTeX specials: \#
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checkRd: (-1) Read.Rd:107: Escaped LaTeX specials: \#
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘linea-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: decomping
> ### Title: decomping
> ### Aliases: decomping
> 
> ### ** Examples
> 
> run_model(data = mtcars,dv = 'mpg',ivs = c('wt','cyl','disp'),decompose=FALSE) %>% decomping()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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
Error(s) in re-building vignettes:
  ...
--- re-building ‘litteR-installation.Rmd’ using rmarkdown
--- finished re-building ‘litteR-installation.Rmd’

--- re-building ‘litteR-manual.Rmd’ using rmarkdown
Quitting from lines 206-212 (litteR-manual.Rmd) 
Error: processing vignette ‘litteR-manual.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘litteR-manual.Rmd’

SUMMARY: processing the following file failed:
  ‘litteR-manual.Rmd’

Error: Vignette re-building failed.
Execution halted
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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: \_
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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
Specified C++11: please drop specification unless essential
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checkRd: (-1) SPSloess.Rd:71: Escaped LaTeX specials: \^ \^
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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: \&
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checkRd: (-1) SandwichAnts.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) SandwichAnts2.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:11: Escaped LaTeX specials: \&
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checkRd: (-1) TrafficFlow.Rd:18: Escaped LaTeX specials: \#
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Running examples in ‘LogConcDEAD-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EMmixlcd
> ### Title: Estimate the mixture proportions and component densities using
> ###   EM algorithm
> ### Aliases: EMmixlcd
> ### Keywords: nonparametric multivariate EM classification
> 
> ### ** Examples
> 
> ##Simple bivariate normal data
>   set.seed( 1 )
>   n = 15
>   d = 2
>   props=c( 0.6, 0.4 )
>   shift=2
>   x <- matrix( rnorm( n*d ), ncol = d )
>   shiftvec <- ifelse( runif( n ) > props[ 1 ], 0, shift )
>   x[,1] <- x[,1] + shiftvec
>   EMmixlcd( x, k = 2, max.iter = 2)
*** buffer overflow detected ***: terminated
Aborted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LogConcDEAD.Rnw’ using Sweave
Loading required package: LogConcDEAD
Loading required package: mvtnorm
*** buffer overflow detected ***: terminated
Aborted
Running examples in ‘logconcens-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: logcon
> ### Title: Compute Log-Concave MLE Based on Censored or Exact Data
> ### Aliases: logcon logconcure logConCens
> 
> ### ** Examples
> 
> # A function for artificially censoring exact data
> censor <- function(y, timemat) {
+   tm <- cbind(0,timemat,Inf)
+   n <- length(y)
+   res <- sapply(1:n, function(i){
+             return( c( max(tm[i,][tm[i,] < y[i]]), min(tm[i,][tm[i,] >= y[i]]) ) ) } )
+   return(t(res))
+ }
> 
> 
> 
> # ------------------------
> #  interval censored data
> # ------------------------
> 
> set.seed(20)
> n <- 100
> # generate exact data:
> y <- rgamma(n,3)
> # generate matrix of inspection times:
> itimes <- matrix(rexp(10*n),n,10)
> itimes <- t(apply(itimes,1,cumsum))
> # transform exact data to interval data
> x <- censor(y, itimes)
> # plot both
> plotint(x, imarks=y)
> 
> # Compute censored log-concave MLE
> # (assuming only the censored data is available to us)
> res <- logcon(x)
Error in clc.fixdom(x, preweights, minw, p0, adapt.p0, reduce, red.thresh,  : 
  DLL requires the use of native symbols
Calls: logcon -> clc.fixdom
Execution halted
Found the following significant warnings:
  veclib.h:316:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/logistf.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic_usage.Rmd’ using rmarkdown
--- finished re-building ‘basic_usage.Rmd’

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

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

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

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

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

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

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

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

--- re-building ‘summarizing_results.Rmd’ using rmarkdown
Quitting from lines 108-112 (summarizing_results.Rmd) 
Error: processing vignette ‘summarizing_results.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘summarizing_results.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) butstrap.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.nri.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.s.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.s.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) nri.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) roc.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) roc.s.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.s.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Model_1.cm’ ‘dambacher.dot’ ‘levins.dot’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scio’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  LowRankQP.c:278:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  LowRankQP_init.c:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LowRankQP.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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: \&
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checkRd: (-1) lpridge.Rd:65: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘kerdiest’
checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: \&
Running examples in ‘LTASR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_table_history
> ### Title: Stratify Person Table with Time Varying Co-variate
> ### Aliases: get_table_history
> 
> ### ** Examples
> 
> library(LTASR)
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> 
> #Import example person file
> person <- person_example %>%
+ mutate(dob = as.Date(dob, format='%m/%d/%Y'),
+          pybegin = as.Date(pybegin, format='%m/%d/%Y'),
+          dlo = as.Date(dlo, format='%m/%d/%Y'))
> 
> #Import example history file
> history <- history_example %>%
+   mutate(begin_dt = as.Date(begin_dt, format='%m/%d/%Y'),
+          end_dt = as.Date(end_dt, format='%m/%d/%Y'))
> 
> #Import default rate object
> rateobj <- us_119ucod_19602020
> 
> #Define exposure of interest. Create exp_strata object.The `employed` variable
> #indicates (0/1) periods of employment and will be summed each day of each exposure
> #period. Therefore, this calculates duration of employment in days. The cut-points
> #used below will stratify by person-time with less than and greater than a
> #year of employment (365 days of employment).
> exp1 <- exp_strata(var = 'employed',
+                    cutpt = c(-Inf, 365, Inf),
+                    lag = 0)
> 
> #Stratify cohort by employed variable.
> py_table <- get_table_history(persondf = person,
+                               rateobj = rateobj,
+                               historydf = history,
+                               exps = list(exp1))

Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: get_table_history ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘BasicStrata.Rmd’ using rmarkdown
--- finished re-building ‘BasicStrata.Rmd’

--- re-building ‘HistFile.Rmd’ using rmarkdown
Quitting from lines 135-139 (HistFile.Rmd) 
Error: processing vignette ‘HistFile.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘HistFile.Rmd’

--- re-building ‘SMRbyStrata.Rmd’ using rmarkdown
Quitting from lines 33-54 (SMRbyStrata.Rmd) 
Error: processing vignette ‘SMRbyStrata.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘SMRbyStrata.Rmd’

SUMMARY: processing the following files failed:
  ‘HistFile.Rmd’ ‘SMRbyStrata.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘depth’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
as_string:
  function(x, ...)
as_string.character:
  function(x, sep, conj)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘MachineShop-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TunedInput
> ### Title: Tuned Model Inputs
> ### Aliases: TunedInput TunedModelRecipe TunedInput.recipe
> 
> ### ** Examples
> 
> library(recipes)
Loading required package: dplyr

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: ‘recipes’

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

    step

> data(Boston, package = "MASS")
> 
> rec <- recipe(medv ~ ., data = Boston) %>%
+   step_pca(all_numeric_predictors(), id = "pca")
> 
> grid <- expand_steps(
+   pca = list(num_comp = 1:2)
+ )
> 
> fit(TunedInput(rec, grid = grid), model = GLMModel)
Error in .fit_optim(object, ...) : DLL requires the use of native symbols
Calls: fit ... tryCatchOne -> <Anonymous> -> throw -> .throw -> .throw.error
Execution halted
Specified C++14: please drop specification unless essential
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: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Found the following significant warnings:
  Warning: replacing previous import ‘golem::pkg_version’ by ‘pkgload::pkg_version’ when loading ‘MainExistingDatasets’
  Warning: replacing previous import ‘golem::pkg_name’ by ‘pkgload::pkg_name’ when loading ‘MainExistingDatasets’
  Warning: replacing previous import ‘golem::pkg_path’ by ‘pkgload::pkg_path’ when loading ‘MainExistingDatasets’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MainExistingDatasets.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: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘MALDIquant-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alignSpectra
> ### Title: Align MassSpectrum objects.
> ### Aliases: alignSpectra
> ### Keywords: methods
> 
> ### ** Examples
> 
> ## load package
> library("MALDIquant")
> 
> ## load example data
> data("fiedler2009subset", package="MALDIquant")
> 
> ## running typical workflow
> 
> ## transform intensities
> spectra <- transformIntensity(fiedler2009subset, method="sqrt")
> 
> ## smooth spectra
> spectra <- smoothIntensity(spectra, method="MovingAverage")
> 
> ## baseline correction
> spectra <- removeBaseline(spectra)
Error in .estimateBaselineSnip(x, y, ...) : 
  DLL requires the use of native symbols
Calls: removeBaseline ... .local -> .estimateBaseline -> .estimateBaselineSnip
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MALDIquant-intro.Rnw’ using knitr
Quitting from lines 230-234 (MALDIquant-intro.Rnw) 
Error: processing vignette ‘MALDIquant-intro.Rnw’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘MALDIquant-intro.Rnw’

SUMMARY: processing the following file failed:
  ‘MALDIquant-intro.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘MALDIrppa-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alignPeaks
> ### Title: Compact peak alignment process for 'MassPeaks' objects
> ### Aliases: alignPeaks
> 
> ### ** Examples
> 
> # Load example data
> 
> data(spectra) # list of MassSpectra class objects
> 
> # Some pre-processing
> 
> spectra <- screenSpectra(spectra)$fspectra
The default of 'doScale' is FALSE now for stability;
  set options(mc_doScale_quiet=TRUE) to suppress this (once per session) message
> spectra <- transformIntensity(spectra, method = "sqrt")
> spectra <- wavSmoothing(spectra)
> spectra <- removeBaseline(spectra)
Error in .estimateBaselineSnip(x, y, ...) : 
  DLL requires the use of native symbols
Calls: removeBaseline ... .local -> .estimateBaseline -> .estimateBaselineSnip
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MALDIrppa_vignette_v105.Rmd’ using rmarkdown
Quitting from lines 130-134 (MALDIrppa_vignette_v105.Rmd) 
Error: processing vignette ‘MALDIrppa_vignette_v105.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘MALDIrppa_vignette_v105.Rmd’

--- re-building ‘MALDIrppa_vignette_v110.Rmd’ using rmarkdown
Quitting from lines 125-129 (MALDIrppa_vignette_v110.Rmd) 
Error: processing vignette ‘MALDIrppa_vignette_v110.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘MALDIrppa_vignette_v110.Rmd’

SUMMARY: processing the following files failed:
  ‘MALDIrppa_vignette_v105.Rmd’ ‘MALDIrppa_vignette_v110.Rmd’

Error: Vignette re-building failed.
Execution halted
'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
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘RGtk2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘user.Rmd’ using rmarkdown
Data sets in package 'manydata':

emperors                Emperors database documentation

Quitting from lines 175-179 (user.Rmd) 
Error: processing vignette ‘user.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘user.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [76s/134s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mapbayr)
  
  Attaching package: 'mapbayr'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("mapbayr")
  
  [==============================================================] ID 2/2 (100%)
                                                                                
  Building pchelle_mod ... done.
  (waiting) ...
  Building mod_getparam ... done.
  Building mod12 ... done.
  
  [=============================================>----------------] ID 3/4 ( 75%)
  [==============================================================] ID 4/4 (100%)
                                                                                
  
  [==============================================================] ID 3/3 (100%)
                                                                                
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 591 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (4)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-check_mapbayr_data.R:40:3'): lloq, LLOQ, and BLQ are checked ───
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─base::`[<-`(`*tmp*`, 1, c("LLOQ", "BLQ"), value = `<dbl>`) at test-check_mapbayr_data.R:40:2
   2. └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, c("LLOQ", "BLQ"), value = `<dbl>`) at test-check_mapbayr_data.R:40:2
   3.   └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   4.     └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   5.       ├─base::withCallingHandlers(...)
   6.       └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 591 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    To do
Specified C++11: please drop specification unless essential
Running examples in ‘maraca-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: maraca
> ### Title: maraca package.
> ### Aliases: maraca
> 
> ### ** Examples
> 
> data(hce_scenario_a)
> hce_test <- maraca(
+   data = hce_scenario_a,
+   tte_outcomes = c("Outcome I", "Outcome II", "Outcome III", "Outcome IV"),
+   continuous_outcome = "Continuous outcome",
+   column_names = c(outcome = "GROUP", arm = "TRTP", value = "AVAL0"),
+   arm_levels = c(active = "Active", control = "Control"),
+   compute_win_odds = TRUE
+ )
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: maraca ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘faq.Rmd’ using rmarkdown
--- finished re-building ‘faq.Rmd’

--- re-building ‘maraca.Rmd’ using rmarkdown
Quitting from lines 98-101 (maraca.Rmd) 
Error: processing vignette ‘maraca.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘maraca.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘markets-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: model_initialization
> ### Title: Model initialization
> ### Aliases: model_initialization initialize,diseq_basic-method
> ###   initialize,diseq_deterministic_adjustment-method
> ###   initialize,diseq_directional-method
> ###   initialize,diseq_stochastic_adjustment-method
> ###   initialize,equilibrium_model-method
> 
> ### ** Examples
> 
> simulated_data <- simulate_data(
+   "diseq_basic", 500, 3, # model type, observed entities, observed time points
+   -0.9, 8.9, c(0.3, -0.2), c(-0.03, -0.01), # demand coefficients
+   0.9, 6.2, c(0.03), c(-0.05, 0.02) # supply coefficients
+ )
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: simulate_data ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic_usage.Rmd’ using rmarkdown
Quitting from lines 31-66 (basic_usage.Rmd) 
Error: processing vignette ‘basic_usage.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘basic_usage.Rmd’

--- re-building ‘market_clearing_assessment.Rmd’ using rmarkdown
Quitting from lines 30-57 (market_clearing_assessment.Rmd) 
Error: processing vignette ‘market_clearing_assessment.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘market_clearing_assessment.Rmd’

--- re-building ‘model_details.Rmd’ using rmarkdown
Quitting from lines 32-67 (model_details.Rmd) 
Error: processing vignette ‘model_details.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘model_details.Rmd’

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

SUMMARY: processing the following files failed:
  ‘basic_usage.Rmd’ ‘market_clearing_assessment.Rmd’
  ‘model_details.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
autoplot:
  function(object, ...)
autoplot.bathy:
  function(x, geom, mapping, coast, ...)

fortify:
  function(model, data, ...)
fortify.bathy:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘flashier’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
Running examples in ‘mateable-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dailyOMP
> ### Title: Calculate daily outcrossed mating potential
> ### Aliases: dailyOMP
> 
> ### ** Examples
> 
> pop <- simulateScene()
> omp <- dailyOMP(pop)
Error in get.knn(scene[idsDi, c("x", "y")], k = nbrs) : 
  DLL requires the use of native symbols
Calls: dailyOMP -> unlist -> get.knn
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘investigateMatingScene.Rmd’ using rmarkdown
Quitting from lines 81-82 (investigateMatingScene.Rmd) 
Error: processing vignette ‘investigateMatingScene.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘investigateMatingScene.Rmd’

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) size_t-class.Rd:6: Escaped LaTeX specials: \_
Running examples in ‘matman-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: expandData
> ### Title: Expands a temporal data frame
> ### Aliases: expandData
> 
> ### ** Examples
> 
> data("Amount")
> expandedItems = expandData(Amount,
+     expand = c("item", "itemgroup"),
+     expandTo = "all",
+     valueColumns = c("amount", "value"),
+     latest_values = TRUE,
+     valueLevels = c(0, 0),
+     timestamp = "date",
+     timestampFormat = "day")
Joining with `by = join_by(date, item, itemgroup)`
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: expandData ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following significant warnings:
  ../Core/cholmod_add.c:34:12: warning: argument 3 of type ‘double[2]’ with mismatched bound [-Warray-parameter=]
  ../Core/cholmod_add.c:35:12: warning: argument 4 of type ‘double[2]’ with mismatched bound [-Warray-parameter=]
  ../Cholesky/cholmod_factorize.c:101:12: warning: argument 2 of type ‘double[2]’ with mismatched bound [-Warray-parameter=]
  ../Cholesky/cholmod_rowfac.c:577:12: warning: argument 3 of type ‘double[2]’ with mismatched bound [-Warray-parameter=]
  ../Cholesky/cholmod_rowfac.c:602:12: warning: argument 3 of type ‘double[2]’ with mismatched bound [-Warray-parameter=]
  ../Cholesky/cholmod_rowfac.c:629:12: warning: argument 3 of type ‘double[2]’ with mismatched bound [-Warray-parameter=]
  ../MatrixOps/cholmod_sdmult.c:59:12: warning: argument 3 of type ‘double[2]’ with mismatched bound [-Warray-parameter=]
  ../MatrixOps/cholmod_sdmult.c:60:12: warning: argument 4 of type ‘double[2]’ with mismatched bound [-Warray-parameter=]
  ../Modify/cholmod_rowadd.c:72:12: warning: argument 3 of type ‘double[2]’ with mismatched bound [-Warray-parameter=]
  ../Modify/cholmod_rowadd.c:116:12: warning: argument 3 of type ‘double[2]’ with mismatched bound [-Warray-parameter=]
  ../Modify/cholmod_rowdel.c:72:12: warning: argument 3 of type ‘double[2]’ with mismatched bound [-Warray-parameter=]
  ../Modify/cholmod_rowdel.c:104:12: warning: argument 3 of type ‘double[2]’ with mismatched bound [-Warray-parameter=]
  ../Supernodal/cholmod_super_numeric.c:102:12: warning: argument 3 of type ‘double[2]’ with mismatched bound [-Warray-parameter=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Matrix.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
File ‘Matrix/libs/Matrix.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘validity.o’

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 nor [v]sprintf.

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: maturation_cm
> ### Title: Maturation and Biobanding Metrics
> ### Aliases: maturation_cm
> 
> ### ** Examples
> 
> maturation_cm(data_sample)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: maturation_cm ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
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
Running examples in ‘MazamaLocationUtils-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: table_updateSingleRecord
> ### Title: Update a single known location record in a table
> ### Aliases: table_updateSingleRecord
> 
> ### ** Examples
> 
> library(MazamaLocationUtils)
> 
> locationTbl <- get(data("wa_monitors_500"))
> 
> # Wenatchee
> wenatcheeRecord <- 
+   locationTbl %>% 
+   dplyr::filter(city == "Wenatchee")
> 
> str(wenatcheeRecord)
tibble [1 × 13] (S3: tbl_df/tbl/data.frame)
 $ locationID  : chr "8e54314f43eb8746"
 $ locationName: chr "us.wa_8e5431"
 $ longitude   : num -120
 $ latitude    : num 47.4
 $ elevation   : num 249
 $ countryCode : chr "US"
 $ stateCode   : chr "WA"
 $ countyName  : chr "Chelan"
 $ timezone    : chr "America/Los_Angeles"
 $ houseNumber : chr NA
 $ street      : chr NA
 $ city        : chr "Wenatchee"
 $ zip         : chr "98801"
> 
> wenatcheeID <- wenatcheeRecord$locationID
> 
> locationTbl <- table_updateSingleRecord(
+   locationTbl,
+   locationList = list(
+     locationID = wenatcheeID,
+     locationName = "Wenatchee-Fifth St"
+   )
+ )
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: table_updateSingleRecord ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(MazamaLocationUtils)
  > 
  > test_check("MazamaLocationUtils")
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 24 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-table_getNearestLocation.R:8:3'): table_getNearestLocation() works ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─base::`[<-`(`*tmp*`, 1, 1, value = `<chr>`) at test-table_getNearestLocation.R:8:2
   2. └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, 1, value = `<chr>`) at test-table_getNearestLocation.R:8:2
   3.   └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   4.     └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   5.       ├─base::withCallingHandlers(...)
   6.       └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test-table_updateSingleRecord.R:10:3'): table_updateSingleRecord() works ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─MazamaLocationUtils::table_updateSingleRecord(...) at test-table_updateSingleRecord.R:10:2
   2.   ├─base::`[<-`(`*tmp*`, row, columnName, value = `<chr>`)
   3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, row, columnName, value = `<chr>`)
   4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   5.       └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   6.         ├─base::withCallingHandlers(...)
   7.         └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 24 ]
  Error: Test failures
  Execution halted
Running examples in ‘MazamaTimeSeries-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mts_combine
> ### Title: Combine multiple _mts_ time series objects
> ### Aliases: mts_combine
> 
> ### ** Examples
> 
> library(MazamaTimeSeries)
> 
> ids1 <- example_mts$meta$deviceDeploymentID[1:5]
> ids2 <- example_mts$meta$deviceDeploymentID[4:6]
> ids3 <- example_mts$meta$deviceDeploymentID[8:10]
> 
> mts1 <-
+   example_mts %>%
+   mts_filterMeta(deviceDeploymentID %in% ids1) %>%
+   mts_filterDate(20190701, 20190703)
> 
> mts2 <-
+   example_mts %>%
+   mts_filterMeta(deviceDeploymentID %in% ids2) %>%
+   mts_filterDate(20190704, 20190706)
> 
> mts3 <-
+   example_mts %>%
+   mts_filterMeta(deviceDeploymentID %in% ids3) %>%
+   mts_filterDate(20190705, 20190708)
> 
> mts <- mts_combine(mts1, mts2, mts3)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: mts_combine ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cplexAPI’
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: \#
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  datablock.h:124:42: warning: pointer used after ‘void operator delete(void*)’ [-Wuse-after-free]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MCMCpack.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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) 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: \&
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial version.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  threat-safe-random.h:58:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  threat-safe-random.h:70:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mdgc.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used Fortran compiler: ‘GNU Fortran (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mriTest.Rd:9: Escaped LaTeX specials: \&
checkRd: (-1) riTest.Rd:9: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MethylCapSig’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(meantables)
  > 
  > test_check("meantables")
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 28 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-mean_format.R:11:1'): (code run outside of `test_that()`) ──────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─mtcars %>% mean_table(mpg) %>% ... at test-mean_format.R:11:0
   2. └─meantables::mean_format(...)
   3.   ├─base::`[<-`(`*tmp*`, i, name, value = `<chr>`)
   4.   └─tibble:::`[<-.tbl_df`(`*tmp*`, i, name, value = `<chr>`)
   5.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   6.       └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   7.         ├─base::withCallingHandlers(...)
   8.         └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 28 ]
  Error: Test failures
  Execution halted
'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: \& \$
Running examples in ‘meconetcomp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: edge_comp
> ### Title: Generate a 'microtable' object with paired nodes distributions
> ###   of edges across networks
> ### Aliases: edge_comp
> 
> ### ** Examples
> 
> data(soil_amp_network)
> test <- edge_comp(soil_amp_network)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: edge_comp ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
residualPlots:
  function(model, ...)
residualPlots.expData:
  function(object, ...)

residualPlots:
  function(model, ...)
residualPlots.neModel:
  function(object, ...)

residualPlot:
  function(model, ...)
residualPlot.neModel:
  function(object, ...)

residualPlot:
  function(model, ...)
residualPlot.expData:
  function(object, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘cost-report-analysis.Rmd’ using rmarkdown
Quitting from lines 197-222 (cost-report-analysis.Rmd) 
Error: processing vignette ‘cost-report-analysis.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘cost-report-analysis.Rmd’

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

SUMMARY: processing the following file failed:
  ‘cost-report-analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
'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
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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) 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
VarCorr:
  function(x, sigma, ...)
VarCorr.merModList:
  function(x, sigma, rdig)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 107-109 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘genuMet’
Running examples in ‘metacoder-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: branches
> ### Title: Get "branch" taxa
> ### Aliases: branches
> 
> ### ** Examples
> 
> # Return indexes of branch taxa
> branches(ex_taxmap)
 d  e  f  h  i  j  k  l 
 3  4  5  7  8  9 10 11 
> 
> # Return indexes for a subset of taxa
> branches(ex_taxmap, subset = 2:17)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: branches ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘adam-mapping.Rmd’ using rmarkdown
--- finished re-building ‘adam-mapping.Rmd’

--- re-building ‘ar-grid.Rmd’ using rmarkdown
Quitting from lines 126-131 (ar-grid.Rmd) 
Error: processing vignette ‘ar-grid.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘ar-grid.Rmd’

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

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

--- re-building ‘mockup-table.Rmd’ using rmarkdown
--- finished re-building ‘mockup-table.Rmd’

SUMMARY: processing the following file failed:
  ‘ar-grid.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘metamer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mean_dist_to
> ### Title: Mean minimum distance
> ### Aliases: mean_dist_to
> 
> ### ** Examples
> 
> target <- data.frame(x = rnorm(100), y = rnorm(100))
> data <- data.frame(x = rnorm(100), y = rnorm(100))
> distance <- mean_dist_to(target)
> distance(data)
Error in FNN::get.knnx(target, as.matrix(data), k = 1) : 
  DLL requires the use of native symbols
Calls: distance -> mean -> <Anonymous>
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running examples in ‘metavcov-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: smd.vcov
> ### Title: Computing Variance-Covariance Matrices for Standardized Mean
> ###   Differences
> ### Aliases: smd.vcov
> 
> ### ** Examples
> 
> ######################################################
> # Example: Geeganage2010 data
> # Preparing covarianceS for multivariate meta-analysis
> ######################################################
> data(Geeganage2010)
> ## set the correlation coefficients list r
> r12 <- 0.71
> r.Gee <- lapply(1:nrow(Geeganage2010), function(i){matrix(c(1, r12, r12, 1), 2, 2)})
> 
> computvcov <- smd.vcov(nt = subset(Geeganage2010, select = c(nt_SBP, nt_DBP)),
+                nc = subset(Geeganage2010, select = c(nc_SBP, nc_DBP)),
+                d = subset(Geeganage2010, select = c(SMD_SBP, SMD_DBP)), r = r.Gee,
+                name = c("SMD_SBP", "SMD_DBP"))
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: smd.vcov ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘testthat.R’ [244s/212s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(meteoland)
  Loading required package: sp
  Loading required package: sf
  Linking to GEOS 3.11.1, GDAL 3.6.2, PROJ 9.1.1; sf_use_s2() is TRUE
  Loading required package: stars
  Loading required package: abind
  Package 'meteoland' [ver. 2.0.0]
  > 
  > test_check("meteoland")
  Starting 2 test processes
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 670 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-03_interpolator_object.R:53:3'): create_meteo_interpolator works as expected ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─base::`[<-`(`*tmp*`, 1:5, "elevation", value = `<lgl>`) at test-03_interpolator_object.R:53:2
   2. └─tibble:::`[<-.tbl_df`(`*tmp*`, 1:5, "elevation", value = `<lgl>`) at test-03_interpolator_object.R:53:2
   3.   └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   4.     └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   5.       ├─base::withCallingHandlers(...)
   6.       └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 670 ]
  Error: Test failures
  Execution halted
checkRd: (-1) dslp.Rd:11: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) cardiac.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) plvol.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) sbp.Rd:16: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Running examples in ‘metools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stattable
> ### Title: Descritive statistic table
> ### Aliases: stattable
> 
> ### ** Examples
> 
> v=data.frame(dataone=c(3,2,5,6,5,4),datatwo=c(33,22,55,66,55,44)
+ ,datathree=c(133,122,155,166,155,144))
> stattable(v) #vertical table
# A tibble: 6 × 4
  Statistic `   dataone` `   datatwo` `  datathree`
  <chr>            <dbl>        <dbl>         <dbl>
1 "Min.   "         2            22            122 
2 "1st Qu."         3.25         35.8          136.
3 "Median "         4.5          49.5          150.
4 "Mean   "         4.17         45.8          146.
5 "3rd Qu."         5            55            155 
6 "Max.   "         6            66            166 
> stattable(v,translate=TRUE) #vertical table translated
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: stattable ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
guide_train:
  function(guide, scale, aesthetic)
guide_train.vector:
  function(guide, scale, output)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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’:
No news entries found.
Running ‘testthat.R’ [2s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(MFO)
  > 
  > test_check("MFO")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-MFO.R:38:3'): output of MFO function ───────────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─MFO::MFO(...) at test-MFO.R:38:2
   2.   ├─base::`[<-`(`*tmp*`, MFO_db$FAT <= 0, 3, value = `<dbl>`)
   3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, MFO_db$FAT <= 0, 3, value = `<dbl>`)
   4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   5.       └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   6.         ├─base::withCallingHandlers(...)
   7.         └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test-MFO_kinetics.R:39:3'): output of MFO Kinetics function ─────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─MFO::MFO(...) at test-MFO_kinetics.R:39:2
   2.   ├─base::`[<-`(`*tmp*`, MFO_db$FAT <= 0, 3, value = `<dbl>`)
   3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, MFO_db$FAT <= 0, 3, value = `<dbl>`)
   4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   5.       └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   6.         ├─base::withCallingHandlers(...)
   7.         └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘MGMS2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: characterize_peak
> ### Title: characterize_peak
> ### Aliases: characterize_peak
> 
> ### ** Examples
> 
> spectra.processed.A <- process_monospectra(
+    file=system.file("extdata", "listA.txt", package="MGMS2"),
+    mass.range=c(1000,2200))
Warning in .replaceNegativeIntensityValues(object) :
  Negative intensity values are replaced by zeros.
Warning in .replaceNegativeIntensityValues(object) :
  Negative intensity values are replaced by zeros.
Warning in .replaceNegativeIntensityValues(object) :
  Negative intensity values are replaced by zeros.
Warning in .replaceNegativeIntensityValues(object) :
  Negative intensity values are replaced by zeros.
Warning in .replaceNegativeIntensityValues(object) :
  Negative intensity values are replaced by zeros.
Warning in .replaceNegativeIntensityValues(object) :
  Negative intensity values are replaced by zeros.
Error in .estimateBaselineSnip(x, y, ...) : 
  DLL requires the use of native symbols
Calls: process_monospectra ... .local -> .estimateBaseline -> .estimateBaselineSnip
Execution halted
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package unavailable to check Rd xrefs: ‘DAPAR’
Specified C++11: please drop specification unless essential
checkRd: (-1) IPDNa.Rd:42: Escaped LaTeX specials: \&
Running examples in ‘miceRanger-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addDatasets
> ### Title: addDatasets
> ### Aliases: addDatasets
> 
> ### ** Examples
> 
> data("sampleMiceDefs")
> miceObj <- addDatasets(
+     sampleMiceDefs
+   , datasets = 1
+   , verbose = FALSE
+   , num.threads = 1
+   , num.trees=5
+ )
Error in addDatasets(sampleMiceDefs, datasets = 1, verbose = FALSE, num.threads = 1,  : 
  Evaluation failed with error <Error in get.knnx(data, query, k, algorithm): DLL requires the use of native symbols
>. This is probably our fault - please open an issue at https://github.com/FarrellDay/miceRanger/issues with a reproduceable example.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  do_nothing.h:4:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  do_nothing.c:11:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:7:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nanotimer.c:88:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/microbenchmark.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘migest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: manila_1970
> ### Title: Manila female population 1970 by age
> ### Aliases: manila_1970
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # match table 6 - perhaps small error in children net migration numbers in the published table?
> net_sr(manila_1970, pop0_col = "pop_1960", pop1_col = "pop_1970", 
+        survival_ratio_col = "phl_census_sr", net_children = TRUE)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: net_sr ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
‘:::’ call which should be ‘::’: ‘parallel:::detectCores’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘mipplot-first-steps.Rmd’ using rmarkdown
Quitting from lines 161-172 (mipplot-first-steps.Rmd) 
Error: processing vignette ‘mipplot-first-steps.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘mipplot-first-steps.Rmd’

SUMMARY: processing the following file failed:
  ‘mipplot-first-steps.Rmd’

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
Running ‘testthat.R’ [34s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(miRetrieve)
  > 
  > test_check("miRetrieve")
  [ FAIL 1 | WARN 14 | SKIP 0 | PASS 207 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_loaddata.R:5:1'): (code run outside of `test_that()`) ──────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─miRetrieve::read_pubmed("pubmed_test.txt") at test_loaddata.R:5:0
   2.   ├─base::`[<-`(`*tmp*`, indices_pubmed, "Abstract_no", value = `<chr>`)
   3.   └─tibble:::`[<-.tbl_df`(...)
   4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   5.       └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   6.         ├─base::withCallingHandlers(...)
   7.         └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 14 | SKIP 0 | PASS 207 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(missMethods)
  > 
  > test_check("missMethods")
  Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
    DLL requires the use of native symbols
  Calls: test_check ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
  Execution halted
Specified C++11: please drop specification unless essential
Running examples in ‘missRanger-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: missRanger
> ### Title: Fast Imputation of Missing Values by Chained Random Forests
> ### Aliases: missRanger
> 
> ### ** Examples
> 
> irisWithNA <- generateNA(iris, seed = 34)
> irisImputed <- missRanger(irisWithNA, pmm.k = 3, num.trees = 100)

Missing value imputation by random forests

  Variables to impute:		Sepal.Length, Sepal.Width, Petal.Length, Petal.Width, Species
  Variables used to impute:	Sepal.Length, Sepal.Width, Petal.Length, Petal.Width, Species
iter 1:	.Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols
Calls: missRanger -> pmm -> knnx.index -> get.knnx
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘censored_variables.Rmd’ using rmarkdown
Quitting from lines 49-82 (censored_variables.Rmd) 
Error: processing vignette ‘censored_variables.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘censored_variables.Rmd’

--- re-building ‘missRanger.Rmd’ using rmarkdown
Quitting from lines 81-82 (missRanger.Rmd) 
Error: processing vignette ‘missRanger.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘missRanger.Rmd’

--- re-building ‘multiple_imputation.Rmd’ using rmarkdown
Quitting from lines 34-53 (multiple_imputation.Rmd) 
Error: processing vignette ‘multiple_imputation.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘multiple_imputation.Rmd’

SUMMARY: processing the following files failed:
  ‘censored_variables.Rmd’ ‘missRanger.Rmd’ ‘multiple_imputation.Rmd’

Error: Vignette re-building failed.
Execution halted
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘l1_similarity’
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: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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.
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
Package which this enhances but not available for checking: ‘AnalyzeFMRI’
Running examples in ‘mixgb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: data_clean
> ### Title: Data cleaning
> ### Aliases: data_clean
> 
> ### ** Examples
> 
> rawdata <- nhanes3
> 
> rawdata[4, 4] <- NaN
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: [<- ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
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
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) ssize.propCI.Rd:38: Escaped LaTeX specials: \&
Found the following significant warnings:
  waveform.c:31:4: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  waveform.c:44:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mlbench.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
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: \^
Running examples in ‘mlbplotR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gt_fmt_mlb_headshot
> ### Title: Render Player Headshots in 'gt' Tables
> ### Aliases: gt_fmt_mlb_headshot
> 
> ### ** Examples
> 
> library(gt)
> library(mlbplotR)
> gt_headshot_example <- mlbplotR::load_headshots() %>%
+   head(5) %>%
+   dplyr::select(player_name, savant_id) %>%
+   gt::gt() %>%
+   gt_fmt_mlb_headshot(columns = "savant_id")
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'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
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
Found the following significant warnings:
  ./mlpack/core/data/save_impl.hpp:107:40: warning: ‘bool arma::Mat<eT>::quiet_save(std::ostream&, arma::file_type) const [with eT = long unsigned int; std::ostream = std::basic_ostream<char>]’ is deprecated [-Wdeprecated-declarations]
  ./mlpack/core/data/save_impl.hpp:128:43: warning: ‘bool arma::Mat<eT>::quiet_save(std::ostream&, arma::file_type) const [with eT = long unsigned int; std::ostream = std::basic_ostream<char>]’ is deprecated [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mlpack.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++14: please drop specification unless essential
Running examples in ‘mlquantify-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PWK
> ### Title: Proportion-weighted k-nearest neighbor
> ### Aliases: PWK
> 
> ### ** Examples
> 
> library(caret)
Loading required package: ggplot2
Loading required package: lattice
> library(FNN)
> cv <- createFolds(aeAegypti$class, 2)
> tr <- aeAegypti[cv$Fold1,]
> ts <- aeAegypti[cv$Fold2,]
> 
> # -- Getting a sample from ts with 80 positive and 20 negative instances --
> ts_sample <- rbind(ts[sample(which(ts$class==1),80),],
+                    ts[sample(which(ts$class==2),20),])
> PWK(train=tr[,-which(names(tr)=="class")], y=tr[,"class"], test= ts[,-which(names(ts)=="class")])
Error in get.knnx(data = train, query = test, k = k, algorithm) : 
  DLL requires the use of native symbols
Calls: PWK -> <Anonymous> -> get.knnx
Execution halted
as_learner:
  function(x, ...)
as_learner.PipeOp:
  function(x, clone)

as_learner:
  function(x, ...)
as_learner.Graph:
  function(x, clone)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘mlr3pipelines-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mlr_pipeops_smote
> ### Title: SMOTE Balancing
> ### Aliases: mlr_pipeops_smote PipeOpSmote
> 
> ### ** Examples
> 
> library("mlr3")
> 
> # Create example task
> data = smotefamily::sample_generator(1000, ratio = 0.80)
> data$result = factor(data$result)
> task = TaskClassif$new(id = "example", backend = data, target = "result")
> task$data()
      result          X1         X2
   1:      n 0.383283394 0.95498800
   2:      n 0.039100055 0.50450503
   3:      n 0.839303908 0.65444498
   4:      n 0.511657630 0.08492106
   5:      n 0.401444120 0.89564630
  ---                              
 996:      n 0.820412443 0.36436475
 997:      n 0.909833827 0.23834935
 998:      n 0.003577045 0.76389997
 999:      p 0.561139086 0.29913830
1000:      n 0.816479665 0.26172111
> table(task$data()$result)

  n   p 
795 205 
> 
> # Generate synthetic data for minority class
> pop = po("smote")
> smotedata = pop$train(list(task))[[1]]$data()
Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols
This happened PipeOp smote's $train()
Calls: <Anonymous> ... knearest -> <Anonymous> -> get.knnx -> .handleSimpleError -> h
Execution halted
rd_info:
  function(obj, ...)
rd_info.Learner:
  function(obj)

rd_info:
  function(obj, ...)
rd_info.Task:
  function(obj, section)

rd_info:
  function(obj, ...)
rd_info.Measure:
  function(obj)
See section ‘Generic functions and methods’ 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
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.pdf’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Flury’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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', 'RandomFieldsUtils', 'MoBPSmaps'
Package suggested but not available for checking: ‘ArchR’
'LazyData' is specified without a 'data' directory
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
train:
  function(x, ...)
train.model_grid:
  function(mg, train_all, resample_seed)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
predictor_vars:
  function(model)
predictor_vars.default:
  function(model, data)

response_var:
  function(model)
response_var.default:
  function(model, data)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started-with-modeltime-ensemble.Rmd’ using rmarkdown
Quitting from lines 104-111 (getting-started-with-modeltime-ensemble.Rmd) 
Error: processing vignette ‘getting-started-with-modeltime-ensemble.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘getting-started-with-modeltime-ensemble.Rmd’

--- re-building ‘nested-ensembles.Rmd’ using rmarkdown
Quitting from lines 158-166 (nested-ensembles.Rmd) 
Error: processing vignette ‘nested-ensembles.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘nested-ensembles.Rmd’

--- re-building ‘recursive-ensembles.Rmd’ using rmarkdown
Quitting from lines 151-160 (recursive-ensembles.Rmd) 
Error: processing vignette ‘recursive-ensembles.Rmd’ failed with diagnostics:
ℹ In argument: `.model_desc == "ACTUAL" | .key == "prediction"`.
Caused by error:
! object ‘.key’ not found
--- failed re-building ‘recursive-ensembles.Rmd’

SUMMARY: processing the following files failed:
  ‘getting-started-with-modeltime-ensemble.Rmd’ ‘nested-ensembles.Rmd’
  ‘recursive-ensembles.Rmd’

Error: Vignette re-building failed.
Execution halted
Could not detect any Conda Python Environments with `reticulate::conda_list()`. Conda is required for 'modeltime.gluonts'. Try using `reticulate::install_miniconda()`.

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
Running examples in ‘modeltime-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arima_boost
> ### Title: General Interface for "Boosted" ARIMA Regression Models
> ### Aliases: arima_boost
> 
> ### ** Examples
> 
> library(tidyverse)
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.0     ✔ readr     2.1.4
✔ forcats   1.0.0     ✔ stringr   1.5.0
✔ ggplot2   3.4.1     ✔ tibble    3.2.0
✔ lubridate 1.9.2     ✔ tidyr     1.3.0
✔ purrr     1.0.1     
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
> library(lubridate)
> library(parsnip)
> library(rsample)
> library(timetk)
> library(modeltime)
> 
> 
> # Data
> m750 <- m4_monthly %>% filter(id == "M750")
> 
> # Split Data 80/20
> splits <- initial_time_split(m750, prop = 0.9)
> 
> # MODEL SPEC ----
> 
> # Set engine and boosting parameters
> model_spec <- arima_boost(
+ 
+     # ARIMA args
+     seasonal_period = 12,
+     non_seasonal_ar = 0,
+     non_seasonal_differences = 1,
+     non_seasonal_ma = 1,
+     seasonal_ar     = 0,
+     seasonal_differences = 1,
+     seasonal_ma     = 1,
+ 
+     # XGBoost Args
+     tree_depth = 6,
+     learn_rate = 0.1
+ ) %>%
+     set_engine(engine = "arima_xgboost")
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started-with-modeltime.Rmd’ using rmarkdown
Quitting from lines 137-141 (getting-started-with-modeltime.Rmd) 
Error: processing vignette ‘getting-started-with-modeltime.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘getting-started-with-modeltime.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started-with-modeltime.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘modeltime.resample-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: modeltime_resample_accuracy
> ### Title: Calculate Accuracy Metrics from Modeltime Resamples
> ### Aliases: modeltime_resample_accuracy
> 
> ### ** Examples
> 
> library(modeltime)
> 
> # Mean (Default)
> m750_training_resamples_fitted %>%
+     modeltime_resample_accuracy() %>%
+     table_modeltime_accuracy(.interactive = FALSE)
Warning: There was 1 warning in `dplyr::summarise()`.
ℹ In argument: `dplyr::across(.fns = summary_fns, ...)`.
Caused by warning:
! Using `across()` without supplying `.cols` was deprecated in dplyr 1.1.0.
ℹ Please supply `.cols` instead.
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
Quitting from lines 138-141 (getting-started.Rmd) 
Error: processing vignette ‘getting-started.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘getting-started.Rmd’

--- re-building ‘panel-data.Rmd’ using rmarkdown
Quitting from lines 152-158 (panel-data.Rmd) 
Error: processing vignette ‘panel-data.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘panel-data.Rmd’

SUMMARY: processing the following files failed:
  ‘getting-started.Rmd’ ‘panel-data.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘modernVA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tdVA
> ### Title: R wrapper that accesses C code to fit temporal dependent
> ###   value-added models for two cohorts
> ### Aliases: tdVA
> 
> ### ** Examples
> 
> # Generate data from model 1 of San Martin el al.
> m <- 25 # number of schools
> ni <- 20 # number of students per school
> N <- m*ni
> 
> # specify parameter values to generate data
> beta1 <- 0.6
> beta2 <- 0.75;
> sig21 <- 100;
> sig22 <- 100;
> tau2 <- 100
> phi02 <- 0;
> phi12 <- 0.75;
> phi01 <- 0
> 
> X1 <- rnorm(N, 0, sqrt(200))
> X2 <- rnorm(N, 0, sqrt(200))
> 
> alpha1 <- rnorm(m, phi01, sqrt(tau2))
> alpha2 <- rnorm(m, phi02 + phi12*alpha1, sqrt(tau2*(1-phi12^2)))
> 
> Y1 <- rep(alpha1, each=ni) + X1*beta1 + rnorm(N, 0, sqrt(sig21))
> Y2 <- rep(alpha2, each=ni) + X2*beta2 + rnorm(N, 0, sqrt(sig22))
> 
> # Create school vector indicating to which school each observation belongs
> school1 <- rep(1:m, each=ni)
> school2 <- rep(1:m, each=ni)
> 
> 
> # design matrix only one covariate and no intercept
> X1i <- cbind(X1)
> X2i <- cbind(X2)
> 
> 
> fit <- tdVA(y1=Y1,xmat1=X1i,y2=Y2,xmat2=X2i,
+               school1=school1,school2=school2, groupID=NULL, model=2,
+               var.global=TRUE, nchains=1)
Error in tdVA(y1 = Y1, xmat1 = X1i, y2 = Y2, xmat2 = X2i, school1 = school1,  : 
  DLL requires the use of native symbols
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_Usage.Rmd’ using rmarkdown
Quitting from lines 65-70 (Basic_Usage.Rmd) 
Error: processing vignette ‘Basic_Usage.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Basic_Usage.Rmd’

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

--- re-building ‘Modification_Usage.Rmd’ using rmarkdown
Quitting from lines 70-94 (Modification_Usage.Rmd) 
Error: processing vignette ‘Modification_Usage.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Modification_Usage.Rmd’

--- re-building ‘problem-definition.Rmd’ using rmarkdown
--- finished re-building ‘problem-definition.Rmd’

--- re-building ‘writing-functions-for-moeadr.Rmd’ using rmarkdown
--- finished re-building ‘writing-functions-for-moeadr.Rmd’

SUMMARY: processing the following files failed:
  ‘Basic_Usage.Rmd’ ‘Modification_Usage.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Running examples in ‘molnet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_drug_response_score
> ### Title: Calculate drug response score
> ### Aliases: get_drug_response_score
> 
> ### ** Examples
> 
> data(drug_gene_interactions)
> drug_target_interaction <- make_drug_target(target_molecules='protein',
+ interaction_table=drug_gene_interactions, match_on='gene_name')
> 
> 
> data(drug_targets_example)
> data(differential_score_graph_example)
> drug_response_score <- get_drug_response_score(differential_score_graph_example,
+ drug_targets_example[["targets"]], drug_target_interaction$interaction_table)
Joining with `by = join_by(drug_name)`
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: get_drug_response_score ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Molnet_Vignette.Rmd’ using rmarkdown
Quitting from lines 320-323 (Molnet_Vignette.Rmd) 
Error: processing vignette ‘Molnet_Vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Molnet_Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'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
Running examples in ‘monoClust-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MonoClust
> ### Title: Monothetic Clustering
> ### Aliases: MonoClust
> 
> ### ** Examples
> 
> # Very simple data set
> library(cluster)
> data(ruspini)
> ruspini4sol <- MonoClust(ruspini, nclusters = 4)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: MonoClust ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘monoclust.Rmd’ using rmarkdown
Quitting from lines 53-58 (monoclust.Rmd) 
Error: processing vignette ‘monoclust.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘monoclust.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  ordsampler.c:59:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:113:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:124:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:386:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:544:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:560:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:710:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ordsampler.c:1102:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sampler.c:52:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sampler.c:149:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sampler.c:158:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sampler.c:729:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/monoreg.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘MortalityLaws’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
Error(s) in re-building vignettes:
  ...
--- re-building ‘movMF.Rnw’ using Sweave
Warning: unable to access index for repository https://datacube.wu.ac.at/src/contrib:
  cannot open URL ‘https://datacube.wu.ac.at/src/contrib/PACKAGES’
Warning: package 'corpus.useR.2008.abstracts' is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages

Error: processing vignette ‘movMF.Rnw’ failed with diagnostics:
 chunk 3 (label = corpus-package) 
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'corpus.useR.2008.abstracts'

--- failed re-building 'movMF.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) Context.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) psyfun.boot.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) psyfun.boot.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
checkRd: (-1) genotype_data.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) phenotype_data.Rd:15: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Import.Rmd’ using rmarkdown
--- finished re-building ‘Import.Rmd’

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

--- re-building ‘Workflow.Rmd’ using rmarkdown
Quitting from lines 247-249 (Workflow.Rmd) 
Error: processing vignette ‘Workflow.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘MSclassifR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PeakDetection
> ### Title: Detection of peaks in 'MassSpectrum' objects.
> ### Aliases: PeakDetection
> ### Keywords: Preprocessing
> 
> ### ** Examples
> 
> library("MALDIquant")

This is MALDIquant version 1.22
Quantitative Analysis of Mass Spectrometry Data
 See ‘?MALDIquant’ for more information about this package.

> library("MALDIquantForeign")
> library("MSclassifR")
> 
> 
> ## Load mass spectra and metadata
> data("CitrobacterRKIspectra", "CitrobacterRKImetadata", package = "MSclassifR")
> 
> ## Pre-processing of mass spectra
> spectra <- SignalProcessing(CitrobacterRKIspectra)
[1] "1- Transform intensities with sqrt method"
[1] "2- Smoothing with Wavelet method"
[1] "3- Remove baseline with SNIP method"
Error in .estimateBaselineSnip(x, y, ...) : 
  DLL requires the use of native symbols
Calls: SignalProcessing ... .local -> .estimateBaseline -> .estimateBaselineSnip
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.txt’
'LazyData' is specified without a 'data' directory
Running examples in ‘MSiP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Weighted.matrixModel
> ### Title: Weighted.matrixModel
> ### Aliases: Weighted.matrixModel
> 
> ### ** Examples
> 
> data(SampleDatInput)
> datScoring <- Weighted.matrixModel(SampleDatInput)
Warning: `summarise_each_()` was deprecated in dplyr 0.7.0.
ℹ Please use `across()` instead.
ℹ The deprecated feature was likely used in the dplyr package.
  Please report the issue at <https://github.com/tidyverse/dplyr/issues>.
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: Weighted.matrixModel ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MSiP_tutorial.Rmd’ using knitr
Quitting from lines 46-49 (MSiP_tutorial.Rmd) 
Error: processing vignette ‘MSiP_tutorial.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘MSiP_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'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: \_
Specified C++11: please drop specification unless essential
'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: ‘rqPen::rq.lasso.fit’
MTElasso: no visible global function definition for ‘rq.lasso.fit’
Undefined global functions or variables:
  rq.lasso.fit
Running examples in ‘MTE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MTElasso
> ### Title: MTE-Lasso estimator
> ### Aliases: MTElasso
> 
> ### ** Examples
> 
> set.seed(2017)
> n=200; d=500
> X=matrix(rnorm(n*d), nrow=n, ncol=d)
> beta=c(rep(2,6), rep(0, d-6))
> y=X%*%beta+c(rnorm(150), rnorm(30,10,10), rnorm(20,0,100))
> output.MTELasso=MTElasso(X, y, p=2, t=0.05, method="MTE")
Error in rq.lasso.fit(x = X, y = as.vector(y), lambda = 0.1, intercept = intercept) : 
  could not find function "rq.lasso.fit"
Calls: MTElasso
Execution halted
'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
Running examples in ‘mudata2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: update_datasets
> ### Title: Add documentation to mudata objects
> ### Aliases: update_datasets update_datasets.default update_locations
> ###   update_locations.default update_params update_params.default
> ###   update_columns update_columns.default
> 
> ### ** Examples
> 
> kentvillegreenwood %>%
+   update_datasets("ecclimate", new_key = "new_value") %>%
+   tbl_datasets()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mudata2.Rmd’ using rmarkdown
--- finished re-building ‘mudata2.Rmd’

--- re-building ‘mudata_create.Rmd’ using rmarkdown
Quitting from lines 142-150 (mudata_create.Rmd) 
Error: processing vignette ‘mudata_create.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘mudata_create.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) MultBiplotR-package.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) MultBiplotR-package.Rd:52: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) print.multcompLetters.Rd:20: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
pull:
  function(.data, var, name, ...)
pull.multidplyr_party_df:
  function(.data, var)

ungroup:
  function(x, ...)
ungroup.multidplyr_party_df:
  function(.data, ...)

collect:
  function(x, ...)
collect.multidplyr_party_df:
  function(.data, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Running ‘testthat.R’ [19s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(multidplyr)
  > 
  > test_check("multidplyr")
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 45 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (7)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-dplyr-dual.R:17:3'): joins match local results ─────────────────
  Error in `cluster_call(cluster, !!code)`: Remote computation failed in worker 2
  Caused by error:
  ! DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-dplyr-dual.R:17:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─pf1 %>% right_join(pf2, by = "x") %>% pull(x)
    5. ├─dplyr::pull(., x)
    6. ├─dplyr::right_join(., pf2, by = "x")
    7. └─multidplyr:::right_join.multidplyr_party_df(., pf2, by = "x")
    8.   └─multidplyr:::shard_call_dual(...)
    9.     └─multidplyr::cluster_send(...)
   10.       └─multidplyr::cluster_call(cluster, !!code)
   11.         └─rlang::abort(message, parent = err)
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 45 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘multimorbidity-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: charlson
> ### Title: Charlson Comorbidities
> ### Aliases: charlson
> 
> ### ** Examples
> 
> charlson(dat = prepared_data, id = patient_id, dx = dx, version = 19,
+ version_var = version, outpatient_two = "yes")
Message: You have specified that for a comorbidity to be positvely coded, an individual must have two outpatient claims with it. Please make sure the levels of your variable denoting outpatient type are either 'ot' or 'OT'
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: charlson ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘multimorbidity.Rmd’ using rmarkdown
Quitting from lines 111-112 (multimorbidity.Rmd) 
Error: processing vignette ‘multimorbidity.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘multimorbidity.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘musclesyneRgies-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sMLE
> ### Title: Short-term maximum Lyapunov exponents
> ### Aliases: sMLE
> 
> ### ** Examples
> 
> # Load some primitives
> data("primitives")
> # Calculate sMLE of motor primitives in the muscle synergy space
> short_term_MLE <- sMLE(primitives,
+   mean_period = 80,
+   future_pts = 200,
+   norm = "z",
+   pts = 30
+ )
Error in FNN::get.knn(P[1:upper_limit, ], k = mean_period) : 
  DLL requires the use of native symbols
Calls: sMLE -> <Anonymous>
Execution halted
Running ‘testthat.R’ [17s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(musclesyneRgies)
  > 
  > test_check("musclesyneRgies")
  [ FAIL 1 | WARN 35 | SKIP 0 | PASS 48 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-sMLE.R:4:3'): sMLE works ───────────────────────────────────────
  Error in `FNN::get.knn(P[1:upper_limit, ], k = mean_period)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-sMLE.R:4:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─musclesyneRgies::sMLE(...)
   5.   └─FNN::get.knn(P[1:upper_limit, ], k = mean_period)
  
  [ FAIL 1 | WARN 35 | SKIP 0 | PASS 48 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘mxnorm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_mx_umap
> ### Title: Visualize UMAP dimension reduction algorithm
> ### Aliases: plot_mx_umap
> 
> ### ** Examples
> 
> mx_data = mx_dataset(mxnorm::mx_sample, "slide_id", "image_id",
+   c("marker1_vals","marker2_vals","marker3_vals"),
+   c("metadata1_vals"))
> mx_data = mx_normalize(mx_data, transform="log10",method="None")
> mx_data = run_reduce_umap(mx_data, table="normalized",
+ c("marker1_vals","marker2_vals","marker3_vals"))
Error in FNN::get.knn(X, k) : DLL requires the use of native symbols
Calls: run_reduce_umap ... data2set -> x2set -> x2nn -> find_nn -> FNN_nn -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mxnorm-vignette.Rmd’ using rmarkdown
Quitting from lines 164-170 (mxnorm-vignette.Rmd) 
Error: processing vignette ‘mxnorm-vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘mxnorm-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Errors_Statistic_and_Handling.Rmd’ using rmarkdown
--- finished re-building ‘Errors_Statistic_and_Handling.Rmd’

--- re-building ‘NADIA_examples_and_motivation.Rmd’ using rmarkdown
Quitting from lines 138-156 (NADIA_examples_and_motivation.Rmd) 
Error: processing vignette ‘NADIA_examples_and_motivation.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
This happened PipeOp impute_missRanger_B's $train()
--- failed re-building ‘NADIA_examples_and_motivation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
Found the following significant warnings:
  namespace.c:4:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/namespace.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘exploring-imputed-values.Rmd’ using rmarkdown
Quitting from lines 78-87 (exploring-imputed-values.Rmd) 
Error: processing vignette ‘exploring-imputed-values.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘exploring-imputed-values.Rmd’

--- re-building ‘getting-started-w-naniar.Rmd’ using rmarkdown
--- finished re-building ‘getting-started-w-naniar.Rmd’

--- re-building ‘naniar-visualisation.Rmd’ using rmarkdown
--- finished re-building ‘naniar-visualisation.Rmd’

--- re-building ‘replace-with-na.Rmd’ using rmarkdown
--- finished re-building ‘replace-with-na.Rmd’

--- re-building ‘special-missing-values.Rmd’ using rmarkdown
--- finished re-building ‘special-missing-values.Rmd’

SUMMARY: processing the following file failed:
  ‘exploring-imputed-values.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spatialClust’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.navigatr_nav_menu:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.navigatr_nav_input:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Package which this enhances but not available for checking: ‘openVA’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘ncdfgeom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculate_area_intersection_weights
> ### Title: Area Weighted Intersection (areal implementation)
> ### Aliases: calculate_area_intersection_weights
> 
> ### ** Examples
> 
> b1 = sf::st_polygon(list(rbind(c(-1,-1), c(1,-1),
+                            c(1,1), c(-1,1),
+                            c(-1,-1))))
> b2 = b1 + 2
> b3 = b1 + c(-0.2, 2)
> b4 = b1 + c(2.2, 0)
> b = sf::st_sfc(b1, b2, b3, b4)
> a1 = b1 * 0.8
> a2 = a1 + c(1, 2)
> a3 = a1 + c(-1, 2)
> a = sf::st_sfc(a1,a2,a3)
> plot(b, border = 'red')
> plot(a, border = 'green', add = TRUE)
> 
> sf::st_crs(b) <- sf::st_crs(a) <- sf::st_crs(5070)
> 
> b <- sf::st_sf(b, data.frame(idb = c(1, 2, 3, 4)))
> a <- sf::st_sf(a, data.frame(ida = c(1, 2, 3)))
> 
> sf::st_agr(a) <- sf::st_agr(b) <- "constant"
> 
> a_b <- calculate_area_intersection_weights(a, b)
Loading required namespace: areal
> b_a <- calculate_area_intersection_weights(b, a)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: calculate_area_intersection_weights ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running examples in ‘nestedmodels-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: augment.nested_model_fit
> ### Title: Augment data with predictions
> ### Aliases: augment.nested_model_fit
> 
> ### ** Examples
> 
> data <- dplyr::filter(example_nested_data, id %in% 1:5)
> 
> nested_data <- tidyr::nest(data, data = -c(id, id2))
> 
> model <- parsnip::linear_reg() %>%
+   parsnip::set_engine("lm") %>%
+   nested()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘nestedmodels-limitations.Rmd’ using rmarkdown
Quitting from lines 34-41 (nestedmodels-limitations.Rmd) 
Error: processing vignette ‘nestedmodels-limitations.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘nestedmodels-limitations.Rmd’

--- re-building ‘nestedmodels.Rmd’ using rmarkdown
Quitting from lines 74-77 (nestedmodels.Rmd) 
Error: processing vignette ‘nestedmodels.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘nestedmodels.Rmd’

SUMMARY: processing the following files failed:
  ‘nestedmodels-limitations.Rmd’ ‘nestedmodels.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) netCoin-package.Rd:38: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Running examples in ‘NetCoupler-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nc_estimate_links
> ### Title: Compute model estimates between an external (exposure or
> ###   outcome) variable and a network.
> ### Aliases: nc_estimate_links nc_estimate_exposure_links
> ###   nc_estimate_outcome_links
> 
> ### ** Examples
> 
> 
> standardized_data <- simulated_data %>%
+     nc_standardize(starts_with("metabolite"))
> 
> metabolite_network <- simulated_data %>%
+     nc_standardize(starts_with("metabolite"),
+                    regressed_on = "age") %>%
+     nc_estimate_network(starts_with("metabolite"))
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [24s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(NetCoupler)
  
  Attaching package: 'NetCoupler'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("NetCoupler")
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 29 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-standardize.R:8:1'): (code run outside of `test_that()`) ───────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─... %>% select(starts_with("metabolite")) at test-standardize.R:8:0
    2. ├─dplyr::select(., starts_with("metabolite"))
    3. ├─NetCoupler::nc_standardize(., starts_with("metabolite"), regressed_on = "age")
    4. │ └─NetCoupler:::replace_with_residuals(...)
    5. │   └─... %>% purrr::reduce(dplyr::full_join, by = ".id_variable")
    6. └─purrr::reduce(., dplyr::full_join, by = ".id_variable")
    7.   └─purrr:::reduce_impl(.x, .f, ..., .init = .init, .dir = .dir)
    8.     ├─dplyr (local) fn(out, elt, ...)
    9.     └─dplyr:::full_join.data.frame(out, elt, ...)
   10.       └─dplyr:::join_mutate(...)
   11.         ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   12.         └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   13.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   14.             └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   15.               ├─base::withCallingHandlers(...)
   16.               └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 29 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
Running examples in ‘NetFACS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multiple_netfacs_network
> ### Title: Creates network objects out of the netfacs data
> ### Aliases: multiple_netfacs_network multiple.netfacs.network
> 
> ### ** Examples
> 
> data(emotions_set)
> emo.faces <- netfacs_multiple(
+   data = emotions_set[[1]],
+   condition = emotions_set[[2]]$emotion,
+   ran.trials = 10, # only for example
+   combination.size = 2
+ )
> 
> emo.nets <- multiple_netfacs_network(emo.faces)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: multiple_netfacs_network ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘netfacs_tutorial.Rmd’ using rmarkdown
Quitting from lines 325-332 (netfacs_tutorial.Rmd) 
Error: processing vignette ‘netfacs_tutorial.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘netfacs_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
‘:::’ call which should be ‘::’: ‘lhs:::maximinLHS’
  See the note in ?`:::` about the use of this operator.
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Running examples in ‘NetworkExtinction-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DegreeDistribution
> ### Title: Degree distribution of the network
> ### Aliases: DegreeDistribution
> 
> ### ** Examples
> 
> library(NetworkExtinction)
> data("chilean_intertidal")
> DegreeDistribution(chilean_intertidal)
Joining with `by = join_by(K, Cumulative, LogK, LogCum, Exp)`
Joining with `by = join_by(K, Cumulative, LogK, LogCum, Exp, LogExp, LogPower)`
Joining with `by = join_by(sigma, isConv, finTol, logLik, AIC, BIC, deviance,
df.residual, nobs, model, Normal.Resid, family, AICcNorm)`
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: DegreeDistribution ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘NetworkExtinction.Rmd’ using rmarkdown
Quitting from lines 250-252 (NetworkExtinction.Rmd) 
Error: processing vignette ‘NetworkExtinction.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘NetworkExtinction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map.png’ ‘maze.html’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘nhdplusTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_plus_network_attributes
> ### Title: Add NHDPlus Network Attributes to a provided network.
> ### Aliases: add_plus_network_attributes
> 
> ### ** Examples
> 
> 
> source(system.file("extdata", "walker_data.R", package = "nhdplusTools"))
> 
> test_flowline <- prepare_nhdplus(walker_flowline, 0, 0, FALSE)
Warning in prepare_nhdplus(walker_flowline, 0, 0, FALSE) :
  removing geometry
Warning in prepare_nhdplus(walker_flowline, 0, 0, FALSE) :
  Removed 0 flowlines that don't apply.
 Includes: Coastlines, non-dendritic paths, 
and networks with drainage area less than 0 sqkm, and drainage basins smaller than FALSE
> 
> test_flowline <- data.frame(
+   comid = test_flowline$COMID,
+   tocomid = test_flowline$toCOMID,
+   nameID = walker_flowline$GNIS_ID,
+   lengthkm = test_flowline$LENGTHKM,
+   areasqkm = walker_flowline$AreaSqKM)
> 
> add_plus_network_attributes(test_flowline)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: add_plus_network_attributes ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
Running examples in ‘nlrx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nl_to_points
> ### Title: Get spatial data from metrics.turtles output
> ### Aliases: nl_to_points
> 
> ### ** Examples
> 
> 
> # Load nl object (with spatial output data already attached) from test data:
> nl <- nl_spatial
> 
> # Convert turtle metrics (pxcor/pycor) to spatial point objects:
> results.sf <- nl_to_points(nl, coords="px")
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: nl_to_points ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) nltm.control.Rd:29: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘DAISIE’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
# NOTE - CRAN check detected: limiting maximum number of cores [2/32]

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  veclib.h:302:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nncc.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Found the following significant warnings:
  geodesic.c:57:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nngeo.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Other ideas
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘noisemodel-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: exp_bor_ln
> ### Title: Exponential borderline label noise
> ### Aliases: exp_bor_ln exp_bor_ln.default exp_bor_ln.formula
> 
> ### ** Examples
> 
> # load the dataset
> data(iris2D)
> 
> # usage of the default method
> set.seed(9)
> outdef <- exp_bor_ln(x = iris2D[,-ncol(iris2D)], y = iris2D[,ncol(iris2D)], level = 0.1)
Error in get.knnx(data = x[id_difclass, ], query = x[idx_noise[i], ],  : 
  DLL requires the use of native symbols
Calls: exp_bor_ln -> exp_bor_ln.default -> bord_noise -> get.knnx
Execution halted
'LazyData' is specified without a 'data' directory
Running examples in ‘noisyr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optimise_window_length
> ### Title: Optimise the elements per window for the count matrix approach
> ### Aliases: optimise_window_length
> 
> ### ** Examples
> 
> optimise_window_length(
+   matrix(1:100+runif(100), ncol=5, byrow=TRUE),
+   window.length.min=3, window.length.max=5, iteration.number=5
+ )
Window length optimisation
    number of windows: 3
    minimum window: 3
    maximum window: 5
    window step: 1
    # of iterations: 5
    minimum similar windows: 3
Calculating expression summary and JSE for each window...
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: optimise_window_length ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_noisyr_counts.Rmd’ using rmarkdown
Quitting from lines 137-141 (vignette_noisyr_counts.Rmd) 
Error: processing vignette ‘vignette_noisyr_counts.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘vignette_noisyr_counts.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette_noisyr_counts.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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:16:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/norm.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used Fortran compiler: ‘GNU Fortran (Debian 12.2.0-14) 12.2.0’
Error(s) in re-building vignettes:
  ...
--- re-building ‘continuous.Rmd’ using rmarkdown
--- finished re-building ‘continuous.Rmd’

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

--- re-building ‘none.Rmd’ using rmarkdown
--- finished re-building ‘none.Rmd’

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

--- re-building ‘output.Rmd’ using rmarkdown
Quitting from lines 393-409 (output.Rmd) 
Error: processing vignette ‘output.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘output.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) prepareplot.Rd:64: Escaped LaTeX specials: \#
checkRd: (-1) prepareplot.Rd:68: Escaped LaTeX specials: \#
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
'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) Ardechedata.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) nsRFA-package.Rd:231: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running examples in ‘numbat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_bulk
> ### Title: Aggregate single-cell data into combined bulk expression and
> ###   allele profile
> ### Aliases: get_bulk
> 
> ### ** Examples
> 
> bulk_example = get_bulk(
+     count_mat = count_mat_example,
+     lambdas_ref = ref_hca,
+     df_allele = df_allele_example,
+     gtf = gtf_hg38)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: get_bulk ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential