'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’
Documented arguments not in \usage in documentation object ‘ADMM_EN2’:
  ‘alpha’

Documented arguments not in \usage in documentation object ‘ADMM_EN_SMW’:
  ‘alpha’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘testRmACD’:
  ‘pStar’
'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
Documented arguments not in \usage in documentation object ‘fitSnpNmfArray’:
  ‘maxIter’ ‘acc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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'
Documented arguments not in \usage in documentation object ‘checkDupSignals’:
  ‘tag.list’

Documented arguments not in \usage in documentation object ‘collectStrays’:
  ‘restart’

Documented arguments not in \usage in documentation object ‘findSecondsPerSection’:
  ‘start.time’

Documented arguments not in \usage in documentation object ‘printExploreRmd’:
  ‘valid.detectiosn’

Documented arguments not in \usage in documentation object ‘printLastArray’:
  ‘input’ ‘sections’

Documented arguments not in \usage in documentation object ‘transformSpatial’:
  ‘file’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in documentation object ‘d1’:
  ‘The’ ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (7) NEWS.Rd:74: Tag \dQuote is invalid in a \code block
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘AdaptGauss-package.Rd’:
  ‘MultiModal-package’
Invalid package aliases in Rd file ‘aslm-package.Rd’:
  ‘aslm-package’ ‘asggm-package’
Argument items with no description in Rd object ‘asggm-internal’:
  ‘ansL’ ‘kNodes’ ‘spP’
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
Documented arguments not in \usage in documentation object ‘print.aTest’:
  ‘how’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘ae_count’:
  ‘patients’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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’
Package which this enhances but not available for checking: ‘asreml’
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: \&
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
Invalid package aliases in Rd file ‘aire.zmvm-deprecated.Rd’:
  ‘aire.zmvm-deprecated-package’
'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
Objects in \usage without \alias in documentation object ‘cmf’:
  ‘fitted.cmf’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
'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
Documented arguments not in \usage in documentation object ‘gs’:
  ‘x’ ‘parallel’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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.
Argument items with no description in Rd object ‘MLS’:
  ‘MSE1’
'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
Invalid package aliases in Rd file ‘amelia.package.Rd’:
  ‘amelia-package’
'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
Documented arguments not in \usage in documentation object ‘check_factors’:
  ‘object’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
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
Auto-generated content requiring editing in Rd object ‘rowVars’:
  \arguments: \dots: ‘~~Describe \code{\dots} here~~’
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: \~
Invalid package aliases in Rd file ‘and-package.Rd’:
  ‘reprex-package’
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in documentation object ‘ggplot_gtable’:
  ‘plot’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘crawl_interpolation’:
  ‘pt.colors’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Documented arguments not in \usage in documentation object ‘alternate.sol3’:
  ‘lambda0’

Documented arguments not in \usage in documentation object ‘check.group’:
  ‘k’

Documented arguments not in \usage in documentation object ‘getrow3’:
  ‘lambda0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object ‘apci’:
  ‘\dots’
Argument items with no description in Rd object ‘apci.bar’:
  ‘\dots’
Argument items with no description in Rd object ‘apci.plot’:
  ‘\dots’
Argument items with no description in Rd object ‘apci.plot.heatmap’:
  ‘\dots’
Argument items with no description in Rd object ‘apci.plot.hexagram’:
  ‘first_age’ ‘first_period’ ‘interval’ ‘first_age_isoline’
  ‘first_period_isoline’ ‘isoline_interval’ ‘line_width’ ‘line_color’
  ‘label_size’ ‘label_color’ ‘scale_units’ ‘wrap_cohort_labels’
  ‘quantile’
Argument items with no description in Rd object ‘apci.plot.raw’:
  ‘\dots’
Argument items with no description in Rd object ‘cohortdeviation’:
  ‘\dots’
Argument items with no description in Rd object ‘compute_xcoordinate’:
  ‘p’
Argument items with no description in Rd object ‘compute_ycoordinate’:
  ‘p’ ‘a’
Argument items with no description in Rd object ‘maineffect’:
  ‘\dots’
Argument items with no description in Rd object ‘temp_model’:
  ‘\dots’
Argument items with no description in Rd object ‘tests’:
  ‘\dots’
Documented arguments not in \usage in documentation object ‘apercu’:
  ‘c’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
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’
Argument items with no description in Rd object ‘change_int’:
  ‘enhanced’ ‘ind’ ‘tree’ ‘alpha’ ‘beta’ ‘epsilon’ ‘lambdaN’ ‘aN’
Argument items with no description in Rd object ‘change_int_eta’:
  ‘enhance’ ‘ind’ ‘tree’ ‘alpha’ ‘beta’ ‘eta’ ‘epsilon’ ‘lambdaN’ ‘aN’
  ‘change’ ‘uns’
Argument items with no description in Rd object ‘enhance’:
  ‘tree’ ‘alpha’ ‘beta’ ‘epsilon’ ‘lambdaN’ ‘aN’
Argument items with no description in Rd object ‘enhance_eta’:
  ‘tree’ ‘alpha’ ‘beta’ ‘eta’ ‘epsilon’ ‘lambdaN’ ‘aN’ ‘uns’
Argument items with no description in Rd object ‘rbactrian’:
  ‘n’ ‘m’
Argument items with no description in Rd object ‘transform’:
  ‘tree’ ‘unsampled’ ‘list_depth’ ‘change_depth’
Argument items with no description in Rd object ‘transform_eta’:
  ‘tree’ ‘unsampled’ ‘eta’ ‘list_depth’ ‘change_depth’
Running ‘testthat.R’ [8s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(archeoViz)
  > 
  > test_check("archeoViz")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 70 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test.do_refits_preprocessing.R:34:3'): .do_refits_preprocessing for 3D plots ──
  res[1, ]$x != res[2, ]$y is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 70 ]
  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
Specified C++11: please drop specification unless essential
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Argument items with no description in Rd object ‘dynamac_pkg_bounds_test’:
  ‘obs’ ‘fstat’ ‘tstat’ ‘case’ ‘k’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
Documented arguments not in \usage in documentation object ‘AromaUnitTabularBinaryFile$allocateFromCdf’:
  ‘path’ ‘tags’ ‘footer’

Documented arguments not in \usage in documentation object ‘byChipType.DChipSnpInformation’:
  ‘rootPath’ ‘pattern’ ‘verbose’

Documented arguments not in \usage in documentation object ‘UgpGenomeInformation$byChipType’:
  ‘version’

Documented arguments not in \usage in documentation object ‘calculateResidualSet.FirmaModel’:
  ‘verbose’

Documented arguments not in \usage in documentation object ‘findByChipType.AromaChipTypeAnnotationFile’:
  ‘chipType’ ‘tags’

Documented arguments not in \usage in documentation object ‘fit.SmoothMultiarrayModel’:
  ‘data’

Documented arguments not in \usage in documentation object ‘getCellIndices.ExonChipEffectFile’:
  ‘units’

Documented arguments not in \usage in documentation object ‘getImage.AffymetrixCelFile’:
  ‘palette’

Documented arguments not in \usage in documentation object ‘getOutputDataSet.Transform’:
  ‘force’

Documented arguments not in \usage in documentation object ‘getUnitTypes.AffymetrixCdfFile’:
  ‘map’

Documented arguments not in \usage in documentation object ‘plotMvsX.AffymetrixCelFile’:
  ‘xlim’ ‘xlab’

Documented arguments not in \usage in documentation object ‘process.BackgroundCorrection’:
  ‘force’ ‘verbose’

Documented arguments not in \usage in documentation object ‘readUnits.CnagCfhFile’:
  ‘cdf’

Documented arguments not in \usage in documentation object ‘setArrays.ArrayExplorer’:
  ‘arrays’

Documented arguments not in \usage in documentation object ‘setRestructor.AffymetrixCdfFile’:
  ‘units’

Documented arguments not in \usage in documentation object ‘setupExampleData’:
  ‘dirs’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘fitOne.MultiSourceCopyNumberNormalization’:
  ‘name’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Documented arguments not in \usage in documentation object ‘fit.CopyNumberSegmentationModel’:
  ‘chromosome’

Documented arguments not in \usage in documentation object ‘getPath.Explorer’:
  ‘create’

Documented arguments not in \usage in documentation object ‘process.AromaTransform’:
  ‘force’ ‘verbose’

Documented arguments not in \usage in documentation object ‘process.ChromosomeExplorer’:
  ‘chromosome’

Documented arguments not in \usage in documentation object ‘process.Explorer’:
  ‘arrays’ ‘verbose’

Documented arguments not in \usage in documentation object ‘setArrays.Explorer’:
  ‘arrays’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘RweaveAsciiSetup’:
  ‘stylepath’

Documented arguments not in \usage in documentation object ‘RweaveOrg’:
  ‘stylepath’

Documented arguments not in \usage in documentation object ‘RweavePandoc’:
  ‘stylepath’

Documented arguments not in \usage in documentation object ‘RweaveReST’:
  ‘stylepath’

Documented arguments not in \usage in documentation object ‘RweaveT2t’:
  ‘stylepath’

Documented arguments not in \usage in documentation object ‘RweaveTextile’:
  ‘stylepath’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
Documented arguments not in \usage in documentation object ‘check.args_’:
  ‘rename_’ ‘arg.update_’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘snpar’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Re-building vignettes had CPU time 4.4 times elapsed time
'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
Running examples in ‘avidaR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert_seq_into_org
> ### Title: Converts a genome instruction sequence into a digital organism
> ###   file
> ### Aliases: convert_seq_into_org
> 
> ### ** 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"
+ )
Error: Server responded with status code '526 - It seems that the server SSL certificate is not valid':
- If error persists, please contact server administrator.
Execution halted
'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
Package suggested but not available for checking: ‘lixoftConnectors’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘write.narrative’:
  ‘trials:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd object ‘BartMixVs-package’:
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Error(s) in re-building vignettes:
  ...
--- re-building ‘baseballr.Rmd’ using rmarkdown
--- finished re-building ‘baseballr.Rmd’

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

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

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

Quitting from lines 38-40 [get-id] (using_statcast_pitch_data.Rmd)
Error: processing vignette ‘using_statcast_pitch_data.Rmd’ failed with diagnostics:
HTTP error 503.
--- failed re-building ‘using_statcast_pitch_data.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Earlier versions
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.
Invalid package aliases in Rd file ‘bayesANOVA-package.Rd’:
  ‘bayesANOVA-package’
'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: \$
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
Package suggested but not available for checking: ‘INLA’
Documented arguments not in \usage in documentation object ‘Q_prime’:
  ‘spdean’

Documented arguments not in \usage in documentation object ‘neg_kappa_fn4’:
  ‘spde_mats’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
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.
'LazyData' is specified without a 'data' directory
File ‘bayesQR/libs/bayesQR.so’:
  Found ‘_gfortran_arandom_r8’, possibly from ‘random_number’ (Fortran)
    Objects: ‘QRb_AL_mcmc.o’, ‘QRb_mcmc.o’, ‘QRc_AL_mcmc.o’,
      ‘QRc_mcmc.o’
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Objects: ‘QRb_AL_mcmc.o’, ‘QRb_mcmc.o’, ‘QRc_AL_mcmc.o’,
      ‘QRc_mcmc.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘setseed.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
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.
Argument items with no description in Rd object ‘hmmeantemp’:
  ‘dat’
checkRd: (-1) bart.Rd:271: Escaped LaTeX specials: \_
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.
Found the following files/directories:
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘fabiabreast.txt’
Package suggested but not available for checking: ‘INLA’
Documented arguments not in \usage in documentation object ‘contour_ggplot_params’:
  ‘pos_legend’

Documented arguments not in \usage in documentation object ‘geom_quad_txt’:
  ‘graph’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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: \_
S3 methods shown with full name in documentation object ‘export.bce’:
  ‘export.bce’

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.
'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
'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
Found the following files/directories:
  ‘dump.txt’
Argument items with no description in Rd object ‘bdw’:
  ‘\dots’
Argument items with no description in Rd object ‘plot.bdw’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.bdw’:
  ‘\dots’
Specified C++11: 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.
'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
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
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘print_summary_gibbs_psd_help’:
  ‘flag=T:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘BFpack/libs/BFpack.so’:
  Found ‘_gfortran_arandom_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘bct_continuous_final.o’
  Found ‘_gfortran_random_r4’, possibly from ‘random_number’ (Fortran)
    Object: ‘bct_prior.o’
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘bct_continuous_final.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Objects: ‘bct_continuous_final.o’, ‘bct_prior.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.
Package suggested but not available for checking: ‘SoDA’
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in documentation object ‘getFpTransforms’:
  ‘%bt%’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
Argument items with no description in Rd object ‘h.pr.u’:
  ‘z’ ‘ih’ ‘mu’ ‘sigma’ ‘pk’ ‘K’ ‘H’ ‘n’
Argument items with no description in Rd object ‘hatpai.u’:
  ‘z’ ‘hk1’ ‘hk0’ ‘ph1’ ‘ph0’ ‘sigma1’ ‘sigma0’ ‘mu1’ ‘mu0’ ‘pai’ ‘H’
  ‘n’
Argument items with no description in Rd object ‘ind.u’:
  ‘pr’
Argument items with no description in Rd object ‘lambda.u’:
  ‘nu’
Argument items with no description in Rd object ‘mu.k.u’:
  ‘k’ ‘ik’ ‘z’ ‘sigma’ ‘mu0’
Argument items with no description in Rd object ‘nu.u’:
  ‘ind’ ‘tau’ ‘H’
Argument items with no description in Rd object ‘pai.u’:
  ‘b’ ‘a.pai’ ‘b.pai’
Argument items with no description in Rd object ‘sig.k.u’:
  ‘k’ ‘ik’ ‘z’ ‘mu0’ ‘a0’ ‘b0’
Argument items with no description in Rd object ‘z.pr.u’:
  ‘z’ ‘hk’ ‘mu’ ‘sigma’ ‘ph’ ‘H’ ‘n’
'LazyData' is specified without a 'data' directory
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘lavaan.survey’
Unknown package ‘lavaan.survey’ in Rd xrefs
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Package suggested but not available for checking: ‘ffbase’
Invalid package aliases in Rd file ‘package_bigdist.Rd’:
  ‘package_bigdist-package’
Package suggested but not available for checking: ‘INLA’
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’
'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
'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:
  ‘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.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘select.cfs’:
  ‘select.cfs’

S3 methods shown with full name in documentation object ‘select.fast.filter’:
  ‘select.fast.filter’

S3 methods shown with full name in documentation object ‘select.forward.Corr’:
  ‘select.forward.Corr’

S3 methods shown with full name in documentation object ‘select.forward.wrapper’:
  ‘select.forward.wrapper’

S3 methods shown with full name in documentation object ‘select.inf.chi2’:
  ‘select.inf.chi2’

S3 methods shown with full name in documentation object ‘select.inf.gain’:
  ‘select.inf.gain’

S3 methods shown with full name in documentation object ‘select.inf.symm’:
  ‘select.inf.symm’

S3 methods shown with full name in documentation object ‘select.process’:
  ‘select.process’

S3 methods shown with full name in documentation object ‘select.relief’:
  ‘select.relief’

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.
Found the following files/directories:
  ‘pointshape.dbf’ ‘pointshape.shp’ ‘pointshape.shx’
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
Documented arguments not in \usage in documentation object ‘predict2.em’:
  ‘na.rm’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘bios2cor-package.Rd’:
  ‘bios2cor-package’
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘ONA_compiled’:
  ‘ATN’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘export.dyadic’:
  ‘blauObj’
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
'LazyData' is specified without 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
Documented arguments not in \usage in documentation object ‘.print.summary.ccc’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object ‘id2rownum’:
  ‘ids’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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’
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘augment_kdb’:
  ‘...’

Documented arguments not in \usage in documentation object ‘graph_connected_components’:
  ‘x’

Documented arguments not in \usage in documentation object ‘graph_subgraph’:
  ‘x’

Documented arguments not in \usage in documentation object ‘map’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
'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
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘check_inputs’:
  ‘h_rs’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
Documented arguments not in \usage in documentation object ‘InternalFunctions’:
  ‘metric’ ‘matrix’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
Documented arguments not in \usage in documentation object ‘info’:
  ‘mod_spec’ ‘pkg_spec’

Documented arguments not in \usage in documentation object ‘path’:
  ‘args’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) bpca.Rd:85: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object ‘xtable.bpca’:
  ‘xtable.bpca’

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
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘b_samp’:
  ‘Y’

Documented arguments not in \usage in documentation object ‘betaBlock’:
  ‘Y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Documented arguments not in \usage in documentation object ‘Utility functions’:
  ‘max.len’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object ‘availability.int’:
  ‘v.set’ ‘dir.set’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘subset.int’:
  ‘subset.int’

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.
'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 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
Documented arguments not in \usage in documentation object ‘bs4Table’:
  ‘headTitles’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘plot.bshazard’:
  ‘\dots’
Argument items with no description in Rd object ‘print.bshazard’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.bshazard’:
  ‘\dots’
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
Documented arguments not in \usage in documentation object ‘count’:
  ‘.data’

Documented arguments not in \usage in documentation object ‘unite’:
  ‘.data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘calcIntegralSurv2_cpp’:
  ‘dsurvival’

Documented arguments not in \usage in documentation object ‘.calcIntegralCif_cpp’:
  ‘cif’ ‘CIF_t’

Documented arguments not in \usage in documentation object ‘validFCTs’:
  ‘super.classes’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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: \& \&
'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’
Documented arguments not in \usage in documentation object ‘get_result’:
  ‘out’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘simulateDelegateCore’:
  ‘replicate’ ‘iterations’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘makeEventHistory’:
  ‘type’
Argument items with no description in Rd object ‘plotSeqCount’:
  ‘segColors’
Found the following files/directories:
  ‘MDA231_tree.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
Objects in \usage without \alias in documentation object ‘aweibull7’:
  ‘fweibull6’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
Invalid package aliases in Rd file ‘EcoLinkPredict.Rd’:
  ‘EcoLinkPredict-package’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘validate_cover_cats’:
  ‘cats_target’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘add_catmaply_slider’:
  ‘text_font_color’ ‘categorical_col’

Documented arguments not in \usage in documentation object ‘add_catmaply_traces’:
  ‘categorical_col’

Documented arguments not in \usage in documentation object ‘catmaply_annotations’:
  ‘fig’ ‘text_font_color’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
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: \&
Documented arguments not in \usage in documentation object ‘check_args_compile_pseudo_pop’:
  ‘data_obj’ ‘ci.appr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
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
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
Packages which this enhances but not available for checking:
  'CirceR', 'Capr'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘buildModel’:
  ‘x’ ‘y’

Documented arguments not in \usage in documentation object ‘modelKrigingInternalPredictor’:
  ‘...’

Documented arguments not in \usage in documentation object ‘selfAdapt’:
  ‘nvaleus’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
Documented arguments not in \usage in documentation object ‘evaluate_rule’:
  ‘class’

Documented arguments not in \usage in documentation object ‘tree_leaf_nodes’:
  ‘classes.’ ‘invert.’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object ‘CensMFM-package’:
  \details: ‘...o use the package, including the most important functions ~~’
Unexported objects imported by ‘:::’ calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Documented arguments not in \usage in documentation object ‘blackboost_train’:
  ‘x’ ‘y’

Documented arguments not in \usage in documentation object ‘survival_prob_mboost’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘centralplot’:
  ‘alpha’
'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
Documented arguments not in \usage in documentation object ‘create_epa’:
  ‘clean_pbp_dat’ ‘df’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
S3 methods shown with full name in documentation object ‘select.cglasso’:
  ‘select.cglasso’

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.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘influence-methods’:
  ‘influence’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file ‘jumpointsVar-package.Rd’:
  ‘jumpointsVar-package’
Objects in \usage without \alias in documentation object ‘internals’:
  ‘seg.lm.fit0.gamma’ ‘max.rss’ ‘print.jumpointsVar’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘internals’:
  ‘max.rss’

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.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘ChangePointAnalyzer-package.Rd’:
  ‘ChangePointAnalyzer-package’
Auto-generated content requiring editing in Rd object ‘ChangePointAnalyzer-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Documented arguments not in \usage in documentation object ‘multiplierDSeqfun’:
  ‘MC’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘wallace’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘darts’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘.chkArgs’:
  ‘mode.’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘countreg’
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘ChIPtest-package.Rd’:
  ‘ChIPtest_1.0-package’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
Argument items with no description in Rd object ‘chngpt.test’:
  ‘by.percentile’ ‘both’ ‘main’ ‘prec.weights’ ‘p.val.method’ ‘boot.B’
  ‘keep.fits’
Argument items with no description in Rd object ‘convert.coef predictx threshold.func’:
  ‘include.intercept’ ‘coef.0’ ‘threshold.type’ ‘get.simultaneous’
  ‘return.boot’ ‘fit’ ‘boot.ci.type’ ‘alpha’ ‘verbose’ ‘coef’ ‘xx’
  ‘x.name’
Argument items with no description in Rd object ‘double.hinge’:
  ‘object’ ‘x’ ‘y’ ‘lower.y’ ‘upper.y’ ‘var.type’ ‘boot.ci.type’
  ‘ci.bootstrap.size’ ‘alpha’ ‘save.boot’ ‘ncpus’ ‘lcol’ ‘lwd’ ‘which’
  ‘xlim’ ‘lty’ ‘add.points’ ‘add.ci’ ‘breaks’ ‘mark.chngpt’ ‘xlab’
  ‘ylab’
Argument items with no description in Rd object ‘hinge.test’:
  ‘formula’ ‘cov.interest’ ‘family’ ‘data’ ‘verbose’
Argument items with no description in Rd object ‘performance.unit.test’:
  ‘formula.1’ ‘formula.2’ ‘family’ ‘data’ ‘B’ ‘I’
Argument items with no description in Rd object ‘sim.chngpt’:
  ‘n’ ‘mu.z’ ‘seed’ ‘weighted’ ‘beta’ ‘e.’ ‘b.transition’ ‘sd’ ‘e’
  ‘beta_e’ ‘f’ ‘beta_f’ ‘logistic.slope’ ‘gamma’
Argument items with no description in Rd object ‘sim.hinge’:
  ‘threshold.type’ ‘family’ ‘thres’ ‘X.ditr’ ‘mu.X’ ‘coef.X’ ‘cov.X’
  ‘eps.sd’ ‘seed’ ‘n’
Problems with news in ‘NEWS.md’:
No news entries found.
Objects in \usage without \alias in documentation object ‘choplump-internal’:
  ‘chooseMatrix’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Documented arguments not in \usage in documentation object ‘SearchEmptyClusters’:
  ‘oldcluster’ ‘SSminvec’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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: ‘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
'LazyData' is specified without 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
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
Objects in \usage without \alias in documentation object ‘clinfun-internal’:
  ‘compareROC.paired’ ‘compareROC.unpaired’ ‘getBoundary’
  ‘gsd.bdryconstant’ ‘gsd.drift.efficacy’ ‘gsd.drift.both’ ‘mrcobj’
  ‘smmrcobj’ ‘rocauc’ ‘smrocauc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘internals’:
  ‘lpm.newton2’ ‘lpm.fit’ ‘lpm.newton’ ‘L_lambda’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘auxiliary_functions’:
  ‘edelist’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Objects in \usage without \alias in documentation object ‘internals’:
  ‘.get_ave_sil_width’ ‘.get_withinSS’ ‘print.clustEff’
  ‘print.summary.clustEff’ ‘print.fpcac’ ‘print.summary.fpcac’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘clusterhap_reports’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘calculate_connectivity’:
  ‘datdf’

Documented arguments not in \usage in documentation object ‘dunn_metric’:
  ‘distance’ ‘method’

Documented arguments not in \usage in documentation object ‘evaluate_all_column_dataset’:
  ‘data’

Documented arguments not in \usage in documentation object ‘information_external’:
  ‘info’

Documented arguments not in \usage in documentation object ‘information_internal’:
  ‘info’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘host’:
  ‘short’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
prepare_Rd: NEWS.Rd:395-396: Dropping empty section ‘Changes in version 1.14.0 (2011-06-07, svn r....)’
checkRd: (-1) dtmvnom.Rd:30: 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
Running ‘testthat.R’ [20m/21m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cmcR)
  > 
  > test_check("cmcR",reporter = SummaryReporter)
    adding: bindata/ (stored 0%)
    adding: bindata/data.bin (deflated 58%)
    adding: main.xml (deflated 62%)
    adding: md5checksum.hex (stored 0%)
    adding: bindata/ (stored 0%)
    adding: bindata/data.bin (deflated 58%)
    adding: main.xml (deflated 62%)
    adding: md5checksum.hex (stored 0%)
  comparison: ..
  decision: ..........
  diagnosticTools: Killed
'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: \#
'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’
Documented arguments not in \usage in documentation object ‘feat_sample’:
  ‘locus_group’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘get_superior’:
  ‘stirng’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘disttree’
Documented arguments not in \usage in documentation object ‘lb_calculation’:
  ‘qu.param’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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’
Documented arguments not in \usage in documentation object ‘cocorresp-internal’:
  ‘Y’ ‘eps’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Unexported object imported by a ‘:::’ call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
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
Argument items with no description in Rd object ‘summary.CommunityClimateInput’:
  ‘object’ ‘\dots’
Argument items with no description in Rd object ‘summary.CommunityClimateStatistics’:
  ‘object’ ‘\dots’
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘comf-internal’:
  ‘calcet’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘CAM’
Documented arguments not in \usage in documentation object ‘CopulaSelection’:
  ‘rhoType’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Rd files without \alias:
  ‘CompoundEvents-package.Rd’
'LazyData' is specified without 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
Auto-generated content requiring editing in Rd object ‘concordancer-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'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
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
Documented arguments not in \usage in documentation object ‘checkCountsWholeNumbers’:
  ‘aggregated.samples’

Documented arguments not in \usage in documentation object ‘getGlobalClusterMarkers’:
  ‘min.percent.samples.expression’

Documented arguments not in \usage in documentation object ‘getPercentGlobalClusters’:
  ‘min.cell.count.per.samples’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘postProcessSys’:
  ‘myFile’

Documented arguments not in \usage in documentation object ‘theta_ll’:
  ‘params’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Documented arguments not in \usage in documentation object ‘print_table’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘.validate_scalar’:
  ‘arg_class’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file ‘coopProductGame-package.Rd’:
  ‘coopProducGame-package’
Package suggested but not available for checking: ‘paleobioDB’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘ft’:
  ‘theta’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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) egde.Rd:26: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object ‘mChoose’:
  ‘mc.est.raw’

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
Package suggested but not available for checking: ‘xcms’
'LazyData' is specified without a 'data' directory
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘dCount_dePril_bi’:
  ‘inheritParams’

Documented arguments not in \usage in documentation object ‘dCount_naive_bi’:
  ‘inheritParams’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Found the following files/directories:
  ‘covfefe_inauguration.txt’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘update_current_test’:
  ‘key’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
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
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘BEST’
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
'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
File ‘crimCV/libs/crimCV.so’:
  Found ‘_gfortran_arandom_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘crimCV.o’
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘crimCV.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘crimCV.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
Documented arguments not in \usage in documentation object ‘pinvGamma’:
  ‘logical;’

Documented arguments not in \usage in documentation object ‘qinvGamma’:
  ‘logical;’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major features
    Minor features
checkRd: (-1) handmovement.Rd:9: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘tool’:
  ‘seq’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Objects in \usage without \alias in documentation object ‘internals’:
  ‘findagoodestimator’ ‘safe.pch’ ‘quickpred’ ‘check.in.ctqr’ ‘start’
  ‘ee.u’ ‘ee.cens’ ‘ee.cens.trunc’ ‘ee.icens’ ‘qr.gs’ ‘nobs.ctqr’
  ‘vcov.ctqr’ ‘coef.ctqr’ ‘print.ctqr’ ‘summary.ctqr’
  ‘print.summary.ctqr’ ‘firstep.ct’ ‘firstep.ic’ ‘asy.qr.ct’
  ‘asy.qr.ic’ ‘safesolve’ ‘regularize_corr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘internals’:
  ‘qr.gs’

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.
'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’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘chi2cub2cov’:
  ‘covar’

Documented arguments not in \usage in documentation object ‘cubpq’:
  ‘summary’

Documented arguments not in \usage in documentation object ‘cubshe’:
  ‘makeplot’ ‘summary’

Documented arguments not in \usage in documentation object ‘kkk’:
  ‘Vector’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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: \_ \_ \_
Documented arguments not in \usage in documentation object ‘cvRiskPlot’:
  ‘estimator’

Documented arguments not in \usage in documentation object ‘matrixMetrics’:
  ‘estimator’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package which this enhances but not available for checking: ‘RGtk2’
Documented arguments not in \usage in documentation object ‘compute_stat’:
  ‘K_0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'gurobi', 'rcbc'
Problems with news in ‘NEWS.md’:
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
Documented arguments not in \usage in documentation object ‘tree.filter’:
  ‘nodeList’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running ‘testthat.R’ [71s/87s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dabestr)
  Loading required package: magrittr
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > 
  > test_check("dabestr")
  [ FAIL 1 | WARN 3 | SKIP 9 | PASS 25 ]
  
  ══ Skipped tests (9) ═══════════════════════════════════════════════════════════
  • On CRAN (9): 'test-aesthetics.R:30:3', 'test-aesthetics.R:161:3',
    'test-cumming-plots.R:86:3', 'test-cumming-plots.R:109:3',
    'test-cumming-plots.R:139:3', 'test-cumming-plots.R:160:3',
    'test-gardner-altman-plots.R:21:3', 'test-gardner-altman-plots.R:61:3',
    'test-unquoting.R:62:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cumming-plots.R:8:3'): Cumming two-groups ──────────────────────
  Error in `.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)`: invalid non-character version specification 'x' (type: double)
  Backtrace:
      ▆
   1. ├─testthat::skip_if(getRversion() == 4.1) at test-cumming-plots.R:8:2
   2. │ └─base::isTRUE(condition)
   3. └─base::Ops.numeric_version(getRversion(), 4.1)
   4.   └─base::as.numeric_version(e2)
   5.     └─base::numeric_version(x)
   6.       └─base::.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)
  
  [ FAIL 1 | WARN 3 | SKIP 9 | PASS 25 ]
  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
Documented arguments not in \usage in documentation object ‘default_params_doc’:
  ‘islands’ ‘sort_clade_sizes’

Documented arguments not in \usage in documentation object ‘integral_peak’:
  ‘...’

Documented arguments not in \usage in documentation object ‘sample_relaxed_rate’:
  ‘relaxed_rate_pars’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘mm_run_reg’:
  ‘all_params’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘DANN_distance’:
  ‘x2’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file ‘dap-package.Rd’:
  ‘dap-package’
'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
Documented arguments not in \usage in documentation object ‘plotDataExplorer.single’:
  ‘obj’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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:
  ‘my new data set.rds’
'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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Datastream DWE - now decommissioned by Refinitiv
    CRAN
Documented arguments not in \usage in documentation object ‘dotgetJSONValue’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘zplot’:
  ‘xlim’ ‘ylim’
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
Documented arguments not in \usage in documentation object ‘win_over’:
  ‘parition’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object ‘dbglm-inl’:
  ‘dbglm.iteration’

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.
'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
Documented arguments not in \usage in documentation object ‘a_dcc_mat_est’:
  ‘param’

Documented arguments not in \usage in documentation object ‘dcc_mat_est’:
  ‘param’

Documented arguments not in \usage in documentation object ‘deco_mat_est’:
  ‘param’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
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
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
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object ‘DDPNA-package’:
  \details: ‘...o use the package, including the most important functions ~~’
Argument items with no description in Rd object ‘DEP_Mod_net_plot’:
  ‘\dots’
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
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘getTriContextFraction’:
  ‘trimer.counts.ref’

Documented arguments not in \usage in documentation object ‘norm.it’:
  ‘trimer.counts’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Documented arguments not in \usage in documentation object ‘degreenet-internal’:
  ‘range’ ‘lims’
Objects in \usage without \alias in documentation object ‘degreenet-internal’:
  ‘bootstrapyule’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Documented arguments not in \usage in documentation object ‘boot_f_cor’:
  ‘fun’

Documented arguments not in \usage in documentation object ‘boot_f_pcor’:
  ‘fun’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
GNU make is a SystemRequirements.
Rd files without \alias:
  ‘densityClust-package.Rd’
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
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
checkRd: (-1) barriers.Rd:127: 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:
  ‘.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’
'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
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
'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
Documented arguments not in \usage in documentation object ‘encode_unit’:
  ‘original’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘Nortonbass_startvalgen’:
  ‘param’ ‘startvalgen’

Documented arguments not in \usage in documentation object ‘seqdiffusion’:
  ‘w’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
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’
Documented arguments not in \usage in documentation object ‘residuals_extrap’:
  ‘n’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Invalid package aliases in Rd file ‘RV.Rd’:
  ‘RV-package’
'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
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.
Documented arguments not in \usage in documentation object ‘reshape_into_long’:
  ‘pred_intvar’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘internals_for_distrEx’:
  ‘namestoGather’ ‘namestoGatherNS’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘internal_mlehelpers_for_distrMod’:
  ‘validity.check’

Objects in \usage without \alias in documentation object ‘internals_for_distrMod’:
  ‘.csimpsum’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Assignments in \usage in documentation object ‘internalGenerics’:
  x <- samplesize(object, value)

Documented arguments not in \usage in documentation object ‘internals_for_distr’:
  ‘DClass’
Objects in \usage without \alias in documentation object ‘internals_for_distr’:
  ‘.consolidategaps’ ‘.List’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘diveMove-internal’:
  ‘.diveMatches’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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: \&
Invalid package aliases in Rd file ‘dmaiIntro.Rd’:
  ‘dmaiIntro-package’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object ‘dml_bagging’:
  ‘y,x,d,data,sed’
Argument items with no description in Rd object ‘dml_boosting’:
  ‘y,x,d,data,sed’
Argument items with no description in Rd object ‘dml_ensemble_lm’:
  ‘y,x,d,data,sed’
Argument items with no description in Rd object ‘dml_ensemble_rf’:
  ‘y,x,d,data,sed’
Argument items with no description in Rd object ‘dml_neural_network’:
  ‘y,x,d,data,sed’
Argument items with no description in Rd object ‘dml_random_forest’:
  ‘y,x,d,data,sed’
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
Invalid package aliases in Rd file ‘dnapath2-package.Rd’:
  ‘dnapath2-package’
Auto-generated content requiring editing in Rd object ‘dnapath2-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
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: \#
S3 methods shown with full name in documentation object ‘add.joint.mean.many’:
  ‘all.cond.mean.PO’ ‘all.cond.mean2.PO’

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.
Argument items with no description in Rd object ‘derivType’:
  ‘L’ ‘mu’ ‘eps’
Argument items with no description in Rd object ‘getNewParams.SC’:
  ‘n.fft’
Argument items with no description in Rd object ‘graph.CTMC’:
  ‘\dots’
Argument items with no description in Rd object ‘num.deriv’:
  ‘\dots’
Argument items with no description in Rd object ‘power.coef.one’:
  ‘\dots’
Documented arguments not in \usage in documentation object ‘concDict’:
  ‘text’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
Documented arguments not in \usage in documentation object ‘check_results’:
  ‘error_on_failure’ ‘error_on_warning’

Documented arguments not in \usage in documentation object ‘function_get_comments’:
  ‘thresholds’

Documented arguments not in \usage in documentation object ‘vignette_results_display’:
  ‘vignette_results’ ‘error_on_failure’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Objects in \usage without \alias in documentation object ‘utilities’:
  ‘generators.character’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New features
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
Auto-generated content requiring editing in Rd object ‘downscaledl-package’:
  \references: ‘~~ Literature or other references for background information ~~’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘show,dparserFunction-method’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘isolate_example’:
  ‘...’

Documented arguments not in \usage in documentation object ‘new_drake_deps’:
  ‘restrict’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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: \&
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
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘forecastCovCompiled’:
  ‘obj’ ‘zero’ ‘trend’ ‘estimation.sample’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
'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.
Objects in \usage without \alias in documentation object ‘d.spls.norm1’:
  ‘d.spls.norm2’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Invalid package aliases in Rd file ‘dynConfiR-package.Rd’:
  ‘dynWEV-package’
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
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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    20181118
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘example_table1.csv’ ‘example_table1.txt’ ‘example_table2.csv’
  ‘example_table2.txt’ ‘example_table3.csv’ ‘example_table3.txt’
  ‘table1.csv’ ‘table2.csv’ ‘table2.txt’ ‘table3.txt’ ‘table4.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
'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
Argument items with no description in Rd object ‘e.cluster.decision’:
  ‘reg_data’ ‘log.lambda’
Argument items with no description in Rd object ‘e.cluster.dendrogram’:
  ‘echelon.obj’ ‘n.sim’ ‘cluster.legend.pos’ ‘cluster_reg’ ‘p_rank’
  ‘para’
Argument items with no description in Rd object ‘e.cluster.map’:
  ‘x’ ‘c_separates’ ‘locs’ ‘coo’ ‘rin’ ‘p_rank’ ‘cluster_reg’ ‘n.sim’
  ‘cluster.type’
Argument items with no description in Rd object ‘e.dendrogram’:
  ‘peaks’ ‘locs’ ‘x’ ‘separates’ ‘c_separates’ ‘number’ ‘parents’
  ‘pare_locs’ ‘progeny’ ‘symbols’ ‘col.symbols’ ‘cex.symbols’ ‘lwd’
  ‘col’ ‘ens’ ‘adj.ens’ ‘col.ens’ ‘cex.ens’ ‘limb’
Argument items with no description in Rd object ‘e.dendrogram.axis’:
  ‘main’ ‘ylab’ ‘yaxes’ ‘ylim’ ‘xaxes’ ‘xdper’ ‘dmai’ ‘peaks’ ‘x’
Argument items with no description in Rd object ‘e.main’:
  ‘x’ ‘rin’ ‘T’
Argument items with no description in Rd object ‘e.monte.bin’:
  ‘rin’ ‘cas’ ‘pop’ ‘n.sim’ ‘K’ ‘cluster.type’
Argument items with no description in Rd object ‘e.monte.poi’:
  ‘rin’ ‘cas’ ‘pop’ ‘ex’ ‘n.sim’ ‘K’ ‘cluster.type’
Argument items with no description in Rd object ‘e.profile’:
  ‘peaks’ ‘parents’ ‘separates’
Argument items with no description in Rd object ‘e.scan’:
  ‘x’ ‘locs’ ‘peaks’ ‘c_separates’ ‘parents’ ‘K’
Argument items with no description in Rd object ‘e.scan.pop’:
  ‘x’ ‘locs’ ‘peaks’ ‘c_separates’ ‘parents’ ‘K’ ‘pop’
Argument items with no description in Rd object ‘nlimb’:
  ‘x’ ‘k2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO:
'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 ‘editbl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rows_delete.tbl_dbi
> ### Title: rows_delete implementation for DBI backends.
> ### Aliases: rows_delete.tbl_dbi
> 
> ### ** 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

> 
> conn <- connectDB()
> artists <- tbl(conn, "Artist")
> DBI::dbBegin(conn)
> y <- data.frame(ArtistId = 999)
> rows_delete(
+      x = artists,
+      y = y,
+      by = "ArtistId",
+      in_place = TRUE)
Error: attempt to write a readonly database
Execution halted
Documented arguments not in \usage in documentation object ‘fcf.env’:
  ‘vars’

Documented arguments not in \usage in documentation object ‘getlevels’:
  ‘editarray’

Documented arguments not in \usage in documentation object ‘parseCatEdit’:
  ‘e’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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++11: please drop specification unless essential
Package suggested but not available for checking: ‘lavaan.survey’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Package suggested but not available for checking: ‘eggCountsExtra’
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object ‘rotate_to_equilibrium’:
  ‘xy_may’

Documented arguments not in \usage in documentation object ‘wide.dyads.to.edgelist’:
  ‘fist.var’

Documented arguments not in \usage in documentation object ‘wide.to.long’:
  ‘last.col’ ‘ego.vars’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file ‘HOF-package.Rd’:
  ‘HOF-package’
'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++14: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘colBoxplot4’:
  ‘id’

Documented arguments not in \usage in documentation object ‘elaborator_server’:
  ‘id’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'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
Documented arguments not in \usage in documentation object ‘bbox_to_sp’:
  ‘bbx’

Documented arguments not in \usage in documentation object ‘get_aws_terrain’:
  ‘bbx’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
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) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘enc-package.Rd’
'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)’
Documented arguments not in \usage in documentation object ‘.calcWeights’:
  ‘Data’

Documented arguments not in \usage in documentation object ‘.cardinalDistance’:
  ‘refLat’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘enmSdmX-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: squareCellRast
> ### Title: Create a raster with square cells
> ### Aliases: squareCellRast
> 
> ### ** Examples
> 
> 
> library(sf)
Linking to GEOS 3.12.0, GDAL 3.7.1, PROJ 9.3.0; sf_use_s2() is TRUE
> library(terra)
terra 1.7.46
> 
> # project outline of Madagascar to equal-area:
> data(mad0)
> mad0Ea <- st_transform(mad0, getCRS('madAlbers'))
> 
> n <- 101
> cellSize_meters <- 10E4
> byNumCells <- squareCellRast(mad0Ea, numCells=n)
Error in squareCellRast(mad0Ea, numCells = n) : 
  no slot of name "ptr" for this object of class "SpatExtent"
Execution halted
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'xcms', 'MSnbase'
Package suggested but not available for checking: ‘RStoolbox’
Documented arguments not in \usage in documentation object ‘div_plot’:
  ‘plot_cols’

Documented arguments not in \usage in documentation object ‘seq_plot’:
  ‘plot_cols’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Auto-generated content requiring editing in Rd object ‘EnviroPRA-package’:
  \details: ‘...o use the package, including the most important functions ~~’
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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
Found export directives that require package ‘methods’:
  ‘exportClasses’ ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘epidict’
Documented arguments not in \usage in documentation object ‘dots_to_charlist’:
  ‘call’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
S3 methods shown with full name in documentation object ‘addDrug.Lexis’:
  ‘addDrug.Lexis’

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.
'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
Invalid package aliases in Rd file ‘equateMultiple-package.Rd’:
  ‘EquateMultiple-package’
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
Documented arguments not in \usage in documentation object ‘subnetwork_templates’:
  ‘nams.vattr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘call.ErgmTerm’:
  ‘A’

Objects in \usage without \alias in documentation object ‘ergm-defunct’:
  ‘sociality’

Documented arguments not in \usage in documentation object ‘ergm-deprecated’:
  ‘fname’ ‘varnames’ ‘vartypes’ ‘defaultvalues’ ‘required’
  ‘nw.bipartiteflag’ ‘requirement’ ‘extramessage’ ‘nw.directedflag’ ‘m’
  ‘response’ ‘new’ ‘from.new’ ‘model’ ‘proposal’ ‘eta0’ ‘control’
  ‘verbose’ ‘update.nws’ ‘Clist’ ‘prev.run’ ‘burnin’ ‘samplesize’
  ‘interval’ ‘maxedges’ ‘attrname’ ‘label’ ‘coord’ ‘jitter’ ‘thresh’
  ‘usearrows’ ‘mode’ ‘displayisolates’ ‘interactive’ ‘xlab’ ‘ylab’
  ‘xlim’ ‘ylim’ ‘pad’ ‘label.pad’ ‘displaylabels’ ‘boxed.labels’
  ‘label.pos’ ‘label.bg’ ‘vertex.sides’ ‘vertex.rot’ ‘arrowhead.cex’
  ‘label.cex’ ‘loop.cex’ ‘vertex.cex’ ‘edge.col’ ‘label.col’
  ‘vertex.col’ ‘label.border’ ‘vertex.border’ ‘edge.lty’ ‘label.lty’
  ‘vertex.lty’ ‘edge.lwd’ ‘label.lwd’ ‘edge.len’ ‘edge.curve’
  ‘edge.steps’ ‘loop.steps’ ‘object.scale’ ‘uselen’ ‘usecurve’
  ‘suppress.axes’ ‘vertices.last’ ‘layout.par’ ‘cex.main’ ‘cex.sub’
  ‘seed’ ‘latent.control’ ‘colornames’ ‘latent’ ‘preserve.eattr’

Documented arguments not in \usage in documentation object ‘ergm_state’:
  ‘nw’

Documented arguments not in \usage in documentation object ‘nodal_attributes-API’:
  ‘l’

Documented arguments not in \usage in documentation object ‘summary.ergm_model’:
  ‘response’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘summary.error_interval’:
  ‘summary.error_interval’

S3 methods shown with full name in documentation object ‘summary.measure’:
  ‘summary.measure’

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.
'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
Invalid package aliases in Rd file ‘esaBcv_package.Rd’:
  ‘esaBcv_package-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
S3 methods shown with full name in documentation object ‘ETAS-internal’:
  ‘Smooth.catalog’

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.
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘poly_clip’:
  ‘x’ ‘y’

Documented arguments not in \usage in documentation object ‘setup_gpar’:
  ‘x’

Documented arguments not in \usage in documentation object ‘setup_grobs’:
  ‘centers’

Documented arguments not in \usage in documentation object ‘update_list’:
  ‘x’ ‘val’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running ‘testthat.R’ [4s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(europepmc)
  > 
  > test_check("europepmc")
  [ FAIL 1 | WARN 0 | SKIP 20 | PASS 0 ]
  
  ══ Skipped tests (20) ══════════════════════════════════════════════════════════
  • On CRAN (20): 'test_annotations_by_id.r:4:3', 'test_epmc_citations.r:4:3',
    'test_epmc_db.r:4:3', 'test_epmc_db_count.r:4:3', 'test_epmc_details.r:4:3',
    'test_epmc_ftxt.r:4:3', 'test_epmc_ftxt_book.r:4:3', 'test_epmc_hits.r:4:3',
    'test_epmc_hits_trend.R:4:3', 'test_epmc_hits_trend.R:30:3',
    'test_epmc_lablinks.r:4:3', 'test_epmc_lablinks_count.r:4:3',
    'test_epmc_profile.r:4:3', 'test_epmc_profile.r:22:3',
    'test_epmc_refs.r:4:3', 'test_epmc_search.r:4:3', 'test_epmc_search.r:54:3',
    'test_epmc_search_by_doi.r:4:3', 'test_epmc_tm.r:4:3',
    'test_epmc_tm_count.r:4:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_epmc_hits_trend.R:39:3'): epmc_hits_trend synonym search works correctly ──
  <http_404/http_400/http_error/error/condition>
  Error in `rebi_GET(path = paste0(rest_path(), "/profile"), query = args)`: Not Found (HTTP 404).
  Backtrace:
      ▆
   1. └─europepmc::epmc_hits_trend("malaria", period = 2012:2016, synonym = FALSE) at test_epmc_hits_trend.R:39:2
   2.   └─base::lapply(...)
   3.     └─europepmc (local) FUN(X[[i]], ...)
   4.       └─europepmc::epmc_profile(queryforall, synonym)
   5.         └─europepmc:::rebi_GET(...)
   6.           └─httr::stop_for_status(req)
  
  [ FAIL 1 | WARN 0 | SKIP 20 | PASS 0 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘doHttrRequest’:
  ‘params’ ‘customConfig’

Documented arguments not in \usage in documentation object ‘errorMessage’:
  ‘test_me’

Documented arguments not in \usage in documentation object ‘isError’:
  ‘test_me’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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 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
Documented arguments not in \usage in documentation object ‘borrOrderingInternal’:
  ‘n.cntrl’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
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: \&
Argument items with no description in Rd object ‘plot.expectreg’:
  ‘\dots’
Argument items with no description in Rd object ‘update.expectreg’:
  ‘\dots’
'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
Package suggested but not available for checking: ‘hoa’
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: \&
Argument items with no description in Rd object ‘fbvpot’:
  ‘cutoff’
checkRd: (-1) outlierPlot.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) outlierPlot.Rd:32: Escaped LaTeX specials: \$
Documented arguments not in \usage in documentation object ‘getQQLimit’:
  ‘N’ ‘rho’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘exuberdata’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Argument items with no description in Rd object ‘complete.log.likelihood_Sj’:
  ‘z’
Auto-generated content requiring editing in Rd object ‘getStuffForDIC’:
  \details: ‘If necessary, more details than the description above’
'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
Auto-generated content requiring editing in Rd object ‘procrustes_switching’:
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd object ‘rsp_exact’:
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd object ‘rsp_full_sa’:
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd object ‘rsp_partial_sa’:
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd object ‘weighted_procrustes_switching’:
  \details: ‘If necessary, more details than the description above.’
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object ‘Factoshiny-package’:
  \references: ‘~~ Literature or other references for background information ~~’
  \seealso: ‘~~ Optional links to other man pages, e.g. ~~’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘jss.Rmd’ using rmarkdown
Error: processing vignette ‘jss.Rmd’ failed with diagnostics:
invalid non-character version specification ‘x’ (type: double)
--- failed re-building ‘jss.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Documented arguments not in \usage in documentation object ‘.get_default_sign_size’:
  ‘outcome_type’

Documented arguments not in \usage in documentation object ‘.get_iteration_data’:
  ‘file_dir’

Documented arguments not in \usage in documentation object ‘extract_model_vimp’:
  ‘feature_similarity_table’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
Documented arguments not in \usage in documentation object ‘check_cache’:
  ‘data’ ‘reset’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘kkk’:
  ‘Vector’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘Get_C_R_K_Q’:
  ‘have_noise’

Documented arguments not in \usage in documentation object ‘Sample_KF_post’:
  ‘C0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
'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: \&
Rd files without \alias:
  ‘FastPCS-package.Rd’
Specified C++11: please drop specification unless essential
checkRd: (-1) Scent.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) Traffic.Rd:44: Escaped LaTeX specials: \&
Invalid package aliases in Rd file ‘fastR-package.Rd’:
  ‘fastR-package’
Specified C++11: please drop specification unless essential
checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
Invalid package aliases in Rd file ‘FastRCS-package.Rd’:
  ‘FastPCS-package’
.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
Documented arguments not in \usage in documentation object ‘bin’:
  ‘Integer’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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.
'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’
Unexported object imported by a ‘:::’ call: ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
Argument items with no description in Rd object ‘getbasispenalty’:
  ‘Lfdobj’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘vert.txt’
S3 methods shown with full name in documentation object ‘xtable.fdt’:
  ‘xtable.fdt’ ‘xtable.fdt.multiple’ ‘xtable.fdt_cat.multiple’

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
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
Documented arguments not in \usage in documentation object ‘url_base’:
  ‘url’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Documented arguments not in \usage in documentation object ‘linregEst’:
  ‘rank_lim’ ‘Umodel’

Documented arguments not in \usage in documentation object ‘m2c’:
  ‘CC’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘checkStream’:
  ‘skipChecks’

Documented arguments not in \usage in documentation object ‘cpp_detectCUSUMMeanSinglePrechange’:
  ‘BL’

Documented arguments not in \usage in documentation object ‘cpp_detectEWMAMeanSinglePrechange’:
  ‘BL’

Documented arguments not in \usage in documentation object ‘makeStreamMeanChangeR’:
  ‘x’

Documented arguments not in \usage in documentation object ‘update_Omega’:
  ‘m_new’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘recode_subquad’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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++11: please drop specification unless essential
Package suggested but not available for checking: ‘MicrobeDS’
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘filename.Rd’:
  ‘filename-package’
'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
Documented arguments not in \usage in documentation object ‘print.data.frame.ff’:
  ‘.data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package 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
Documented arguments not in \usage in documentation object ‘plot_data_type’:
  ‘client_id’ ‘client_secret’ ‘refresh_token’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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:
  'nCDunnett', '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
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
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: \&
'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
Invalid package aliases in Rd file ‘FLPS-package.Rd’:
  ‘FLPS-package’
Malformed Description field: should contain one or more complete sentences.
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
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
Documented arguments not in \usage in documentation object ‘RD_impData’:
  ‘cutoff’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘hl.factor.number’:
  ‘w’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
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
File ‘frailtypack/libs/frailtypack.so’:
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Objects: ‘Integrale_mult_scl.o’, ‘autres_fonctions.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘autres_fonctions.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.
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
Documented arguments not in \usage in documentation object ‘assert.surface’:
  ‘surf’

Documented arguments not in \usage in documentation object ‘check.dtype.for.data’:
  ‘silent’

Documented arguments not in \usage in documentation object ‘fread3’:
  ‘filehandle:’

Documented arguments not in \usage in documentation object ‘fwrite3’:
  ‘filehandle:’ ‘data:’

Documented arguments not in \usage in documentation object ‘polygon.soup.to.indexed.mesh’:
  ‘face_vertex_coords’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘freqdom.transpose’:
  ‘S’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Packages suggested but not available for checking: 'dggrids', 'INLA'
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘draw.colorbar’:
  ‘coloredmesh’

Documented arguments not in \usage in documentation object ‘extend_neighbors’:
  ‘min_dotp_threshold’

Documented arguments not in \usage in documentation object ‘surf.sphere.spatialfilter’:
  ‘gaussian_weight’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
Argument items with no description in Rd object ‘fsdam’:
  ‘verbose’ ‘which’
Argument items with no description in Rd object ‘plot.classes’:
  ‘\dots’
Argument items with no description in Rd object ‘predict.fsim’:
  ‘\dots’
Argument items with no description in Rd object ‘predict.lm’:
  ‘\dots’
Argument items with no description in Rd object ‘predict.sfpl’:
  ‘\dots’
Argument items with no description in Rd object ‘predict.sfplsim.FASSMR’:
  ‘\dots’
Argument items with no description in Rd object ‘print.summary.mfplsim’:
  ‘\dots’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘imp_small_gaps_WMA’:
  ‘Data’ ‘univariate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Objects in \usage without \alias in documentation object ‘funData-constructor’:
  ‘funData’

Objects in \usage without \alias in documentation object ‘irregFunData-constructor’:
  ‘irregFunData’

Objects in \usage without \alias in documentation object ‘multiFunData-constructor’:
  ‘multiFunData’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘plot.funData’:
  ‘plot.funData’

S3 methods shown with full name in documentation object ‘plot.irregFunData’:
  ‘plot.irregFunData’

S3 methods shown with full name in documentation object ‘plot.multiFunData’:
  ‘plot.multiFunData’

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.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘build_limits_lookup’:
  ‘min_preds’ ‘max_preds’ ‘min_ratio’ ‘max_ratio’ ‘draw_unadjusted’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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’
Documented arguments not in \usage in documentation object ‘loggedOutput’:
  ‘future’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘mandelbrot’:
  ‘Z’ ‘xmid’ ‘ymid’ ‘side’ ‘resolution’ ‘maxIter’ ‘tau’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Package required but not available: ‘cBioPortalData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid package aliases in Rd file ‘GAabbreviate-internal.Rd’:
  ‘GAabbreviation-package’
Documented arguments not in \usage in documentation object ‘splitQTL_comment’:
  ‘output_qtls’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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: \_
Invalid package aliases in Rd file ‘gamlss.mx.package.Rd’:
  ‘gamlss.mix-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
Documented arguments not in \usage in documentation object ‘as.gapdata’:
  ‘labels_df’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Documented arguments not in \usage in documentation object ‘lrr_plot’:
  ‘plot_cols’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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: \&
Documented arguments not in \usage in documentation object ‘align_peaks’:
  ‘gc_peak_df’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
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
Objects in \usage without \alias in documentation object ‘geepack-internal’:
  ‘genZcor’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Auto-generated content requiring editing in Rd object ‘gemlog-package’:
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
'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
Invalid package aliases in Rd file ‘GenBinom-package.Rd’:
  ‘GenbinomApps-package’
Package suggested but not available for checking: ‘genderdata’
Documented arguments not in \usage in documentation object ‘CirDisp’:
  ‘x’

Documented arguments not in \usage in documentation object ‘CirKurt’:
  ‘x’ ‘na.rm’

Documented arguments not in \usage in documentation object ‘CirSD’:
  ‘x’

Documented arguments not in \usage in documentation object ‘CirSkew’:
  ‘x’

Documented arguments not in \usage in documentation object ‘CirVar’:
  ‘x’

Documented arguments not in \usage in documentation object ‘MeanDir’:
  ‘x’

Documented arguments not in \usage in documentation object ‘impact’:
  ‘na.rm’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘expand’:
  ‘x’

Documented arguments not in \usage in documentation object ‘%bq%’:
  ‘x’

Documented arguments not in \usage in documentation object ‘%bt%’:
  ‘x’

Documented arguments not in \usage in documentation object ‘stftcalc’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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) SandP500.Rd:4: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object ‘generalizedwendland-internal’:
  ‘numint.abstol (default: 1e-3)’ ‘numint.reltol (default: 1e-3)’
  ‘numint.qag_key (default: 0)’ ‘numint.subintervals (default: 0)’
  ‘interp.method (default: 'none')’ ‘interp.num_support (default: 0)’
  ‘cov.reparameterize (default: TRUE)’ ‘cov.eps (default:
  .Machine$double.eps^0.5)’ ‘cov.d_value (default: 2)’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file ‘GenlibR-package.Rd’:
  ‘GenlibR-package’
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘bin.levels’:
  ‘variable’

Documented arguments not in \usage in documentation object ‘info.mox’:
  ‘y:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Documented arguments not in \usage in documentation object ‘adj_spconsist_arr_window_globstd’:
  ‘a’

Documented arguments not in \usage in documentation object ‘elsa_fuzzy_vector’:
  ‘nbslitw’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
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
Documented arguments not in \usage in documentation object ‘variables_query’:
  ‘variables’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) getopt.Rd:60: Escaped LaTeX specials: \#
Package suggested but not available for checking: ‘argon2’
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘attract_by_distance’:
  ‘prop_start’ ‘prop_end’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [10s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggasym)
  > 
  > test_check("ggasym")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 260 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-asymmetrise_stats.R:14:3'): stats asymmetrization works ────────
  Error in `.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)`: invalid non-character version specification 'x' (type: double)
  Backtrace:
      ▆
   1. └─base::Ops.numeric_version(utils::packageVersion("broom"), 0.7) at test-asymmetrise_stats.R:14:2
   2.   └─base::as.numeric_version(e2)
   3.     └─base::numeric_version(x)
   4.       └─base::.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 260 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggasym-corrr.Rmd’ using rmarkdown
--- finished re-building ‘ggasym-corrr.Rmd’

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

Quitting from lines 82-84 [prep_results] (ggasym-stats.Rmd)
Error: processing vignette ‘ggasym-stats.Rmd’ failed with diagnostics:
invalid non-character version specification ‘x’ (type: double)
--- failed re-building ‘ggasym-stats.Rmd’

SUMMARY: processing the following file failed:
  ‘ggasym-stats.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
Documented arguments not in \usage in documentation object ‘labels.rpart’:
  ‘pretty:’

Documented arguments not in \usage in documentation object ‘rpart_labels’:
  ‘model’ ‘...’

Documented arguments not in \usage in documentation object ‘rpart_segments’:
  ‘model’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
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
Documented arguments not in \usage in documentation object ‘interpolateDataFrame’:
  ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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.
Argument items with no description in Rd object ‘isADMG’:
  ‘amat’
Argument items with no description in Rd object ‘isAG’:
  ‘amat’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘package-ggparallel.Rd’:
  ‘package-ggparallel-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  'captioner', 'lixoftConnectors'
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘operator’:
  ‘x’ ‘y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
Documented arguments not in \usage in documentation object ‘decoration’:
  ‘nudge_npcx’ ‘nudge_npcy’

Documented arguments not in \usage in documentation object ‘generic_plot’:
  ‘pc.out’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘ggplot_gtable’:
  ‘plot’

Documented arguments not in \usage in documentation object ‘zzz-internal’:
  ‘latex’ ‘ggplot’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
Documented arguments not in \usage in documentation object ‘add_scale’:
  ‘domain’

Documented arguments not in \usage in documentation object ‘bin_vector’:
  ‘width’ ‘origin’ ‘closed’ ‘pad’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Unknown package ‘IC2’ 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
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
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mlr3proba’
Argument items with no description in Rd object ‘GLD.lm.full.surv’:
  ‘maxit’
Argument items with no description in Rd object ‘GLD.lm.surv’:
  ‘maxit’
Documented arguments not in \usage in documentation object ‘getBeta’:
  ‘thetaConrol’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
checkRd: (-1) glmc.control.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) glmc.control.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object ‘VarCorr.glmmTMB’:
  ‘extra’

Documented arguments not in \usage in documentation object ‘expandDoubleVert’:
  ‘a’

Documented arguments not in \usage in documentation object ‘mkTMBStruc’:
  ‘zioffset’ ‘doffset’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘glmpathcr-internal’:
  ‘fit’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘fun.svd_1’:
  ‘X’

Documented arguments not in \usage in documentation object ‘fun.svd_2’:
  ‘X’

Documented arguments not in \usage in documentation object ‘fun.svd_3’:
  ‘X’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘gmeta/libs/gmeta.so’:
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘confdistint.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘confdistint.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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'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
Rd files without \alias:
  ‘goodpractice-package.Rd’
Package suggested but not available for checking: ‘ganalytics’
Documented arguments not in \usage in documentation object ‘doHttrRequest’:
  ‘session’ ‘params’

Documented arguments not in \usage in documentation object ‘get_google_token’:
  ‘shiny_return_token’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Documented arguments not in \usage in documentation object ‘maxLevelBP’:
  ‘org’

Documented arguments not in \usage in documentation object ‘maxLevelCC’:
  ‘org’

Documented arguments not in \usage in documentation object ‘maxLevelMF’:
  ‘org’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file ‘00.GPArotateDF.Rd’:
  ‘00.GPArotateDF-package’
Documented arguments not in \usage in documentation object ‘estimate_noise_nn’:
  ‘n_thread’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
'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
Documented arguments not in \usage in documentation object ‘fmpareto_HR_MLE’:
  ‘method’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object ‘HistPCA’:
  ‘ggplot’
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/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(greenclust)
  > 
  > test_check("greenclust")
  Step 1:  Cluster 1 + 6
  
            [,1] [,2]
  1            1    7
  2            2    8
  3            3    9
  4            4   10
  Cluster 1   11   23
  
  Chi-squared: 1.64 
  p-value: 0.8014 
  R-squared: 0.9887 
  
  
  Step 2:  Cluster 2 + 4
  
            [,1] [,2]
  1            1    7
  2            2    8
  Cluster 2    7   19
  Cluster 1   11   23
  
  Chi-squared: 1.6 
  p-value: 0.6596 
  R-squared: 0.9635 
  
  
  Step 3:  Cluster 3 + 2
  
            [,1] [,2]
  Cluster 3    3   15
  Cluster 2    7   19
  Cluster 1   11   23
  
  Chi-squared: 1.47 
  p-value: 0.479 
  R-squared: 0.8869 
  
  
  Step 4:  Cluster 4 + Cluster 1
  
            [,1] [,2]
  Cluster 3    3   15
  Cluster 4   18   42
  
  Chi-squared: 1.25 
  p-value: 0.2633 
  R-squared: 0.7539 
  
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 127 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-greenclust-main.R:48:5'): greenclust stops when x has an initial chi-squared of zero ──
  Error in `.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)`: invalid non-character version specification 'x' (type: double)
  Backtrace:
      ▆
   1. └─testthat::skip_if_not_installed("greenclust", minimum_version = 1.1) at test-greenclust-main.R:48:4
   2.   └─base::Ops.numeric_version(installed_version, minimum_version)
   3.     └─base::as.numeric_version(e2)
   4.       └─base::numeric_version(x)
   5.         └─base::.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 127 ]
  Error: Test failures
  Execution halted
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object ‘load_map’:
  ‘unity’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘prCaSetRownames’:
  ‘rownames.fn’

Documented arguments not in \usage in documentation object ‘prClearPCAclass’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
S3 methods shown with full name in documentation object ‘groc.fit’:
  ‘groc.fit’

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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘groupsubsetselection/libs/groupsubsetselection.so’:
  Found ‘_gfortran_random_r4’, possibly from ‘random_number’ (Fortran)
    Object: ‘gss.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.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘fit_grp.Rd’:
  ‘grplasso-package’
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’
Objects in \usage without \alias in documentation object ‘GSA-internal’:
  ‘est.s0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file ‘gsb-package.Rd’:
  ‘gsb-package’
'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
'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
Documented arguments not in \usage in documentation object ‘traits’:
  ‘efo_id’ ‘trait’ ‘uri’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) luzdat.Rd:21: Escaped LaTeX specials: \~
File ‘GWEX/libs/GWEX.so’:
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘GWex_disag.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
'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
'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
Documented arguments not in \usage in documentation object ‘num_knots_generator’:
  ‘d’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Argument items with no description in Rd object ‘haplo.em.fitter’:
  ‘random.start ’
Argument items with no description in Rd object ‘haplo.model.frame’:
  ‘control’
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘modeling-package.Rd’:
  ‘modeling-package’
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
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'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
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GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
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
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Documented arguments not in \usage in documentation object ‘check_arg_for_hyperslab_func’:
  ‘cur_arg’

Documented arguments not in \usage in documentation object ‘extract_dim’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
Documented arguments not in \usage in documentation object ‘compute_counts’:
  ‘init’ ‘inflow’

Documented arguments not in \usage in documentation object ‘compute_values’:
  ‘counts’

Documented arguments not in \usage in documentation object ‘create_demographic_table’:
  ‘...’

Documented arguments not in \usage in documentation object ‘eval_strategy_newdata’:
  ‘model’

Documented arguments not in \usage in documentation object ‘get_state_value_names’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Objects in \usage without \alias in documentation object ‘autocomplete-defunct’:
  ‘autocomplete’

Objects in \usage without \alias in documentation object ‘set_auth-defunct’:
  ‘set_auth’

Objects in \usage without \alias in documentation object ‘set_proxy-defunct’:
  ‘set_proxy’

Objects in \usage without \alias in documentation object ‘traffic-defunct’:
  ‘traffic’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘check.id_attributes’:
  ‘inner_class’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘check_known_repos’:
  ‘known_packages’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘defunct’:
  ‘anova.mean’ ‘print.glht.mmc.multicomp’ ‘coef.arima.HH’ ‘glht.mmc’
  ‘plot.odds.ratio’ ‘persp.plane’ ‘persp.floor’ ‘persp.back.wall.x’
  ‘persp.back.wall.y’ ‘persp.setup’ ‘plot.hov’ ‘plot.hov.bf’
  ‘plot.matchMMC’ ‘seqplot.forecast’

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.
Argument items with no description in Rd object ‘residual.plots.lattice’:
  ‘X’
Found export directives that require package ‘methods’:
  ‘exportClasses’ ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'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’
Argument items with no description in Rd object ‘qcplate’:
  ‘dat’
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
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd object ‘HistDAWass-package’:
  \details: ‘...o use the package, including the most important functions ~~’
Invalid package aliases in Rd file ‘histogram-package.Rd’:
  ‘histogramtools-package’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘trackr’
Package which this enhances but not available for checking: ‘HadoopStreaming’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
html_describe_con: multiple local function definitions for ‘g’ with
  different formal arguments
Argument items with no description in Rd object ‘bpower’:
  ‘odds.ratio’ ‘percent.reduction’ ‘n1’
Argument items with no description in Rd object ‘describe’:
  ‘data’ ‘subset’
Argument items with no description in Rd object ‘find.matches’:
  ‘xcase’ ‘ycase’ ‘idcase’
Argument items with no description in Rd object ‘labcurve’:
  ‘x’ ‘width’ ‘col.’ ‘empty.method’ ‘xlab’
Argument items with no description in Rd object ‘varclus’:
  ‘data’ ‘subset’ ‘lty’ ‘col’
Documented arguments not in \usage in documentation object ‘bootstrapfun’:
  ‘DoF’ ‘n_sample’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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: \&
Auto-generated content requiring editing in Rd object ‘HMVD-package’:
  \details: ‘...o use the package, including the most important functions ~~’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
Invalid package aliases in Rd file ‘hoardeR-package.Rd’:
  ‘R/hoardeR-package’
Argument items with no description in Rd object ‘bid2’:
  ‘numattable1’ ‘playerseats1’ ‘blinds1’ ‘dealer1’ ‘b3’ ‘b4’ ‘round1’
  ‘ntable1’ ‘decision1’
Argument items with no description in Rd object ‘calcwin1’:
  ‘numattable1’ ‘playerseats1’ ‘b3’ ‘b7’
Argument items with no description in Rd object ‘mycount1’:
  ‘x’
Argument items with no description in Rd object ‘mygraphics1’:
  ‘numattable1’ ‘playerseats1’ ‘chips1’ ‘blinds1’ ‘dealer1’ ‘b3’ ‘b4’
  ‘b5’ ‘b6’ ‘b7’ ‘chips2’ ‘ntable1’ ‘myfast1’ ‘chipstart1’ ‘name1’
  ‘lowercut1’
Argument items with no description in Rd object ‘nothing1’:
  ‘x’
Argument items with no description in Rd object ‘onepair1’:
  ‘x’
Argument items with no description in Rd object ‘straight1’:
  ‘x’
Argument items with no description in Rd object ‘straightdraw1’:
  ‘x’
Argument items with no description in Rd object ‘strflsh1’:
  ‘x’ ‘y’
Argument items with no description in Rd object ‘trip1’:
  ‘x’
Argument items with no description in Rd object ‘twopair1’:
  ‘x’
Argument items with no description in Rd object ‘writebets1’:
  ‘b9’ ‘y1’ ‘numattable1’ ‘b3’ ‘playerseats1’ ‘chips1’ ‘chips2’ ‘over1’
  ‘myfast1’ ‘name1’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘plot.hopitCP’:
  ‘plotf’

Documented arguments not in \usage in documentation object ‘sigma.hopit’:
  ‘model’

Documented arguments not in \usage in documentation object ‘summary.hopit’:
  ‘control’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘hpoPlot-package.Rd’
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘.E3’:
  ‘i’ ‘M’

Documented arguments not in \usage in documentation object ‘.E4’:
  ‘i’ ‘M’

Documented arguments not in \usage in documentation object ‘hrm.0w.2s’:
  ‘group’

Documented arguments not in \usage in documentation object ‘hrm.0w.3s’:
  ‘group’

Documented arguments not in \usage in documentation object ‘hrm.0w.4s’:
  ‘group’

Documented arguments not in \usage in documentation object ‘hrm.0w.5s’:
  ‘group’

Documented arguments not in \usage in documentation object ‘hrm.1f’:
  ‘group’

Documented arguments not in \usage in documentation object ‘hrm.1w.0f’:
  ‘factor1’

Documented arguments not in \usage in documentation object ‘hrm.2w.2f’:
  ‘factor’

Documented arguments not in \usage in documentation object ‘hrm.mv.1w.1f’:
  ‘H’ ‘text’

Documented arguments not in \usage in documentation object ‘hrm.mv.internal’:
  ‘alpha’ ‘H’ ‘text’

Documented arguments not in \usage in documentation object ‘hrm.test.1.none’:
  ‘factor1’ ‘factor2’

Documented arguments not in \usage in documentation object ‘hrm.test.1.one’:
  ‘group’ ‘factor2’

Documented arguments not in \usage in documentation object ‘hrm.test.2.one’:
  ‘factor2’

Documented arguments not in \usage in documentation object ‘hrm.test.2.two’:
  ‘group’

Documented arguments not in \usage in documentation object ‘hrm.test.3.three’:
  ‘group’

Documented arguments not in \usage in documentation object ‘hrm.test.4.four’:
  ‘group’

Documented arguments not in \usage in documentation object ‘hrm.test.5.five’:
  ‘group’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘imageplot’:
  ‘\dots’
'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
Documented arguments not in \usage in documentation object ‘prGetStyle’:
  ‘styles’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘FramedHTML’:
  ‘DiagnosticsPath’
Invalid package aliases in Rd file ‘httkpop.Rd’:
  ‘httkpop-package’
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
Documented arguments not in \usage in documentation object ‘as.redactor’:
  ‘expr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘as.redactor’:
  ‘expr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
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
Running ‘testthat.R’ [21s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hyd1d)
  'df.gauging_data' locally stored at
  /tmp/RtmpBMzUDn/df.gauging_data_latest.RDS
  was last downloaded 2023-09-08 15:12:51 CEST
  > 
  > test_check("hyd1d")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 136 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_getW.R:83:5'): getPegelonlineW ─────────────────────────────────
  Error: unable to find an inherited method for function 'fromJSON' for signature 'content = "logical", handler = "missing"'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test_getW.R:83:4
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─hyd1d::getPegelonlineW("SCHOENA", Sys.Date() - 10)
   5.   └─RJSONIO::fromJSON(w_string)
   6.     └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 136 ]
  Error: Test failures
  Execution halted
Invalid package aliases in Rd file ‘HydroMe-package.Rd’:
  ‘HydroMe2-package’
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: \#
Documented arguments not in \usage in documentation object ‘scan.txt.Witec’:
  ‘nwl’ ‘remove.zerospc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘print.Hypervolume’:
  ‘...’
Argument items with no description in Rd object ‘summary.Hypervolume’:
  ‘...’
'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: ‘gutenbergr’
Objects in \usage without \alias in documentation object ‘btibgen’:
  ‘ibdgen’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘pairSum’:
  ‘cov1’ ‘cov2’
'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
Documented arguments not in \usage in documentation object ‘GetCustomKmerCounts’:
  ‘custom.range’

Documented arguments not in \usage in documentation object ‘GetMutationLoadsFromStrelkaIDVCFs’:
  ‘list.of.vcfs’

Documented arguments not in \usage in documentation object ‘GetMutationLoadsFromStrelkaSBSVCFs’:
  ‘split.vcfs’

Documented arguments not in \usage in documentation object ‘PlotPPM’:
  ‘pwm’

Documented arguments not in \usage in documentation object ‘PlotPPMToPdf’:
  ‘list.of.pwm’

Documented arguments not in \usage in documentation object ‘ReadStrelkaSBSVCF’:
  ‘suppress.discarded.variants.warnings’

Documented arguments not in \usage in documentation object ‘ReadVCF’:
  ‘num.of.cores’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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: \$
S3 methods shown with full name in documentation object ‘orlm’:
  ‘orlm.forboot.fixed’ ‘orlm.forboot’

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.
'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) pulmonary.Rd:13: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rggobi’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in documentation object ‘internals’:
  ‘iplotMain’ ‘segments.circle’ ‘griddat’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘internals’:
  ‘plot.page’

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.
Package suggested but not available for checking: ‘IFCdata’
Documented arguments not in \usage in documentation object ‘fastAny’:
  ‘obj’

Documented arguments not in \usage in documentation object ‘getSTATSREPORT’:
  ‘...’

Documented arguments not in \usage in documentation object ‘split_feat’:
  ‘operators’

Documented arguments not in \usage in documentation object ‘toXML2_features_def’:
  ‘features’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘.compl’:
  ‘imgfile’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Invalid package aliases in Rd file ‘image-package.Rd’:
  ‘image-package’
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: ‘accdata’
Documented arguments not in \usage in documentation object ‘new_impactr_peaks’:
  ‘acc_signal:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Rd files without \alias:
  ‘imputeYn-package.Rd’
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++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: \&
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
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Argument items with no description in Rd object ‘combine.NULL’:
  ‘x’ ‘y’
Argument items with no description in Rd object ‘combine’:
  ‘x’ ‘y’
Argument items with no description in Rd object ‘combine.character’:
  ‘x’ ‘y’
Argument items with no description in Rd object ‘combine.list’:
  ‘x’ ‘y’
Argument items with no description in Rd object ‘findGeneric’:
  ‘fname’ ‘envir’
Argument items with no description in Rd object ‘fixPackageFileNames’:
  ‘list’
Argument items with no description in Rd object ‘forfun’:
  ‘FUN’
Argument items with no description in Rd object ‘get_S3_primitive_generics’:
  ‘include_group_generics’
Argument items with no description in Rd object ‘get_internal_S3_generics’:
  ‘primitive’
Argument items with no description in Rd object ‘is_primitive_in_base’:
  ‘fname’
Argument items with no description in Rd object ‘prefixed.lines’:
  ‘src’ ‘\dots’
Argument items with no description in Rd object ‘print.allfun’:
  ‘x’ ‘\dots’
Argument items with no description in Rd object ‘whole.word’:
  ‘\dots’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
Package suggested but not available for checking: ‘cmdstanr’
Malformed Title field: should not end in a period.
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
'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
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object ‘IntervalSurgeon-package’:
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
Error(s) in re-building vignettes:
  ...
--- re-building ‘inTextSummaryTable-advanced.Rmd’ using rmarkdown
--- finished re-building ‘inTextSummaryTable-advanced.Rmd’

--- re-building ‘inTextSummaryTable-aesthetics.Rmd’ using rmarkdown
--- finished re-building ‘inTextSummaryTable-aesthetics.Rmd’

--- re-building ‘inTextSummaryTable-createTables.Rmd’ using rmarkdown
--- finished re-building ‘inTextSummaryTable-createTables.Rmd’

--- re-building ‘inTextSummaryTable-exportTables.Rmd’ using rmarkdown
--- finished re-building ‘inTextSummaryTable-exportTables.Rmd’

--- re-building ‘inTextSummaryTable-introduction.Rmd’ using rmarkdown
--- finished re-building ‘inTextSummaryTable-introduction.Rmd’

--- re-building ‘inTextSummaryTable-standardTables.Rmd’ using rmarkdown
--- finished re-building ‘inTextSummaryTable-standardTables.Rmd’

--- re-building ‘inTextSummaryTable-visualization.Rmd’ using rmarkdown

Quitting from lines 152-169 [visualization-a4document] (inTextSummaryTable-visualization.Rmd)
Error: processing vignette ‘inTextSummaryTable-visualization.Rmd’ failed with diagnostics:
invalid non-character version specification ‘x’ (type: double)
--- failed re-building ‘inTextSummaryTable-visualization.Rmd’

SUMMARY: processing the following file failed:
  ‘inTextSummaryTable-visualization.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object ‘selectRuleRRF’:
  ‘target’
'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
Documented arguments not in \usage in documentation object ‘rawAvgCost-deprecated’:
  ‘cost.transf’ ‘in.millions’ ‘confidence.interval’ ‘minimum.year’
  ‘maximum.year’ ‘final.year’ ‘incomplete.year.threshold’
  ‘incomplete.year.weights’ ‘gam.k’ ‘mars.nprune’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘surveyspec’
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
Documented arguments not in \usage in documentation object ‘chars_collapse’:
  ‘collapse’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘iprior_package.Rd’:
  ‘iprior_package-package’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object ‘mrbayes’:
  ‘unlink’ ‘constraint’
Argument items with no description in Rd object ‘mrbayes.lset’:
  ‘partition’
Argument items with no description in Rd object ‘multistate’:
  ‘model’
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
Documented arguments not in \usage in documentation object ‘print.cat_output’:
  ‘object’

Documented arguments not in \usage in documentation object ‘[[<-,Itempool,numeric,missing-method’:
  ‘...’

Documented arguments not in \usage in documentation object ‘[[<-,Response_set,numeric,missing-method’:
  ‘...’

Documented arguments not in \usage in documentation object ‘[[<-,Testlet,numeric,missing-method’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘print.Item’:
  ‘print.Item’

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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘xcms’
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘islasso-internal’:
  ‘modelX’ ‘.checkinput’ ‘.startpoint’ ‘.islasso’
  ‘checkinput.islasso.path’ ‘startpoint.islasso.path’
  ‘islasso.path.fit.glm’ ‘islasso.path.fitter2’ ‘interpolate’ ‘makeHyp’
  ‘printHyp’ ‘cislasso’ ‘ci.fitted.islasso’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘.assignmentMaker’:
  ‘.precip_raster’ ‘.precip_SD_raster’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
GNU make is a SystemRequirements.
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’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Invalid package aliases in Rd file ‘ivprobit-package.Rd’:
  ‘ivProbit-package’
Auto-generated content requiring editing in Rd object ‘ivregEX-package’:
  \references: ‘~~ Literature or other references for background information ~~’
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.
Rd files without \alias:
  ‘jackknifeKME-package.Rd’
'LazyData' is specified without a 'data' directory
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
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
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’
Documented arguments not in \usage in documentation object ‘paste_coef’:
  ‘parlemts’

Documented arguments not in \usage in documentation object ‘paste_linpred’:
  ‘parlemts’ ‘matname’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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:
    pre-release juicr (2017 - 2021)
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
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
Rd files without \alias:
  ‘karaoke-package.Rd’
Found the following files/directories:
  ‘song.wav’ ‘song4karaoke.wav’
'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
prepare_Rd: NEWS.Rd:58: Dropping empty section ‘kelvin INITIAL VERSION 1.0-0 (2012-05-30)’
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘covQualNested’:
  ‘covBet’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘bw.abram.temp’:
  ‘bw.abram.temp’

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.
Documented arguments not in \usage in documentation object ‘calc_PGtheta_R’:
  ‘model’ ‘iter’

Documented arguments not in \usage in documentation object ‘make_wsz_cpp’:
  ‘info’ ‘initialized’

Documented arguments not in \usage in documentation object ‘read_dfm_cpp’:
  ‘W_raw’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘b_wincred_get’:
  ‘backend’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    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
S3 methods shown with full name in documentation object ‘unlist.constr’:
  ‘unlist.constr’

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.
'LazyData' is specified without a 'data' directory
'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
Invalid package aliases in Rd file ‘knotR-package.Rd’:
  ‘knot-package’
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘variablekey.Rnw’ using Sweave
Error: processing vignette ‘variablekey.Rnw’ failed with diagnostics:
Running ‘texi2dvi’ on ‘variablekey.tex’ failed.
LaTeX errors:
! TeX capacity exceeded, sorry [input stack size=10000].
\protect ->\noexpand \protect 
                              \noexpand 
l.662 ... variable key\label{sec:Editing-the-key}}
                                                  
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'variablekey.Rnw'

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

Error: Vignette re-building failed.
Execution halted
S3 methods shown with full name in documentation object ‘stat.functions’:
  ‘kappa.cor’

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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘extract_and_augment_context’:
  ‘...additional’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
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
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.
Packages suggested but not available for checking:
  'akmedoids', 'clusterCrit'
Unknown packages ‘clusterCrit’, ‘akmedoids’ in Rd xrefs
Objects in \usage without \alias in documentation object ‘latrend-generics’:
  ‘nClusters’ ‘clusterProportions’ ‘clusterTrajectories’ ‘compose’
  ‘converged’ ‘externalMetric’ ‘estimationTime’ ‘fit’
  ‘fittedTrajectories’ ‘getArgumentDefaults’ ‘getArgumentExclusions’
  ‘getLabel’ ‘getLcMethod’ ‘getName’ ‘getShortName’ ‘idVariable’
  ‘metric’ ‘plotFittedTrajectories’ ‘plotClusterTrajectories’ ‘postFit’
  ‘postprob’ ‘predictAssignments’ ‘predictForCluster’ ‘predictPostprob’
  ‘prepareData’ ‘preFit’ ‘qqPlot’ ‘responseVariable’ ‘strip’
  ‘timeVariable’ ‘trajectoryAssignments’ ‘validate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Documented arguments not in \usage in documentation object ‘moments2’:
  ‘...’

Documented arguments not in \usage in documentation object ‘skeleton’:
  ‘endogeneous’ ‘...’

Documented arguments not in \usage in documentation object ‘vcov2-internal’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
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
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’
Packages suggested but not available for checking: 'xcms', 'MSnbase'
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘H_inv’:
  ‘trunc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘.choose_best_subjects’:
  ‘best’ ‘candidate’

Documented arguments not in \usage in documentation object ‘.normalize_props’:
  ‘keep_all_items’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘top.topic.words’:
  ‘alpha’
'LazyData' is specified without 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
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
Invalid package aliases in Rd file ‘LEANR-package.Rd’:
  ‘LEAN-package’
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
Invalid package aliases in Rd file ‘learnn.Rd’:
  ‘learnn-package’
Documented arguments not in \usage in documentation object ‘backward_step’:
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in documentation object ‘backward_step_IM’:
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in documentation object ‘forward_step’:
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in documentation object ‘forward_step_IM’:
  ‘empty_start_dataset’ ‘fit’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object ‘lemon-ggproto’:
  ‘side’ ‘is.primary’

Documented arguments not in \usage in documentation object ‘render_gpar’:
  ‘name’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘get_generic’:
  ‘mismatch’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gpclib’
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
Documented arguments not in \usage in documentation object ‘CoordInBounds’:
  ‘direction’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'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: \# \#
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S3 methods shown with full name in documentation object ‘BIC.threshold’:
  ‘BIC.threshold’

S3 methods shown with full name in documentation object ‘BIC.threshold.ggm’:
  ‘BIC.threshold.ggm’

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.
'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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Documented arguments not in \usage in documentation object ‘MassAcylCer’:
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Documented arguments not in \usage in documentation object ‘MassPEo’:
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Documented arguments not in \usage in documentation object ‘findMS2precursor’:
  ‘minint’ ‘maxint’

Documented arguments not in \usage in documentation object ‘joinAnnotationResults’:
  ‘simplifyAnnotation’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘get_variable’:
  ‘x’ ‘name’ ‘mustExist’ ‘create’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
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Found the following files/directories:
  ‘tTestTable.rda’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Author
    Maintainer
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Invalid package aliases in Rd file ‘Lock5Data-package.Rd’:
  ‘Lock5Data-package’
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Argument items with no description in Rd object ‘spec.emb’:
  ‘A’
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘dlogitnorm’:
  ‘sigma’
Argument items with no description in Rd object ‘invlogit’:
  ‘q’ ‘\dots’
Argument items with no description in Rd object ‘logit’:
  ‘p’ ‘\dots’
Argument items with no description in Rd object ‘plogitnorm’:
  ‘sigma’ ‘\dots’
Argument items with no description in Rd object ‘qlogitnorm’:
  ‘sigma’ ‘\dots’
Argument items with no description in Rd object ‘twCoefLogitnorm’:
  ‘\dots’
Argument items with no description in Rd object ‘twCoefLogitnormE’:
  ‘\dots’
'LazyData' is specified without a 'data' directory
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Argument items with no description in Rd object ‘levopt’:
  ‘x’ ‘alpha’ ‘fmax’ ‘tm’
Argument items with no description in Rd object ‘pershow’:
  ‘object’
Argument items with no description in Rd object ‘norpt’:
  ‘alist’
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
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Auto-generated content requiring editing in Rd object ‘LoopAnalyst-package’:
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Found the following files/directories:
  ‘Model_1.cm’ ‘dambacher.dot’ ‘levins.dot’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘importance_sampling.array’:
  ‘is_method’

Documented arguments not in \usage in documentation object ‘importance_sampling.default’:
  ‘is_method’

Documented arguments not in \usage in documentation object ‘importance_sampling.matrix’:
  ‘is_method’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Argument items with no description in Rd object ‘LotkasXX’:
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Argument items with no description in Rd object ‘LotkasXY’:
  ‘Table’
'LazyData' is specified without a 'data' directory
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Argument items with no description in Rd object ‘followx’:
  ‘Xi’ ‘x0’ ‘h’ ‘t0’ ‘iter’ ‘way’ ‘weights’ ‘pen’ ‘phi’
  ‘lasteigenvector’ ‘rho0’ ‘boundary’ ‘convergence.at’ ‘cross’
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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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'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘setlogdata’:
  ‘logdata’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test’
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Package suggested but not available for checking: ‘depth’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
Packages suggested but not available for checking: 'lpjmlkit', 'quitte'
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Argument items with no description in Rd object ‘plot.magree’:
  ‘xlab’ ‘ylab’ ‘main’ ‘\dots’
Argument items with no description in Rd object ‘print.summary.magree’:
  ‘x’ ‘\dots’
Argument items with no description in Rd object ‘summary.magree’:
  ‘object’ ‘\dots’
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
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Package unavailable to check Rd xrefs: ‘INLA’
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Argument items with no description in Rd object ‘alignPeaks’:
  ‘\dots’
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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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
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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Argument items with no description in Rd object ‘map.scale’:
  ‘x’
GNU make is a SystemRequirements.
checkRd: (-1) sw_sfac.Rd:24: Escaped LaTeX specials: \_
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Argument items with no description in Rd object ‘bias.factor’:
  ‘RRud’ ‘RReu’ ‘rr’ ‘s2’
'LazyData' is specified without a 'data' directory
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checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
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S3 methods shown with full name in documentation object ‘set.scale’:
  ‘scale.dm’ ‘scale.par’

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
Documented arguments not in \usage in documentation object ‘mark_my_dir’:
  ‘mark_file’

Documented arguments not in \usage in documentation object ‘path_type’:
  ‘github_token’

Documented arguments not in \usage in documentation object ‘read_assignment_yml’:
  ‘path’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘marssTMB’
Objects in \usage without \alias in documentation object ‘utility.functions’:
  ‘fully.spec.x’ ‘marssMODEL.to.list’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘flashier’
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Package suggested but not available for checking: ‘wallace’
'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
Invalid package aliases in Rd file ‘NewPackage-package.Rd’:
  ‘NewPackage-package’
Auto-generated content requiring editing in Rd object ‘NewPackage-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Package suggested but not available for checking: ‘gurobi’
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
'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
Documented arguments not in \usage in documentation object ‘x_OP_y’:
  ‘idxs’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'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
Argument items with no description in Rd object ‘mr.smd’:
  ‘structural.cost’
'LazyData' is specified without 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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Auto-generated content requiring editing in Rd object ‘mccca-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'LazyData' is specified without a 'data' directory
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Missing link or links in documentation object ‘CoupledHeatedmcmcabn.Rd’:
  ‘[abn:build_score_cache]{buildScoreCache}’
  ‘[abn:search_heuristic]{searchHeuristic}’

Missing link or links in documentation object ‘abnCache_asia.Rd’:
  ‘[abn:build_score_cache]{buildScoreCache}’

Missing link or links in documentation object ‘mcmc.Rd’:
  ‘[abn:build_score_cache]{buildScoreCache}’
  ‘[abn:search_heuristic]{searchHeuristic}’

Missing link or links in documentation object ‘mcmc_asia.Rd’:
  ‘[abn:build_score_cache]{buildScoreCache}’

See section ‘Cross-references’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘mcmcabn.Rmd’ using rmarkdown

Quitting from lines 143-149 [unnamed-chunk-7] (mcmcabn.Rmd)
Error: processing vignette ‘mcmcabn.Rmd’ failed with diagnostics:
`data.df` and `object` provided but can only accept one of them.
--- failed re-building ‘mcmcabn.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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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: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘geom_cp_density’:
  ‘include’

Documented arguments not in \usage in documentation object ‘get_simulate’:
  ‘par_trials’ ‘pars_pop’ ‘pars_varying’

Documented arguments not in \usage in documentation object ‘pp_eval’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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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
'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
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
'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
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'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
Documented arguments not in \usage in documentation object ‘buildModelMatrix’:
  ‘character’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
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: ‘xcms’
Invalid package aliases in Rd file ‘taxa-package.Rd’:
  ‘taxa-package’
Documented arguments not in \usage in documentation object ‘limited_print’:
  ‘trunc’

Documented arguments not in \usage in documentation object ‘parse_heirarchies_to_taxonomy’:
  ‘A’

Documented arguments not in \usage in documentation object ‘parse_raw_heirarchies_to_taxonomy’:
  ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Documented arguments not in \usage in documentation object ‘ClusterMF-deprecated’:
  ‘formula’ ‘data’ ‘vi’ ‘study’ ‘whichweights’ ‘num.trees’ ‘mtry’
  ‘method’ ‘tau2’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘plot.metaplot_gtable’:
  ‘y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) dslp.Rd:11: Escaped LaTeX specials: \&
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File ‘MEtest/libs/MEtest.so’:
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘TScomp.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘TScomp.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.
checkRd: (-1) cardiac.Rd:15: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Package suggested but not available for checking: ‘INLA’
Documented arguments not in \usage in documentation object ‘wmata_api’:
  ‘type’ ‘endpoint’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
Package suggested but not available for checking: ‘mvPot’
Documented arguments not in \usage in documentation object ‘.gev.postpred’:
  ‘vector’

Documented arguments not in \usage in documentation object ‘.gpd_2D_fit’:
  ‘...other’

Documented arguments not in \usage in documentation object ‘.mvasym.check’:
  ‘vector’

Documented arguments not in \usage in documentation object ‘.rPexstud’:
  ‘Sigma’

Documented arguments not in \usage in documentation object ‘.rPsite’:
  ‘index’ ‘param’

Documented arguments not in \usage in documentation object ‘.rdirspec’:
  ‘rho’

Documented arguments not in \usage in documentation object ‘.rexstudspec’:
  ‘index’ ‘Sigma’

Documented arguments not in \usage in documentation object ‘.rhrspec’:
  ‘index’

Documented arguments not in \usage in documentation object ‘.rmevA1’:
  ‘param’

Documented arguments not in \usage in documentation object ‘.rmevA2’:
  ‘param’

Documented arguments not in \usage in documentation object ‘.rmevasy’:
  ‘param’

Documented arguments not in \usage in documentation object ‘.rmevspec_cpp’:
  ‘param’

Documented arguments not in \usage in documentation object ‘.wecdf’:
  ‘ord’

Documented arguments not in \usage in documentation object ‘tem.corr’:
  ‘fran’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Argument items with no description in Rd object ‘predict.mfp’:
  ‘safe’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Invalid package aliases in Rd file ‘Rpackage-package.Rd’:
  ‘Rpackage-package’
Auto-generated content requiring editing in Rd object ‘Rpackage-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
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No news entries found.
Package suggested but not available for checking: ‘DAPAR’
S3 methods shown with full name in documentation object ‘complete.miceadds’:
  ‘complete.mids.nmi’ ‘complete.mids.1chain’

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
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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
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Documented arguments not in \usage in documentation object ‘changeDevSettings’:
  ‘defaultsSettings’

Documented arguments not in \usage in documentation object ‘getResultPerScheme’:
  ‘criteria’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘micSimParallel’:
  ‘transitionMatrix’ ‘absStates’ ‘varInitStates’ ‘initStatesProb’
  ‘fixInitStates’ ‘maxAge’ ‘simHorizon’ ‘fertTr’
'LazyData' is specified without a 'data' directory
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Auto-generated content requiring editing in Rd object ‘MIDASwrappeR-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
Package suggested but not available for checking: ‘midfielddata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘gurobi’
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'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘getvol’:
  ‘data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
‘:::’ 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
Documented arguments not in \usage in documentation object ‘logAdd’:
  ‘x’ ‘y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘l1_similarity’
Argument items with no description in Rd object ‘randomizationTest’:
  ‘R’
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Documented arguments not in \usage in documentation object ‘mixAR-internal’:
  ‘p’ ‘value’ ‘tau’ ‘etk’ ‘parscore’ ‘sigma’ ‘logpdf’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘rigaussian’:
  ‘mu’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘Sn_A’:
  ‘data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
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
Auto-generated content requiring editing in Rd object ‘mixl-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘mixRasch’
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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:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
Documented arguments not in \usage in documentation object ‘mlr_assertions’:
  ‘resample_result’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘cpoTemplate’:
  ‘affect.names’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Argument items with no description in Rd object ‘mlVARsim0’:
  ‘nPerson’ ‘nNode’ ‘nTime’ ‘sparsity’ ‘parRange’ ‘propPositive’
  ‘diagPositive’ ‘diagIncluded’ ‘sdRange’ ‘shrinkFactor’
  ‘residualStyle’ ‘residualShared’ ‘residualSDrange’ ‘verbose’
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
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Auto-generated content requiring editing in Rd object ‘mmeln-package’:
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
'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
Rd files without \alias:
  ‘mnlfa-package.Rd’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Flury’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘alstructure’

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Package suggested but not available for checking: ‘ArchR’
Documented arguments not in \usage in documentation object ‘simplifiedSampleTile’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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Error(s) in re-building vignettes:
  ...
--- re-building ‘modelplotr.Rmd’ using rmarkdown

Quitting from lines 484-485 [plot_roi] (modelplotr.Rmd)
Error: processing vignette ‘modelplotr.Rmd’ failed with diagnostics:
invalid non-character version specification ‘x’ (type: double)
--- failed re-building ‘modelplotr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Documented arguments not in \usage in documentation object ‘check_augment_data_specification’:
  ‘strict’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Warning: no function found corresponding to methods exports from ‘moko’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Problems with news in ‘NEWS.md’:
No news entries found.
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'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
Argument items with no description in Rd object ‘as.difftime’:
  ‘tim’ ‘format’
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'LazyData' is specified without a 'data' directory
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Documented arguments not in \usage in documentation object ‘create_barrier_cs’:
  ‘fields’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
Specified C++11: please drop specification unless essential
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Rd files without \alias:
  ‘MPLikelihoodWB-package.Rd’
Documented arguments not in \usage in documentation object ‘addHeaderToSavedata’:
  ‘director’

Documented arguments not in \usage in documentation object ‘extractIndirect’:
  ‘curFile’

Documented arguments not in \usage in documentation object ‘extractIndirect_section’:
  ‘curFile’

Documented arguments not in \usage in documentation object ‘graphModel’:
  ‘The’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘internals’:
  ‘check.in’ ‘check.out’ ‘start.theta’ ‘iMqr.internal’ ‘cov.theta’
  ‘iobjfun’ ‘sortH’ ‘isigma’ ‘iMqr.newton’ ‘num.fun’ ‘make.bfun’
  ‘apply_bfun’ ‘p.bisec’ ‘slp.basis’ ‘is.slp’ ‘iqr.waldtest’
  ‘extract.p’ ‘pred.beta’ ‘print.iMqr’ ‘print.summary.iMqr’
  ‘terms.iMqr’ ‘model.matrix.iMqr’ ‘vcov.iMqr’ ‘nobs.iMqr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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GNU make is a SystemRequirements.
Auto-generated content requiring editing in Rd object ‘mrbsizer-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'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
Argument items with no description in Rd object ‘msda’:
  ‘sml’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘CalcMPDynamics’:
  ‘M_ageArray’ ‘TAC_f’ ‘E_f’ ‘SizeLim_f’ ‘FinF’ ‘Spat_targ’
  ‘CAL_binsmid’ ‘Linf’ ‘Len_age’ ‘maxage’ ‘nareas’ ‘Asize’ ‘nCALbins’
  ‘qs’ ‘qvar’ ‘qinc’

Documented arguments not in \usage in documentation object ‘popdynCPP’:
  ‘SSBcurr’

Documented arguments not in \usage in documentation object ‘popdynOneMICE’:
  ‘nyears’

Documented arguments not in \usage in documentation object ‘qestMICE’:
  ‘mod’ ‘plusgroup.’ ‘WtC’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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: \&
Argument items with no description in Rd object ‘DAGOSTINO’:
  ‘data’
Argument items with no description in Rd object ‘HZ.test’:
  ‘data’
Argument items with no description in Rd object ‘MardiaTest’:
  ‘data’
Argument items with no description in Rd object ‘Royston.test’:
  ‘data’
Argument items with no description in Rd object ‘gen.var’:
  ‘\dots’
Argument items with no description in Rd object ‘larg.ellip’:
  ‘n’ ‘box’ ‘add’ ‘xlim’ ‘ylim’ ‘zlim’ ‘xlab’ ‘ylab’ ‘zlab’ ‘col’
  ‘alpha’ ‘\dots’
Argument items with no description in Rd object ‘prism’:
  ‘add’
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: \_
Invalid package aliases in Rd file ‘ms_sev-package.Rd’:
  ‘ms_sev-package’
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
S3 methods shown with full name in documentation object ‘pca.plot.wrap’:
  ‘lda.plot.wrap.1’

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) mkjnw.Rd:3: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘diagPlot’:
  ‘hvt.results.model’

Documented arguments not in \usage in documentation object ‘getOptimalCentroids’:
  ‘depth’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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checkRd: (-1) MultBiplotR-package.Rd:52: Escaped LaTeX specials: \&
Argument items with no description in Rd object ‘BinaryLogBiplotJoint’:
  ‘lambda’
Argument items with no description in Rd object ‘ConstrainedOrdinalLogisticBiplot’:
  ‘show’
Argument items with no description in Rd object ‘ContinuousProximities’:
  ‘ysup’
Argument items with no description in Rd object ‘Multiquad’:
  ‘nnodes’ ‘dims’
Argument items with no description in Rd object ‘PLSR1Bin’:
  ‘grouping’
Argument items with no description in Rd object ‘Unfolding’:
  ‘lambda’ ‘omega’ ‘plot’
Argument items with no description in Rd object ‘plot.CCA.sol’:
  ‘x’ ‘A1’ ‘A2’ ‘ShowAxis’ ‘margin’ ‘PlotSites’ ‘PlotSpecies’ ‘PlotEnv’
  ‘LabelSites’ ‘LabelSpecies’ ‘LabelEnv’ ‘TypeSites’ ‘SpeciesQuality’
  ‘MinQualityVars’ ‘dp’ ‘pr’ ‘PlotAxis’ ‘TypeScale’ ‘ValuesScale’
  ‘mode’ ‘CexSites’ ‘CexSpecies’ ‘CexVar’ ‘ColorSites’ ‘ColorSpecies’
  ‘ColorVar’ ‘PchSites’ ‘PchSpecies’ ‘PchVar’ ‘SizeQualSites’
  ‘SizeQualSpecies’ ‘SizeQualVars’ ‘ColorQualSites’ ‘ColorQualSpecies’
  ‘ColorQualVars’ ‘SmartLabels’
Argument items with no description in Rd object ‘plot.CanonicalDistanceAnalysis’:
  ‘SmartLabels’
Argument items with no description in Rd object ‘plot.Principal.Coordinates’:
  ‘ShowAxis’ ‘PlotBinaryMeans’ ‘MinIncidence’ ‘ShowBox’
  ‘ColorSupContVars’ ‘ColorSupBinVars’ ‘ColorSupOrdVars’ ‘TypeScale’
  ‘SupMode’ ‘PlotSupVars’
Argument items with no description in Rd object ‘plot.Unfolding’:
  ‘SpeciesQuality’ ‘dp’ ‘PlotAxis’ ‘TypeScale’ ‘ValuesScale’ ‘mode’
  ‘CexSites’ ‘CexSpecies’ ‘CexVar’ ‘ColorSites’ ‘ColorSpecies’
  ‘ColorVar’ ‘PchSites’ ‘PchSpecies’ ‘PchVar’ ‘SizeQualSites’
  ‘SizeQualSpecies’ ‘SizeQualVars’ ‘ColorQualSites’ ‘ColorQualSpecies’
  ‘ColorQualVars’ ‘SmartLabels’ ‘PlotTol’ ‘...’
Argument items with no description in Rd object ‘scores.CCA.sol’:
  ‘CCA.sol’
Argument items with no description in Rd object ‘summary.Canonical.Biplot’:
  ‘object’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘plotBoxes’:
  ‘lwd’ ‘T.base’ ‘font.family’ ‘fig’ ‘mar’

Documented arguments not in \usage in documentation object ‘plotLetters’:
  ‘width’ ‘lwd’ ‘label.groups’ ‘T.base’ ‘orientation’

Documented arguments not in \usage in documentation object ‘plotTs’:
  ‘font.family’ ‘fig’ ‘mar’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘RegularizedSCA’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘Trace’:
  ‘x’

Documented arguments not in \usage in documentation object ‘iteraite_fun_Iter’:
  ‘The’

Documented arguments not in \usage in documentation object ‘prepare_data’:
  ‘The’

Documented arguments not in \usage in documentation object ‘project’:
  ‘x’

Documented arguments not in \usage in documentation object ‘select_initial_Iter’:
  ‘X’ ‘parametrs’

Documented arguments not in \usage in documentation object ‘similarity_function’:
  ‘x’

Documented arguments not in \usage in documentation object ‘similarity_noncum’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘cmdstanr’
'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
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++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘check_mnsl’:
  ‘fix’

Documented arguments not in \usage in documentation object ‘text_colour’:
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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: \# \# \#
'LazyData' is specified without a 'data' directory
checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rTubeDB’
Package unavailable to check Rd xrefs: ‘rTubeDB’
'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’
Argument items with no description in Rd object ‘check_subject_pattern’:
  ‘subject.vec’ ‘pattern’
Argument items with no description in Rd object ‘names_or_error’:
  ‘pattern’
Argument items with no description in Rd object ‘only_captures’:
  ‘match.mat’ ‘pattern’
Argument items with no description in Rd object ‘stop_for_names’:
  ‘pattern’
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
GNU make is a SystemRequirements.
Invalid package aliases in Rd file ‘NBBttest-package.Rd’:
  ‘NBBtatest-package’
'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.
Documented arguments not in \usage in documentation object ‘Moth’:
  ‘delta.ident’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘assignClasses’:
  ‘df’

Documented arguments not in \usage in documentation object ‘dateConvert’:
  ‘use_fasstime’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
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
‘:::’ 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
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
Argument items with no description in Rd object ‘print.networkDynamic’:
  ‘\dots’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map.png’ ‘maze.html’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘network-internal’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
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
Invalid package aliases in Rd file ‘NH-MSAR-package.Rd’:
  ‘NH-MSAR-package’
Argument items with no description in Rd object ‘ENu_graph’:
  ‘N.s.data’
Argument items with no description in Rd object ‘Estep.MSAR.VM’:
  ‘verbose’
Auto-generated content requiring editing in Rd object ‘NH-MSAR-package’:
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Argument items with no description in Rd object ‘init.theta.MSAR (NH-MSAR)’:
  ‘\dots’
Argument items with no description in Rd object ‘init.theta.MSAR.VM’:
  ‘\dots’
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
Objects in \usage without \alias in documentation object ‘getPossibleR’:
  ‘brkCalc’ ‘findPowerR’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
Documented arguments not in \usage in documentation object ‘nldoc_write_nldoc’:
  ‘number_ections’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) nltm.control.Rd:29: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Documented arguments not in \usage in documentation object ‘searchColRow’:
  ‘use.rds’ ‘applyFilters’ ‘recover.cols’ ‘details’ ‘col.row’ ‘quiet’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘mail’
Documented arguments not in \usage in documentation object ‘ccSpec’:
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘NMOF-internal’:
  ‘mRU’ ‘mRN’ ‘mcList’ ‘repair1c’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘logistf-package.Rd’:
  ‘logistf-package’ ‘{logistf}-package’
'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
Auto-generated content requiring editing in Rd object ‘noise-package’:
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 41-45 [specific-dataset] (introduction.Rmd)
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
cannot open the connection to ‘https://www.nomisweb.co.uk/api/v01/dataset/NM_893_1/def.sdmx.json’
--- 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
Documented arguments not in \usage in documentation object ‘get_max_stat’:
  ‘statfunc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘StatQQVPC’:
  ‘mapping’ ‘data’ ‘geom’ ‘position’ ‘na.rm’ ‘show.legend’
  ‘inherit.aes’ ‘...’

Documented arguments not in \usage in documentation object ‘StatQQnorm’:
  ‘mapping’ ‘data’ ‘geom’ ‘position’ ‘na.rm’ ‘show.legend’
  ‘inherit.aes’ ‘...’

Documented arguments not in \usage in documentation object ‘StatQQrefline’:
  ‘mapping’ ‘data’ ‘geom’ ‘position’ ‘na.rm’ ‘show.legend’
  ‘inherit.aes’ ‘...’

Documented arguments not in \usage in documentation object ‘covload.sub.table’:
  ‘nrows’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Auto-generated content requiring editing in Rd object ‘nose-package’:
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Documented arguments not in \usage in documentation object ‘FunctionSanityChecks’:
  ‘structure’

Documented arguments not in \usage in documentation object ‘newLine’:
  ‘current.in’

Documented arguments not in \usage in documentation object ‘nosoiSimConstructor’:
  ‘pres.time’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘read’:
  ‘dots’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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.
Documented arguments not in \usage in documentation object ‘Create_P’:
  ‘y_zx_dependent’

Documented arguments not in \usage in documentation object ‘make_proposer’:
  ‘N’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
Documented arguments not in \usage in documentation object ‘exp_hclust’:
  ‘df_allele’

Documented arguments not in \usage in documentation object ‘log_mem’:
  ‘msg’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
File ‘numOSL/libs/numOSL.so’:
  Found ‘_gfortran_arandom_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘diffev.o’
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Objects: ‘mcCAM.o’, ‘mcFMM2.o’, ‘mcFMM3.o’, ‘mcFMM4.o’, ‘mcMam3.o’,
      ‘mcMam4.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Objects: ‘mcCAM.o’, ‘mcFMM2.o’, ‘mcFMM3.o’, ‘mcFMM4.o’, ‘mcMam3.o’,
      ‘mcMam4.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
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
Documented arguments not in \usage in documentation object ‘cust.colorbar’:
  ‘\code{input.mode}’ ‘\code{force.figdim.widget}’ ‘\code{xpos}’
  ‘region’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘plot.comphat’:
  ‘\dots’
Rd files without \alias:
  ‘odbc-package.Rd’
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
Rd files without \alias:
  ‘ontologyPlot-package.Rd’
'LazyData' is specified without 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.
'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘openNLPmodels.en’
Documented arguments not in \usage in documentation object ‘clique_color_pals’:
  ‘aplha’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘bertinBase’:
  ‘x’ ‘ratings’ ‘trim’

Documented arguments not in \usage in documentation object ‘biplot3dBase2’:
  ‘ext.sphere’

Documented arguments not in \usage in documentation object ‘convertImportObjectToRepGridObject’:
  ‘x’

Documented arguments not in \usage in documentation object ‘convertScivescoImportObjectToRepGridObject’:
  ‘x’

Documented arguments not in \usage in documentation object ‘mapCoordinatesToColor’:
  ‘color’

Documented arguments not in \usage in documentation object ‘quasiDistributionDistanceSlater’:
  ‘rep’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘assign_binIDs’:
  ‘id:’ ‘binID:’ ‘lastbit:’

Documented arguments not in \usage in documentation object ‘calcCatchmArea_assignNetID’:
  ‘netID’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
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
Argument items with no description in Rd object ‘dsevdist’:
  ‘x’ ‘sevdist’
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’
Documented arguments not in \usage in documentation object ‘distsuml2’:
  ‘partial’

Documented arguments not in \usage in documentation object ‘distsumlp’:
  ‘partial’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘dosepred’:
  ‘w’

Documented arguments not in \usage in documentation object ‘surv_dm_solver’:
  ‘bw_optim’

Documented arguments not in \usage in documentation object ‘surv_forward_solver’:
  ‘Phit’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Rd files without \alias:
  ‘otp-package.Rd’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘packagetracker.Rd’:
  ‘packagetracker-package’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘prediction_regression’:
  ‘dataset’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Argument items with no description in Rd object ‘joint_estimate’:
  ‘\dots’
Argument items with no description in Rd object ‘only_A_estimate’:
  ‘\dots’
Argument items with no description in Rd object ‘only_F_estimate’:
  ‘\dots’
Argument items with no description in Rd object ‘plot.Full_PAFit_result’:
  ‘\dots’
Argument items with no description in Rd object ‘plot.PAFit_net’:
  ‘\dots’
Argument items with no description in Rd object ‘plot.PAFit_result’:
  ‘\dots’
Argument items with no description in Rd object ‘plot.PA_result’:
  ‘\dots’
Argument items with no description in Rd object ‘print.CV_Result’:
  ‘\dots’
Argument items with no description in Rd object ‘print.CV_Data’:
  ‘\dots’
Argument items with no description in Rd object ‘print.Full_PAFit_result’:
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Argument items with no description in Rd object ‘print.PAFit_data’:
  ‘\dots’
Argument items with no description in Rd object ‘print.PAFit_net’:
  ‘\dots’
Argument items with no description in Rd object ‘print.PAFit_result’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.CV_Data’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.CV_Result’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.Full_PAFit_result’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.PAFit_data’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.PAFit_net’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.PAFit_result’:
  ‘\dots’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘CorShrink’
Documented arguments not in \usage in documentation object ‘other’:
  ‘trial’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘dplyr_verbs’:
  ‘funs’ ‘.dots’ ‘keep_attributes’

Documented arguments not in \usage in documentation object ‘nest_tdc’:
  ‘vars’ ‘id’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘pamr-internal’:
  ‘print.nsc’ ‘print.nsccv’

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.
'LazyData' is specified without a 'data' directory
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Documented arguments not in \usage in documentation object ‘getOption2’:
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Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
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Documented arguments not in \usage in documentation object ‘expect_missing_argument’:
  ‘message’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++14: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
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Documented arguments not in \usage in documentation object ‘as_partition’:
  ‘.partition_step’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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’
Documented arguments not in \usage in documentation object ‘fixvar_of_red_mod’:
  ‘data’

Documented arguments not in \usage in documentation object ‘get_ndf’:
  ‘data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘vec_cast.partial_time’:
  ‘vec_cast.partial_time’

S3 methods shown with full name in documentation object ‘vec_cast.timespan’:
  ‘vec_cast.timespan’

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
Documented arguments not in \usage in documentation object ‘help_console’:
  ‘which’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \# \# \#
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \#
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Package suggested but not available for checking: ‘anomalize’
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GNU make is a SystemRequirements.
Argument items with no description in Rd object ‘markbouts.acclist’:
  ‘extreme’
S3 methods shown with full name in documentation object ‘ped’:
  ‘ped.markerNames’

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.
'LazyData' is specified without 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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Malformed Description field: should contain one or more complete sentences.
'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
GNU make is a SystemRequirements.
Objects in \usage without \alias in documentation object ‘internals’:
  ‘CumSum’ ‘myapply’ ‘makebreaks.ct’ ‘makebreaks.ic’ ‘pois.loglik’
  ‘icpch.loglik’ ‘convert.Surv’ ‘break.y’ ‘pois.fit’ ‘pch.fit.ct’
  ‘pch.fit.ic’ ‘newton’ ‘cleanlambda’ ‘predF.pch’ ‘predQ.pch’ ‘sim.pch’
  ‘build.splinex’ ‘predict.splinex’ ‘logLik.pch’ ‘nobs.pch’ ‘vcov.pch’
  ‘coef.pch’ ‘print.pch’ ‘summary.pch’ ‘print.summary.pch’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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Documented arguments not in \usage in documentation object ‘getResponse’:
  ‘model’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘ODACATH.estimate’:
  ‘ODACAT.estimate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘PythonInR’
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Argument items with no description in Rd object ‘PoissonLoss’:
  ‘count’ ‘seg.mean’ ‘weight’
Argument items with no description in Rd object ‘getPath’:
  ‘A’
Argument items with no description in Rd object ‘PoissonLoss’:
  ‘count’ ‘seg.mean’ ‘weight’
Argument items with no description in Rd object ‘featureMatrixJoint’:
  ‘profile.list’
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Argument items with no description in Rd object ‘PoissonLoss’:
  ‘count’ ‘seg.mean’ ‘weight’
Argument items with no description in Rd object ‘oracleModelComplexity’:
  ‘bases’ ‘segments’
S3 methods shown with full name in documentation object ‘format.relation’:
  ‘format.relation’

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.
Package suggested but not available for checking: ‘georob’
Invalid package aliases in Rd file ‘pedSimulte-package.Rd’:
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GNU make is a SystemRequirements.
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Error(s) in re-building vignettes:
  ...
--- re-building ‘intro-to-penppml.Rmd’ using rmarkdown

Quitting from lines 140-155 [plot regularization path] (intro-to-penppml.Rmd)
Error: processing vignette ‘intro-to-penppml.Rmd’ failed with diagnostics:
object ‘last.bumpup’ not found
--- failed re-building ‘intro-to-penppml.Rmd’

SUMMARY: processing the following file failed:
  ‘intro-to-penppml.Rmd’

Error: Vignette re-building failed.
Execution halted
Argument items with no description in Rd object ‘lmres’:
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Argument items with no description in Rd object ‘simpleSlope’:
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Argument items with no description in Rd object ‘summary.lmres’:
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Documented arguments not in \usage in documentation object ‘allTrees’:
  ‘dist’

Documented arguments not in \usage in documentation object ‘getNode’:
  ‘hc’ ‘pair’

Documented arguments not in \usage in documentation object ‘switchEntries’:
  ‘pair’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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Invalid package aliases in Rd file ‘perspective-package.Rd’:
  ‘perspective-package’
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
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Invalid package aliases in Rd file ‘00_PH1XBAR-package.Rd’:
  ‘00_PH1XBAR-package’
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Found the following files/directories:
  ‘animation.gif’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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  ‘test.pdf’
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Documented arguments not in \usage in documentation object ‘process_season’:
  ‘d’ ‘options_season’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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Auto-generated content requiring editing in Rd object ‘phm-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
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Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
Documented arguments not in \usage in documentation object ‘adaptive_smoothing’:
  ‘smooth.limt’ ‘smooth.thershold’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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No news entries found.
Documented arguments not in \usage in documentation object ‘TungUbRF’:
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Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘ggsubplot’
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Documented arguments not in \usage in documentation object ‘make_pgk_cache_subdir_for_all_relative_files’:
  ‘relative_filenames’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in documentation object ‘imports_env’:
  ‘path’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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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’
'LazyData' is specified without a 'data' directory
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Running examples in ‘pliman-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: efourier
> ### Title: Elliptical Fourier Analysis
> ### Aliases: efourier
> 
> ### ** Examples
> 
> library(pliman)
> leaf1 <- contours[[4]]
> plot_polygon(leaf1)
> 
> #### default options
> # 10 harmonics (default)
> # without alignment
> 
> ef <- efourier(leaf1)
> efourier_coefs(ef)
           an           bn          cn           dn
1  21.1298663 -382.7540180 -364.126202 -21.29189747
2   1.6804167  151.6255507  -40.467153  10.80476561
3   4.3779839   -0.9870311 -129.212508   3.20445130
4  -3.1329537  -46.3028113  -26.380285  -4.12257511
5  -1.6548827    3.6997248   19.343685  -3.32106033
6   4.9296483   39.2656639  -15.461424   0.48631684
7   1.2043295    0.5415148  -15.556049   0.96104147
8   0.5959547  -13.0422412  -18.885184   1.42268431
9  -0.8187422    3.9795071   -4.368973   0.04457129
10 -0.3849895   -5.7461417   -2.553430  -1.11528942
> 
> # object is aligned along the major caliper with `poly_align()`
> # object is centered on the origin with `poly_center()`
> # using a list of object coordinates
> ef2 <- efourier(contours, align = TRUE, center = TRUE)
Error in eval(substitute(list(...)), `_data`, parent.frame()) : 
  object 'X1' not found
Calls: efourier ... transform.default -> transform.data.frame -> eval -> eval
Execution halted
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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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Invalid package aliases in Rd file ‘plsgenomics-deprecated.Rd’:
  ‘plsgenomics-deprecated-package’
Invalid package aliases in Rd file ‘plsgenomics-internal.Rd’:
  ‘plsgenomics-internal-package’
Specified C++11: please drop specification unless essential
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Documented arguments not in \usage in documentation object ‘eval.quoted’:
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Documented arguments not in \usage in documentation object ‘indexed_df’:
  ‘env’

Documented arguments not in \usage in documentation object ‘list_to_dataframe’:
  ‘idname’

Documented arguments not in \usage in documentation object ‘split_indices’:
  ‘index’

Documented arguments not in \usage in documentation object ‘split_labels’:
  ‘list’ ‘whether’

Documented arguments not in \usage in documentation object ‘tryapply’:
  ‘f’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘MSnbase’
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'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘sample_store’:
  ‘subjects_ids’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Objects in \usage without \alias in documentation object ‘PMwR-internal’:
  ‘.timestamp<-’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
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Unknown package ‘gpclib’ in Rd xrefs
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Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
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Documented arguments not in \usage in documentation object ‘initialize,genclone-method’:
  ‘gen’ ‘loc’ ‘treatOther’ ‘quiet’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘popsom/libs/popsom.so’:
  Found ‘_gfortran_random_r4’, possibly from ‘random_number’ (Fortran)
    Object: ‘vsom.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘vsom.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.
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
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: \&
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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
Objects in \usage without \alias in documentation object ‘ppmlasso-internal’:
  ‘spatRes’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
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
Documented arguments not in \usage in documentation object ‘local_test_setup’:
  ‘use_precommmit’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package which this enhances but not available for checking: ‘ffbase’
Unknown package ‘ffbase’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
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: 'gurobi', 'rcbc'
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘validate_inputs’:
  ‘required_vars’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cin’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘bitAND’:
  ‘a’ ‘b’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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’
Documented arguments not in \usage in documentation object ‘.marxan_data_reader’:
  ‘parameter’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file ‘granova-package.Rd’:
  ‘granova-package’
Documented arguments not in \usage in documentation object ‘estimateDeltaLOH.PairedPSCBS’:
  ‘scale’

Documented arguments not in \usage in documentation object ‘getLocusData.AbstractCBS’:
  ‘splitters’

Documented arguments not in \usage in documentation object ‘getSegments.AbstractCBS’:
  ‘simplify’ ‘splitters’

Documented arguments not in \usage in documentation object ‘mergeTwoSegments.AbstractCBS’:
  ‘left’ ‘update’ ‘verbose’

Documented arguments not in \usage in documentation object ‘plotTracks.PairedPSCBS’:
  ‘x’ ‘tracks’ ‘scatter’ ‘calls’ ‘pch’ ‘col’ ‘cex’ ‘changepoints’
  ‘grid’ ‘quantiles’ ‘xlim’ ‘Clim’ ‘Blim’ ‘xScale’ ‘add’ ‘subplots’
  ‘verbose’

Documented arguments not in \usage in documentation object ‘updateMeansTogether.AbstractCBS’:
  ‘idxList’ ‘verbose’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘kepner_robinson_test_internal’:
  ‘group’ ‘alternative’ ‘trend’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘pspline.sample.scalars’:
  ‘time’

Documented arguments not in \usage in documentation object ‘pspline.sample.timeseries’:
  ‘time’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Invalid package aliases in Rd file ‘00.psych-package.Rd’:
  ‘00.psych-package’
Documented arguments not in \usage in documentation object ‘GetFitHReg’:
  ‘z’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file ‘package-ptf.Rd’:
  ‘package-ptf-package’
Documented arguments not in \usage in documentation object ‘assert_correct_attributes’:
  ‘expected_colnames’

Documented arguments not in \usage in documentation object ‘geopath_to_tibble’:
  ‘route’

Documented arguments not in \usage in documentation object ‘run_to_tibble’:
  ‘route’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Invalid package aliases in Rd file ‘PVAClone-package.Rd’:
  ‘PVA-package’ ‘pva-package’ ‘Pva-package’
'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: \&
Documented arguments not in \usage in documentation object ‘http_was_redirected’:
  ‘response’

Documented arguments not in \usage in documentation object ‘permutations’:
  ‘nset’

Documented arguments not in \usage in documentation object ‘pxweb_split_query’:
  ‘pxweb_metadata’

Documented arguments not in \usage in documentation object ‘split_dimensions_left_right’:
  ‘pxq’

Documented arguments not in \usage in documentation object ‘str_pad’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘lagm’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘get_names_MV’:
  ‘path_matrix’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘internals’:
  ‘expit’ ‘logit’ ‘pmax0’ ‘num.fun’ ‘format.perc’ ‘Ltau’ ‘minabs’
  ‘invJ’ ‘tensorX’ ‘buildTau’ ‘callwtau’ ‘callQ’ ‘start.Qest’
  ‘start.Qest.family’ ‘rq.fit.br2’ ‘Qest.sgs.internal’
  ‘Qest.gs.internal’ ‘Qest.gs’ ‘Qest.newton’ ‘Qlm.bfun’ ‘start.Qlm’
  ‘scalevars.Qlm’ ‘descalecoef.Qlm’ ‘Qlm.sgs.internal’
  ‘Qlm.gs.internal’ ‘Qlm.gs’ ‘Qlm.newton’ ‘plfcox’ ‘scalevars.Qcoxph’
  ‘descalecoef.Qcoxph’ ‘check.singularities’ ‘starting.points.Qcox’
  ‘adjust.coef’ ‘agsurv.Qcoxph’ ‘coxsurv.fit.Qcoxph’ ‘seg.lm.fit1’ ‘gs’
  ‘myg’ ‘dlist’ ‘omega’ ‘choose_eps’ ‘derQtheta’ ‘der2Qtheta’ ‘intA’
  ‘findp’ ‘findAp’ ‘A_beta_fun’ ‘A_gamma_fun’ ‘A_beta_beta_fun’
  ‘A_gamma_gamma_mix_fun’ ‘A_gamma_gamma_fun’ ‘A_beta_gamma_fun’
  ‘coxBB’ ‘derQtheta.gamma’ ‘der2Qtheta.gamma’ ‘findAp.gamma’
  ‘QestGamma.ee.u’ ‘QestGamma.ee.c’ ‘QestGamma.ee.ct’ ‘tau.pois’
  ‘ppoisC’ ‘dpoisC’ ‘qpoisC.955’ ‘qpoisC.me’ ‘qpoisC.bisec’ ‘qpoisC’
  ‘derQtheta.pois’ ‘der2Qtheta.pois’ ‘findp.pois’ ‘findAp.pois’
  ‘QestPois.ee.u’ ‘QestUnif.ee.u’ ‘QestNorm.ee.u’ ‘QestNorm.ee.c’
  ‘QestNorm.ee.ct’ ‘Qest.ee.u’ ‘Qest.ee.c’ ‘Qest.ee.ct’ ‘QCox.ee.c’
  ‘QCox.ee.ct’ ‘Qlm.ee.u’ ‘Qest.covar’ ‘Qcox.covar’ ‘Qlm.covar’ ‘Loss’
  ‘coxLoss’ ‘qlmLoss’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘internals’:
  ‘format.perc’

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.
'LazyData' is specified without 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: ‘spDataLarge’
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘ad.simudata’:
  ‘SimuNum’
'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
Objects in \usage without \alias in documentation object ‘internals’:
  ‘Q’ ‘funQ1’ ‘check.fun’ ‘boot’ ‘predBeta’ ‘grad3’ ‘grad2’ ‘num.int’
  ‘integr’ ‘bisec’ ‘Bfun’ ‘bfun’ ‘funGrad’ ‘Fun’ ‘armijo’ ‘check.in.2’
  ‘check.out.2’ ‘piqr.newton’ ‘piqr.ee’ ‘pciqr.ee’ ‘pctiqr.ee’
  ‘plotCoef’ ‘nonzeroCoef’ ‘cov.theta.2’ ‘plot.piqr2’
  ‘divide.et.impera.2’ ‘print.niqr’ ‘print.summary.niqr’ ‘print.piqr’
  ‘print.summary.piqr’ ‘terms.piqr’ ‘coef.piqr’ ‘model.matrix.piqr’
  ‘nobs.piqr’
Assignments in \usage in documentation object ‘internals’:
  start.theta.niqr <- function(fun, x0, X, y, control = list()) piqr.internal(mf, 
      cl, formula.p, tol = 1e-06, maxit = 100, s, segno = 1, lambda = 0, 
      check = FALSE, A, st.theta = FALSE, theta0)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘internals’:
  ‘plot.piqr2’

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.
Objects in \usage without \alias in documentation object ‘internals’:
  ‘check.in.iqr’ ‘check.in0.iqrL’ ‘check.in.iqrL’ ‘check.out’
  ‘start.iqr’ ‘start.iqrL’ ‘ctiqr.internal’ ‘iqrL.internal’ ‘iqrL.fit’
  ‘iqr.ee’ ‘ciqr.ee’ ‘ctiqr.ee’ ‘iobjfun’ ‘iobjfun.ct’ ‘cov.fun.iqr’
  ‘iqrL.ee’ ‘cov.fun.iqrL’ ‘iqr.newton’ ‘divide.et.impera’
  ‘iqrL.newton’ ‘pmax0’ ‘maxind’ ‘num.fun’ ‘make.bfun’ ‘apply_bfun’
  ‘p.bisec’ ‘p.bisec.internal’ ‘slp.basis’ ‘is.slp’ ‘safesolve’
  ‘iqr.waldtest’ ‘extract.p’ ‘pred.beta’ ‘km’ ‘alpha’ ‘test.unif.ct’
  ‘findagoodestimator’ ‘quickpred’ ‘trans’ ‘alpha.bisec’
  ‘alpha.bisec.out’ ‘ks’ ‘print.iqr’ ‘print.summary.iqr’ ‘terms.iqr’
  ‘model.matrix.iqr’ ‘vcov.iqr’ ‘nobs.iqr’ ‘predict.iqrL.internal’
  ‘print.iqrL’ ‘print.summary.iqrL’ ‘terms.iqrL’ ‘model.matrix.iqrL’
  ‘vcov.iqrL’ ‘nobs.iqrL’ ‘qc.penalty’ ‘fixqc’ ‘print.qc.iqr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘internals’:
  ‘predict.iqrL.internal’

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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) NEWS.Rd:15: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘mmer_adapted’:
  ‘void’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘export_responses_filedownload’:
  ‘requestID’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘convert-wrappers’:
  ‘...’

Documented arguments not in \usage in documentation object ‘corpus-class’:
  ‘if’

Documented arguments not in \usage in documentation object ‘dfm-class’:
  ‘drop_docid’

Documented arguments not in \usage in documentation object ‘dictionary2-class’:
  ‘object’

Documented arguments not in \usage in documentation object ‘matrix2fcm’:
  ‘slots’

Documented arguments not in \usage in documentation object ‘meta_system’:
  ‘source’

Documented arguments not in \usage in documentation object ‘search_index’:
  ‘regex’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘wordcloud_comparison’:
  ‘random.color’ ‘ordered.colors’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Auto-generated content requiring editing in Rd object ‘quhomology-package’:
  \details: ‘...o use the package, including the most important functions ~~’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘fastshp’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘qut-package.Rd’:
  ‘QUT-package’
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
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 calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
Documented arguments not in \usage in documentation object ‘bugs.inits’:
  ‘inits.file’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
Documented arguments not in \usage in documentation object ‘.armaRidgeP’:
  ‘alpha’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘print.ramchoiceRevealAtte’:
  ‘object’

Documented arguments not in \usage in documentation object ‘print.ramchoiceRevealPref’:
  ‘object’

Documented arguments not in \usage in documentation object ‘print.ramchoiceRevealPrefModel’:
  ‘object’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Invalid package aliases in Rd file ‘randtests-package.Rd’:
  ‘randomtests-package’
Package suggested but not available for checking: ‘googlesheets’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘get_parameters’:
  ‘parameters_def’

Documented arguments not in \usage in documentation object ‘print.rapi_api’:
  ‘...further’

Documented arguments not in \usage in documentation object ‘print.rapi_operation’:
  ‘...further’

Documented arguments not in \usage in documentation object ‘print.rapi_schema_function’:
  ‘...further’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object ‘RApiDatetime-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘# Optional simple examples of the most important functions’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Objects in \usage without \alias in documentation object ‘cache’:
  ‘\S4method{cache}{RapData,character,ANY}’
  ‘\S4method{cache}{RapData,character,missing}’
  ‘\S4method{cache}{RapResults,character,ANY}’
  ‘\S4method{cache}{RapResults,character,missing}’

Objects in \usage without \alias in documentation object ‘is.cached’:
  ‘\S4method{is.cached}{RapData,character}’
  ‘\S4method{is.cached}{RapResults,character}’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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.
Documented arguments not in \usage in documentation object ‘mpaRaoS’:
  ‘rasterm’

Objects in \usage without \alias in documentation object ‘paRaoP’:
  ‘paRaoS’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
Documented arguments not in \usage in documentation object ‘convert_to_native_raster’:
  ‘ncol’ ‘nrow’

Documented arguments not in \usage in documentation object ‘pad_to_fit’:
  ‘heightmap’ ‘pad’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘onb_from_w’:
  ‘v’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘init_time’:
  ‘verbose’ ‘message’

Documented arguments not in \usage in documentation object ‘print_time’:
  ‘message’

Documented arguments not in \usage in documentation object ‘process_point_series_1d’:
  ‘points’

Documented arguments not in \usage in documentation object ‘process_point_series_2d’:
  ‘points’

Documented arguments not in \usage in documentation object ‘tween’:
  ‘type’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘gen_fractal_perlin’:
  ‘image’

Documented arguments not in \usage in documentation object ‘generate_base_shape’:
  ‘image’

Documented arguments not in \usage in documentation object ‘generate_cloud_layer’:
  ‘image’

Documented arguments not in \usage in documentation object ‘make_base_triangulated’:
  ‘zscale’

Documented arguments not in \usage in documentation object ‘raymarch_cloud_layer’:
  ‘image’

Documented arguments not in \usage in documentation object ‘render_snapshot_software’:
  ‘ground_size’

Documented arguments not in \usage in documentation object ‘transform_into_heightmap_coords’:
  ‘image’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘generate_toon_outline’:
  ‘angle’ ‘order_rotation’

Documented arguments not in \usage in documentation object ‘init_time’:
  ‘verbose’ ‘message’

Documented arguments not in \usage in documentation object ‘merge_scene’:
  ‘scene’

Documented arguments not in \usage in documentation object ‘print_time’:
  ‘message’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘Min_Max_Inverse_Scale_Vec’:
  ‘mat’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
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.
'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
S3 methods shown with full name in documentation object ‘export.default’:
  ‘export.default’

S3 methods shown with full name in documentation object ‘export.listpoly’:
  ‘export.listpoly’

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.
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’
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’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘makeTitle’:
  ‘string:’ ‘length:’ ‘prefix.length:’ ‘char:’

Documented arguments not in \usage in documentation object ‘messageConsole’:
  ‘message:’

Documented arguments not in \usage in documentation object ‘tkEmptyLine’:
  ‘tk.object:’ ‘row:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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.
Invalid package aliases in Rd file ‘RcmdrPlugin.coin-package.Rd’:
  ‘RcmdrcoinPlugin-package’
S3 methods shown with full name in documentation object ‘editDataset.design’:
  ‘editDataset.design’

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.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘Rcmdr.HH-package.Rd’:
  ‘Rcmdr.HH-package’
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
Invalid package aliases in Rd file ‘RcmdrPlugin.SCDA-package.Rd’:
  ‘RcmdrSCDAPlugin-package’
Argument items with no description in Rd object ‘aovreml’:
  ‘formula’ ‘data’ ‘Lconfint’ ‘REML’ ‘\dots’
Argument items with no description in Rd object ‘aovremm’:
  ‘formula’ ‘data’ ‘\dots’
Argument items with no description in Rd object ‘characRV’:
  ‘D’ ‘charact’ ‘moment’ ‘cmoment’
Argument items with no description in Rd object ‘plotRegions’:
  ‘D’ ‘add’ ‘regions’ ‘col’ ‘legend’ ‘legend.pos’ ‘to.draw.arg’
  ‘verticals’ ‘ngrid’ ‘cex.points’ ‘mfColRow’ ‘lwd’ ‘\dots’
Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package suggested but not available for checking: ‘conics’
Auto-generated content requiring editing in Rd object ‘RcppAnnoy-package’:
  \examples: ‘# Optional simple examples of the most important functions’
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file ‘RcppHnsw-package.Rd’:
  ‘RcppHnsw-package’
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
NEWS.Rd:46: First argument to \href must be verbatim URL
problem found in ‘NEWS.Rd’
Auto-generated content requiring editing in Rd object ‘RcppSpdlog-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
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
GNU make is a SystemRequirements.
Invalid package aliases in Rd file ‘Rd2markdown-package.Rd’:
  ‘Rd2markdown-package’
'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
Documented arguments not in \usage in documentation object ‘h_opt_density_res’:
  ‘x’ ‘dgp_F1’ ‘dgp_Fp1’ ‘f_low’ ‘f_up’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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:
  ‘devAll’
Documented arguments not in \usage in documentation object ‘favicon’:
  ‘file’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘rdoc_options.Rd’:
  ‘rdoc_options-package’
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object ‘RDocumentation-package’:
  \details: ‘...o use the package, including the most important functions ~~’
'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: ‘DIDmultiplegt’
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
Documented arguments not in \usage in documentation object ‘.readAcquFile’:
  ‘file’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Auto-generated content requiring editing in Rd object ‘readmnist-package’:
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
'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
Documented arguments not in \usage in documentation object ‘add_docid’:
  ‘impute_types’

Documented arguments not in \usage in documentation object ‘texts’:
  ‘spacer’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘rearrr_fn_’:
  ‘overwrite’

Documented arguments not in \usage in documentation object ‘rev_windows_rearranger_’:
  ‘keep_windows’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Auto-generated content requiring editing in Rd object ‘recom-package’:
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'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
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
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘EDM.Rd’:
  ‘EDM-package’
'LazyData' is specified without a 'data' directory
Running examples in ‘red-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aoo
> ### Title: Area of Occupancy (AOO).
> ### Aliases: aoo
> 
> ### ** Examples
> 
> range = red.examples("red.range")
> aoo(range)
Error in data.frame(x = spData@ptr$coordinates()[[1]], y = spData@ptr$coordinates()[[2]]) : 
  no slot of name "ptr" for this object of class "SpatVector"
Calls: aoo -> data.frame
Execution halted
Invalid package aliases in Rd file ‘RED.Rd’:
  ‘RED-package’
Auto-generated content requiring editing in Rd object ‘referenceIntervals-package’:
  \references: ‘~~ Literature or other references for background information ~~’
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘Estep’:
  ‘adaptive_quad’

Documented arguments not in \usage in documentation object ‘d_bernoulli’:
  ‘pred.data’ ‘num.quad’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
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
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
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: \$
Invalid package aliases in Rd file ‘Renvlp.Rd’:
  ‘Revnlp-package’
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.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘REPPlab-package.Rd’:
  ‘R/EPP-lab-package’
'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 ‘reReg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.reReg
> ### Title: Plot the Baseline Cumulative Rate Function and the Baseline
> ###   Cumulative Hazard Function
> ### Aliases: plot.reReg
> ### Keywords: Plots
> 
> ### ** Examples
> 
> data(simDat)
> fm <- Recur(t.start %to% t.stop, id, event, status) ~ x1 + x2
> 
> fit <- reReg(fm, data = simDat, B = 0)
> plot(fit)
> plot(fit, xlab = "Time (days)", smooth = TRUE)
> 
> ## Predicted cumulative rate and hazard given covariates
> newdata <- expand.grid(x1 = 0:1, x2 = mean(simDat$x2))
> plot(fit, newdata = newdata, showName = TRUE)
Error in get(method[[1]]) : object 'last.bumpup' not found
Calls: <Anonymous> ... drawDetails -> drawDetails.dlgrob -> apply.method -> get
Execution halted
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘gaussian_process_cv’:
  ‘ncomp’

Documented arguments not in \usage in documentation object ‘get_samples_from_strata’:
  ‘starta’

Documented arguments not in \usage in documentation object ‘ith_subsets_ortho_diss’:
  ‘remove’

Documented arguments not in \usage in documentation object ‘pca_nipals’:
  ‘Y’

Documented arguments not in \usage in documentation object ‘predict_gaussian_process’:
  ‘b’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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: \_ \_
Documented arguments not in \usage in documentation object ‘time_roll’:
  ‘df’

Documented arguments not in \usage in documentation object ‘validate_auto_rate’:
  ‘df’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘get.V’:
  ‘ct.lst’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Re-building vignettes had CPU time 3.3 times elapsed time
Rd files without \alias:
  ‘retry-package.Rd’
'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
Documented arguments not in \usage in documentation object ‘compareChecksum.GenericDataFile’:
  ‘verbose’

Documented arguments not in \usage in documentation object ‘dim.GenericTabularFile’:
  ‘...’

Documented arguments not in \usage in documentation object ‘dsApplyInPairs.GenericDataFileSet’:
  ‘ds’

Documented arguments not in \usage in documentation object ‘GenericDataFile$fromFile’:
  ‘unknown’

Documented arguments not in \usage in documentation object ‘gzip.GenericDataFile’:
  ‘verbose’

Documented arguments not in \usage in documentation object ‘readChecksum.ChecksumFile’:
  ‘verbose’

Documented arguments not in \usage in documentation object ‘writeChecksum.GenericDataFile’:
  ‘verbose’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CardioRiskFactors.Rd:35: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘obs2Optim’:
  ‘BIC’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Documented arguments not in \usage in documentation object ‘rgl.fns’:
  ‘tag’ ‘tags’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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: \$
Argument items with no description in Rd object ‘MapBackground’:
  ‘lat’ ‘lon’
Argument items with no description in Rd object ‘plotOSM’:
  ‘add’ ‘removeMargin’
Argument items with no description in Rd object ‘plotOSMtile’:
  ‘add’ ‘raster’
Argument items with no description in Rd object ‘qbbox’:
  ‘TYPE’ ‘verbose’
'LazyData' is specified without a 'data' directory
'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:
  ‘mydata.rda’ ‘thedata.rda’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘dimnames.AbstractFileArray’:
  ‘...’

Documented arguments not in \usage in documentation object ‘length.AbstractFileArray’:
  ‘...’

Documented arguments not in \usage in documentation object ‘readContiguousValues.AbstractFileArray’:
  ‘length’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
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
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
Objects in \usage without \alias in documentation object ‘rioja-internal’:
  ‘.rmse’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘inner_t_index_calculation’:
  ‘param_’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
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
Invalid package aliases in Rd file ‘rkt-package.Rd’:
  ‘tkt-package’
'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: \$
Documented arguments not in \usage in documentation object ‘ns_env’:
  ‘env’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
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
S3 methods shown with full name in documentation object ‘fitted.values.margint’:
  ‘fitted.values.margint’

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.
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
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
Documented arguments not in \usage in documentation object ‘bind’:
  ‘.single_on_bind’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following calls to attach():
File ‘Rmosek/R/builder.R’:
  attach(builderenv, pos, name, warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
Documented arguments not in \usage in documentation object ‘WeightsFun_1C_1AIR’:
  ‘x’

Documented arguments not in \usage in documentation object ‘assert_col_vec_3C’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘ols’:
  ‘penalty’
Argument items with no description in Rd object ‘rmsMisc’:
  ‘fit1’
Argument items with no description in Rd object ‘val.surv’:
  ‘xlim’
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rnaturalearthhires’
Malformed Title field: should not end in a period.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘SanitizeURL’:
  ‘bad.str’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
Documented arguments not in \usage in documentation object ‘internals_for_RobAStBase_plot’:
  ‘panelFirst’

Documented arguments not in \usage in documentation object ‘internals_for_RobAStBase’:
  ‘L2fam’
Objects in \usage without \alias in documentation object ‘internals_for_RobAStBase’:
  ‘.evalListRec’ ‘.filterEargsWEargList’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file ‘0RobRDA-package.Rd’:
  ‘RobRDA-package’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘internal_interpolate_helpers_for_RobExtremes’:
  ‘upRad.s’
Objects in \usage without \alias in documentation object ‘internal_interpolate_helpers_for_RobExtremes’:
  ‘.getPsi.wL’ ‘.getPsi.P’

Objects in \usage without \alias in documentation object ‘rescaleFunction-methods’:
  ‘rescaleFunction’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘createITPSplineResult’:
  ‘measure’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
checkRd: (7) NEWS.Rd:320: Tag \bold is invalid in a \code block
Argument items with no description in Rd object ‘nlrob.control’:
  ‘\dots’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘Sample’:
  ‘interval_data’

Objects in \usage without \alias in documentation object ‘neg_log_marginal_post_approx_ref_ppgasp’:
  ‘neg_log_marginal_post_approx_ref’

Objects in \usage without \alias in documentation object ‘separable_multi_kernel’:
  ‘separable_kernel’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘choose.test’:
  ‘Xpaired’ ‘Ypaired’ ‘Xextra’ ‘Yextra’ ‘mc.rep’
Argument items with no description in Rd object ‘multinom.test’:
  ‘X’ ‘Y’ ‘alternative’ ‘correct’ ‘perm’ ‘mc.rep’ ‘method’ ‘verbose’
  ‘mode’ ‘useC’
Argument items with no description in Rd object ‘mw.mw.2.perm’:
  ‘X’ ‘Y’ ‘Xprime’ ‘Yprime’ ‘.corr’ ‘mc.rep’ ‘alternative’ ‘verbose’
Argument items with no description in Rd object ‘pm.wilcox.test’:
  ‘Xpaired’ ‘Ypaired’ ‘Xextra’ ‘Yextra’ ‘alternative’ ‘verbose’
Argument items with no description in Rd object ‘sim.partially.matched’:
  ‘meanRatio’ ‘sdRatio’ ‘within.sd’ ‘type’ ‘hyp’
Argument items with no description in Rd object ‘wmw.paired.replicates.test’:
  ‘X’ ‘Y’ ‘alternative’ ‘correct’ ‘perm’ ‘mc.rep’ ‘method’ ‘verbose’
  ‘mode’ ‘useC’
Problems with news in ‘NEWS.md’:
No news entries found.
Objects in \usage without \alias in documentation object ‘gettptnfpfn-defunct’:
  ‘gettptnfpfn’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
Documented arguments not in \usage in documentation object ‘add_matches_columns’:
  ‘Matches’

Documented arguments not in \usage in documentation object ‘run_checks_two’:
  ‘lookback’ ‘standard_deviaion’ ‘match_on’ ‘model_type’

Documented arguments not in \usage in documentation object ‘trim_pool’:
  ‘standard_deviaion’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Auto-generated content requiring editing in Rd object ‘roloc-package’:
  \references: ‘~~ Literature or other references for background information ~~’
  \seealso: ‘~~ Optional links to other man pages, e.g. ~~’
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
Documented arguments not in \usage in documentation object ‘DOLLAR.Class’:
  ‘...’

Documented arguments not in \usage in documentation object ‘DOLLAR< -.Class’:
  ‘...’

Documented arguments not in \usage in documentation object ‘getMethods.Class’:
  ‘unqiue’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
Documented arguments not in \usage in documentation object ‘internal_interpolate_helpers’:
  ‘upRad.s’ ‘withSmooth’
Assignments in \usage in documentation object ‘internal_interpolate_helpers’:
  .readGridFromCSV <- function(fromFileCSV) .generateInterpGrid(thGrid, 
      PFam, toFileCSV = "temp.csv", getFun = .getLMGrid, ..., modifyfct, 
      nameInSysdata, GridFileName, withPrint = TRUE, len = 13)

Objects in \usage without \alias in documentation object ‘internals_for_ROptEst_robest’:
  ‘.constructArg.list’ ‘.fix.in.defaults’ ‘.pretreat’ ‘.check.eps’
  ‘.isOKsteps’ ‘.isOKfsCor’

Documented arguments not in \usage in documentation object ‘internals_for_ROptEst_Cniperplots’:
  ‘origCl’

Objects in \usage without \alias in documentation object ‘internals_for_ROptEst’:
  ‘.isVirginW’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file ‘A.Introduction-RoughSets.Rd’:
  ‘A.Introduction-RoughSets-package’
Invalid package aliases in Rd file ‘B.Introduction-FuzzyRoughSets.Rd’:
  ‘B.Introduction-FuzzyRoughSets-package’
'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
Objects in \usage without \alias in documentation object ‘rpart-internal’:
  ‘rpart.anova’ ‘rpart.class’ ‘rpart.poisson’ ‘rpartco’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Argument items with no description in Rd object ‘anova.phylopars.lm’:
  ‘\dots’
Argument items with no description in Rd object ‘logLik.phylopars’:
  ‘\dots’
Argument items with no description in Rd object ‘logLik.phylopars.lm’:
  ‘\dots’
Argument items with no description in Rd object ‘print.SSC’:
  ‘\dots’
Argument items with no description in Rd object ‘print.phylopars’:
  ‘\dots’
Argument items with no description in Rd object ‘print.phylopars.lm’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.phylopars’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.phylopars.lm’:
  ‘\dots’
Error(s) in re-building vignettes:
  ...
--- re-building ‘a-getting-started.Rmd’ using rmarkdown
--- finished re-building ‘a-getting-started.Rmd’

--- re-building ‘b-advanced-ggplot.Rmd’ using rmarkdown

Quitting from lines 182-189 [unnamed-chunk-14] (b-advanced-ggplot.Rmd)
Error: processing vignette ‘b-advanced-ggplot.Rmd’ failed with diagnostics:
Problem while setting up geom.
ℹ Error occurred in the 2nd layer.
Caused by error in `handle_url()`:
! Must specify at least one of url or handle
--- failed re-building ‘b-advanced-ggplot.Rmd’

--- re-building ‘c-advanced-base.Rmd’ using rmarkdown

Quitting from lines 259-260 [unnamed-chunk-20] (c-advanced-base.Rmd)
Error: processing vignette ‘c-advanced-base.Rmd’ failed with diagnostics:
Must specify at least one of url or handle
--- failed re-building ‘c-advanced-base.Rmd’

SUMMARY: processing the following files failed:
  ‘b-advanced-ggplot.Rmd’ ‘c-advanced-base.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘pgCheckGeom’:
  ‘namechar’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
Documented arguments not in \usage in documentation object ‘rrcov-utils’:
  ‘tol’ ‘sv’ ‘n’ ‘p’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘RNAPlot’:
  ‘seqTF’
Argument items with no description in Rd object ‘aptPlotCT’:
  ‘seqTF’
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
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘[.RspDocument’:
  ‘...’

Documented arguments not in \usage in documentation object ‘RspEvalDirective’:
  ‘attributes’

Documented arguments not in \usage in documentation object ‘RspExpression’:
  ‘object’

Documented arguments not in \usage in documentation object ‘RspIncludeDirective’:
  ‘attributes’

Documented arguments not in \usage in documentation object ‘buildNonSweaveVignette’:
  ‘pathname’

Documented arguments not in \usage in documentation object ‘buildNonSweaveVignettes’:
  ‘path’ ‘pattern’

Documented arguments not in \usage in documentation object ‘exprToCode.RspSourceCodeFactory’:
  ‘expr’

Documented arguments not in \usage in documentation object ‘getContent.RspText’:
  ‘unescaped’

Documented arguments not in \usage in documentation object ‘toSourceCode.RspSourceCodeFactory’:
  ‘expr’

Documented arguments not in \usage in documentation object ‘trim.RspDocument’:
  ‘envir’

Documented arguments not in \usage in documentation object ‘writeResponse.RspResponse’:
  ‘collapse’ ‘sep’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘rrum_helper’:
  ‘deltas’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘create_tool’:
  ‘character’

Documented arguments not in \usage in documentation object ‘update_parameters_file’:
  ‘param’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'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 16.0.6 (11)’
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
Documented arguments not in \usage in documentation object ‘ApiRequest’:
  ‘report.description’

Documented arguments not in \usage in documentation object ‘BuildLineItemSegment’:
  ‘elements’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
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
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
Argument items with no description in Rd object ‘SetHash’:
  ‘\dots’
Invalid package aliases in Rd file ‘Rstpm2-package.Rd’:
  ‘Rstpm2-package’
Documented arguments not in \usage in documentation object ‘calculate.var.np’:
  ‘sone’ ‘szero’ ‘yone’ ‘yzero’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘summary.trimbatch’:
  ‘x’

Documented arguments not in \usage in documentation object ‘trim_workhorse’:
  ‘max_beta’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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.
Found the following files/directories:
  ‘Tsttwalk.dat’
Documented arguments not in \usage in documentation object ‘TWIT_paginate_max_id’:
  ‘parse’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘tidy_pi_traces’:
  ‘mix_indiv_tib’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘MEM_MIDAS_lr_pred_no_skew’:
  ‘daily_ret’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object ‘printHTML.trackInfo’:
  ‘printHTML.trackInfo’

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.
Found the following files/directories:
  ‘results’
Documented arguments not in \usage in documentation object ‘.is_datetime_valid’:
  ‘(`character`)’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘hsize’:
  ‘sizes’ ‘digits’ ‘units’ ‘bytes’

Documented arguments not in \usage in documentation object ‘timestamp.Verbose’:
  ‘stamp’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Package suggested but not available for checking: ‘gpuR’
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in documentation object ‘summary.rv’:
  ‘all.levels’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘matmult’:
  ‘%*%.rv’

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.
'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
Documented arguments not in \usage in documentation object ‘wind.fit_int’:
  ‘X’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Documented arguments not in \usage in documentation object ‘rxErrTypeCombine’:
  ‘newTransform’

Documented arguments not in \usage in documentation object ‘rxRepR0_’:
  ‘number’

Documented arguments not in \usage in documentation object ‘rxSetupScale’:
  ‘inits’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘.LoadDataFile’:
  ‘remapcells’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object ‘predict.s2netR’:
  ‘...’
Argument items with no description in Rd object ‘print.s2Data’:
  ‘\dots’
Specified C++11: please drop specification unless essential
matrixOps:
  function(x, y)
matrixOps.S7_object:
  function(e1, e2)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
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
Documented arguments not in \usage in documentation object ‘file_status’:
  ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd object ‘SAMM-package’:
  \seealso: ‘~~ Optional links to other man pages, e.g. ~~’
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘santoku-cast’:
  ‘santoku_cast_common.default’ ‘santoku_cast_common.double’
  ‘santoku_cast_common.Date’ ‘santoku_cast_common.POSIXct’
  ‘santoku_cast_common.ts’ ‘santoku_cast_common.zoo’
  ‘santoku_cast_common.integer64’ ‘santoku_cast_common.hexmode’
  ‘santoku_cast_common.octmode’

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.
'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: \&
Argument items with no description in Rd object ‘creer_graphe’:
  ‘groupes’
Argument items with no description in Rd object ‘fichiers’:
  ‘groupes’
‘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
Documented arguments not in \usage in documentation object ‘item_rm_recursive’:
  ‘sb_id’

Documented arguments not in \usage in documentation object ‘session_age’:
  ‘sb_id’ ‘...’

Documented arguments not in \usage in documentation object ‘session_expired’:
  ‘sb_id’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Re-building vignettes had CPU time 2.5 times elapsed time
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'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.
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
S3 methods shown with full name in documentation object ‘plot’:
  ‘plot.discretization’

S3 methods shown with full name in documentation object ‘predict’:
  ‘predict.discretization’ ‘predict.reject_infered’

S3 methods shown with full name in documentation object ‘summary’:
  ‘summary.discretization’

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.
'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
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
Problems with news in ‘NEWS.md’:
No news entries found.
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
Documented arguments not in \usage in documentation object ‘parse_search_analytics’:
  ‘pn’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘%>%’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
S3 methods shown with full name in documentation object ‘min.abs’:
  ‘min.abs’

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.
'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.
Auto-generated content requiring editing in Rd object ‘seqCBS-package’:
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
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’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Argument items with no description in Rd object ‘sequential.design’:
  ‘\dots’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) 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
Documented arguments not in \usage in documentation object ‘SingleCorPlot’:
  ‘rows.highight’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘jc_clc_perm_impl’:
  ‘a’

Documented arguments not in \usage in documentation object ‘local_g_spt’:
  ‘n_sim’

Documented arguments not in \usage in documentation object ‘permute_listw’:
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 44-48 [unnamed-chunk-3] (introduction.Rmd)
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error in `loadNamespace()`:
! there is no package called 'prettymapr'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
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
Invalid package aliases in Rd file ‘package_sgmodel.Rd’:
  ‘package_sgmodel-package’
'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: \^
'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’
'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
Documented arguments not in \usage in documentation object ‘shiny_models’:
  ‘original_data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Found the following files/directories:
  ‘MM.csv’ ‘Simul.csv’ ‘catalytic.csv’
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’
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object ‘estThetaRow’:
  ‘theta’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘print_info’:
  ‘line’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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.
Documented arguments not in \usage in documentation object ‘make_kernel_dist’:
  ‘Umax’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.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
Documented arguments not in \usage in documentation object ‘interval_labels’:
  ‘format’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
Auto-generated content requiring editing in Rd object ‘SimplifyStats-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Found the following files/directories:
  ‘SimRAD-exampleRefSeq-Fasta.fa’ ‘SimRAD-exampleRefSeq.fa’
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’
Invalid package aliases in Rd file ‘SimReg-package.Rd’:
  ‘SimReg3-package’
Documented arguments not in \usage in documentation object ‘sim_founderRVstatus’:
  ‘intro_RV’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
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
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'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
Argument items with no description in Rd object ‘management.prob’:
  ‘...’
Argument items with no description in Rd object ‘mng.tree.removal’:
  ‘\dots’
Argument items with no description in Rd object ‘prep.common.vars.fun’:
  ‘\dots’
Argument items with no description in Rd object ‘recr.BBG2008’:
  ‘common.vars’
Documented arguments not in \usage in documentation object ‘to_shiny_tag’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ‘:::’ call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object ‘calculate_gefficiency’:
  ‘RunMatrix’

Documented arguments not in \usage in documentation object ‘constructRunMatrix’:
  ‘Levelvector’

Documented arguments not in \usage in documentation object ‘effectpower’:
  ‘X’

Documented arguments not in \usage in documentation object ‘gen_momentsmatrix’:
  ‘Levelvector’

Documented arguments not in \usage in documentation object ‘generate_noise_block’:
  ‘RunMatrix’

Documented arguments not in \usage in documentation object ‘genhypmatrix’:
  ‘Parameters’ ‘Levels’ ‘G’

Documented arguments not in \usage in documentation object ‘genparammatrix’:
  ‘Parameters’ ‘Levels’ ‘G’

Documented arguments not in \usage in documentation object ‘priorlevels’:
  ‘Levelvector’

Documented arguments not in \usage in documentation object ‘reduceRunMatrix’:
  ‘ModelMatrix’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘texPreview’
Unknown package ‘texPreview’ 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
Documented arguments not in \usage in documentation object ‘capacity_logreg_testing’:
  ‘maxNWts’

Documented arguments not in \usage in documentation object ‘mi_logreg_testing’:
  ‘maxNWts’

Documented arguments not in \usage in documentation object ‘output_graphs_main’:
  ‘path’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) ex0723.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ex0915.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) ex1515.Rd:4: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘captioner’
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’
Auto-generated content requiring editing in Rd object ‘smallstuff-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
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
Documented arguments not in \usage in documentation object ‘aux_cs’:
  ‘dists’

Documented arguments not in \usage in documentation object ‘aux_gauss’:
  ‘dists’

Documented arguments not in \usage in documentation object ‘aux_gw’:
  ‘dists’

Documented arguments not in \usage in documentation object ‘aux_mat’:
  ‘mat_list1’ ‘mat_list2’ ‘x’ ‘y’ ‘return_single’

Documented arguments not in \usage in documentation object ‘aux_matern’:
  ‘dists’

Documented arguments not in \usage in documentation object ‘aux_pexp’:
  ‘dists’

Documented arguments not in \usage in documentation object ‘aux_spher’:
  ‘dists’

Documented arguments not in \usage in documentation object ‘aux_tapmat’:
  ‘dists’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file ‘SMLE-package.Rd’:
  ‘smle-package’
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
Auto-generated content requiring editing in Rd object ‘smoke-package’:
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
'LazyData' is specified without a 'data' directory
File ‘SmoothHazard/libs/SmoothHazard.so’:
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘bgos.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.
checkRd: (-1) hoods2dsmooth.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dmeitsjer.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dsmooth.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) smoothie-package.Rd:42: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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
Auto-generated content requiring editing in Rd object ‘smotefamily-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Found the following files/directories:
  ‘my_new_social_media_plot.png’
Objects in \usage without \alias in documentation object ‘sm-internal’:
  ‘sm.check.data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
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’
Documented arguments not in \usage in documentation object ‘som.nn.do.train’:
  ‘model’

Documented arguments not in \usage in documentation object ‘som.nn.som.internal’:
  ‘rlen’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘plot.predictions’:
  ‘plot.predictions’

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.
'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
Documented arguments not in \usage in documentation object ‘path2name’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘averageMatrices’:
  ‘aggFun’

Documented arguments not in \usage in documentation object ‘.detectNLP’:
  ‘orig_x’

Documented arguments not in \usage in documentation object ‘getSmoothSpectrum’:
  ‘a’

Documented arguments not in \usage in documentation object ‘htmlPlots’:
  ‘myfolder’ ‘myfiles’

Documented arguments not in \usage in documentation object ‘interpolate’:
  ‘manualUnvoiced’

Documented arguments not in \usage in documentation object ‘parabPeakInterpol’:
  ‘points’

Documented arguments not in \usage in documentation object ‘processAudio’:
  ‘summaryFun’

Documented arguments not in \usage in documentation object ‘pseudoLog’:
  ‘approximate’

Documented arguments not in \usage in documentation object ‘pseudoLog_undo’:
  ‘approximate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘r2cytoscape’
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘NLMR’
Documented arguments not in \usage in documentation object ‘.findModuleName’:
  ‘modules’

Documented arguments not in \usage in documentation object ‘.runCodeChecks’:
  ‘message’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
'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
'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
Documented arguments not in \usage in documentation object ‘logit’:
  ‘theta’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object ‘binarizer’:
  ‘\dots’
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
checkRd: (-1) NEWS.Rd:137: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘spDataLarge’
Documented arguments not in \usage in documentation object ‘hazard’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Documented arguments not in \usage in documentation object ‘%matches%’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘changeDevSettings’:
  ‘defaultsSettings’

Documented arguments not in \usage in documentation object ‘checkMethod’:
  ‘allowedMethod’

Documented arguments not in \usage in documentation object ‘convertListToS4’:
  ‘names’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘i_is_index’:
  ‘max_length’

Documented arguments not in \usage in documentation object ‘i_read_asd_spectra’:
  ‘format’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.neig’
Objects in \usage without \alias in documentation object ‘add_details’:
  ‘\S4method{add_details}{spflow_model}’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
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’
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checkRd: (-1) PimaIndiansDiabetes_wide.Rd:16: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘split_feasibility.Rd’:
  ‘split_feasibility-package’
'LazyData' is specified without a 'data' directory
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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
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Documented arguments not in \usage in documentation object ‘obis_search’:
  ‘scientificname’

Documented arguments not in \usage in documentation object ‘spocc_objects’:
  ‘n’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘basketball_center_circle_fill’:
  ‘linethickness’

Documented arguments not in \usage in documentation object ‘basketball_free_throw_circle_dash’:
  ‘end_angleThe’

Documented arguments not in \usage in documentation object ‘basketball_painted_area’:
  ‘free_throw_lane_boundary_line_thickness’

Documented arguments not in \usage in documentation object ‘curling_features_set_colors’:
  ‘sheet’ ‘ring_1’ ‘ring_2’ ‘ring_3’

Documented arguments not in \usage in documentation object ‘football_field_border’:
  ‘boundary_thickness’

Documented arguments not in \usage in documentation object ‘football_field_border_outline’:
  ‘boundary_thickness’

Documented arguments not in \usage in documentation object ‘hockey_features_set_colors’:
  ‘boards_color’ ‘center_line_color’ ‘blue_line_color’
  ‘goal_line_color’ ‘goalkeepers_restricted_area_color’
  ‘goal_crease_outline_color’ ‘goal_crease_fill_color’
  ‘referee_crease_color’ ‘center_faceoff_spot_color’
  ‘faceoff_spot_outer_ring_color’ ‘faceoff_spot_fill_color’
  ‘center_faceoff_circle_color’ ‘non_center_faceoff_circle_color’
  ‘faceoff_line_color’ ‘goal_color’ ‘goal_fill_color’

Documented arguments not in \usage in documentation object ‘lacrosse_off_field_officials_box’:
  ‘feature_thickness’

Documented arguments not in \usage in documentation object ‘lacrosse_penalty_box_outline’:
  ‘feature_thickness’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘checkFunEvalsDesignSize’:
  ‘fun’ ‘upper’

Documented arguments not in \usage in documentation object ‘print.spotBOModel’:
  ‘object’

Documented arguments not in \usage in documentation object ‘print.spotGaussianProcessModel’:
  ‘object’

Documented arguments not in \usage in documentation object ‘print.spotLOESS’:
  ‘object’

Documented arguments not in \usage in documentation object ‘print.spotLassoModel’:
  ‘object’

Documented arguments not in \usage in documentation object ‘print.spotLinearModel’:
  ‘object’

Documented arguments not in \usage in documentation object ‘print.spotRSM’:
  ‘object’

Documented arguments not in \usage in documentation object ‘print.spotRandomForest’:
  ‘object’

Documented arguments not in \usage in documentation object ‘print.spotRanger’:
  ‘object’

Documented arguments not in \usage in documentation object ‘print.spotSeverity’:
  ‘object’

Documented arguments not in \usage in documentation object ‘print.spotTreeModel’:
  ‘object’

Documented arguments not in \usage in documentation object ‘simulationSpectral’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
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.
Argument items with no description in Rd object ‘sim.kong’:
  ‘gamma’ ‘beta’ ‘design’ ‘rho’ ‘seed’ ‘impute’ ‘ppi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘Expected time series dynamics’:
  ‘logs2’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
Documented arguments not in \usage in documentation object ‘namesMultiple’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Documented arguments not in \usage in documentation object ‘stack_predict’:
  ‘type’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘connect,report_mig-method’:
  ‘h’ ‘...’

Documented arguments not in \usage in documentation object ‘print,report_mig-method’:
  ‘h’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘which_class’:
  ‘character’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    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
Invalid package aliases in Rd file ‘statcheck-package.Rd’:
  ‘{statcheck}-package’
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Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Documented arguments not in \usage in documentation object ‘estEffsCPP’:
  ‘y’ ‘w’ ‘x’ ‘ncores’

Documented arguments not in \usage in documentation object ‘updateFA’:
  ‘Y’ ‘WStart’ ‘m’ ‘PStart’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘imputeMissings’
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
'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
Argument items with no description in Rd object ‘d.sum.of.mixtures.EXPLN’:
  ‘p.vector’
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object ‘strategicplayers-package’:
  \details: ‘...o use the package, including the most important functions ~~’
  \references: ‘~~ Literature or other references for background information ~~’
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
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Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘get_groups’:
  ‘groups’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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: \&
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Invalid package aliases in Rd file ‘StructFDR-package.Rd’:
  ‘TreeFDR-package’
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘size.penalize’:
  ‘size.penalize’

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.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘subsamp’:
  ‘x:’ ‘y:’ ‘s:’ ‘m:’ ‘qnum:’ ‘wplot:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Auto-generated content requiring editing in Rd object ‘supcluster-package’:
  \references: ‘~~ Literature or other references for background information ~~’
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
Documented arguments not in \usage in documentation object ‘check_package’:
  ‘X’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
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surfaceSimulate : phytransform: no visible global function definition
  for ‘rescale’
Undefined global functions or variables:
  rescale
'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: 'INLA', 'gpclib'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'
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
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
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
File ‘swdpwr/libs/swdpwr.so’:
  Found ‘_gfortran_random_r4’, possibly from ‘random_number’ (Fortran)
    Object: ‘auxillary.o’
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘auxillary.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.
Package suggested but not available for checking: ‘swephRdata’
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
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Invalid package aliases in Rd file ‘syncrng-package.Rd’:
  ‘syncrng-package’
'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
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
Documented arguments not in \usage in documentation object ‘table_params_circle’:
  ‘d’

Documented arguments not in \usage in documentation object ‘table_params_rect’:
  ‘d’ ‘scale_breaks’ ‘r_max’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘plot.prEntries’:
  ‘plot.margin’ ‘sizeAdjust’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
S3 methods shown with full name in documentation object ‘designMatrices’:
  ‘print.designMatrices’

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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘default_db_ref’:
  ‘name’ ‘url’ ‘desc’ ‘id_regex’

Documented arguments not in \usage in documentation object ‘limited_print’:
  ‘trunc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'LazyData' is specified without a 'data' directory
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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: \^
checkRd: (-1) run.cor.examp.Rd:10: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:31: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'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
Documented arguments not in \usage in documentation object ‘extract_sptensor’:
  ‘idxmat’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘safe_digest’:
  ‘filename’

Documented arguments not in \usage in documentation object ‘with_mock’:
  ‘.local_env’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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Documented arguments not in \usage in documentation object ‘CompileLatexDir’:
  ‘engine:’ ‘compile.dir:’

Documented arguments not in \usage in documentation object ‘GetLayerSampleIndexes’:
  ‘NamesOfListToSample’ ‘isRandomized’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
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'LazyData' is specified without a 'data' directory
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Problems with news in ‘NEWS.md’:
No news entries found.
Rd file 'textEmbedReduce.Rd':
  \usage lines wider than 90 characters:
         "https://raw.githubusercontent.com/adithya8/ContextualEmbeddingDR/master/models/fb20/scalar.csv",
         "https://raw.githubusercontent.com/adithya8/ContextualEmbeddingDR/master/models/fb20/rpca_roberta_768_D_20.csv"

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Unknown package ‘textreadr’ in Rd xrefs
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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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Objects in \usage without \alias in documentation object ‘tframe.timeSeries’:
  ‘tbind.timeSeries’

Objects in \usage without \alias in documentation object ‘tframe.tis’:
  ‘tfstart.tis’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘witcherMap’:
  ‘palettes’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘poisson_likelihood’:
  ‘rate_exp’ ‘rate_ref’ ‘rate_pla’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
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checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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
Documented arguments not in \usage in documentation object ‘hclust_fit’:
  ‘h’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘gate_interactive_chr_int’:
  ‘gate_list’

Documented arguments not in \usage in documentation object ‘gate_programmatic’:
  ‘...’

Documented arguments not in \usage in documentation object ‘gate_programmatic_chr_int’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘deprecated-se’:
  ‘expand_cols’

Documented arguments not in \usage in documentation object ‘tidyr_legacy’:
  ‘nm’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘vars_select’:
  ‘args’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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 16.0.6 (11)’
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd object ‘timeperiodsR-package’:
  \details: ‘...o use the package, including the most important functions ~~’
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
Invalid package aliases in Rd file ‘timeSeq_1.0.4-package.Rd’:
  ‘timeSeq_1.0.4-package’
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘tm.plugin.alceste-package.Rd’:
  ‘tm.plugin.europresse-package’
'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
Documented arguments not in \usage in documentation object ‘TNRS_core’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Package suggested but not available for checking: ‘corpus.JSS.papers’
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in documentation object ‘createLink’:
  ‘hits’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘moveVis’
Unknown package ‘moveVis’ in Rd xrefs
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Enhancements
    Other changes
Argument items with no description in Rd object ‘noblabrams’:
  ‘prior’ ‘change’
Argument items with no description in Rd object ‘absoluteIncreaseALL’:
  ‘storedev’ ‘\dots’
Argument items with no description in Rd object ‘boundaryLineALL’:
  ‘\dots’
Argument items with no description in Rd object ‘growthAveragingALL’:
  ‘\dots’
Argument items with no description in Rd object ‘plotFirstYears’:
  ‘\dots’
Argument items with no description in Rd object ‘plotRelease’:
  ‘\dots’
Argument items with no description in Rd object ‘splechtnaALL’:
  ‘\dots’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taxidata’
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object ‘seqimplic’:
  ‘ylim’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in documentation object ‘transport-internal’:
  ‘gif.generate’ ‘plot_pgrid_wpp’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Packages suggested but not available for checking:
  'Eunomia', 'CohortGenerator', 'CirceR'
Documented arguments not in \usage in documentation object ‘clean_data’:
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
Documented arguments not in \usage in documentation object ‘correct_continuous’:
  ‘x’

Documented arguments not in \usage in documentation object ‘tc_correlation’:
  ‘p’

Documented arguments not in \usage in documentation object ‘tc_efunc’:
  ‘p’

Documented arguments not in \usage in documentation object ‘tc_mfunc’:
  ‘p’

Documented arguments not in \usage in documentation object ‘tc_response’:
  ‘p’

Documented arguments not in \usage in documentation object ‘truncate_input’:
  ‘moving’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Auto-generated content requiring editing in Rd object ‘treemisc-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
Specified C++11: please drop specification unless essential
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
Documented arguments not in \usage in documentation object ‘check_variables’:
  ‘ncol’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [139s/51s]
Running R code in ‘testthat.R’ had CPU time 2.7 times elapsed time
Documented arguments not in \usage in documentation object ‘dvinecopula_objective’:
  ‘udata’

Documented arguments not in \usage in documentation object ‘wobjective’:
  ‘vt’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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: \&
Objects in \usage without \alias in documentation object ‘nlar.struct’:
  ‘getNUsed’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘tseriesTARMA/libs/tseriesTARMA.so’:
  Found ‘_gfortran_arandom_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘TARMA_MOD.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
S3 methods shown with full name in documentation object ‘tsibble-vctrs’:
  ‘vec_ptype2.tbl_ts’ ‘vec_cast.tbl_ts’ ‘vec_cast.yearmonth’
  ‘vec_ptype2.yearmonth’ ‘vec_cast.yearquarter’
  ‘vec_ptype2.yearquarter’ ‘vec_cast.yearweek’ ‘vec_ptype2.yearweek’

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.
'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
Invalid package aliases in Rd file ‘tsoutliers-package.Rd’:
  ‘tsouliers-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Invalid package aliases in Rd file ‘TTAinterface-package.Rd’:
  ‘TTAinterface-package’
'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
Package which this enhances but not available for checking: ‘sl3’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in documentation object ‘generate_parameter’:
  ‘SIMINT_PARAMETERS_TV’ ‘SIMINT_PARAMETERS_IIV_VALUE’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
'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
Argument items with no description in Rd object ‘HC’:
  ‘X’ ‘K’
Argument items with no description in Rd object ‘KA’:
  ‘X’ ‘K’ ‘distancemetric’
Argument items with no description in Rd object ‘SOMs’:
  ‘X’ ‘K’ ‘topo’ ‘rlen’ ‘alpha’ ‘n.hood’
Argument items with no description in Rd object ‘binarise’:
  ‘U’ ‘K’ ‘technique’ ‘parameter’
Argument items with no description in Rd object ‘closestToSquareFactors’:
  ‘n’
Argument items with no description in Rd object ‘clustDist’:
  ‘U1’ ‘U2’ ‘X’ ‘criterion’
Argument items with no description in Rd object ‘clustVec2partMat’:
  ‘C’
Argument items with no description in Rd object ‘clusterDataset’:
  ‘X’ ‘K’ ‘D’ ‘methods’
Argument items with no description in Rd object ‘factors’:
  ‘n’ ‘primeonly’
Argument items with no description in Rd object ‘fixnans’:
  ‘X’ ‘type’
Argument items with no description in Rd object ‘fuzzystretch’:
  ‘X’ ‘x0’
Argument items with no description in Rd object ‘generateCoPaM’:
  ‘U’ ‘relabel_technique’ ‘w’ ‘X’ ‘distCriterion’ ‘K’ ‘GDM’
Argument items with no description in Rd object ‘isValidBPM’:
  ‘U’
Argument items with no description in Rd object ‘isempty’:
  ‘X’
Argument items with no description in Rd object ‘isnullorempty’:
  ‘X’
Argument items with no description in Rd object ‘kmeansKA’:
  ‘X’ ‘K’ ‘distancemetric’ ‘iter.max’ ‘nstart’ ‘algorithm’ ‘trace’
Argument items with no description in Rd object ‘mnplots’:
  ‘Vmse’ ‘mseCache’ ‘subplotdim’ ‘subplotind’ ‘minimiseDistance’
Argument items with no description in Rd object ‘mseclusters’:
  ‘X’ ‘B’ ‘normalise’
Argument items with no description in Rd object ‘normaliseMatrix’:
  ‘X’ ‘type’
Argument items with no description in Rd object ‘partMat2clustVec’:
  ‘U’ ‘skipValidity’
Argument items with no description in Rd object ‘permutations’:
  ‘n’
Argument items with no description in Rd object ‘relabelClusts’:
  ‘ref’ ‘input’ ‘technique’ ‘X’ ‘distCriterion’
Documented arguments not in \usage in documentation object ‘sqrtm’:
  ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Rd files without \alias:
  ‘ungroup.Rd’
Documented arguments not in \usage in documentation object ‘MortSmooth_tpower’:
  ‘vector’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘as.character.bullet’:
  ‘pre’

Documented arguments not in \usage in documentation object ‘capture_output’:
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Running ‘testthat.R’ [20s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(useful)
  Loading required package: ggplot2
  > 
  > test_check("useful")
  Error in detach("package:coefplot", unload = TRUE) : 
    invalid 'name' argument
  [ FAIL 1 | WARN 30 | SKIP 2 | PASS 740 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-load-packages.R:11:5', 'test-load-packages.R:18:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-shiftColumn.r:6:5'): shift.column returns data.frames (or appropriate errors) ──
  Error in `.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)`: invalid non-character version specification 'x' (type: double)
  Backtrace:
      ▆
   1. ├─testthat::skip_if(getRversion() <= 3.4) at test-shiftColumn.r:6:4
   2. │ └─base::isTRUE(condition)
   3. └─base::Ops.numeric_version(getRversion(), 3.4)
   4.   └─base::as.numeric_version(e2)
   5.     └─base::numeric_version(x)
   6.       └─base::.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)
  
  [ FAIL 1 | WARN 30 | SKIP 2 | PASS 740 ]
  Error: Test failures
  Execution halted
Documented arguments not in \usage in documentation object ‘use_course_details’:
  ‘destdir’ ‘zipfile’

Documented arguments not in \usage in documentation object ‘write-this’:
  ‘contents’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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: \_ \_ \_
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checkRd: (-1) babies.Rd:28: Escaped LaTeX specials: \&
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checkRd: (-1) cabinet.Rd:25: Escaped LaTeX specials: \$
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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
Documented arguments not in \usage in documentation object ‘countDNAPatternInAlt’:
  ‘trascriptsTable’

Documented arguments not in \usage in documentation object ‘countDNAPatternInAltOneVariant’:
  ‘trascriptsTable’

Documented arguments not in \usage in documentation object ‘getAltSequence’:
  ‘trascriptsTable’

Documented arguments not in \usage in documentation object ‘getCodonInAlt’:
  ‘trascriptsTable’ ‘codonPositionsColumnn’

Documented arguments not in \usage in documentation object ‘getCodonInAltOneVariant’:
  ‘trascriptsTable’ ‘codonPositionsColumnn’

Documented arguments not in \usage in documentation object ‘getTSSKozakOneVariant’:
  ‘variantsTable’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Rd files without \alias:
  ‘valaddin.Rd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
Documented arguments not in \usage in documentation object ‘.PKGOPT’:
  ‘varlist:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘vctrs-conditions’:
  ‘subclass’

Documented arguments not in \usage in documentation object ‘vec_as_subscript’:
  ‘location’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘syntab’:
  ‘print.syntab’

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.
Documented arguments not in \usage in documentation object ‘vein-deprecated’:
  ‘object’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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: \&
Missing link or links in documentation object ‘profilevglm.Rd’:
  ‘[MASS]{plot.profile}’

See section ‘Cross-references’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Argument items with no description in Rd object ‘learnPartitionWithLLR’:
  ‘type’ ‘procedure’ ‘ql’ ‘qq’ ‘BinaryLearningProcedure’
Argument items with no description in Rd object ‘plotClassifRule’:
  ‘object’
Documented arguments not in \usage in documentation object ‘boxplot_VICI’:
  ‘res_2plot’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘draw_map_shiny’:
  ‘rigth.lim’

Documented arguments not in \usage in documentation object ‘map_summary’:
  ‘rigth.lim’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘insert_preview’:
  ‘input’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Documented arguments not in \usage in documentation object ‘cpp_vol2bird_version’:
  ‘path’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object ‘blendColor’:
  ‘color’ ‘percent’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘get.wal.mipmap.heights’:
  ‘height_mm’

Documented arguments not in \usage in documentation object ‘get.wal.mipmap.widths’:
  ‘width_mm’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘WaveDjF’:
  ‘y_fft’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Auto-generated content requiring editing in Rd object ‘maxithresh’:
  \details: ‘~~ If necessary, more details than the description above ~~’
  \arguments: data: ‘~~Describe \code{data} here~~’
  \arguments: g: ‘~~Describe \code{g} here~~’
  \arguments: L: ‘~~Describe \code{L} here~~’
  \arguments: F: ‘~~Describe \code{F} here~~’
  \arguments: eta: ‘~~Describe \code{eta} here~~’
'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
Documented arguments not in \usage in documentation object ‘train_spectra’:
  ‘save.model’ ‘vector.input’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
Invalid package aliases in Rd file ‘wce-package.Rd’:
  ‘wce-package’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘prepr’
Problems with news in ‘NEWS.md’:
No news entries found.
Argument items with no description in Rd object ‘plotByRate’:
  ‘baseTimeCol’ ‘baseDataCol’ ‘baseBaseRateCol’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘read_img’:
  ‘imgfile’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file ‘print.webpower.Rd’:
  ‘print.webpower-package’
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
Argument items with no description in Rd object ‘zdifference_ordinal’:
  ‘na.rm’
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘sampledHierarchicalConsensusModules’:
  ‘consensusTOMFilePattern’
S3 methods shown with full name in documentation object ‘QIC.gee’:
  ‘QIC.gee’

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.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
Package suggested but not available for checking: ‘anomalize’
Documented arguments not in \usage in documentation object ‘remove_empty’:
  ‘quiet’

Documented arguments not in \usage in documentation object ‘undoHistory’:
  ‘class’ ‘btn_class’ ‘back_text’ ‘fwd_text’ ‘back_title’ ‘fwd_title’
  ‘back_icon’ ‘fwd_icon’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘displayDataTable’:
  ‘id’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'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
Documented arguments not in \usage in documentation object ‘new_givens_path’:
  ‘generate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Documented arguments not in \usage in documentation object ‘sample_me’:
  ‘middle_name’ ‘M_rs’ ‘M_rf’ ‘M_rm’ ‘alpha’ ‘me_race’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘Cut.off’:
  ‘main’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘xbreed/libs/xbreed.so’:
  Found ‘_gfortran_random_r4’, possibly from ‘random_number’ (Fortran)
    Object: ‘hp.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘hp.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.
Found the following files/directories:
  ‘RP2_data_1.txt’ ‘RP2_data_4.txt’ ‘RP2_qtl_1.txt’ ‘RP2_qtl_4.txt’
  ‘hp1_effect_qtl.txt’ ‘hp1_freq_mrk.txt’ ‘hp1_freq_qtl.txt’
  ‘hp1_genome.txt’ ‘hp1_last_hp_data.txt’ ‘hp1_lm_mrk.txt’
  ‘hp1_lm_qtl.txt’ ‘hp1_lm_qtl_mrk.txt’ ‘hp1_mrk.txt’ ‘hp1_qtl.txt’
  ‘hp2_effect_qtl.txt’ ‘hp2_freq_mrk.txt’ ‘hp2_freq_qtl.txt’
  ‘hp2_genome.txt’ ‘hp2_last_hp_data.txt’ ‘hp2_lm_mrk.txt’
  ‘hp2_lm_qtl.txt’ ‘hp2_lm_qtl_mrk.txt’ ‘hp2_mrk.txt’ ‘hp2_qtl.txt’
  ‘my_RP_data_1.txt’ ‘my_RP_data_4.txt’ ‘my_RP_mrk_1.txt’
  ‘my_RP_mrk_4.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xgb.txt’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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
Documented arguments not in \usage in documentation object ‘local_cli_theme’:
  ‘`[environment(1)]`\cr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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: \_
Documented arguments not in \usage in documentation object ‘xpose.create.title’:
  ‘plot.text’ ‘main’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘check_problem’:
  ‘xpdb’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file ‘XRjulia-package.Rd’:
  ‘XRjulia-package’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
Argument items with no description in Rd object ‘getCondition’:
  ‘object’
Argument items with no description in Rd object ‘screen’:
  ‘fac’ ‘condition’ ‘position’
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
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.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘IC’:
  ‘\dots’
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.
Auto-generated content requiring editing in Rd object ‘ZIBseq-package’:
  \seealso: ‘~~ Optional links to other man pages, e.g. ~~ ~~ \code{\link...’
'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
Documented arguments not in \usage in documentation object ‘plot_curves’:
  ‘fix.x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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: \_
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
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’
Documented arguments not in \usage in documentation object ‘ADMM_EN2’:
  ‘alpha’

Documented arguments not in \usage in documentation object ‘ADMM_EN_SMW’:
  ‘alpha’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘testRmACD’:
  ‘pStar’
'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
Documented arguments not in \usage in documentation object ‘fitSnpNmfArray’:
  ‘maxIter’ ‘acc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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'
Documented arguments not in \usage in documentation object ‘checkDupSignals’:
  ‘tag.list’

Documented arguments not in \usage in documentation object ‘collectStrays’:
  ‘restart’

Documented arguments not in \usage in documentation object ‘findSecondsPerSection’:
  ‘start.time’

Documented arguments not in \usage in documentation object ‘printExploreRmd’:
  ‘valid.detectiosn’

Documented arguments not in \usage in documentation object ‘printLastArray’:
  ‘input’ ‘sections’

Documented arguments not in \usage in documentation object ‘transformSpatial’:
  ‘file’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Packages required but not available:
  'BSgenome', 'BSgenome.Hsapiens.UCSC.hg19',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm9',
  'BSgenome.Mmusculus.UCSC.mm10'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in documentation object ‘d1’:
  ‘The’ ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (7) NEWS.Rd:74: Tag \dQuote is invalid in a \code block
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘AdaptGauss-package.Rd’:
  ‘MultiModal-package’
Invalid package aliases in Rd file ‘aslm-package.Rd’:
  ‘aslm-package’ ‘asggm-package’
Argument items with no description in Rd object ‘asggm-internal’:
  ‘ansL’ ‘kNodes’ ‘spP’
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
Documented arguments not in \usage in documentation object ‘print.aTest’:
  ‘how’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘ae_count’:
  ‘patients’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘phytools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘HiTC’
'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.
Package suggested but not available for checking: ‘glmmTMB’
'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’
Missing or unexported object: ‘Matrix::crossprod’
Package which this enhances but not available for checking: ‘asreml’
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: \&
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
Package suggested but not available for checking: ‘glmmTMB’
Package required but not available: ‘ALDEx2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid package aliases in Rd file ‘aire.zmvm-deprecated.Rd’:
  ‘aire.zmvm-deprecated-package’
'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
Package required but not available: ‘GenomicAlignments’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/albatross.Rcheck/00install.out’ for details.
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
'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
Missing or unexported objects:
  ‘Matrix::crossprod’ ‘Matrix::tcrossprod’
Package suggested but not available for checking: ‘lfe’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘gs’:
  ‘x’ ‘parallel’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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.
Argument items with no description in Rd object ‘MLS’:
  ‘MSE1’
'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
Invalid package aliases in Rd file ‘amelia.package.Rd’:
  ‘amelia-package’
'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
Documented arguments not in \usage in documentation object ‘check_factors’:
  ‘object’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
Package required but not available: ‘DESeq2’

See section ‘The DESCRIPTION file’ 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
Package required but not available: ‘Seurat’

Package suggested but not available for checking: ‘Signac’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Auto-generated content requiring editing in Rd object ‘rowVars’:
  \arguments: \dots: ‘~~Describe \code{\dots} here~~’
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: \~
Invalid package aliases in Rd file ‘and-package.Rd’:
  ‘reprex-package’
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in documentation object ‘ggplot_gtable’:
  ‘plot’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘crawl_interpolation’:
  ‘pt.colors’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Documented arguments not in \usage in documentation object ‘alternate.sol3’:
  ‘lambda0’

Documented arguments not in \usage in documentation object ‘check.group’:
  ‘k’

Documented arguments not in \usage in documentation object ‘getrow3’:
  ‘lambda0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
GNU make is a SystemRequirements.
Package required but not available: ‘MBESS’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘apaTables’
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object ‘apci’:
  ‘\dots’
Argument items with no description in Rd object ‘apci.bar’:
  ‘\dots’
Argument items with no description in Rd object ‘apci.plot’:
  ‘\dots’
Argument items with no description in Rd object ‘apci.plot.heatmap’:
  ‘\dots’
Argument items with no description in Rd object ‘apci.plot.hexagram’:
  ‘first_age’ ‘first_period’ ‘interval’ ‘first_age_isoline’
  ‘first_period_isoline’ ‘isoline_interval’ ‘line_width’ ‘line_color’
  ‘label_size’ ‘label_color’ ‘scale_units’ ‘wrap_cohort_labels’
  ‘quantile’
Argument items with no description in Rd object ‘apci.plot.raw’:
  ‘\dots’
Argument items with no description in Rd object ‘cohortdeviation’:
  ‘\dots’
Argument items with no description in Rd object ‘compute_xcoordinate’:
  ‘p’
Argument items with no description in Rd object ‘compute_ycoordinate’:
  ‘p’ ‘a’
Argument items with no description in Rd object ‘maineffect’:
  ‘\dots’
Argument items with no description in Rd object ‘temp_model’:
  ‘\dots’
Argument items with no description in Rd object ‘tests’:
  ‘\dots’
Package suggested but not available for checking: ‘phangorn’
Error(s) in re-building vignettes:
  ...
--- re-building ‘DrawingPhylogenies.Rnw’ using Sweave
--- finished re-building ‘DrawingPhylogenies.Rnw’

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

--- re-building ‘RandomTopologies.Rnw’ using Sweave

Error: processing vignette ‘RandomTopologies.Rnw’ failed with diagnostics:
 chunk 10 
Error in library(phangorn) : there is no package called ‘phangorn’

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

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

Error: Vignette re-building failed.
Execution halted
Documented arguments not in \usage in documentation object ‘apercu’:
  ‘c’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
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’
Argument items with no description in Rd object ‘change_int’:
  ‘enhanced’ ‘ind’ ‘tree’ ‘alpha’ ‘beta’ ‘epsilon’ ‘lambdaN’ ‘aN’
Argument items with no description in Rd object ‘change_int_eta’:
  ‘enhance’ ‘ind’ ‘tree’ ‘alpha’ ‘beta’ ‘eta’ ‘epsilon’ ‘lambdaN’ ‘aN’
  ‘change’ ‘uns’
Argument items with no description in Rd object ‘enhance’:
  ‘tree’ ‘alpha’ ‘beta’ ‘epsilon’ ‘lambdaN’ ‘aN’
Argument items with no description in Rd object ‘enhance_eta’:
  ‘tree’ ‘alpha’ ‘beta’ ‘eta’ ‘epsilon’ ‘lambdaN’ ‘aN’ ‘uns’
Argument items with no description in Rd object ‘rbactrian’:
  ‘n’ ‘m’
Argument items with no description in Rd object ‘transform’:
  ‘tree’ ‘unsampled’ ‘list_depth’ ‘change_depth’
Argument items with no description in Rd object ‘transform_eta’:
  ‘tree’ ‘unsampled’ ‘eta’ ‘list_depth’ ‘change_depth’
Package required but not available: ‘phytools’

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

See section ‘The DESCRIPTION file’ 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
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Argument items with no description in Rd object ‘dynamac_pkg_bounds_test’:
  ‘obs’ ‘fstat’ ‘tstat’ ‘case’ ‘k’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 ‘ar.matrix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Q.AR1
> ### Title: Precision matrix for an AR1 process
> ### Aliases: Q.AR1 r.AR1
> 
> ### ** Examples
> 
> require("ggplot2")
Loading required package: ggplot2
> # simulate AR1 GMRF
> obs <- r.AR1(100, M=30, sigma=1, rho=.98)
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arm.Rcheck/00install.out’ for details.
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:
  'oligo', 'oligoClasses', 'pdInfoBuilder'
Packages unavailable to check Rd xrefs: ‘oligo’, ‘oligoClasses’
Documented arguments not in \usage in documentation object ‘AromaUnitTabularBinaryFile$allocateFromCdf’:
  ‘path’ ‘tags’ ‘footer’

Documented arguments not in \usage in documentation object ‘byChipType.DChipSnpInformation’:
  ‘rootPath’ ‘pattern’ ‘verbose’

Documented arguments not in \usage in documentation object ‘UgpGenomeInformation$byChipType’:
  ‘version’

Documented arguments not in \usage in documentation object ‘calculateResidualSet.FirmaModel’:
  ‘verbose’

Documented arguments not in \usage in documentation object ‘findByChipType.AromaChipTypeAnnotationFile’:
  ‘chipType’ ‘tags’

Documented arguments not in \usage in documentation object ‘fit.SmoothMultiarrayModel’:
  ‘data’

Documented arguments not in \usage in documentation object ‘getCellIndices.ExonChipEffectFile’:
  ‘units’

Documented arguments not in \usage in documentation object ‘getImage.AffymetrixCelFile’:
  ‘palette’

Documented arguments not in \usage in documentation object ‘getOutputDataSet.Transform’:
  ‘force’

Documented arguments not in \usage in documentation object ‘getUnitTypes.AffymetrixCdfFile’:
  ‘map’

Documented arguments not in \usage in documentation object ‘plotMvsX.AffymetrixCelFile’:
  ‘xlim’ ‘xlab’

Documented arguments not in \usage in documentation object ‘process.BackgroundCorrection’:
  ‘force’ ‘verbose’

Documented arguments not in \usage in documentation object ‘readUnits.CnagCfhFile’:
  ‘cdf’

Documented arguments not in \usage in documentation object ‘setArrays.ArrayExplorer’:
  ‘arrays’

Documented arguments not in \usage in documentation object ‘setRestructor.AffymetrixCdfFile’:
  ‘units’

Documented arguments not in \usage in documentation object ‘setupExampleData’:
  ‘dirs’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘fitOne.MultiSourceCopyNumberNormalization’:
  ‘name’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Documented arguments not in \usage in documentation object ‘fit.CopyNumberSegmentationModel’:
  ‘chromosome’

Documented arguments not in \usage in documentation object ‘getPath.Explorer’:
  ‘create’

Documented arguments not in \usage in documentation object ‘process.AromaTransform’:
  ‘force’ ‘verbose’

Documented arguments not in \usage in documentation object ‘process.ChromosomeExplorer’:
  ‘chromosome’

Documented arguments not in \usage in documentation object ‘process.Explorer’:
  ‘arrays’ ‘verbose’

Documented arguments not in \usage in documentation object ‘setArrays.Explorer’:
  ‘arrays’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package required but not available: ‘Morpho’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [14s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > 
  > library("arules")
  Loading required package: Matrix
  
  Attaching package: 'arules'
  
  The following objects are masked from 'package:base':
  
      abbreviate, write
  
  > test_check("arules")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 286 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • fim4r cannot be loaded (1): 'test-fim4r.R:4:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-matrix.R:66:1'): (code run outside of `test_that()`) ───────────
  Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-matrix.R:66:0
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─methods::as(...)
   5.   └─methods:::.class1(object)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 286 ]
  Error: Test failures
  Execution halted
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘RweaveAsciiSetup’:
  ‘stylepath’

Documented arguments not in \usage in documentation object ‘RweaveOrg’:
  ‘stylepath’

Documented arguments not in \usage in documentation object ‘RweavePandoc’:
  ‘stylepath’

Documented arguments not in \usage in documentation object ‘RweaveReST’:
  ‘stylepath’

Documented arguments not in \usage in documentation object ‘RweaveT2t’:
  ‘stylepath’

Documented arguments not in \usage in documentation object ‘RweaveTextile’:
  ‘stylepath’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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: ‘sem’
Package which this enhances but not available for checking: ‘asreml’
Documented arguments not in \usage in documentation object ‘check.args_’:
  ‘rename_’ ‘arg.update_’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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: ‘trtf’
Unknown package ‘snpar’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Re-building vignettes had CPU time 2.5 times elapsed time
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages required but not available:
  'DESeq2', 'GSVA', 'SummarizedExperiment'

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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘avidaR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert_seq_into_org
> ### Title: Converts a genome instruction sequence into a digital organism
> ###   file
> ### Aliases: convert_seq_into_org
> 
> ### ** 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"
+ )
Error: Server responded with status code '526 - It seems that the server SSL certificate is not valid':
- If error persists, please contact server administrator.
Execution halted
'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
Package suggested but not available for checking: ‘lixoftConnectors’
Packages required but not available: 'beastier', 'mauricer', 'phangorn'

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
Documented arguments not in \usage in documentation object ‘write.narrative’:
  ‘trials:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DESeq2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Differential-Synth.Rmd’ using rmarkdown

Quitting from lines 29-42 [setup] (Differential-Synth.Rmd)
Error: processing vignette ‘Differential-Synth.Rmd’ failed with diagnostics:
there is no package called 'DESeq2'
--- failed re-building ‘Differential-Synth.Rmd’

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

--- re-building ‘Getting-Started.Rmd’ using rmarkdown
--- finished re-building ‘Getting-Started.Rmd’

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

Quitting from lines 32-46 [setup] (NSS.Rmd)
Error: processing vignette ‘NSS.Rmd’ failed with diagnostics:
there is no package called 'DESeq2'
--- failed re-building ‘NSS.Rmd’

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

--- re-building ‘bakR-Fn.Rmd’ using rmarkdown
--- finished re-building ‘bakR-Fn.Rmd’

--- re-building ‘bakR-Quickstart.Rmd’ using rmarkdown
--- finished re-building ‘bakR-Quickstart.Rmd’

SUMMARY: processing the following files failed:
  ‘Differential-Synth.Rmd’ ‘NSS.Rmd’

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Package suggested but not available for checking: ‘ArrayExpress’
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [22s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (require(testthat, quietly = TRUE)) {
  +   require(bartCause)
  +   test_check("bartCause")
  + } else {
  +   cat("package 'testthat' not available; cannot run unit tests\n")
  + }
  Loading required package: bartCause
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 393 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-11-stan4bart.R:14:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (???): semiparametric predict works ───────────────────────────────────
  Error: 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. └─bartCause:::getBartTreatmentFit(...)
   2.   ├─dbarts::extract(bartFit, combine_chains = combineChains)
   3.   └─stan4bart:::extract.stan4bartFit(bartFit, combine_chains = combineChains)
   4.     └─stan4bart:::fitted_random(...)
   5.       └─base::array(...)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 393 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd object ‘BartMixVs-package’:
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Error(s) in re-building vignettes:
  ...
--- re-building ‘baseballr.Rmd’ using rmarkdown
--- finished re-building ‘baseballr.Rmd’

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

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

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

Quitting from lines 38-40 [get-id] (using_statcast_pitch_data.Rmd)
Error: processing vignette ‘using_statcast_pitch_data.Rmd’ failed with diagnostics:
HTTP error 503.
--- failed re-building ‘using_statcast_pitch_data.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Earlier versions
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.
Invalid package aliases in Rd file ‘bayesANOVA-package.Rd’:
  ‘bayesANOVA-package’
'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: \&
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checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘arm’
Error(s) in re-building vignettes:
  ...
--- re-building ‘compare_lme4.Rmd’ using knitr

Quitting from lines 34-37 [unnamed-chunk-2] (compare_lme4.Rmd)
Error: processing vignette ‘compare_lme4.Rmd’ failed with diagnostics:
there is no package called 'arm'
--- failed re-building ‘compare_lme4.Rmd’

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

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

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

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

SUMMARY: processing the following file failed:
  ‘compare_lme4.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘INLA’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BayesfMRI.Rcheck/00install.out’ for details.
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘BugReports.Rmd’ using rmarkdown
--- finished re-building ‘BugReports.Rmd’

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

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Error: processing vignette ‘GetStarted.Rmd’ failed with diagnostics:
Something went wrong (see the error message above). Perhaps you transformed numeric variables to factors or vice versa within the model formula? If yes, please convert your variables beforehand. Or did you use a grouping factor also for a different purpose? If yes, please make sure that its factor levels are correct also in the new data you may have provided.
--- 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.
Package suggested but not available for checking: ‘qtlnet’
'LazyData' is specified without a 'data' directory
File ‘bayesQR/libs/bayesQR.so’:
  Found ‘_gfortran_arandom_r8’, possibly from ‘random_number’ (Fortran)
    Objects: ‘QRb_AL_mcmc.o’, ‘QRb_mcmc.o’, ‘QRc_AL_mcmc.o’,
      ‘QRc_mcmc.o’
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Objects: ‘QRb_AL_mcmc.o’, ‘QRb_mcmc.o’, ‘QRc_AL_mcmc.o’,
      ‘QRc_mcmc.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘setseed.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
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: \$
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BayesS5.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Argument items with no description in Rd object ‘hmmeantemp’:
  ‘dat’
Package suggested but not available for checking: ‘glmmTMB’
checkRd: (-1) bart.Rd:271: Escaped LaTeX specials: \_
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
Package required but not available: ‘Seurat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘fabiabreast.txt’
Package suggested but not available for checking: ‘INLA’
Documented arguments not in \usage in documentation object ‘contour_ggplot_params’:
  ‘pos_legend’

Documented arguments not in \usage in documentation object ‘geom_quad_txt’:
  ‘graph’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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: \_
S3 methods shown with full name in documentation object ‘export.bce’:
  ‘export.bce’

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.
'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
'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
Found the following files/directories:
  ‘dump.txt’
Package required but not available: ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Argument items with no description in Rd object ‘bdw’:
  ‘\dots’
Argument items with no description in Rd object ‘plot.bdw’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.bdw’:
  ‘\dots’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package required but not available: ‘phangorn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘beast_plot_toy.pdf’
GNU make is a SystemRequirements.
'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
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
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘print_summary_gibbs_psd_help’:
  ‘flag=T:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘BFpack/libs/BFpack.so’:
  Found ‘_gfortran_arandom_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘bct_continuous_final.o’
  Found ‘_gfortran_random_r4’, possibly from ‘random_number’ (Fortran)
    Object: ‘bct_prior.o’
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘bct_continuous_final.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Objects: ‘bct_continuous_final.o’, ‘bct_prior.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.
Package suggested but not available for checking: ‘SoDA’
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in documentation object ‘getFpTransforms’:
  ‘%bt%’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
Running examples in ‘bgsmtr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bgsmtr
> ### Title: Bayesian Group Sparse Multi-Task Regression for Imaging Genetics
> ### Aliases: bgsmtr
> 
> ### ** Examples
> 
> data(bgsmtr_example_data)
> names(bgsmtr_example_data)
[1] "SNP_data"               "SNP_groups"             "BrainMeasures"         
[4] "neighborhood_structure"
> ## Don't show: 
> ## Toy example with a small subset of the data for routine CRAN testing
> ## reduce the number of SNPs to 5, subjects to 5, phenotypes to 5
> fit = bgsmtr(X = bgsmtr_example_data$SNP_data[1:5,1:5], Y = bgsmtr_example_data$BrainMeasures[1:5,1:5],
+ group = bgsmtr_example_data$SNP_groups[1:5], tuning = 'WAIC', lam_1_fixed = 2, lam_2_fixed = 2,
+ iter_num = 5, burn_in = 1)
Computing Initial Values 
time:  0.007 s 
Gibbs Sampler Initialized and Running 
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
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
Argument items with no description in Rd object ‘h.pr.u’:
  ‘z’ ‘ih’ ‘mu’ ‘sigma’ ‘pk’ ‘K’ ‘H’ ‘n’
Argument items with no description in Rd object ‘hatpai.u’:
  ‘z’ ‘hk1’ ‘hk0’ ‘ph1’ ‘ph0’ ‘sigma1’ ‘sigma0’ ‘mu1’ ‘mu0’ ‘pai’ ‘H’
  ‘n’
Argument items with no description in Rd object ‘ind.u’:
  ‘pr’
Argument items with no description in Rd object ‘lambda.u’:
  ‘nu’
Argument items with no description in Rd object ‘mu.k.u’:
  ‘k’ ‘ik’ ‘z’ ‘sigma’ ‘mu0’
Argument items with no description in Rd object ‘nu.u’:
  ‘ind’ ‘tau’ ‘H’
Argument items with no description in Rd object ‘pai.u’:
  ‘b’ ‘a.pai’ ‘b.pai’
Argument items with no description in Rd object ‘sig.k.u’:
  ‘k’ ‘ik’ ‘z’ ‘mu0’ ‘a0’ ‘b0’
Argument items with no description in Rd object ‘z.pr.u’:
  ‘z’ ‘hk’ ‘mu’ ‘sigma’ ‘ph’ ‘H’ ‘n’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘bibliometrix’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bibliometrix.Rcheck/00install.out’ for details.
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘lavaan.survey’
Unknown package ‘lavaan.survey’ in Rd xrefs
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Package suggested but not available for checking: ‘ffbase’
Invalid package aliases in Rd file ‘package_bigdist.Rd’:
  ‘package_bigdist-package’
Package suggested but not available for checking: ‘INLA’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/biglasso.Rcheck/00install.out’ for details.
Found the following calls to data() loading into the global environment:
File ‘biglm/R/bigglm.R’:
  data(reset = TRUE)
  data(reset = FALSE)
See section ‘Good practice’ in ‘?data’.
Specified C++14: please drop specification unless essential
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:
  ‘outputs’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [8s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bigsparser)
  > 
  > test_check("bigsparser")
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 316 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test-add-columns.R:97:3', 'test-solve.R:5:3',
    'test-solve.R:35:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-SFBM-compact.R:113:3'): products between an SFBM_compact and a vector work ──
  Error: 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-SFBM-compact.R:113:2
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::as.vector(Matrix::crossprod(spmat, y))
  ── Error ('test-SFBM.R:62:3'): products between an SFBM and a vector work ──────
  Error: 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-SFBM.R:62:2
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::as.vector(Matrix::crossprod(spmat, y))
  
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 316 ]
  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
'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:
  ‘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.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘select.cfs’:
  ‘select.cfs’

S3 methods shown with full name in documentation object ‘select.fast.filter’:
  ‘select.fast.filter’

S3 methods shown with full name in documentation object ‘select.forward.Corr’:
  ‘select.forward.Corr’

S3 methods shown with full name in documentation object ‘select.forward.wrapper’:
  ‘select.forward.wrapper’

S3 methods shown with full name in documentation object ‘select.inf.chi2’:
  ‘select.inf.chi2’

S3 methods shown with full name in documentation object ‘select.inf.gain’:
  ‘select.inf.gain’

S3 methods shown with full name in documentation object ‘select.inf.symm’:
  ‘select.inf.symm’

S3 methods shown with full name in documentation object ‘select.process’:
  ‘select.process’

S3 methods shown with full name in documentation object ‘select.relief’:
  ‘select.relief’

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.
Found the following files/directories:
  ‘pointshape.dbf’ ‘pointshape.shp’ ‘pointshape.shx’
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
Documented arguments not in \usage in documentation object ‘predict2.em’:
  ‘na.rm’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bioregion.Rcheck/00install.out’ for details.
Invalid package aliases in Rd file ‘bios2cor-package.Rd’:
  ‘bios2cor-package’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘micemd’
Specified C++11: please drop specification unless essential
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/birankr.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘Seurat’
GNU make is a SystemRequirements.
Package required but not available: ‘phytools’

Package suggested but not available for checking: ‘mvMORPH’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Argument items with no description in Rd object ‘ONA_compiled’:
  ‘ATN’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘export.dyadic’:
  ‘blauObj’
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
Package required but not available: ‘arm’

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
Missing or unexported objects:
  ‘Matrix::crossprod’ ‘Matrix::tcrossprod’
'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 required but not available: ‘sem’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in documentation object ‘.print.summary.ccc’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object ‘id2rownum’:
  ‘ids’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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’
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘augment_kdb’:
  ‘...’

Documented arguments not in \usage in documentation object ‘graph_connected_components’:
  ‘x’

Documented arguments not in \usage in documentation object ‘graph_subgraph’:
  ‘x’

Documented arguments not in \usage in documentation object ‘map’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package required but not available: ‘semPlot’

See section ‘The DESCRIPTION file’ 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
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘check_inputs’:
  ‘h_rs’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
Documented arguments not in \usage in documentation object ‘InternalFunctions’:
  ‘metric’ ‘matrix’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package required but not available: ‘phangorn’

See section ‘The DESCRIPTION file’ 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
Documented arguments not in \usage in documentation object ‘info’:
  ‘mod_spec’ ‘pkg_spec’

Documented arguments not in \usage in documentation object ‘path’:
  ‘args’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) bpca.Rd:85: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object ‘xtable.bpca’:
  ‘xtable.bpca’

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
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘b_samp’:
  ‘Y’

Documented arguments not in \usage in documentation object ‘betaBlock’:
  ‘Y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Documented arguments not in \usage in documentation object ‘Utility functions’:
  ‘max.len’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bravo.Rcheck/00install.out’ for details.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object ‘availability.int’:
  ‘v.set’ ‘dir.set’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘subset.int’:
  ‘subset.int’

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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'cmdstanr', 'arm'
Missing or unexported object: ‘Matrix::tcrossprod’
Packages suggested but not available for checking: 'glmmTMB', 'lfe'
Packages suggested but not available for checking: 'glmmADMB', 'glmmTMB'
Package suggested but not available for checking: ‘lfe’
checkRd: (-1) brr-package.Rd:33: Escaped LaTeX specials: \&
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'.
Packages required but not available: 'DiffBind', 'DESeq2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘bs4Table’:
  ‘headTitles’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘plot.bshazard’:
  ‘\dots’
Argument items with no description in Rd object ‘print.bshazard’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.bshazard’:
  ‘\dots’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Package required but not available: ‘phangorn’

See section ‘The DESCRIPTION file’ 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
Package suggested but not available for checking: ‘gvcm.cat’
Specified C++11: please drop specification unless essential
Unknown package ‘gvcm.cat’ in Rd xrefs
Package suggested but not available for checking: ‘udpipe’
'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: ‘glmmTMB’
Package required but not available: ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘count’:
  ‘.data’

Documented arguments not in \usage in documentation object ‘unite’:
  ‘.data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘calcIntegralSurv2_cpp’:
  ‘dsurvival’

Documented arguments not in \usage in documentation object ‘.calcIntegralCif_cpp’:
  ‘cif’ ‘CIF_t’

Documented arguments not in \usage in documentation object ‘validFCTs’:
  ‘super.classes’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Package required but not available: ‘Seurat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
'LazyData' is specified without a 'data' directory
Package required but not available: ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
Documented arguments not in \usage in documentation object ‘get_result’:
  ‘out’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Seurat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in documentation object ‘simulateDelegateCore’:
  ‘replicate’ ‘iterations’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taxize’
Package required but not available: ‘phyloregion’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Argument items with no description in Rd object ‘makeEventHistory’:
  ‘type’
Argument items with no description in Rd object ‘plotSeqCount’:
  ‘segColors’
Packages suggested but not available for checking:
  'Seurat', 'SingleCellExperiment', 'SummarizedExperiment', 'scater',
  'batchelor', 'scran'
Running ‘testthat.R’ [36s/57s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Canek)
  > 
  > test_check("Canek")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 74 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_RunCanek.R:2:1'): (code run outside of `test_that()`) ──────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'Seurat'
  Backtrace:
      ▆
   1. ├─base::lapply(...) at test_RunCanek.R:2:0
   2. │ └─Canek (local) FUN(X[[i]], ...)
   3. └─base::loadNamespace(x) at test_RunCanek.R:3:2
   4.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   5.     └─base (local) withOneRestart(expr, restarts[[1L]])
   6.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 74 ]
  Error: Test failures
  Execution halted
Found the following files/directories:
  ‘MDA231_tree.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
Objects in \usage without \alias in documentation object ‘aweibull7’:
  ‘fweibull6’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
Invalid package aliases in Rd file ‘EcoLinkPredict.Rd’:
  ‘EcoLinkPredict-package’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘validate_cover_cats’:
  ‘cats_target’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sparsepca’

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
Documented arguments not in \usage in documentation object ‘add_catmaply_slider’:
  ‘text_font_color’ ‘categorical_col’

Documented arguments not in \usage in documentation object ‘add_catmaply_traces’:
  ‘categorical_col’

Documented arguments not in \usage in documentation object ‘catmaply_annotations’:
  ‘fig’ ‘text_font_color’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
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: \&
Documented arguments not in \usage in documentation object ‘check_args_compile_pseudo_pop’:
  ‘data_obj’ ‘ci.appr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
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
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
Packages which this enhances but not available for checking:
  'CirceR', 'Capr'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘buildModel’:
  ‘x’ ‘y’

Documented arguments not in \usage in documentation object ‘modelKrigingInternalPredictor’:
  ‘...’

Documented arguments not in \usage in documentation object ‘selfAdapt’:
  ‘nvaleus’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
Package required but not available: ‘sdcTable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Seurat', 'DESeq2'
Documented arguments not in \usage in documentation object ‘evaluate_rule’:
  ‘class’

Documented arguments not in \usage in documentation object ‘tree_leaf_nodes’:
  ‘classes.’ ‘invert.’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running ‘testthat.R’ [7s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cellpypes)
  > 
  > test_check("cellpypes")
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 53 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-pseudobulk.R:10:3'): class_to_deseq2 example working ─────────
  `{ ... }` threw an unexpected error.
  Message: Install DESeq2 to use class_to_deseq2 function.
  Class:   simpleError/error/condition
  Backtrace:
      ▆
   1. ├─testthat::expect_error(...) at test-pseudobulk.R:10:2
   2. │ └─testthat:::expect_condition_matching(...)
   3. │   └─testthat:::quasi_capture(...)
   4. │     ├─testthat (local) .capture(...)
   5. │     │ └─base::withCallingHandlers(...)
   6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   7. └─cellpypes::class_to_deseq2(obj, meta_data, "T", ~treatment) at test-pseudobulk.R:20:6
  ── Error ('test-pseudobulk.R:61:3'): class_to_deseq2 stops gracefully if class has zero cells. ──
  Error in `class_to_deseq2(dds, meta_data, "T", ~treatment)`: Install DESeq2 to use class_to_deseq2 function.
  Backtrace:
      ▆
   1. ├─testthat::expect_error(...) at test-pseudobulk.R:61:2
   2. │ └─testthat:::expect_condition_matching(...)
   3. │   └─testthat:::quasi_capture(...)
   4. │     ├─testthat (local) .capture(...)
   5. │     │ └─base::withCallingHandlers(...)
   6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   7. └─cellpypes::class_to_deseq2(dds, meta_data, "T", ~treatment)
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 53 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object ‘CensMFM-package’:
  \details: ‘...o use the package, including the most important functions ~~’
Unexported objects imported by ‘:::’ calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Documented arguments not in \usage in documentation object ‘blackboost_train’:
  ‘x’ ‘y’

Documented arguments not in \usage in documentation object ‘survival_prob_mboost’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘centralplot’:
  ‘alpha’
'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
Documented arguments not in \usage in documentation object ‘create_epa’:
  ‘clean_pbp_dat’ ‘df’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
S3 methods shown with full name in documentation object ‘select.cglasso’:
  ‘select.cglasso’

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.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘influence-methods’:
  ‘influence’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file ‘jumpointsVar-package.Rd’:
  ‘jumpointsVar-package’
Objects in \usage without \alias in documentation object ‘internals’:
  ‘seg.lm.fit0.gamma’ ‘max.rss’ ‘print.jumpointsVar’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘internals’:
  ‘max.rss’

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.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘ChangePointAnalyzer-package.Rd’:
  ‘ChangePointAnalyzer-package’
Auto-generated content requiring editing in Rd object ‘ChangePointAnalyzer-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Documented arguments not in \usage in documentation object ‘multiplierDSeqfun’:
  ‘MC’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘wallace’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘darts’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘hillR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in documentation object ‘.chkArgs’:
  ‘mode.’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'GenomicInteractions', 'Gviz', 'countreg'
Missing or unexported objects:
  ‘Matrix::crossprod’ ‘Matrix::tcrossprod’
'LazyData' is specified without a 'data' directory
Running examples in ‘chinese.misc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_ttm
> ### Title: Create Term-Term Matrix (Term-Cooccurrence Matrix)
> ### Aliases: create_ttm
> 
> ### ** Examples
> 
> x <- c(
+   "Hello, what do you want to drink?", 
+   "drink a bottle of milk", 
+   "drink a cup of coffee", 
+   "drink some water")
> dtm <- corp_or_dtm(x, from = "v", type = "dtm")
CHECKING ARGUMENTS
PROCESSING CHARACTER VECTOR
GENERATING CORPUS
PROCESSING CORPUS
MAKING DTM/TDM
DONE
> ttm1 <- create_ttm(dtm)
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Invalid package aliases in Rd file ‘ChIPtest-package.Rd’:
  ‘ChIPtest_1.0-package’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
Argument items with no description in Rd object ‘chngpt.test’:
  ‘by.percentile’ ‘both’ ‘main’ ‘prec.weights’ ‘p.val.method’ ‘boot.B’
  ‘keep.fits’
Argument items with no description in Rd object ‘convert.coef predictx threshold.func’:
  ‘include.intercept’ ‘coef.0’ ‘threshold.type’ ‘get.simultaneous’
  ‘return.boot’ ‘fit’ ‘boot.ci.type’ ‘alpha’ ‘verbose’ ‘coef’ ‘xx’
  ‘x.name’
Argument items with no description in Rd object ‘double.hinge’:
  ‘object’ ‘x’ ‘y’ ‘lower.y’ ‘upper.y’ ‘var.type’ ‘boot.ci.type’
  ‘ci.bootstrap.size’ ‘alpha’ ‘save.boot’ ‘ncpus’ ‘lcol’ ‘lwd’ ‘which’
  ‘xlim’ ‘lty’ ‘add.points’ ‘add.ci’ ‘breaks’ ‘mark.chngpt’ ‘xlab’
  ‘ylab’
Argument items with no description in Rd object ‘hinge.test’:
  ‘formula’ ‘cov.interest’ ‘family’ ‘data’ ‘verbose’
Argument items with no description in Rd object ‘performance.unit.test’:
  ‘formula.1’ ‘formula.2’ ‘family’ ‘data’ ‘B’ ‘I’
Argument items with no description in Rd object ‘sim.chngpt’:
  ‘n’ ‘mu.z’ ‘seed’ ‘weighted’ ‘beta’ ‘e.’ ‘b.transition’ ‘sd’ ‘e’
  ‘beta_e’ ‘f’ ‘beta_f’ ‘logistic.slope’ ‘gamma’
Argument items with no description in Rd object ‘sim.hinge’:
  ‘threshold.type’ ‘family’ ‘thres’ ‘X.ditr’ ‘mu.X’ ‘coef.X’ ‘cov.X’
  ‘eps.sd’ ‘seed’ ‘n’
Problems with news in ‘NEWS.md’:
No news entries found.
Objects in \usage without \alias in documentation object ‘choplump-internal’:
  ‘chooseMatrix’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Package suggested but not available for checking: ‘Seurat’
Note: skipping ‘CIARA.Rmd’ due to unavailable dependencies: 'Seurat'
Documented arguments not in \usage in documentation object ‘SearchEmptyClusters’:
  ‘oldcluster’ ‘SSminvec’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Seurat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ChIPseeker', 'DESeq2', 'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ 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
Package required but not available: ‘phytools’

See section ‘The DESCRIPTION file’ 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
Package required but not available: ‘udpipe’

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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/clevr.Rcheck/00install.out’ for details.
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
Packages suggested but not available for checking: 'gosset', 'PlackettLuce'
Objects in \usage without \alias in documentation object ‘clinfun-internal’:
  ‘compareROC.paired’ ‘compareROC.unpaired’ ‘getBoundary’
  ‘gsd.bdryconstant’ ‘gsd.drift.efficacy’ ‘gsd.drift.both’ ‘mrcobj’
  ‘smmrcobj’ ‘rocauc’ ‘smrocauc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘internals’:
  ‘lpm.newton2’ ‘lpm.fit’ ‘lpm.newton’ ‘L_lambda’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Missing or unexported object: ‘Matrix::tcrossprod’
Running examples in ‘clubSandwich-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vcovCR.lmerMod
> ### Title: Cluster-robust variance-covariance matrix for an lmerMod object.
> ### Aliases: vcovCR.lmerMod
> 
> ### ** Examples
> 
> 
> if (requireNamespace("lme4", quietly = TRUE)) {
+ 
+ library(lme4)
+ sleep_fit <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
+ vcovCR(sleep_fit, type = "CR2")
+ 
+ }
Loading required package: Matrix
Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘auxiliary_functions’:
  ‘edelist’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘Seurat’
Running examples in ‘ClustAssess-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_clustering_difference
> ### Title: Graph Clustering Method Stability
> ### Aliases: get_clustering_difference
> 
> ### ** Examples
> 
> set.seed(2021)
> # create an artificial expression matrix
> expr_matrix = matrix(runif(100*10), nrow = 100)
> rownames(expr_matrix) = as.character(1:100)
> 
> adj_matrix = Seurat::FindNeighbors(expr_matrix,
+     k.param = 10,
+     nn.method = "rann",
+     verbose = FALSE,
+     compute.SNN = FALSE)$nn
Error in loadNamespace(x) : there is no package called ‘Seurat’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ClustAssess.Rmd’ using rmarkdown

Quitting from lines 22-27 [setup] (ClustAssess.Rmd)
Error: processing vignette ‘ClustAssess.Rmd’ failed with diagnostics:
there is no package called 'Seurat'
--- failed re-building ‘ClustAssess.Rmd’

--- re-building ‘comparing-soft-and-hierarchical.Rmd’ using rmarkdown
--- finished re-building ‘comparing-soft-and-hierarchical.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Objects in \usage without \alias in documentation object ‘internals’:
  ‘.get_ave_sil_width’ ‘.get_withinSS’ ‘print.clustEff’
  ‘print.summary.clustEff’ ‘print.fpcac’ ‘print.summary.fpcac’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘clusterhap_reports’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘calculate_connectivity’:
  ‘datdf’

Documented arguments not in \usage in documentation object ‘dunn_metric’:
  ‘distance’ ‘method’

Documented arguments not in \usage in documentation object ‘evaluate_all_column_dataset’:
  ‘data’

Documented arguments not in \usage in documentation object ‘information_external’:
  ‘info’

Documented arguments not in \usage in documentation object ‘information_internal’:
  ‘info’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages required but not available: 'GSVA', 'singscore'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in documentation object ‘host’:
  ‘short’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
prepare_Rd: NEWS.Rd:395-396: Dropping empty section ‘Changes in version 1.14.0 (2011-06-07, svn r....)’
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
Packages suggested but not available for checking:
  'SingleCellExperiment', 'Seurat', 'SummarizedExperiment'
'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
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: \#
'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.
Packages required but not available: 'GenomicInteractions', 'rtracklayer'

Packages suggested but not available for checking:
  'InteractionSet', 'GenomicFeatures', 'BSgenome.Hsapiens.UCSC.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘PopGenome’
Documented arguments not in \usage in documentation object ‘feat_sample’:
  ‘locus_group’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package required but not available: ‘phangorn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in documentation object ‘get_superior’:
  ‘stirng’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘disttree’
Documented arguments not in \usage in documentation object ‘lb_calculation’:
  ‘qu.param’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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’
Documented arguments not in \usage in documentation object ‘cocorresp-internal’:
  ‘Y’ ‘eps’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Package required but not available: ‘susieR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Unexported object imported by a ‘:::’ call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
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
Package suggested but not available for checking: ‘Seurat’
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘summary.CommunityClimateInput’:
  ‘object’ ‘\dots’
Argument items with no description in Rd object ‘summary.CommunityClimateStatistics’:
  ‘object’ ‘\dots’
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘comf-internal’:
  ‘calcet’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘CAM’
Documented arguments not in \usage in documentation object ‘CopulaSelection’:
  ‘rhoType’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Rd files without \alias:
  ‘CompoundEvents-package.Rd’
'LazyData' is specified without 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
Auto-generated content requiring editing in Rd object ‘concordancer-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'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
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without 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: 'phangorn', 'TreeSearch'
'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
Package required but not available: ‘rmgarch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'conosPanel', 'DESeq2', 'p2data', 'Seurat', 'SummarizedExperiment'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘checkCountsWholeNumbers’:
  ‘aggregated.samples’

Documented arguments not in \usage in documentation object ‘getGlobalClusterMarkers’:
  ‘min.percent.samples.expression’

Documented arguments not in \usage in documentation object ‘getPercentGlobalClusters’:
  ‘min.cell.count.per.samples’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘postProcessSys’:
  ‘myFile’

Documented arguments not in \usage in documentation object ‘theta_ll’:
  ‘params’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Missing or unexported object: ‘Matrix::crossprod’
Running examples in ‘conText-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compute_transform
> ### Title: Compute transformation matrix A
> ### Aliases: compute_transform
> ### Keywords: compute_transform
> 
> ### ** Examples
> 
> 
> library(quanteda)
Package version: 3.3.1
Unicode version: 15.0
ICU version: 72.1
Parallel computing: 3 of 32 threads used.
See https://quanteda.io for tutorials and examples.
> 
> # note, cr_sample_corpus is too small to produce sensical word vectors
> 
> # tokenize
> toks <- tokens(cr_sample_corpus)
> 
> # construct feature-co-occurrence matrix
> toks_fcm <- fcm(toks, context = "window", window = 6,
+ count = "weighted", weights = 1 / (1:6), tri = FALSE)
> 
> # you will generally want to estimate a new (corpus-specific)
> # GloVe model, we will use cr_glove_subset instead
> # see the Quick Start Guide to see a full example.
> 
> # estimate transform
> local_transform <- compute_transform(x = toks_fcm,
+ pre_trained = cr_glove_subset, weighting = 'log')
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown

Quitting from lines 106-118 [unnamed-chunk-8] (quickstart.Rmd)
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
‘crossprod’ is not an exported object from ‘namespace:Matrix’
--- failed re-building ‘quickstart.Rmd’

SUMMARY: processing the following file failed:
  ‘quickstart.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
Documented arguments not in \usage in documentation object ‘print_table’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'geiger', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘.validate_scalar’:
  ‘arg_class’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file ‘coopProductGame-package.Rd’:
  ‘coopProducGame-package’
Package suggested but not available for checking: ‘paleobioDB’
Missing or unexported objects:
  ‘Matrix::crossprod’ ‘Matrix::tcrossprod’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘ft’:
  ‘theta’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages required but not available: 'phangorn', 'phytools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) egde.Rd:26: Escaped LaTeX specials: \&
S3 methods shown with full name in documentation object ‘mChoose’:
  ‘mc.est.raw’

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
Package suggested but not available for checking: ‘xcms’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ICAMS’
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
Package required but not available: ‘MBESS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tram', 'mlt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘trtf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Seurat’
Running examples in ‘countland-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Cluster
> ### Title: Perform spectral clustering on dot products.
> ### Aliases: Cluster
> 
> ### ** Examples
> 
> gold_path <- system.file("testdata", package = "countland", mustWork = TRUE)
> gold.data <- Seurat::Read10X(data.dir = gold_path)
Error in loadNamespace(x) : there is no package called ‘Seurat’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Documented arguments not in \usage in documentation object ‘dCount_dePril_bi’:
  ‘inheritParams’

Documented arguments not in \usage in documentation object ‘dCount_naive_bi’:
  ‘inheritParams’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Found the following files/directories:
  ‘covfefe_inauguration.txt’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘update_current_test’:
  ‘key’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
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
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘BEST’
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
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘udpipe’
Specified C++11: please drop specification unless essential
File ‘crimCV/libs/crimCV.so’:
  Found ‘_gfortran_arandom_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘crimCV.o’
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘crimCV.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘crimCV.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 required but not available: ‘rtracklayer’

Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Seurat', 'SoupX'
Documented arguments not in \usage in documentation object ‘pinvGamma’:
  ‘logical;’

Documented arguments not in \usage in documentation object ‘qinvGamma’:
  ‘logical;’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
Package required but not available: ‘ensembldb’

Package suggested but not available for checking: ‘EnsDb.Hsapiens.v86’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major features
    Minor features
checkRd: (-1) handmovement.Rd:9: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Seurat', 'MAST'

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
Documented arguments not in \usage in documentation object ‘tool’:
  ‘seq’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Missing or unexported object: ‘Matrix::tcrossprod’
'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: ‘phytools’
Objects in \usage without \alias in documentation object ‘internals’:
  ‘findagoodestimator’ ‘safe.pch’ ‘quickpred’ ‘check.in.ctqr’ ‘start’
  ‘ee.u’ ‘ee.cens’ ‘ee.cens.trunc’ ‘ee.icens’ ‘qr.gs’ ‘nobs.ctqr’
  ‘vcov.ctqr’ ‘coef.ctqr’ ‘print.ctqr’ ‘summary.ctqr’
  ‘print.summary.ctqr’ ‘firstep.ct’ ‘firstep.ic’ ‘asy.qr.ct’
  ‘asy.qr.ic’ ‘safesolve’ ‘regularize_corr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘internals’:
  ‘qr.gs’

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.
'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’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘chi2cub2cov’:
  ‘covar’

Documented arguments not in \usage in documentation object ‘cubpq’:
  ‘summary’

Documented arguments not in \usage in documentation object ‘cubshe’:
  ‘makeplot’ ‘summary’

Documented arguments not in \usage in documentation object ‘kkk’:
  ‘Vector’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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: \_ \_ \_
Missing or unexported object: ‘Matrix::tcrossprod’
Documented arguments not in \usage in documentation object ‘cvRiskPlot’:
  ‘estimator’

Documented arguments not in \usage in documentation object ‘matrixMetrics’:
  ‘estimator’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘cvCovEst-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cvFrobeniusLoss
> ### Title: Cross-Validation Function for Aggregated Frobenius Loss
> ### Aliases: cvFrobeniusLoss
> 
> ### ** Examples
> 
> library(MASS)
> library(origami)
origami v1.0.7: Generalized Framework for Cross-Validation
> library(rlang)
> 
> # generate 10x10 covariance matrix with unit variances and off-diagonal
> # elements equal to 0.5
> Sigma <- matrix(0.5, nrow = 10, ncol = 10) + diag(0.5, nrow = 10)
> 
> # sample 50 observations from multivariate normal with mean = 0, var = Sigma
> dat <- mvrnorm(n = 50, mu = rep(0, 10), Sigma = Sigma)
> 
> # generate a single fold using MC-cv
> resub <- make_folds(dat,
+   fold_fun = folds_vfold,
+   V = 2
+ )[[1]]
> cvFrobeniusLoss(
+   fold = resub,
+   dat = dat,
+   estimator_funs = rlang::quo(c(
+     linearShrinkEst, thresholdingEst, sampleCovEst
+   )),
+   estimator_params = list(
+     linearShrinkEst = list(alpha = c(0, 1)),
+     thresholdingEst = list(gamma = c(0, 1))
+   )
+ )
Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Package which this enhances but not available for checking: ‘RGtk2’
Documented arguments not in \usage in documentation object ‘compute_stat’:
  ‘K_0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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'
Package required but not available: ‘Morpho’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘tree.filter’:
  ‘nodeList’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running ‘testthat.R’ [48s/66s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dabestr)
  Loading required package: magrittr
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > 
  > test_check("dabestr")
  [ FAIL 1 | WARN 3 | SKIP 9 | PASS 25 ]
  
  ══ Skipped tests (9) ═══════════════════════════════════════════════════════════
  • On CRAN (9): 'test-aesthetics.R:30:3', 'test-aesthetics.R:161:3',
    'test-cumming-plots.R:86:3', 'test-cumming-plots.R:109:3',
    'test-cumming-plots.R:139:3', 'test-cumming-plots.R:160:3',
    'test-gardner-altman-plots.R:21:3', 'test-gardner-altman-plots.R:61:3',
    'test-unquoting.R:62:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cumming-plots.R:8:3'): Cumming two-groups ──────────────────────
  Error in `.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)`: invalid non-character version specification 'x' (type: double)
  Backtrace:
      ▆
   1. ├─testthat::skip_if(getRversion() == 4.1) at test-cumming-plots.R:8:2
   2. │ └─base::isTRUE(condition)
   3. └─base::Ops.numeric_version(getRversion(), 4.1)
   4.   └─base::as.numeric_version(e2)
   5.     └─base::numeric_version(x)
   6.       └─base::.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)
  
  [ FAIL 1 | WARN 3 | SKIP 9 | PASS 25 ]
  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
Package required but not available: ‘DAISIE’

Package suggested but not available for checking: ‘corHMM’

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

Package suggested but not available for checking: ‘phytools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in documentation object ‘mm_run_reg’:
  ‘all_params’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘DANN_distance’:
  ‘x2’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file ‘dap-package.Rd’:
  ‘dap-package’
'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
Documented arguments not in \usage in documentation object ‘plotDataExplorer.single’:
  ‘obj’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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:
  ‘my new data set.rds’
'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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Datastream DWE - now decommissioned by Refinitiv
    CRAN
Documented arguments not in \usage in documentation object ‘dotgetJSONValue’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘zplot’:
  ‘xlim’ ‘ylim’
Packages required but not available:
  'phangorn', 'phytools', 'ips', 'geiger', 'paleotree', 'taxize'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Documented arguments not in \usage in documentation object ‘win_over’:
  ‘parition’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
S3 methods shown with full name in documentation object ‘dbglm-inl’:
  ‘dbglm.iteration’

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.
'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
Documented arguments not in \usage in documentation object ‘a_dcc_mat_est’:
  ‘param’

Documented arguments not in \usage in documentation object ‘dcc_mat_est’:
  ‘param’

Documented arguments not in \usage in documentation object ‘deco_mat_est’:
  ‘param’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘phangorn’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing or unexported object: ‘Matrix::crossprod’
Running examples in ‘ddml-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: crosspred
> ### Title: Cross-Predictions using Stacking.
> ### Aliases: crosspred
> 
> ### ** Examples
> 
> # Construct variables from the included Angrist & Evans (1998) data
> y = AE98[, "worked"]
> X = AE98[, c("morekids", "age","agefst","black","hisp","othrace","educ")]
> 
> # Compute cross-predictions using stacking with base learners ols and lasso.
> #     Two stacking approaches are simultaneously computed: Equally
> #     weighted (ensemble_type = "average") and MSPE-minimizing with weights
> #     in the unit simplex (ensemble_type = "nnls1"). Predictions for each
> #     learner are also calculated.
> crosspred_res <- crosspred(y, X,
+                            learners = list(list(fun = ols),
+                                            list(fun = mdl_glmnet)),
+                            ensemble_type = c("average",
+                                              "nnls1",
+                                              "singlebest"),
+                            compute_predictions_bylearner = TRUE,
+                            sample_folds = 2,
+                            cv_folds = 2,
+                            silent = TRUE)
Warning in MASS::ginv(X) : restarting interrupted promise evaluation
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object ‘DDPNA-package’:
  \details: ‘...o use the package, including the most important functions ~~’
Argument items with no description in Rd object ‘DEP_Mod_net_plot’:
  ‘\dots’
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
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'BSgenome', 'BSgenome.Hsapiens.UCSC.hg19'

Package suggested but not available for checking: ‘VariantAnnotation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Missing or unexported object: ‘Matrix::crossprod’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘phytools’

Packages suggested but not available for checking: 'paleotree', 'dispRity'

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

Packages suggested but not available for checking: 'tram', 'cotram'

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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘degreenet-internal’:
  ‘range’ ‘lims’
Objects in \usage without \alias in documentation object ‘degreenet-internal’:
  ‘bootstrapyule’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package required but not available: ‘glmmTMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Package which this enhances but not available for checking: ‘phangorn’
Documented arguments not in \usage in documentation object ‘boot_f_cor’:
  ‘fun’

Documented arguments not in \usage in documentation object ‘boot_f_pcor’:
  ‘fun’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
GNU make is a SystemRequirements.
Rd files without \alias:
  ‘densityClust-package.Rd’
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
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
checkRd: (-1) barriers.Rd:127: 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:
  ‘.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’
'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
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
Package required but not available: ‘MLInterfaces’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘zFPKM’
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
Packages suggested but not available for checking: 'spaMM', 'glmmTMB'
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘encode_unit’:
  ‘original’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Missing or unexported objects:
  ‘Matrix::crossprod’ ‘Matrix::tcrossprod’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Two-Stage-Difference-in-Differences.Rmd’ using rmarkdown

Quitting from lines 144-153 [static] (Two-Stage-Difference-in-Differences.Rmd)
Error: processing vignette ‘Two-Stage-Difference-in-Differences.Rmd’ failed with diagnostics:
error in evaluating the argument ‘a’ in selecting a method for function ‘solve’: ‘crossprod’ is not an exported object from ‘namespace:Matrix’
--- failed re-building ‘Two-Stage-Difference-in-Differences.Rmd’

SUMMARY: processing the following file failed:
  ‘Two-Stage-Difference-in-Differences.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
Documented arguments not in \usage in documentation object ‘Nortonbass_startvalgen’:
  ‘param’ ‘startvalgen’

Documented arguments not in \usage in documentation object ‘seqdiffusion’:
  ‘w’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'SingleCellExperiment', 'SummarizedExperiment', 'zinbwave'

Packages suggested but not available for checking:
  'DelayedArray', 'DelayedMatrixStats', 'HDF5Array'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bibliometrix’
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’
Documented arguments not in \usage in documentation object ‘residuals_extrap’:
  ‘n’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Packages required but not available: 'SingleCellExperiment', 'TSCAN'

Package suggested but not available for checking: ‘Seurat’

See section ‘The DESCRIPTION file’ 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
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
Invalid package aliases in Rd file ‘RV.Rd’:
  ‘RV-package’
'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
Packages required but not available: 'Claddis', 'phangorn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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.
Documented arguments not in \usage in documentation object ‘reshape_into_long’:
  ‘pred_intvar’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘internals_for_distrEx’:
  ‘namestoGather’ ‘namestoGatherNS’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘internal_mlehelpers_for_distrMod’:
  ‘validity.check’

Objects in \usage without \alias in documentation object ‘internals_for_distrMod’:
  ‘.csimpsum’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Assignments in \usage in documentation object ‘internalGenerics’:
  x <- samplesize(object, value)

Documented arguments not in \usage in documentation object ‘internals_for_distr’:
  ‘DClass’
Objects in \usage without \alias in documentation object ‘internals_for_distr’:
  ‘.consolidategaps’ ‘.List’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘diveMove-internal’:
  ‘.diveMatches’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘geiger’
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: \&
Invalid package aliases in Rd file ‘dmaiIntro.Rd’:
  ‘dmaiIntro-package’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object ‘dml_bagging’:
  ‘y,x,d,data,sed’
Argument items with no description in Rd object ‘dml_boosting’:
  ‘y,x,d,data,sed’
Argument items with no description in Rd object ‘dml_ensemble_lm’:
  ‘y,x,d,data,sed’
Argument items with no description in Rd object ‘dml_ensemble_rf’:
  ‘y,x,d,data,sed’
Argument items with no description in Rd object ‘dml_neural_network’:
  ‘y,x,d,data,sed’
Argument items with no description in Rd object ‘dml_random_forest’:
  ‘y,x,d,data,sed’
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
Invalid package aliases in Rd file ‘dnapath2-package.Rd’:
  ‘dnapath2-package’
Auto-generated content requiring editing in Rd object ‘dnapath2-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
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: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object ‘add.joint.mean.many’:
  ‘all.cond.mean.PO’ ‘all.cond.mean2.PO’

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.
Argument items with no description in Rd object ‘derivType’:
  ‘L’ ‘mu’ ‘eps’
Argument items with no description in Rd object ‘getNewParams.SC’:
  ‘n.fft’
Argument items with no description in Rd object ‘graph.CTMC’:
  ‘\dots’
Argument items with no description in Rd object ‘num.deriv’:
  ‘\dots’
Argument items with no description in Rd object ‘power.coef.one’:
  ‘\dots’
Documented arguments not in \usage in documentation object ‘concDict’:
  ‘text’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘udpipe’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘check_results’:
  ‘error_on_failure’ ‘error_on_warning’

Documented arguments not in \usage in documentation object ‘function_get_comments’:
  ‘thresholds’

Documented arguments not in \usage in documentation object ‘vignette_results_display’:
  ‘vignette_results’ ‘error_on_failure’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Objects in \usage without \alias in documentation object ‘utilities’:
  ‘generators.character’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Morpho’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New features
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
Auto-generated content requiring editing in Rd object ‘downscaledl-package’:
  \references: ‘~~ Literature or other references for background information ~~’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'alakazam', 'phangorn', 'shazam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in documentation object ‘show,dparserFunction-method’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘isolate_example’:
  ‘...’

Documented arguments not in \usage in documentation object ‘new_drake_deps’:
  ‘restrict’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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: \&
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.
Packages required but not available:
  'GenomicFeatures', 'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Hsapiens.UCSC.hg38.knownGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DESeq2', 'SummarizedExperiment'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘forecastCovCompiled’:
  ‘obj’ ‘zero’ ‘trend’ ‘estimation.sample’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
'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.
Objects in \usage without \alias in documentation object ‘d.spls.norm1’:
  ‘d.spls.norm2’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Seurat', 'MAST', 'SummarizedExperiment'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘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
Invalid package aliases in Rd file ‘dynConfiR-package.Rd’:
  ‘dynWEV-package’
Package suggested but not available for checking: ‘lle’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Seurat', 'SingleCellExperiment', 'SummarizedExperiment'
'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
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
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    20181118
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘example_table1.csv’ ‘example_table1.txt’ ‘example_table2.csv’
  ‘example_table2.txt’ ‘example_table3.csv’ ‘example_table3.txt’
  ‘table1.csv’ ‘table2.csv’ ‘table2.txt’ ‘table3.txt’ ‘table4.txt’
Package required but not available: ‘diffcoexp’

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

Package suggested but not available for checking: ‘RegSDC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Running examples in ‘ecb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_description
> ### Title: Get full, human-readable description of a series
> ### Aliases: get_description
> 
> ### ** Examples
> 
> get_description("ICP.M.DE.N.000000+XEF000.4.ANR")
No encoding supplied: defaulting to UTF-8.
Error in check_status(req) : HTTP failure: 504
<html lang="en"><head><title>European Central Bank</title><style type="text/css"> body{ font-family: "Droid Sans", sans-serif; margin:0; padding:0; background-color: #9099ab; text-align: center; } h1{  font-size:38px; font-weight: normal; color:#003299; }  @media screen and (max-width: 480px) { h1{ font-size: 30px; } }  p { font-size: 15px; line-height: 20px; color: #333; margin-bottom: 20px; }  p.signature{ font-style: italic; color:#DF0101; }  .centredFrame { margin: 0 auto; text-align: center; width: 70%;   } .content{ margin-top:40px; padding:40px; background-color: #fff; border:1px solid #CDE3E0; -moz-border-radius: 20px; border-radius: 20px; } </style><link href="//fonts.googleapis.com/css?family=Droid+Sans" rel="stylesheet" type="text/css"></head><body><div class="centredFrame"><div class="content"><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAASwAAACACAYAAACx1FRUAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JQAAgIMAAPn/AACA6QAAdTAAAOpgAAA6mAAAF2+SX8VG
Calls: get_description ... vapply -> get_dimensions -> make_request -> check_status
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘e.cluster.decision’:
  ‘reg_data’ ‘log.lambda’
Argument items with no description in Rd object ‘e.cluster.dendrogram’:
  ‘echelon.obj’ ‘n.sim’ ‘cluster.legend.pos’ ‘cluster_reg’ ‘p_rank’
  ‘para’
Argument items with no description in Rd object ‘e.cluster.map’:
  ‘x’ ‘c_separates’ ‘locs’ ‘coo’ ‘rin’ ‘p_rank’ ‘cluster_reg’ ‘n.sim’
  ‘cluster.type’
Argument items with no description in Rd object ‘e.dendrogram’:
  ‘peaks’ ‘locs’ ‘x’ ‘separates’ ‘c_separates’ ‘number’ ‘parents’
  ‘pare_locs’ ‘progeny’ ‘symbols’ ‘col.symbols’ ‘cex.symbols’ ‘lwd’
  ‘col’ ‘ens’ ‘adj.ens’ ‘col.ens’ ‘cex.ens’ ‘limb’
Argument items with no description in Rd object ‘e.dendrogram.axis’:
  ‘main’ ‘ylab’ ‘yaxes’ ‘ylim’ ‘xaxes’ ‘xdper’ ‘dmai’ ‘peaks’ ‘x’
Argument items with no description in Rd object ‘e.main’:
  ‘x’ ‘rin’ ‘T’
Argument items with no description in Rd object ‘e.monte.bin’:
  ‘rin’ ‘cas’ ‘pop’ ‘n.sim’ ‘K’ ‘cluster.type’
Argument items with no description in Rd object ‘e.monte.poi’:
  ‘rin’ ‘cas’ ‘pop’ ‘ex’ ‘n.sim’ ‘K’ ‘cluster.type’
Argument items with no description in Rd object ‘e.profile’:
  ‘peaks’ ‘parents’ ‘separates’
Argument items with no description in Rd object ‘e.scan’:
  ‘x’ ‘locs’ ‘peaks’ ‘c_separates’ ‘parents’ ‘K’
Argument items with no description in Rd object ‘e.scan.pop’:
  ‘x’ ‘locs’ ‘peaks’ ‘c_separates’ ‘parents’ ‘K’ ‘pop’
Argument items with no description in Rd object ‘nlimb’:
  ‘x’ ‘k2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taxize’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/economiccomplexity.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘glmmTMB’
'LazyData' is specified without a 'data' directory
Missing or unexported object: ‘Matrix::tcrossprod’
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘editbl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rows_delete.tbl_dbi
> ### Title: rows_delete implementation for DBI backends.
> ### Aliases: rows_delete.tbl_dbi
> 
> ### ** 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

> 
> conn <- connectDB()
> artists <- tbl(conn, "Artist")
> DBI::dbBegin(conn)
> y <- data.frame(ArtistId = 999)
> rows_delete(
+      x = artists,
+      y = y,
+      by = "ArtistId",
+      in_place = TRUE)
Error: attempt to write a readonly database
Execution halted
Documented arguments not in \usage in documentation object ‘fcf.env’:
  ‘vars’

Documented arguments not in \usage in documentation object ‘getlevels’:
  ‘editarray’

Documented arguments not in \usage in documentation object ‘parseCatEdit’:
  ‘e’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘lavaan.survey’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Package required but not available: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘eggCountsExtra’
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object ‘rotate_to_equilibrium’:
  ‘xy_may’

Documented arguments not in \usage in documentation object ‘wide.dyads.to.edgelist’:
  ‘fist.var’

Documented arguments not in \usage in documentation object ‘wide.to.long’:
  ‘last.col’ ‘ego.vars’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file ‘HOF-package.Rd’:
  ‘HOF-package’
'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++14: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘colBoxplot4’:
  ‘id’

Documented arguments not in \usage in documentation object ‘elaborator_server’:
  ‘id’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sparseFLMM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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
Documented arguments not in \usage in documentation object ‘bbox_to_sp’:
  ‘bbx’

Documented arguments not in \usage in documentation object ‘get_aws_terrain’:
  ‘bbx’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
'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.
Packages required but not available:
  'minfi', 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19',
  'IlluminaHumanMethylation450kanno.ilmn12.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  emd-rubner.c:810:20: warning: ‘minI’ is used uninitialized [-Wuninitialized]
  emd-rubner.c:810:26: warning: ‘minJ’ is used uninitialized [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/emdist.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-2) 13.2.0’
'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 export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
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) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘enc-package.Rd’
'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)’
Documented arguments not in \usage in documentation object ‘.calcWeights’:
  ‘Data’

Documented arguments not in \usage in documentation object ‘.cardinalDistance’:
  ‘refLat’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘enmSdmX-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: squareCellRast
> ### Title: Create a raster with square cells
> ### Aliases: squareCellRast
> 
> ### ** Examples
> 
> 
> library(sf)
Linking to GEOS 3.12.0, GDAL 3.7.1, PROJ 9.3.0; sf_use_s2() is TRUE
> library(terra)
terra 1.7.46
> 
> # project outline of Madagascar to equal-area:
> data(mad0)
> mad0Ea <- st_transform(mad0, getCRS('madAlbers'))
> 
> n <- 101
> cellSize_meters <- 10E4
> byNumCells <- squareCellRast(mad0Ea, numCells=n)
Error in squareCellRast(mad0Ea, numCells = n) : 
  no slot of name "ptr" for this object of class "SpatExtent"
Execution halted
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'xcms', 'MSnbase'
Package suggested but not available for checking: ‘RStoolbox’
Documented arguments not in \usage in documentation object ‘div_plot’:
  ‘plot_cols’

Documented arguments not in \usage in documentation object ‘seq_plot’:
  ‘plot_cols’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Auto-generated content requiring editing in Rd object ‘EnviroPRA-package’:
  \details: ‘...o use the package, including the most important functions ~~’
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’
Package required but not available: ‘phangorn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
Found export directives that require package ‘methods’:
  ‘exportClasses’ ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘epidict’
Documented arguments not in \usage in documentation object ‘dots_to_charlist’:
  ‘call’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Package required but not available: ‘qgcomp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object ‘addDrug.Lexis’:
  ‘addDrug.Lexis’

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.
'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’
Package required but not available: ‘ciTools’

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
Invalid package aliases in Rd file ‘equateMultiple-package.Rd’:
  ‘EquateMultiple-package’
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
Documented arguments not in \usage in documentation object ‘subnetwork_templates’:
  ‘nams.vattr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘call.ErgmTerm’:
  ‘A’

Objects in \usage without \alias in documentation object ‘ergm-defunct’:
  ‘sociality’

Documented arguments not in \usage in documentation object ‘ergm-deprecated’:
  ‘fname’ ‘varnames’ ‘vartypes’ ‘defaultvalues’ ‘required’
  ‘nw.bipartiteflag’ ‘requirement’ ‘extramessage’ ‘nw.directedflag’ ‘m’
  ‘response’ ‘new’ ‘from.new’ ‘model’ ‘proposal’ ‘eta0’ ‘control’
  ‘verbose’ ‘update.nws’ ‘Clist’ ‘prev.run’ ‘burnin’ ‘samplesize’
  ‘interval’ ‘maxedges’ ‘attrname’ ‘label’ ‘coord’ ‘jitter’ ‘thresh’
  ‘usearrows’ ‘mode’ ‘displayisolates’ ‘interactive’ ‘xlab’ ‘ylab’
  ‘xlim’ ‘ylim’ ‘pad’ ‘label.pad’ ‘displaylabels’ ‘boxed.labels’
  ‘label.pos’ ‘label.bg’ ‘vertex.sides’ ‘vertex.rot’ ‘arrowhead.cex’
  ‘label.cex’ ‘loop.cex’ ‘vertex.cex’ ‘edge.col’ ‘label.col’
  ‘vertex.col’ ‘label.border’ ‘vertex.border’ ‘edge.lty’ ‘label.lty’
  ‘vertex.lty’ ‘edge.lwd’ ‘label.lwd’ ‘edge.len’ ‘edge.curve’
  ‘edge.steps’ ‘loop.steps’ ‘object.scale’ ‘uselen’ ‘usecurve’
  ‘suppress.axes’ ‘vertices.last’ ‘layout.par’ ‘cex.main’ ‘cex.sub’
  ‘seed’ ‘latent.control’ ‘colornames’ ‘latent’ ‘preserve.eattr’

Documented arguments not in \usage in documentation object ‘ergm_state’:
  ‘nw’

Documented arguments not in \usage in documentation object ‘nodal_attributes-API’:
  ‘l’

Documented arguments not in \usage in documentation object ‘summary.ergm_model’:
  ‘response’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘summary.error_interval’:
  ‘summary.error_interval’

S3 methods shown with full name in documentation object ‘summary.measure’:
  ‘summary.measure’

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.
'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
Invalid package aliases in Rd file ‘esaBcv_package.Rd’:
  ‘esaBcv_package-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
S3 methods shown with full name in documentation object ‘ETAS-internal’:
  ‘Smooth.catalog’

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.
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘poly_clip’:
  ‘x’ ‘y’

Documented arguments not in \usage in documentation object ‘setup_gpar’:
  ‘x’

Documented arguments not in \usage in documentation object ‘setup_grobs’:
  ‘centers’

Documented arguments not in \usage in documentation object ‘update_list’:
  ‘x’ ‘val’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running ‘testthat.R’ [3s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(europepmc)
  > 
  > test_check("europepmc")
  [ FAIL 1 | WARN 0 | SKIP 20 | PASS 0 ]
  
  ══ Skipped tests (20) ══════════════════════════════════════════════════════════
  • On CRAN (20): 'test_annotations_by_id.r:4:3', 'test_epmc_citations.r:4:3',
    'test_epmc_db.r:4:3', 'test_epmc_db_count.r:4:3', 'test_epmc_details.r:4:3',
    'test_epmc_ftxt.r:4:3', 'test_epmc_ftxt_book.r:4:3', 'test_epmc_hits.r:4:3',
    'test_epmc_hits_trend.R:4:3', 'test_epmc_hits_trend.R:30:3',
    'test_epmc_lablinks.r:4:3', 'test_epmc_lablinks_count.r:4:3',
    'test_epmc_profile.r:4:3', 'test_epmc_profile.r:22:3',
    'test_epmc_refs.r:4:3', 'test_epmc_search.r:4:3', 'test_epmc_search.r:54:3',
    'test_epmc_search_by_doi.r:4:3', 'test_epmc_tm.r:4:3',
    'test_epmc_tm_count.r:4:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_epmc_hits_trend.R:39:3'): epmc_hits_trend synonym search works correctly ──
  <http_404/http_400/http_error/error/condition>
  Error in `rebi_GET(path = paste0(rest_path(), "/profile"), query = args)`: Not Found (HTTP 404).
  Backtrace:
      ▆
   1. └─europepmc::epmc_hits_trend("malaria", period = 2012:2016, synonym = FALSE) at test_epmc_hits_trend.R:39:2
   2.   └─base::lapply(...)
   3.     └─europepmc (local) FUN(X[[i]], ...)
   4.       └─europepmc::epmc_profile(queryforall, synonym)
   5.         └─europepmc:::rebi_GET(...)
   6.           └─httr::stop_for_status(req)
  
  [ FAIL 1 | WARN 0 | SKIP 20 | PASS 0 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘doHttrRequest’:
  ‘params’ ‘customConfig’

Documented arguments not in \usage in documentation object ‘errorMessage’:
  ‘test_me’

Documented arguments not in \usage in documentation object ‘isError’:
  ‘test_me’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
Packages required but not available: 'geiger', 'phytools'

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

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

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
Running ‘testthat.R’ [46s/103s]
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(EWSmethods)
  > 
  > test_check("EWSmethods")
  data successfully aggregated into monthly time steps
  
  data successfully aggregated into monthly time steps
  
  data successfully aggregated into monthly time steps
  
  RETICULATE_AUTOCONFIGURE set to FALSE
  + /tmp/check-CRAN-regular-hornik/data/r-miniconda/bin/conda 'create' '--yes' '--name' 'test_env' 'python=3.9' '--quiet'
  Collecting package metadata (current_repodata.json): ...working... failed
  
  NoSpaceLeftError: No space left on devices.
  
  trying URL 'https://drive.google.com/u/0/uc?export=download&confirm=EoIm&id=19OuqzrY1LQxZusByf4ACPj-yiex4LY2e'
  Content type 'application/zip' length 223054273 bytes (212.7 MB)
  ==================================================
  downloaded 212.7 MB
  
  Model weights downloaded
  Model weights removed
  [ FAIL 1 | WARN 27 | SKIP 0 | PASS 61 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ewsnet_init.R:18:3'): EWSNet can be correctly initialised ──────
  Error: Error creating conda environment 'test_env' [exit code 1]
  Backtrace:
      ▆
   1. └─EWSmethods::ewsnet_init(envname = "test_env", auto = TRUE) at test-ewsnet_init.R:18:2
   2.   └─reticulate::conda_create(...)
   3.     └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
  
  [ FAIL 1 | WARN 27 | SKIP 0 | PASS 61 ]
  Error: Test failures
  Execution halted
Documented arguments not in \usage in documentation object ‘borrOrderingInternal’:
  ‘n.cntrl’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
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
Package required but not available: ‘GenomicAlignments’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘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: \&
Argument items with no description in Rd object ‘plot.expectreg’:
  ‘\dots’
Argument items with no description in Rd object ‘update.expectreg’:
  ‘\dots’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package required but not available: ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [7s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(explor)
  > 
  > test_check("explor")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 102 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_prepare_results_textmodel_ca.R:8:1'): (code run outside of `test_that()`) ──
  Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─quanteda.textmodels::textmodel_ca(dfmat, nd = 7) at test_prepare_results_textmodel_ca.R:8:0
   2. └─quanteda.textmodels:::textmodel_ca.dfm(dfmat, nd = 7)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 102 ]
  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: ‘hoa’
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: \&
Argument items with no description in Rd object ‘fbvpot’:
  ‘cutoff’
checkRd: (-1) outlierPlot.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) outlierPlot.Rd:32: Escaped LaTeX specials: \$
Documented arguments not in \usage in documentation object ‘getQQLimit’:
  ‘N’ ‘rho’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘exuberdata’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Package suggested but not available for checking: ‘glmmTMB’
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
Missing or unexported object: ‘Matrix::tcrossprod’
Running examples in ‘ez-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ezPredict
> ### Title: Compute predicted values from the fixed effects of a mixed
> ###   effects model
> ### Aliases: ezPredict
> 
> ### ** Examples
> 
> library(lme4)
Loading required package: Matrix
> 
> #Read in the ANT data (see ?ANT).
> data(ANT)
> head(ANT)
  subnum     group block trial     cue     flank location direction       rt
1      1 Treatment     1     1    None   Neutral       up      left 398.6773
2      1 Treatment     1     2  Center   Neutral       up      left 389.1822
3      1 Treatment     1     3  Double   Neutral       up      left 333.2186
4      1 Treatment     1     4 Spatial   Neutral       up      left 419.7640
5      1 Treatment     1     5    None Congruent       up      left 446.4754
6      1 Treatment     1     6  Center Congruent       up      left 338.9766
  error
1     0
2     0
3     0
4     0
5     0
6     0
> 
> #fit a mixed effects model to the rt data
> rt_fit = lmer(
+     formula = rt ~ cue*flank*group + (1|subnum)
+     , data = ANT[ANT$error==0,]
+ )
boundary (singular) fit: see help('isSingular')
> 
> #obtain the predictions from the model
> rt_preds = ezPredict(
+     fit = rt_fit
+ )
Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
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
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object ‘complete.log.likelihood_Sj’:
  ‘z’
Auto-generated content requiring editing in Rd object ‘getStuffForDIC’:
  \details: ‘If necessary, more details than the description above’
'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
Auto-generated content requiring editing in Rd object ‘procrustes_switching’:
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd object ‘rsp_exact’:
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd object ‘rsp_full_sa’:
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd object ‘rsp_partial_sa’:
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd object ‘weighted_procrustes_switching’:
  \details: ‘If necessary, more details than the description above.’
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object ‘Factoshiny-package’:
  \references: ‘~~ Literature or other references for background information ~~’
  \seealso: ‘~~ Optional links to other man pages, e.g. ~~’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘jss.Rmd’ using rmarkdown
Error: processing vignette ‘jss.Rmd’ failed with diagnostics:
invalid non-character version specification ‘x’ (type: double)
--- failed re-building ‘jss.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Documented arguments not in \usage in documentation object ‘.get_default_sign_size’:
  ‘outcome_type’

Documented arguments not in \usage in documentation object ‘.get_iteration_data’:
  ‘file_dir’

Documented arguments not in \usage in documentation object ‘extract_model_vimp’:
  ‘feature_similarity_table’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
Documented arguments not in \usage in documentation object ‘check_cache’:
  ‘data’ ‘reset’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package required but not available: ‘sem’

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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘kkk’:
  ‘Vector’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘Get_C_R_K_Q’:
  ‘have_noise’

Documented arguments not in \usage in documentation object ‘Sample_KF_post’:
  ‘C0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
'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: \&
Rd files without \alias:
  ‘FastPCS-package.Rd’
Specified C++11: please drop specification unless essential
checkRd: (-1) Scent.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) Traffic.Rd:44: Escaped LaTeX specials: \&
Invalid package aliases in Rd file ‘fastR-package.Rd’:
  ‘fastR-package’
Specified C++11: please drop specification unless essential
checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
Invalid package aliases in Rd file ‘FastRCS-package.Rd’:
  ‘FastPCS-package’
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
Documented arguments not in \usage in documentation object ‘bin’:
  ‘Integer’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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.
Package suggested but not available for checking: ‘DESeq2’
'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’
Unexported object imported by a ‘:::’ call: ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
Argument items with no description in Rd object ‘getbasispenalty’:
  ‘Lfdobj’
Package suggested but not available for checking: ‘refund’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘vert.txt’
S3 methods shown with full name in documentation object ‘xtable.fdt’:
  ‘xtable.fdt’ ‘xtable.fdt.multiple’ ‘xtable.fdt_cat.multiple’

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
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
Documented arguments not in \usage in documentation object ‘url_base’:
  ‘url’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Documented arguments not in \usage in documentation object ‘linregEst’:
  ‘rank_lim’ ‘Umodel’

Documented arguments not in \usage in documentation object ‘m2c’:
  ‘CC’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘checkStream’:
  ‘skipChecks’

Documented arguments not in \usage in documentation object ‘cpp_detectCUSUMMeanSinglePrechange’:
  ‘BL’

Documented arguments not in \usage in documentation object ‘cpp_detectEWMAMeanSinglePrechange’:
  ‘BL’

Documented arguments not in \usage in documentation object ‘makeStreamMeanChangeR’:
  ‘x’

Documented arguments not in \usage in documentation object ‘update_Omega’:
  ‘m_new’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘recode_subquad’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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++11: please drop specification unless essential
Package suggested but not available for checking: ‘MicrobeDS’
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘filename.Rd’:
  ‘filename-package’
'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
Documented arguments not in \usage in documentation object ‘print.data.frame.ff’:
  ‘.data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘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: \&
Missing or unexported object: ‘Matrix::tcrossprod’
Running examples in ‘FinNet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FF.binary.management
> ### Title: Create a binary firm-firm (FF) matrix for board interlocks
> ### Aliases: FF.binary.management
> 
> ### ** Examples
> 
> 
> # Create the binary FF matrix of Berkshire Hathaway's holdings by boards interlock
> data('firms_BKB')
> FF <- FF.binary.management(firms_BKB)
Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
Execution halted
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
Packages required but not available: 'geiger', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'geiger', 'hisse', 'phytools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘plot_data_type’:
  ‘client_id’ ‘client_secret’ ‘refresh_token’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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:
  'nCDunnett', '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
Package suggested but not available for checking: ‘lfe’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
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: \&
'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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/flexrsurv.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘FLPS-package.Rd’:
  ‘FLPS-package’
Malformed Description field: should contain one or more complete sentences.
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
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
Documented arguments not in \usage in documentation object ‘RD_impData’:
  ‘cutoff’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘hl.factor.number’:
  ‘w’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    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
Package required but not available: ‘TreeSim’

Package suggested but not available for checking: ‘paleotree’

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

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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘refund’
'LazyData' is specified without a 'data' directory
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
File ‘frailtypack/libs/frailtypack.so’:
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Objects: ‘Integrale_mult_scl.o’, ‘autres_fonctions.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘autres_fonctions.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.
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
Documented arguments not in \usage in documentation object ‘assert.surface’:
  ‘surf’

Documented arguments not in \usage in documentation object ‘check.dtype.for.data’:
  ‘silent’

Documented arguments not in \usage in documentation object ‘fread3’:
  ‘filehandle:’

Documented arguments not in \usage in documentation object ‘fwrite3’:
  ‘filehandle:’ ‘data:’

Documented arguments not in \usage in documentation object ‘polygon.soup.to.indexed.mesh’:
  ‘face_vertex_coords’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘freqdom.transpose’:
  ‘S’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Packages suggested but not available for checking: 'dggrids', 'INLA'
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘draw.colorbar’:
  ‘coloredmesh’

Documented arguments not in \usage in documentation object ‘extend_neighbors’:
  ‘min_dotp_threshold’

Documented arguments not in \usage in documentation object ‘surf.sphere.spatialfilter’:
  ‘gaussian_weight’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'arm', 'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo',
  'rrlda'
Argument items with no description in Rd object ‘fsdam’:
  ‘verbose’ ‘which’
Argument items with no description in Rd object ‘plot.classes’:
  ‘\dots’
Argument items with no description in Rd object ‘predict.fsim’:
  ‘\dots’
Argument items with no description in Rd object ‘predict.lm’:
  ‘\dots’
Argument items with no description in Rd object ‘predict.sfpl’:
  ‘\dots’
Argument items with no description in Rd object ‘predict.sfplsim.FASSMR’:
  ‘\dots’
Argument items with no description in Rd object ‘print.summary.mfplsim’:
  ‘\dots’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘imp_small_gaps_WMA’:
  ‘Data’ ‘univariate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Objects in \usage without \alias in documentation object ‘funData-constructor’:
  ‘funData’

Objects in \usage without \alias in documentation object ‘irregFunData-constructor’:
  ‘irregFunData’

Objects in \usage without \alias in documentation object ‘multiFunData-constructor’:
  ‘multiFunData’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘plot.funData’:
  ‘plot.funData’

S3 methods shown with full name in documentation object ‘plot.irregFunData’:
  ‘plot.irregFunData’

S3 methods shown with full name in documentation object ‘plot.multiFunData’:
  ‘plot.multiFunData’

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.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘refund’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in documentation object ‘build_limits_lookup’:
  ‘min_preds’ ‘max_preds’ ‘min_ratio’ ‘max_ratio’ ‘draw_unadjusted’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘phytools’

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

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
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’
Documented arguments not in \usage in documentation object ‘loggedOutput’:
  ‘future’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘mandelbrot’:
  ‘Z’ ‘xmid’ ‘ymid’ ‘side’ ‘resolution’ ‘maxIter’ ‘tau’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lfe’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: ‘cBioPortalData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid package aliases in Rd file ‘GAabbreviate-internal.Rd’:
  ‘GAabbreviation-package’
Package required but not available: ‘rtracklayer’

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
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: \_
Invalid package aliases in Rd file ‘gamlss.mx.package.Rd’:
  ‘gamlss.mix-package’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
Documented arguments not in \usage in documentation object ‘as.gapdata’:
  ‘labels_df’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Documented arguments not in \usage in documentation object ‘lrr_plot’:
  ‘plot_cols’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages required but not available: 'SSBtools', 'RegSDC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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: \&
Documented arguments not in \usage in documentation object ‘align_peaks’:
  ‘gc_peak_df’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
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
Objects in \usage without \alias in documentation object ‘geepack-internal’:
  ‘genZcor’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package required but not available: ‘phytools’

Package suggested but not available for checking: ‘TreeSim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Auto-generated content requiring editing in Rd object ‘gemlog-package’:
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
'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
Packages required but not available: 'phangorn', 'ShortRead'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid package aliases in Rd file ‘GenBinom-package.Rd’:
  ‘GenbinomApps-package’
Package suggested but not available for checking: ‘genderdata’
Documented arguments not in \usage in documentation object ‘CirDisp’:
  ‘x’

Documented arguments not in \usage in documentation object ‘CirKurt’:
  ‘x’ ‘na.rm’

Documented arguments not in \usage in documentation object ‘CirSD’:
  ‘x’

Documented arguments not in \usage in documentation object ‘CirSkew’:
  ‘x’

Documented arguments not in \usage in documentation object ‘CirVar’:
  ‘x’

Documented arguments not in \usage in documentation object ‘MeanDir’:
  ‘x’

Documented arguments not in \usage in documentation object ‘impact’:
  ‘na.rm’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘expand’:
  ‘x’

Documented arguments not in \usage in documentation object ‘%bq%’:
  ‘x’

Documented arguments not in \usage in documentation object ‘%bt%’:
  ‘x’

Documented arguments not in \usage in documentation object ‘stftcalc’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rtracklayer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object ‘generalizedwendland-internal’:
  ‘numint.abstol (default: 1e-3)’ ‘numint.reltol (default: 1e-3)’
  ‘numint.qag_key (default: 0)’ ‘numint.subintervals (default: 0)’
  ‘interp.method (default: 'none')’ ‘interp.num_support (default: 0)’
  ‘cov.reparameterize (default: TRUE)’ ‘cov.eps (default:
  .Machine$double.eps^0.5)’ ‘cov.d_value (default: 2)’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file ‘GenlibR-package.Rd’:
  ‘GenlibR-package’
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘bin.levels’:
  ‘variable’

Documented arguments not in \usage in documentation object ‘info.mox’:
  ‘y:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Documented arguments not in \usage in documentation object ‘adj_spconsist_arr_window_globstd’:
  ‘a’

Documented arguments not in \usage in documentation object ‘elsa_fuzzy_vector’:
  ‘nbslitw’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
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
Documented arguments not in \usage in documentation object ‘variables_query’:
  ‘variables’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘geomarocdata’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) getopt.Rd:60: Escaped LaTeX specials: \#
Package suggested but not available for checking: ‘argon2’
Package suggested but not available for checking: ‘lfe’
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘attract_by_distance’:
  ‘prop_start’ ‘prop_end’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [7s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggasym)
  > 
  > test_check("ggasym")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 260 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-asymmetrise_stats.R:14:3'): stats asymmetrization works ────────
  Error in `.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)`: invalid non-character version specification 'x' (type: double)
  Backtrace:
      ▆
   1. └─base::Ops.numeric_version(utils::packageVersion("broom"), 0.7) at test-asymmetrise_stats.R:14:2
   2.   └─base::as.numeric_version(e2)
   3.     └─base::numeric_version(x)
   4.       └─base::.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 260 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggasym-corrr.Rmd’ using rmarkdown
--- finished re-building ‘ggasym-corrr.Rmd’

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

Quitting from lines 82-84 [prep_results] (ggasym-stats.Rmd)
Error: processing vignette ‘ggasym-stats.Rmd’ failed with diagnostics:
invalid non-character version specification ‘x’ (type: double)
--- failed re-building ‘ggasym-stats.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggbio', 'rtracklayer', 'BSgenome', 'GenomicAlignments'

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘labels.rpart’:
  ‘pretty:’

Documented arguments not in \usage in documentation object ‘rpart_labels’:
  ‘model’ ‘...’

Documented arguments not in \usage in documentation object ‘rpart_segments’:
  ‘model’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
Package suggested but not available for checking: ‘glmmTMB’
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
Documented arguments not in \usage in documentation object ‘interpolateDataFrame’:
  ‘A’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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.
Argument items with no description in Rd object ‘isADMG’:
  ‘amat’
Argument items with no description in Rd object ‘isAG’:
  ‘amat’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘package-ggparallel.Rd’:
  ‘package-ggparallel-package’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ALDEx2', 'DESeq2', 'lefser', 'Maaslin2', 'SummarizedExperiment'

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
Packages suggested but not available for checking:
  'captioner', 'lixoftConnectors'
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘operator’:
  ‘x’ ‘y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Package required but not available: ‘Seurat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Documented arguments not in \usage in documentation object ‘decoration’:
  ‘nudge_npcx’ ‘nudge_npcy’

Documented arguments not in \usage in documentation object ‘generic_plot’:
  ‘pc.out’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘ggplot_gtable’:
  ‘plot’

Documented arguments not in \usage in documentation object ‘zzz-internal’:
  ‘latex’ ‘ggplot’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
Documented arguments not in \usage in documentation object ‘add_scale’:
  ‘domain’

Documented arguments not in \usage in documentation object ‘bin_vector’:
  ‘width’ ‘origin’ ‘closed’ ‘pad’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: ‘phytools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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
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.
Packages suggested but not available for checking:
  'rtracklayer', 'BSgenome', 'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
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’
Argument items with no description in Rd object ‘GLD.lm.full.surv’:
  ‘maxit’
Argument items with no description in Rd object ‘GLD.lm.surv’:
  ‘maxit’
Documented arguments not in \usage in documentation object ‘getBeta’:
  ‘thetaConrol’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Package suggested but not available for checking: ‘glmmTMB’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Package required but not available: ‘glmmTMB’

Package suggested but not available for checking: ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/glmmTMB.Rcheck/00install.out’ for details.
Documented arguments not in \usage in documentation object ‘glmpathcr-internal’:
  ‘fit’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘fun.svd_1’:
  ‘X’

Documented arguments not in \usage in documentation object ‘fun.svd_2’:
  ‘X’

Documented arguments not in \usage in documentation object ‘fun.svd_3’:
  ‘X’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘gmeta/libs/gmeta.so’:
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘confdistint.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘confdistint.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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
Package required but not available: ‘glmmTMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'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
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
Rd files without \alias:
  ‘goodpractice-package.Rd’
Package suggested but not available for checking: ‘ganalytics’
Documented arguments not in \usage in documentation object ‘doHttrRequest’:
  ‘session’ ‘params’

Documented arguments not in \usage in documentation object ‘get_google_token’:
  ‘shiny_return_token’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Package required but not available: ‘PlackettLuce’

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
Malformed Description field: should contain one or more complete sentences.
Documented arguments not in \usage in documentation object ‘maxLevelBP’:
  ‘org’

Documented arguments not in \usage in documentation object ‘maxLevelCC’:
  ‘org’

Documented arguments not in \usage in documentation object ‘maxLevelMF’:
  ‘org’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file ‘00.GPArotateDF.Rd’:
  ‘00.GPArotateDF-package’
Documented arguments not in \usage in documentation object ‘estimate_noise_nn’:
  ‘n_thread’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gps.Rcheck/00install.out’ for details.
Specified C++11: please drop specification unless essential
Missing or unexported objects:
  ‘Matrix::crossprod’ ‘Matrix::tcrossprod’
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)
> calculate_posterior_VL(z,vecchia.approx,"gaussian",covparms=c(1,2,.5))
Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GPvecchia_vignette.Rmd’ using rmarkdown

Quitting from lines 85-86 [paramm-est] (GPvecchia_vignette.Rmd)
Error: processing vignette ‘GPvecchia_vignette.Rmd’ failed with diagnostics:
‘crossprod’ is not an exported object from ‘namespace:Matrix’
--- 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
Packages suggested but not available for checking: 'Seurat', 'DESeq2'
Package unavailable to check Rd xrefs: ‘DESeq2’
'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
Documented arguments not in \usage in documentation object ‘fmpareto_HR_MLE’:
  ‘method’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object ‘HistPCA’:
  ‘ggplot’
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/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(greenclust)
  > 
  > test_check("greenclust")
  Step 1:  Cluster 1 + 6
  
            [,1] [,2]
  1            1    7
  2            2    8
  3            3    9
  4            4   10
  Cluster 1   11   23
  
  Chi-squared: 1.64 
  p-value: 0.8014 
  R-squared: 0.9887 
  
  
  Step 2:  Cluster 2 + 4
  
            [,1] [,2]
  1            1    7
  2            2    8
  Cluster 2    7   19
  Cluster 1   11   23
  
  Chi-squared: 1.6 
  p-value: 0.6596 
  R-squared: 0.9635 
  
  
  Step 3:  Cluster 3 + 2
  
            [,1] [,2]
  Cluster 3    3   15
  Cluster 2    7   19
  Cluster 1   11   23
  
  Chi-squared: 1.47 
  p-value: 0.479 
  R-squared: 0.8869 
  
  
  Step 4:  Cluster 4 + Cluster 1
  
            [,1] [,2]
  Cluster 3    3   15
  Cluster 4   18   42
  
  Chi-squared: 1.25 
  p-value: 0.2633 
  R-squared: 0.7539 
  
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 127 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-greenclust-main.R:48:5'): greenclust stops when x has an initial chi-squared of zero ──
  Error in `.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)`: invalid non-character version specification 'x' (type: double)
  Backtrace:
      ▆
   1. └─testthat::skip_if_not_installed("greenclust", minimum_version = 1.1) at test-greenclust-main.R:48:4
   2.   └─base::Ops.numeric_version(installed_version, minimum_version)
   3.     └─base::as.numeric_version(e2)
   4.       └─base::numeric_version(x)
   5.         └─base::.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 127 ]
  Error: Test failures
  Execution halted
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object ‘load_map’:
  ‘unity’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘prCaSetRownames’:
  ‘rownames.fn’

Documented arguments not in \usage in documentation object ‘prClearPCAclass’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
S3 methods shown with full name in documentation object ‘groc.fit’:
  ‘groc.fit’

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.
Package suggested but not available for checking: ‘phangorn’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘groupsubsetselection/libs/groupsubsetselection.so’:
  Found ‘_gfortran_random_r4’, possibly from ‘random_number’ (Fortran)
    Object: ‘gss.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.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘fit_grp.Rd’:
  ‘grplasso-package’
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’
Objects in \usage without \alias in documentation object ‘GSA-internal’:
  ‘est.s0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file ‘gsb-package.Rd’:
  ‘gsb-package’
Packages required but not available: 'Seurat', 'CelliD'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘taxize’
'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
Documented arguments not in \usage in documentation object ‘traits’:
  ‘efo_id’ ‘trait’ ‘uri’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) luzdat.Rd:21: Escaped LaTeX specials: \~
File ‘GWEX/libs/GWEX.so’:
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘GWex_disag.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
'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
Packages required but not available: 'cxhull', 'Morpho'

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
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-gcc/Work/PKGS/hal9001.Rcheck/00install.out’ for details.
Package required but not available: ‘hal9001’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Argument items with no description in Rd object ‘haplo.em.fitter’:
  ‘random.start ’
Argument items with no description in Rd object ‘haplo.model.frame’:
  ‘control’
Package required but not available: ‘phangorn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘modeling-package.Rd’:
  ‘modeling-package’
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
Packages suggested but not available for checking:
  'SingleCellExperiment', 'Seurat'
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
'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) 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
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘check_arg_for_hyperslab_func’:
  ‘cur_arg’

Documented arguments not in \usage in documentation object ‘extract_dim’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
Documented arguments not in \usage in documentation object ‘compute_counts’:
  ‘init’ ‘inflow’

Documented arguments not in \usage in documentation object ‘compute_values’:
  ‘counts’

Documented arguments not in \usage in documentation object ‘create_demographic_table’:
  ‘...’

Documented arguments not in \usage in documentation object ‘eval_strategy_newdata’:
  ‘model’

Documented arguments not in \usage in documentation object ‘get_state_value_names’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘autocomplete-defunct’:
  ‘autocomplete’

Objects in \usage without \alias in documentation object ‘set_auth-defunct’:
  ‘set_auth’

Objects in \usage without \alias in documentation object ‘set_proxy-defunct’:
  ‘set_proxy’

Objects in \usage without \alias in documentation object ‘traffic-defunct’:
  ‘traffic’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages required but not available: 'DESeq2', 'SummarizedExperiment'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Missing or unexported objects:
  ‘Matrix::crossprod’ ‘Matrix::tcrossprod’
Running examples in ‘hero-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: assemble
> ### Title: Assemble spline ingredients for sandwich smooth
> ### Aliases: assemble assemble.hero_bspline assemble.hero_radspline
> ###   assemble.list
> 
> ### ** Examples
> 
> # construct b-spline
> object1 = bspline(nbasis = 10)
> # sequence to evaluate
> x1 = seq(0, 1, len = 11)
> # assemble b-spline information
> spline1 = assemble(object1, x1)
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘check.id_attributes’:
  ‘inner_class’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘check_known_repos’:
  ‘known_packages’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘defunct’:
  ‘anova.mean’ ‘print.glht.mmc.multicomp’ ‘coef.arima.HH’ ‘glht.mmc’
  ‘plot.odds.ratio’ ‘persp.plane’ ‘persp.floor’ ‘persp.back.wall.x’
  ‘persp.back.wall.y’ ‘persp.setup’ ‘plot.hov’ ‘plot.hov.bf’
  ‘plot.matchMMC’ ‘seqplot.forecast’

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.
Argument items with no description in Rd object ‘residual.plots.lattice’:
  ‘X’
Found export directives that require package ‘methods’:
  ‘exportClasses’ ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'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’
Argument items with no description in Rd object ‘qcplate’:
  ‘dat’
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
Package required but not available: ‘geiger’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Missing or unexported object: ‘Matrix::tcrossprod’
Packages required but not available:
  'phytools', 'paleotree', 'geiger', 'phangorn', 'TreeSim', 'corHMM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd object ‘HistDAWass-package’:
  \details: ‘...o use the package, including the most important functions ~~’
Invalid package aliases in Rd file ‘histogram-package.Rd’:
  ‘histogramtools-package’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘trackr’
Package which this enhances but not available for checking: ‘HadoopStreaming’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
html_describe_con: multiple local function definitions for ‘g’ with
  different formal arguments
Argument items with no description in Rd object ‘bpower’:
  ‘odds.ratio’ ‘percent.reduction’ ‘n1’
Argument items with no description in Rd object ‘describe’:
  ‘data’ ‘subset’
Argument items with no description in Rd object ‘find.matches’:
  ‘xcase’ ‘ycase’ ‘idcase’
Argument items with no description in Rd object ‘labcurve’:
  ‘x’ ‘width’ ‘col.’ ‘empty.method’ ‘xlab’
Argument items with no description in Rd object ‘varclus’:
  ‘data’ ‘subset’ ‘lty’ ‘col’
Documented arguments not in \usage in documentation object ‘bootstrapfun’:
  ‘DoF’ ‘n_sample’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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: \&
Missing or unexported objects:
  ‘Matrix::crossprod’ ‘Matrix::tcrossprod’
Auto-generated content requiring editing in Rd object ‘HMVD-package’:
  \details: ‘...o use the package, including the most important functions ~~’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
Invalid package aliases in Rd file ‘hoardeR-package.Rd’:
  ‘R/hoardeR-package’
Argument items with no description in Rd object ‘bid2’:
  ‘numattable1’ ‘playerseats1’ ‘blinds1’ ‘dealer1’ ‘b3’ ‘b4’ ‘round1’
  ‘ntable1’ ‘decision1’
Argument items with no description in Rd object ‘calcwin1’:
  ‘numattable1’ ‘playerseats1’ ‘b3’ ‘b7’
Argument items with no description in Rd object ‘mycount1’:
  ‘x’
Argument items with no description in Rd object ‘mygraphics1’:
  ‘numattable1’ ‘playerseats1’ ‘chips1’ ‘blinds1’ ‘dealer1’ ‘b3’ ‘b4’
  ‘b5’ ‘b6’ ‘b7’ ‘chips2’ ‘ntable1’ ‘myfast1’ ‘chipstart1’ ‘name1’
  ‘lowercut1’
Argument items with no description in Rd object ‘nothing1’:
  ‘x’
Argument items with no description in Rd object ‘onepair1’:
  ‘x’
Argument items with no description in Rd object ‘straight1’:
  ‘x’
Argument items with no description in Rd object ‘straightdraw1’:
  ‘x’
Argument items with no description in Rd object ‘strflsh1’:
  ‘x’ ‘y’
Argument items with no description in Rd object ‘trip1’:
  ‘x’
Argument items with no description in Rd object ‘twopair1’:
  ‘x’
Argument items with no description in Rd object ‘writebets1’:
  ‘b9’ ‘y1’ ‘numattable1’ ‘b3’ ‘playerseats1’ ‘chips1’ ‘chips2’ ‘over1’
  ‘myfast1’ ‘name1’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘plot.hopitCP’:
  ‘plotf’

Documented arguments not in \usage in documentation object ‘sigma.hopit’:
  ‘model’

Documented arguments not in \usage in documentation object ‘summary.hopit’:
  ‘control’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd files without \alias:
  ‘hpoPlot-package.Rd’
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘.E3’:
  ‘i’ ‘M’

Documented arguments not in \usage in documentation object ‘.E4’:
  ‘i’ ‘M’

Documented arguments not in \usage in documentation object ‘hrm.0w.2s’:
  ‘group’

Documented arguments not in \usage in documentation object ‘hrm.0w.3s’:
  ‘group’

Documented arguments not in \usage in documentation object ‘hrm.0w.4s’:
  ‘group’

Documented arguments not in \usage in documentation object ‘hrm.0w.5s’:
  ‘group’

Documented arguments not in \usage in documentation object ‘hrm.1f’:
  ‘group’

Documented arguments not in \usage in documentation object ‘hrm.1w.0f’:
  ‘factor1’

Documented arguments not in \usage in documentation object ‘hrm.2w.2f’:
  ‘factor’

Documented arguments not in \usage in documentation object ‘hrm.mv.1w.1f’:
  ‘H’ ‘text’

Documented arguments not in \usage in documentation object ‘hrm.mv.internal’:
  ‘alpha’ ‘H’ ‘text’

Documented arguments not in \usage in documentation object ‘hrm.test.1.none’:
  ‘factor1’ ‘factor2’

Documented arguments not in \usage in documentation object ‘hrm.test.1.one’:
  ‘group’ ‘factor2’

Documented arguments not in \usage in documentation object ‘hrm.test.2.one’:
  ‘factor2’

Documented arguments not in \usage in documentation object ‘hrm.test.2.two’:
  ‘group’

Documented arguments not in \usage in documentation object ‘hrm.test.3.three’:
  ‘group’

Documented arguments not in \usage in documentation object ‘hrm.test.4.four’:
  ‘group’

Documented arguments not in \usage in documentation object ‘hrm.test.5.five’:
  ‘group’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘imageplot’:
  ‘\dots’
'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
Documented arguments not in \usage in documentation object ‘prGetStyle’:
  ‘styles’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘FramedHTML’:
  ‘DiagnosticsPath’
Package suggested but not available for checking: ‘HTSFilter’
Package required but not available: ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid package aliases in Rd file ‘httkpop.Rd’:
  ‘httkpop-package’
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
Documented arguments not in \usage in documentation object ‘as.redactor’:
  ‘expr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘as.redactor’:
  ‘expr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
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
Invalid package aliases in Rd file ‘HydroMe-package.Rd’:
  ‘HydroMe2-package’
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: \#
Documented arguments not in \usage in documentation object ‘scan.txt.Witec’:
  ‘nwl’ ‘remove.zerospc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘print.Hypervolume’:
  ‘...’
Argument items with no description in Rd object ‘summary.Hypervolume’:
  ‘...’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ciTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gutenbergr’
Objects in \usage without \alias in documentation object ‘btibgen’:
  ‘ibdgen’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘pairSum’:
  ‘cov1’ ‘cov2’
'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
Package required but not available: ‘BSgenome’

Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'

See section ‘The DESCRIPTION file’ 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 required but not available: ‘glmmTMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘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: \$
S3 methods shown with full name in documentation object ‘orlm’:
  ‘orlm.forboot.fixed’ ‘orlm.forboot’

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.
'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) pulmonary.Rd:13: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rggobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘phytools’
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in documentation object ‘internals’:
  ‘iplotMain’ ‘segments.circle’ ‘griddat’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘internals’:
  ‘plot.page’

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.
Package suggested but not available for checking: ‘IFCdata’
Documented arguments not in \usage in documentation object ‘fastAny’:
  ‘obj’

Documented arguments not in \usage in documentation object ‘getSTATSREPORT’:
  ‘...’

Documented arguments not in \usage in documentation object ‘split_feat’:
  ‘operators’

Documented arguments not in \usage in documentation object ‘toXML2_features_def’:
  ‘features’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package required but not available: ‘MBESS’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: graph_match_Umeyama
> ### Title: Spectral Graph Matching Methods: Umeyama Algorithm
> ### Aliases: graph_match_Umeyama
> ### Keywords: internal
> 
> ### ** Examples
> 
> # match G_1 & G_2 using Umeyama algorithm
> G <- sample_correlated_gnp_pair(10, .9, .5)
> g1 <- G$graph1
> g2 <- G$graph2
> startm <- matrix(0, 10, 10)
> diag(startm)[1:4] <- 1
> 
> GM_Umeyama <- gm(g1, g2, similarity = startm, method = "Umeyama")
Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘.compl’:
  ‘imgfile’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Invalid package aliases in Rd file ‘image-package.Rd’:
  ‘image-package’
Specified C++11: please drop specification unless essential
Packages required but not available:
  'SingleCellExperiment', 'SummarizedExperiment'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘accdata’
Documented arguments not in \usage in documentation object ‘new_impactr_peaks’:
  ‘acc_signal:’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Rd files without \alias:
  ‘imputeYn-package.Rd’
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++11: please drop specification unless essential
Package unavailable to check Rd xrefs: ‘minfi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Missing or unexported object: ‘Matrix::crossprod’
Running examples in ‘influenceR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ens
> ### Title: Burt's Effective Network Size and Constraint index. The next two
> ###   functions below provide ways to measure the actors' access to
> ###   structural holes in a network. Structural holes "provide
> ###   opportunities to broker connections between people" (Burt 2008).
> ### Aliases: ens
> 
> ### ** Examples
> 
> ig.ex <- igraph::erdos.renyi.game(100, p.or.m=0.3) # generate an undirected 'igraph' object
> ens(ig.ex) # Effective Network Size scores for each node in the graph
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(influenceR)
  > 
  > test_check("influenceR")
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 4 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_metrics.R:9:3'): metrics work as expected ──────────────────────
  Error: 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(influenceR::ens(flo_graph), flo_ens) at test_metrics.R:9:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─influenceR::ens(flo_graph)
  ── Error ('test_reference.R:57:3'): ens matches reference function ─────────────
  Error: 'crossprod' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(influenceR::ens(flo_graph), ens_test(flo_graph)) at test_reference.R:57:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─influenceR::ens(flo_graph)
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
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’
Packages required but not available: 'spaMM', 'blackbox'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Missing or unexported object: ‘Matrix::crossprod’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Argument items with no description in Rd object ‘combine.NULL’:
  ‘x’ ‘y’
Argument items with no description in Rd object ‘combine’:
  ‘x’ ‘y’
Argument items with no description in Rd object ‘combine.character’:
  ‘x’ ‘y’
Argument items with no description in Rd object ‘combine.list’:
  ‘x’ ‘y’
Argument items with no description in Rd object ‘findGeneric’:
  ‘fname’ ‘envir’
Argument items with no description in Rd object ‘fixPackageFileNames’:
  ‘list’
Argument items with no description in Rd object ‘forfun’:
  ‘FUN’
Argument items with no description in Rd object ‘get_S3_primitive_generics’:
  ‘include_group_generics’
Argument items with no description in Rd object ‘get_internal_S3_generics’:
  ‘primitive’
Argument items with no description in Rd object ‘is_primitive_in_base’:
  ‘fname’
Argument items with no description in Rd object ‘prefixed.lines’:
  ‘src’ ‘\dots’
Argument items with no description in Rd object ‘print.allfun’:
  ‘x’ ‘\dots’
Argument items with no description in Rd object ‘whole.word’:
  ‘\dots’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'glmmTMB', 'lfe', 'merTools'
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
Package suggested but not available for checking: ‘cmdstanr’
Malformed Title field: should not end in a period.
Package required but not available: ‘ciTools’

See section ‘The DESCRIPTION file’ 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:
  ‘Error_Estimation_Response_1.tiff’ ‘Error_Estimation_Response_2.tiff’
  ‘Error_Estimation_Response_3.tiff’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lfe’

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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object ‘IntervalSurgeon-package’:
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
Error(s) in re-building vignettes:
  ...
--- re-building ‘inTextSummaryTable-advanced.Rmd’ using rmarkdown
--- finished re-building ‘inTextSummaryTable-advanced.Rmd’

--- re-building ‘inTextSummaryTable-aesthetics.Rmd’ using rmarkdown
--- finished re-building ‘inTextSummaryTable-aesthetics.Rmd’

--- re-building ‘inTextSummaryTable-createTables.Rmd’ using rmarkdown
--- finished re-building ‘inTextSummaryTable-createTables.Rmd’

--- re-building ‘inTextSummaryTable-exportTables.Rmd’ using rmarkdown
--- finished re-building ‘inTextSummaryTable-exportTables.Rmd’

--- re-building ‘inTextSummaryTable-introduction.Rmd’ using rmarkdown
--- finished re-building ‘inTextSummaryTable-introduction.Rmd’

--- re-building ‘inTextSummaryTable-standardTables.Rmd’ using rmarkdown
--- finished re-building ‘inTextSummaryTable-standardTables.Rmd’

--- re-building ‘inTextSummaryTable-visualization.Rmd’ using rmarkdown

Quitting from lines 152-169 [visualization-a4document] (inTextSummaryTable-visualization.Rmd)
Error: processing vignette ‘inTextSummaryTable-visualization.Rmd’ failed with diagnostics:
invalid non-character version specification ‘x’ (type: double)
--- failed re-building ‘inTextSummaryTable-visualization.Rmd’

SUMMARY: processing the following file failed:
  ‘inTextSummaryTable-visualization.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object ‘selectRuleRRF’:
  ‘target’
'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
Documented arguments not in \usage in documentation object ‘rawAvgCost-deprecated’:
  ‘cost.transf’ ‘in.millions’ ‘confidence.interval’ ‘minimum.year’
  ‘maximum.year’ ‘final.year’ ‘incomplete.year.threshold’
  ‘incomplete.year.weights’ ‘gam.k’ ‘mars.nprune’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Missing or unexported object: ‘Matrix::tcrossprod’
Package suggested but not available for checking: ‘surveyspec’
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
Documented arguments not in \usage in documentation object ‘chars_collapse’:
  ‘collapse’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘iprior_package.Rd’:
  ‘iprior_package-package’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘phangorn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/irtQ.Rcheck/00install.out’ for details.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘print.cat_output’:
  ‘object’

Documented arguments not in \usage in documentation object ‘[[<-,Itempool,numeric,missing-method’:
  ‘...’

Documented arguments not in \usage in documentation object ‘[[<-,Response_set,numeric,missing-method’:
  ‘...’

Documented arguments not in \usage in documentation object ‘[[<-,Testlet,numeric,missing-method’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘print.Item’:
  ‘print.Item’

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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘xcms’
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘islasso-internal’:
  ‘modelX’ ‘.checkinput’ ‘.startpoint’ ‘.islasso’
  ‘checkinput.islasso.path’ ‘startpoint.islasso.path’
  ‘islasso.path.fit.glm’ ‘islasso.path.fitter2’ ‘interpolate’ ‘makeHyp’
  ‘printHyp’ ‘cislasso’ ‘ci.fitted.islasso’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘.assignmentMaker’:
  ‘.precip_raster’ ‘.precip_SD_raster’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Package required but not available: ‘spaMM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
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 required but not available: ‘lfe’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Invalid package aliases in Rd file ‘ivprobit-package.Rd’:
  ‘ivProbit-package’
Auto-generated content requiring editing in Rd object ‘ivregEX-package’:
  \references: ‘~~ Literature or other references for background information ~~’
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.
Rd files without \alias:
  ‘jackknifeKME-package.Rd’
Package required but not available: ‘rsvd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
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
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
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
Package suggested but not available for checking: ‘semPlot’
'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’
Documented arguments not in \usage in documentation object ‘paste_coef’:
  ‘parlemts’

Documented arguments not in \usage in documentation object ‘paste_linpred’:
  ‘parlemts’ ‘matname’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘scran’

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
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:
    pre-release juicr (2017 - 2021)
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
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
Rd files without \alias:
  ‘karaoke-package.Rd’
Found the following files/directories:
  ‘song.wav’ ‘song4karaoke.wav’
Packages required but not available:
  'SingleCellExperiment', 'SummarizedExperiment'

See section ‘The DESCRIPTION file’ 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
prepare_Rd: NEWS.Rd:58: Dropping empty section ‘kelvin INITIAL VERSION 1.0-0 (2012-05-30)’
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘covQualNested’:
  ‘covBet’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘bw.abram.temp’:
  ‘bw.abram.temp’

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.
Missing or unexported object: ‘Matrix::tcrossprod’
Documented arguments not in \usage in documentation object ‘calc_PGtheta_R’:
  ‘model’ ‘iter’

Documented arguments not in \usage in documentation object ‘make_wsz_cpp’:
  ‘info’ ‘initialized’

Documented arguments not in \usage in documentation object ‘read_dfm_cpp’:
  ‘W_raw’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘b_wincred_get’:
  ‘backend’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
Package suggested but not available for checking: ‘semPlot’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rtracklayer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘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
S3 methods shown with full name in documentation object ‘unlist.constr’:
  ‘unlist.constr’

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.
'LazyData' is specified without a 'data' directory
'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
Invalid package aliases in Rd file ‘knotR-package.Rd’:
  ‘knot-package’
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘variablekey.Rnw’ using Sweave
Error: processing vignette ‘variablekey.Rnw’ failed with diagnostics:
Running ‘texi2dvi’ on ‘variablekey.tex’ failed.
LaTeX errors:
! TeX capacity exceeded, sorry [input stack size=10000].
\protect ->\noexpand \protect 
                              \noexpand 
l.662 ... variable key\label{sec:Editing-the-key}}
                                                  
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'variablekey.Rnw'

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

Error: Vignette re-building failed.
Execution halted
S3 methods shown with full name in documentation object ‘stat.functions’:
  ‘kappa.cor’

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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘extract_and_augment_context’:
  ‘...additional’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: ‘EGAnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Packages suggested but not available for checking:
  'akmedoids', 'clusterCrit'
Unknown packages ‘clusterCrit’, ‘akmedoids’ in Rd xrefs
Objects in \usage without \alias in documentation object ‘latrend-generics’:
  ‘nClusters’ ‘clusterProportions’ ‘clusterTrajectories’ ‘compose’
  ‘converged’ ‘externalMetric’ ‘estimationTime’ ‘fit’
  ‘fittedTrajectories’ ‘getArgumentDefaults’ ‘getArgumentExclusions’
  ‘getLabel’ ‘getLcMethod’ ‘getName’ ‘getShortName’ ‘idVariable’
  ‘metric’ ‘plotFittedTrajectories’ ‘plotClusterTrajectories’ ‘postFit’
  ‘postprob’ ‘predictAssignments’ ‘predictForCluster’ ‘predictPostprob’
  ‘prepareData’ ‘preFit’ ‘qqPlot’ ‘responseVariable’ ‘strip’
  ‘timeVariable’ ‘trajectoryAssignments’ ‘validate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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: \$
Package required but not available: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘moments2’:
  ‘...’

Documented arguments not in \usage in documentation object ‘skeleton’:
  ‘endogeneous’ ‘...’

Documented arguments not in \usage in documentation object ‘vcov2-internal’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
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
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’
Packages suggested but not available for checking: 'xcms', 'MSnbase'
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘H_inv’:
  ‘trunc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘semPlot’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in documentation object ‘.choose_best_subjects’:
  ‘best’ ‘candidate’

Documented arguments not in \usage in documentation object ‘.normalize_props’:
  ‘keep_all_items’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘top.topic.words’:
  ‘alpha’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘phangorn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘VariantAnnotation’
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
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
Invalid package aliases in Rd file ‘LEANR-package.Rd’:
  ‘LEAN-package’
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
Invalid package aliases in Rd file ‘learnn.Rd’:
  ‘learnn-package’
Package required but not available: ‘phytools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in documentation object ‘backward_step’:
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in documentation object ‘backward_step_IM’:
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in documentation object ‘forward_step’:
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in documentation object ‘forward_step_IM’:
  ‘empty_start_dataset’ ‘fit’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Documented arguments not in \usage in documentation object ‘lemon-ggproto’:
  ‘side’ ‘is.primary’

Documented arguments not in \usage in documentation object ‘render_gpar’:
  ‘name’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘get_generic’:
  ‘mismatch’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘corpustools’
Packages suggested but not available for checking:
  'DESeq2', 'SummarizedExperiment'
Error(s) in re-building vignettes:
  ...
--- re-building ‘lfc_vignette.Rmd’ using rmarkdown

Quitting from lines 35-47 [unnamed-chunk-1] (lfc_vignette.Rmd)
Error: processing vignette ‘lfc_vignette.Rmd’ failed with diagnostics:
there is no package called 'DESeq2'
--- failed re-building ‘lfc_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lfe.Rcheck/00install.out’ for details.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gpclib’
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
Package required but not available: ‘phangorn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘CoordInBounds’:
  ‘direction’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'LazyData' is specified without a 'data' directory
Package required but not available: ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
S3 methods shown with full name in documentation object ‘BIC.threshold’:
  ‘BIC.threshold’

S3 methods shown with full name in documentation object ‘BIC.threshold.ggm’:
  ‘BIC.threshold.ggm’

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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: \&
Documented arguments not in \usage in documentation object ‘MassAcylCer’:
  ‘glccer’

Documented arguments not in \usage in documentation object ‘MassPEo’:
  ‘PEp’

Documented arguments not in \usage in documentation object ‘findMS2precursor’:
  ‘minint’ ‘maxint’

Documented arguments not in \usage in documentation object ‘joinAnnotationResults’:
  ‘simplifyAnnotation’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘get_variable’:
  ‘x’ ‘name’ ‘mustExist’ ‘create’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) MHDI.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
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
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: \$
checkRd: (-1) HomesForSaleCA.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleCanton.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleNY.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:24: Escaped LaTeX specials: \$
checkRd: (-1) SalaryGender.Rd:9: Escaped LaTeX specials: \$
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Invalid package aliases in Rd file ‘Lock5Data-package.Rd’:
  ‘Lock5Data-package’
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  ‘A’
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘dlogitnorm’:
  ‘sigma’
Argument items with no description in Rd object ‘invlogit’:
  ‘q’ ‘\dots’
Argument items with no description in Rd object ‘logit’:
  ‘p’ ‘\dots’
Argument items with no description in Rd object ‘plogitnorm’:
  ‘sigma’ ‘\dots’
Argument items with no description in Rd object ‘qlogitnorm’:
  ‘sigma’ ‘\dots’
Argument items with no description in Rd object ‘twCoefLogitnorm’:
  ‘\dots’
Argument items with no description in Rd object ‘twCoefLogitnormE’:
  ‘\dots’
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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Argument items with no description in Rd object ‘levopt’:
  ‘x’ ‘alpha’ ‘fmax’ ‘tm’
Argument items with no description in Rd object ‘pershow’:
  ‘object’
Argument items with no description in Rd object ‘norpt’:
  ‘alist’
Package required but not available: ‘glmmTMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
checkRd: (-1) butstrap.Rd:44: Escaped LaTeX specials: \&
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Package required but not available: ‘refund’

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
Auto-generated content requiring editing in Rd object ‘LoopAnalyst-package’:
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Found the following files/directories:
  ‘Model_1.cm’ ‘dambacher.dot’ ‘levins.dot’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘importance_sampling.array’:
  ‘is_method’

Documented arguments not in \usage in documentation object ‘importance_sampling.default’:
  ‘is_method’

Documented arguments not in \usage in documentation object ‘importance_sampling.matrix’:
  ‘is_method’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Argument items with no description in Rd object ‘LotkasXX’:
  ‘Table’
Argument items with no description in Rd object ‘LotkasXY’:
  ‘Table’
'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
Argument items with no description in Rd object ‘followx’:
  ‘Xi’ ‘x0’ ‘h’ ‘t0’ ‘iter’ ‘way’ ‘weights’ ‘pen’ ‘phi’
  ‘lasteigenvector’ ‘rho0’ ‘boundary’ ‘convergence.at’ ‘cross’
'LazyData' is specified without a 'data' directory
checkRd: (-1) lpepa.Rd:32: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
Package required but not available: ‘rsvd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
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'LazyData' is specified without a 'data' directory
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
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Package required but not available: ‘rsvd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘arm’
'LazyData' is specified without a 'data' directory
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
Documented arguments not in \usage in documentation object ‘setlogdata’:
  ‘logdata’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test’
Specified C++11: please drop specification unless essential
Package required but not available: ‘semPlot’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘orthogene’
Package unavailable to check Rd xrefs: ‘orthogene’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'lpjmlkit', 'quitte'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dittoSeq’
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Argument items with no description in Rd object ‘plot.magree’:
  ‘xlab’ ‘ylab’ ‘main’ ‘\dots’
Argument items with no description in Rd object ‘print.summary.magree’:
  ‘x’ ‘\dots’
Argument items with no description in Rd object ‘summary.magree’:
  ‘object’ ‘\dots’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘alignPeaks’:
  ‘\dots’
'LazyData' is specified without a 'data' directory
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Packages suggested but not available for checking: 'semPlot', 'semptools'
'LazyData' is specified without a 'data' directory
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
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Argument items with no description in Rd object ‘map.scale’:
  ‘x’
GNU make is a SystemRequirements.
checkRd: (-1) sw_sfac.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) Interpolation-class.Rd:41: Escaped LaTeX specials: \#
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Package suggested but not available for checking: ‘glmmTMB’
Argument items with no description in Rd object ‘bias.factor’:
  ‘RRud’ ‘RReu’ ‘rr’ ‘s2’
'LazyData' is specified without a 'data' directory
checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
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checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Undocumented S4 methods:
  generic 'crossprod' and siglist 'dgeMatrix,dtTMatrix'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘set.scale’:
  ‘scale.dm’ ‘scale.par’

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
Documented arguments not in \usage in documentation object ‘mark_my_dir’:
  ‘mark_file’

Documented arguments not in \usage in documentation object ‘path_type’:
  ‘github_token’

Documented arguments not in \usage in documentation object ‘read_assignment_yml’:
  ‘path’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘marssTMB’
Objects in \usage without \alias in documentation object ‘utility.functions’:
  ‘fully.spec.x’ ‘marssMODEL.to.list’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome', 'BSgenome.Hsapiens.NCBI.GRCh38', 'MAST', 'wiggleplotr'
Package suggested but not available for checking: ‘flashier’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘wallace’
'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
Invalid package aliases in Rd file ‘NewPackage-package.Rd’:
  ‘NewPackage-package’
Auto-generated content requiring editing in Rd object ‘NewPackage-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Package suggested but not available for checking: ‘gurobi’
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
'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
Documented arguments not in \usage in documentation object ‘x_OP_y’:
  ‘idxs’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘utilities.R’
Package required but not available: ‘beastier’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) maxControl.Rd:83: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
'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
Package required but not available: ‘sem’

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
Packages required but not available: 'babette', 'beastier', 'mauricer'

Package suggested but not available for checking: ‘phangorn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd object ‘mccca-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'LazyData' is specified without a 'data' directory
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: \#
Specified C++14: please drop specification unless essential
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Missing link or links in documentation object ‘CoupledHeatedmcmcabn.Rd’:
  ‘[abn:build_score_cache]{buildScoreCache}’
  ‘[abn:search_heuristic]{searchHeuristic}’

Missing link or links in documentation object ‘abnCache_asia.Rd’:
  ‘[abn:build_score_cache]{buildScoreCache}’

Missing link or links in documentation object ‘mcmc.Rd’:
  ‘[abn:build_score_cache]{buildScoreCache}’
  ‘[abn:search_heuristic]{searchHeuristic}’

Missing link or links in documentation object ‘mcmc_asia.Rd’:
  ‘[abn:build_score_cache]{buildScoreCache}’

See section ‘Cross-references’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘mcmcabn.Rmd’ using rmarkdown

Quitting from lines 143-149 [unnamed-chunk-7] (mcmcabn.Rmd)
Error: processing vignette ‘mcmcabn.Rmd’ failed with diagnostics:
`data.df` and `object` provided but can only accept one of them.
--- failed re-building ‘mcmcabn.Rmd’

SUMMARY: processing the following file failed:
  ‘mcmcabn.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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘geom_cp_density’:
  ‘include’

Documented arguments not in \usage in documentation object ‘get_simulate’:
  ‘par_trials’ ‘pars_pop’ ‘pars_varying’

Documented arguments not in \usage in documentation object ‘pp_eval’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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: \&
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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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checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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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
'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
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
Package suggested but not available for checking: ‘glmmTMB’
Package suggested but not available for checking: ‘arm’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
Found the following files/directories:
  ‘Data_Correlation.txt’ ‘correlation_FDR_table.txt’
'LazyData' is specified without a 'data' directory
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
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ 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.
Packages suggested but not available for checking: 'ropls', 'xcms'
Package required but not available: ‘taxize’

Packages suggested but not available for checking: 'traits', 'DESeq2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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
Documented arguments not in \usage in documentation object ‘ClusterMF-deprecated’:
  ‘formula’ ‘data’ ‘vi’ ‘study’ ‘whichweights’ ‘num.trees’ ‘mtry’
  ‘method’ ‘tau2’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘glmmTMB’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘plot.metaplot_gtable’:
  ‘y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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: ‘DESeq2’
Package suggested but not available for checking: ‘semPlot’
GNU make is a SystemRequirements.
checkRd: (-1) dslp.Rd:11: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
File ‘MEtest/libs/MEtest.so’:
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘TScomp.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘TScomp.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.
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’
Package suggested but not available for checking: ‘INLA’
Documented arguments not in \usage in documentation object ‘wmata_api’:
  ‘type’ ‘endpoint’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
Package suggested but not available for checking: ‘mvPot’
Documented arguments not in \usage in documentation object ‘.gev.postpred’:
  ‘vector’

Documented arguments not in \usage in documentation object ‘.gpd_2D_fit’:
  ‘...other’

Documented arguments not in \usage in documentation object ‘.mvasym.check’:
  ‘vector’

Documented arguments not in \usage in documentation object ‘.rPexstud’:
  ‘Sigma’

Documented arguments not in \usage in documentation object ‘.rPsite’:
  ‘index’ ‘param’

Documented arguments not in \usage in documentation object ‘.rdirspec’:
  ‘rho’

Documented arguments not in \usage in documentation object ‘.rexstudspec’:
  ‘index’ ‘Sigma’

Documented arguments not in \usage in documentation object ‘.rhrspec’:
  ‘index’

Documented arguments not in \usage in documentation object ‘.rmevA1’:
  ‘param’

Documented arguments not in \usage in documentation object ‘.rmevA2’:
  ‘param’

Documented arguments not in \usage in documentation object ‘.rmevasy’:
  ‘param’

Documented arguments not in \usage in documentation object ‘.rmevspec_cpp’:
  ‘param’

Documented arguments not in \usage in documentation object ‘.wecdf’:
  ‘ord’

Documented arguments not in \usage in documentation object ‘tem.corr’:
  ‘fran’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Missing or unexported objects:
  ‘Matrix::crossprod’ ‘Matrix::tcrossprod’
Running examples in ‘MFPCA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MFPCA
> ### Title: Multivariate functional principal component analysis for
> ###   functions on different (dimensional) domains
> ### Aliases: MFPCA
> 
> ### ** Examples
> 
> oldPar <- par(no.readonly = TRUE)
> 
> set.seed(1)
> 
> ### simulate data (one-dimensional domains)
> sim <-  simMultiFunData(type = "split", argvals = list(seq(0,1,0.01), seq(-0.5,0.5,0.02)),
+                         M = 5, eFunType = "Poly", eValType = "linear", N = 100)
> 
> # MFPCA based on univariate FPCA
> uFPCA <- MFPCA(sim$simData, M = 5, uniExpansions = list(list(type = "uFPCA"),
+                                                                   list(type = "uFPCA")))
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Argument items with no description in Rd object ‘predict.mfp’:
  ‘safe’
'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
Invalid package aliases in Rd file ‘Rpackage-package.Rd’:
  ‘Rpackage-package’
Auto-generated content requiring editing in Rd object ‘Rpackage-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'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 suggested but not available for checking: ‘DAPAR’
Package suggested but not available for checking: ‘MBESS’

Package which this enhances but not available for checking: ‘micemd’
S3 methods shown with full name in documentation object ‘complete.miceadds’:
  ‘complete.mids.nmi’ ‘complete.mids.1chain’

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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/micemd.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'DESeq2', 'SummarizedExperiment', 'phangorn'

Package suggested but not available for checking: ‘dada2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Documented arguments not in \usage in documentation object ‘changeDevSettings’:
  ‘defaultsSettings’

Documented arguments not in \usage in documentation object ‘getResultPerScheme’:
  ‘criteria’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘micSimParallel’:
  ‘transitionMatrix’ ‘absStates’ ‘varInitStates’ ‘initStatesProb’
  ‘fixInitStates’ ‘maxAge’ ‘simHorizon’ ‘fertTr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd object ‘MIDASwrappeR-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
Package suggested but not available for checking: ‘midfielddata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'mi', 'arm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Documented arguments not in \usage in documentation object ‘getvol’:
  ‘data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
'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
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Missing or unexported object: ‘Matrix::crossprod’
Running examples in ‘MiRKAT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GLMMMiRKAT
> ### Title: The Microbiome Regression-based Kernel Association Test Based on
> ###   the Generalized Linear Mixed Model
> ### Aliases: GLMMMiRKAT
> 
> ### ** Examples
> 
> 
> 
> ## Example with Gaussian (e.g., body mass index) traits
> ## For non-Gaussian traits, see vignette. 
> 
> # Import example microbiome data with Gaussian traits
> data(nordata)
> otu.tab <- nordata$nor.otu.tab
> meta <- nordata$nor.meta
> 
> # Create kernel matrices and run analysis 
> if (requireNamespace("vegan")) {
+  library(vegan)
+  D_BC = as.matrix(vegdist(otu.tab, 'bray'))
+  K_BC = D2K(D_BC)
+  GLMMMiRKAT(y = meta$y, X = cbind(meta$x1, meta$x2), id = meta$id, 
+           Ks = K_BC, model = "gaussian", nperm = 500)
+ } else {
+ # Computation time is longer for phylogenetic kernels 
+  tree <- nordata$nor.tree
+  unifracs <- GUniFrac::GUniFrac(otu.tab, tree, alpha=c(1))$unifracs
+  D_W <- unifracs[,,"d_1"] 
+  K_W = D2K(D_W)
+  GLMMMiRKAT(y = meta$y, X = cbind(meta$x1, meta$x2), id = meta$id, 
+           Ks = K_W, model = "gaussian", nperm = 500)
+ }
Loading required package: permute
Loading required package: lattice
This is vegan 2.6-4
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MiRKAT_Vignette.Rmd’ using rmarkdown

Quitting from lines 347-354 [unnamed-chunk-21] (MiRKAT_Vignette.Rmd)
Error: processing vignette ‘MiRKAT_Vignette.Rmd’ failed with diagnostics:
‘crossprod’ is not an exported object from ‘namespace:Matrix’
--- failed re-building ‘MiRKAT_Vignette.Rmd’

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

Error: Vignette re-building failed.
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
Documented arguments not in \usage in documentation object ‘logAdd’:
  ‘x’ ‘y’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package required but not available: ‘mi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘l1_similarity’
Argument items with no description in Rd object ‘randomizationTest’:
  ‘R’
checkRd: (-1) AKMCS.Rd:215: Escaped LaTeX specials: \&
checkRd: (-1) BMP.Rd:164: Escaped LaTeX specials: \&
checkRd: (-1) IRW.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) IRW.Rd:151: Escaped LaTeX specials: \&
checkRd: (-1) MP.Rd:142: Escaped LaTeX specials: \&
checkRd: (-1) MetropolisHastings.Rd:58: Escaped LaTeX specials: \&
checkRd: (-1) SubsetSimulation.Rd:152: Escaped LaTeX specials: \&
checkRd: (-1) oscillator_d6.Rd:14: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘glmmTMB’
Packages suggested but not available for checking:
  'karyoploteR', 'regioneR'
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘mixAR-internal’:
  ‘p’ ‘value’ ‘tau’ ‘etk’ ‘parscore’ ‘sigma’ ‘logpdf’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘rigaussian’:
  ‘mu’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘Sn_A’:
  ‘data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
Packages required but not available:
  'scran', 'Seurat', 'SingleCellExperiment', 'scuttle'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Auto-generated content requiring editing in Rd object ‘mixl-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
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
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) Texture.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:33: 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
Packages suggested but not available for checking:
  'minfi', 'IlluminaHumanMethylation450kmanifest'
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
Running ‘testthat.R’ [95s/178s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (requireNamespace("testthat", quietly = TRUE)) {
  +   library("testthat")
  +   library("mlr3learners")
  +   test_check("mlr3learners")
  + }
  Loading required package: mlr3
  # weights:  18 (10 variable)
  initial  value 164.791843 
  iter  10 value 16.177348
  iter  20 value 7.111438
  iter  30 value 6.182999
  iter  40 value 5.984028
  iter  50 value 5.961278
  iter  60 value 5.954900
  iter  70 value 5.951851
  iter  80 value 5.950343
  iter  90 value 5.949904
  iter 100 value 5.949867
  final  value 5.949867 
  stopped after 100 iterations
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 651 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_regr_ranger.R:7:3'): autotest ────────────────────────────────
  `result` is not TRUE
  
  `actual` is a list
  `expected` is a logical vector (TRUE)
  [predict()] learner 'regr.ranger:se' on task 'feat_single_logical' failed: predict log has errors: 'tcrossprod' is not an exported object from 'namespace:Matrix'
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 651 ]
  Error: Test failures
  Execution halted
Documented arguments not in \usage in documentation object ‘mlr_assertions’:
  ‘resample_result’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘cpoTemplate’:
  ‘affect.names’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘refund’
Package required but not available: ‘mlt’

Package suggested but not available for checking: ‘tram’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mlt.Rcheck/00install.out’ for details.
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ 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
Package required but not available: ‘refund’

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
Auto-generated content requiring editing in Rd object ‘mmeln-package’:
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
'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
Package required but not available: ‘mlVAR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Rd files without \alias:
  ‘mnlfa-package.Rd’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Flury’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘alstructure’

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Packages required but not available:
  'plyranges', 'RaggedExperiment', 'MultiAssayExperiment',
  'SummarizedExperiment', 'ggbio', 'GenomicFeatures', 'OrganismDbi',
  'biovizBase', 'ensembldb', 'BSgenome'

Packages suggested but not available for checking:
  'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene',
  'BSgenome.Hsapiens.UCSC.hg19', 'chromVAR', 'glmmTMB'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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
Package suggested but not available for checking: ‘glmmTMB’
'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
Error(s) in re-building vignettes:
  ...
--- re-building ‘modelplotr.Rmd’ using rmarkdown

Quitting from lines 484-485 [plot_roi] (modelplotr.Rmd)
Error: processing vignette ‘modelplotr.Rmd’ failed with diagnostics:
invalid non-character version specification ‘x’ (type: double)
--- failed re-building ‘modelplotr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘lfe’
Documented arguments not in \usage in documentation object ‘check_augment_data_specification’:
  ‘strict’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘arm’
Running examples in ‘modnets-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: intsPlot
> ### Title: Plot confidence intervals for interaction terms
> ### Aliases: intsPlot
> 
> ### ** Examples
> 
> fit <- fitNetwork(ggmDat, 'M')
> plot(fit, 'ints', y = 'all')
Error in loadNamespace(x) : there is no package called ‘arm’
Calls: plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: no function found corresponding to methods exports from ‘moko’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    * efourier with default norm=TRUE now messages about how wrong it may be
Argument items with no description in Rd object ‘as.difftime’:
  ‘tim’ ‘format’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'phytools', 'phangorn', 'taxize'

Package suggested but not available for checking: ‘paleotree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Arothron', 'Morpho'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Morpho.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘MBESS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘create_barrier_cs’:
  ‘fields’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
Specified C++11: please drop specification unless essential
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: \_
Rd files without \alias:
  ‘MPLikelihoodWB-package.Rd’
Documented arguments not in \usage in documentation object ‘addHeaderToSavedata’:
  ‘director’

Documented arguments not in \usage in documentation object ‘extractIndirect’:
  ‘curFile’

Documented arguments not in \usage in documentation object ‘extractIndirect_section’:
  ‘curFile’

Documented arguments not in \usage in documentation object ‘graphModel’:
  ‘The’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘qgcomp’
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘internals’:
  ‘check.in’ ‘check.out’ ‘start.theta’ ‘iMqr.internal’ ‘cov.theta’
  ‘iobjfun’ ‘sortH’ ‘isigma’ ‘iMqr.newton’ ‘num.fun’ ‘make.bfun’
  ‘apply_bfun’ ‘p.bisec’ ‘slp.basis’ ‘is.slp’ ‘iqr.waldtest’
  ‘extract.p’ ‘pred.beta’ ‘print.iMqr’ ‘print.summary.iMqr’
  ‘terms.iMqr’ ‘model.matrix.iMqr’ ‘vcov.iMqr’ ‘nobs.iMqr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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.
Auto-generated content requiring editing in Rd object ‘mrbsizer-package’:
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'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 required but not available: ‘phangorn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Argument items with no description in Rd object ‘msda’:
  ‘sml’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘CalcMPDynamics’:
  ‘M_ageArray’ ‘TAC_f’ ‘E_f’ ‘SizeLim_f’ ‘FinF’ ‘Spat_targ’
  ‘CAL_binsmid’ ‘Linf’ ‘Len_age’ ‘maxage’ ‘nareas’ ‘Asize’ ‘nCALbins’
  ‘qs’ ‘qvar’ ‘qinc’

Documented arguments not in \usage in documentation object ‘popdynCPP’:
  ‘SSBcurr’

Documented arguments not in \usage in documentation object ‘popdynOneMICE’:
  ‘nyears’

Documented arguments not in \usage in documentation object ‘qestMICE’:
  ‘mod’ ‘plusgroup.’ ‘WtC’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘test.txt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ICAMS’
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  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
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Argument items with no description in Rd object ‘DAGOSTINO’:
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Argument items with no description in Rd object ‘HZ.test’:
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Argument items with no description in Rd object ‘MardiaTest’:
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Argument items with no description in Rd object ‘Royston.test’:
  ‘data’
Argument items with no description in Rd object ‘gen.var’:
  ‘\dots’
Argument items with no description in Rd object ‘larg.ellip’:
  ‘n’ ‘box’ ‘add’ ‘xlim’ ‘ylim’ ‘zlim’ ‘xlab’ ‘ylab’ ‘zlab’ ‘col’
  ‘alpha’ ‘\dots’
Argument items with no description in Rd object ‘prism’:
  ‘add’
Problems with news in ‘NEWS.md’:
No news entries found.
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Invalid package aliases in Rd file ‘ms_sev-package.Rd’:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MTAR.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘pca.plot.wrap’:
  ‘lda.plot.wrap.1’

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.
Package required but not available: ‘glmmTMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Documented arguments not in \usage in documentation object ‘diagPlot’:
  ‘hvt.results.model’

Documented arguments not in \usage in documentation object ‘getOptimalCentroids’:
  ‘depth’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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No news entries found.
'LazyData' is specified without a 'data' directory
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checkRd: (-1) MultBiplotR-package.Rd:52: Escaped LaTeX specials: \&
Argument items with no description in Rd object ‘BinaryLogBiplotJoint’:
  ‘lambda’
Argument items with no description in Rd object ‘ConstrainedOrdinalLogisticBiplot’:
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Argument items with no description in Rd object ‘ContinuousProximities’:
  ‘ysup’
Argument items with no description in Rd object ‘Multiquad’:
  ‘nnodes’ ‘dims’
Argument items with no description in Rd object ‘PLSR1Bin’:
  ‘grouping’
Argument items with no description in Rd object ‘Unfolding’:
  ‘lambda’ ‘omega’ ‘plot’
Argument items with no description in Rd object ‘plot.CCA.sol’:
  ‘x’ ‘A1’ ‘A2’ ‘ShowAxis’ ‘margin’ ‘PlotSites’ ‘PlotSpecies’ ‘PlotEnv’
  ‘LabelSites’ ‘LabelSpecies’ ‘LabelEnv’ ‘TypeSites’ ‘SpeciesQuality’
  ‘MinQualityVars’ ‘dp’ ‘pr’ ‘PlotAxis’ ‘TypeScale’ ‘ValuesScale’
  ‘mode’ ‘CexSites’ ‘CexSpecies’ ‘CexVar’ ‘ColorSites’ ‘ColorSpecies’
  ‘ColorVar’ ‘PchSites’ ‘PchSpecies’ ‘PchVar’ ‘SizeQualSites’
  ‘SizeQualSpecies’ ‘SizeQualVars’ ‘ColorQualSites’ ‘ColorQualSpecies’
  ‘ColorQualVars’ ‘SmartLabels’
Argument items with no description in Rd object ‘plot.CanonicalDistanceAnalysis’:
  ‘SmartLabels’
Argument items with no description in Rd object ‘plot.Principal.Coordinates’:
  ‘ShowAxis’ ‘PlotBinaryMeans’ ‘MinIncidence’ ‘ShowBox’
  ‘ColorSupContVars’ ‘ColorSupBinVars’ ‘ColorSupOrdVars’ ‘TypeScale’
  ‘SupMode’ ‘PlotSupVars’
Argument items with no description in Rd object ‘plot.Unfolding’:
  ‘SpeciesQuality’ ‘dp’ ‘PlotAxis’ ‘TypeScale’ ‘ValuesScale’ ‘mode’
  ‘CexSites’ ‘CexSpecies’ ‘CexVar’ ‘ColorSites’ ‘ColorSpecies’
  ‘ColorVar’ ‘PchSites’ ‘PchSpecies’ ‘PchVar’ ‘SizeQualSites’
  ‘SizeQualSpecies’ ‘SizeQualVars’ ‘ColorQualSites’ ‘ColorQualSpecies’
  ‘ColorQualVars’ ‘SmartLabels’ ‘PlotTol’ ‘...’
Argument items with no description in Rd object ‘scores.CCA.sol’:
  ‘CCA.sol’
Argument items with no description in Rd object ‘summary.Canonical.Biplot’:
  ‘object’
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Packages suggested but not available for checking: 'tram', 'glmmTMB'
Documented arguments not in \usage in documentation object ‘plotBoxes’:
  ‘lwd’ ‘T.base’ ‘font.family’ ‘fig’ ‘mar’

Documented arguments not in \usage in documentation object ‘plotLetters’:
  ‘width’ ‘lwd’ ‘label.groups’ ‘T.base’ ‘orientation’

Documented arguments not in \usage in documentation object ‘plotTs’:
  ‘font.family’ ‘fig’ ‘mar’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘SSBtools’

Package suggested but not available for checking: ‘RegularizedSCA’

See section ‘The DESCRIPTION file’ 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
Package required but not available: ‘sparseFLMM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in documentation object ‘Trace’:
  ‘x’

Documented arguments not in \usage in documentation object ‘iteraite_fun_Iter’:
  ‘The’

Documented arguments not in \usage in documentation object ‘prepare_data’:
  ‘The’

Documented arguments not in \usage in documentation object ‘project’:
  ‘x’

Documented arguments not in \usage in documentation object ‘select_initial_Iter’:
  ‘X’ ‘parametrs’

Documented arguments not in \usage in documentation object ‘similarity_function’:
  ‘x’

Documented arguments not in \usage in documentation object ‘similarity_noncum’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘cmdstanr’
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'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
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Documented arguments not in \usage in documentation object ‘check_mnsl’:
  ‘fix’

Documented arguments not in \usage in documentation object ‘text_colour’:
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘sem’
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
Package required but not available: ‘phytools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
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checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
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Package suggested but not available for checking: ‘rTubeDB’
Package unavailable to check Rd xrefs: ‘rTubeDB’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Missing or unexported object: ‘Matrix::tcrossprod’
Package suggested but not available for checking: ‘re2r’
Argument items with no description in Rd object ‘check_subject_pattern’:
  ‘subject.vec’ ‘pattern’
Argument items with no description in Rd object ‘names_or_error’:
  ‘pattern’
Argument items with no description in Rd object ‘only_captures’:
  ‘match.mat’ ‘pattern’
Argument items with no description in Rd object ‘stop_for_names’:
  ‘pattern’
Package suggested but not available for checking: ‘udpipe’
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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’
Package required but not available: ‘Morpho’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘DEXSeq’
Invalid package aliases in Rd file ‘NBBttest-package.Rd’:
  ‘NBBtatest-package’
Package unavailable to check Rd xrefs: ‘DEXSeq’
'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
Package required but not available: ‘spaMM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in documentation object ‘Moth’:
  ‘delta.ident’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘MBESS’

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

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
Documented arguments not in \usage in documentation object ‘assignClasses’:
  ‘df’

Documented arguments not in \usage in documentation object ‘dateConvert’:
  ‘use_fasstime’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
GNU make is a SystemRequirements.
Missing or unexported object: ‘Matrix::crossprod’
Running examples in ‘net4pg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cc_composition
> ### Title: Get peptides and peptide-to-protein mappings for each connected
> ###   component
> ### Aliases: cc_composition
> 
> ### ** Examples
> 
> # Read the tab-delimited file containing the proteome incidence matrix
> incM_filename <- system.file("extdata"
+                              , "incM_example"
+                              , package = "net4pg"
+                              , mustWork = TRUE)
> rownames_filename <- system.file("extdata"
+                                   , "peptideIDs_incM_example"
+                                   , package = "net4pg"
+                                   , mustWork = TRUE)
> colnames_filename <- system.file("extdata"
+                                  , "proteinIDs_incM_example"
+                                  , package = "net4pg"
+                                  , mustWork = TRUE)
> incM <- read_inc_matrix(incM_filename = incM_filename
+                  , colnames_filename = colnames_filename
+                  , rownames_filename = rownames_filename)
> # Only retain proteins with at least one shared peptide and all peptides
> # mapping on such proteins.
> incM_reduced <- reduce_inc_matrix(incM)
> # Generate adjacency matrix describing protein-to-protein mappings
> adjM <- get_adj_matrix(incM_reduced)
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_To_net4pg.Rmd’ using rmarkdown

Quitting from lines 198-200 [unnamed-chunk-5] (Intro_To_net4pg.Rmd)
Error: processing vignette ‘Intro_To_net4pg.Rmd’ failed with diagnostics:
‘crossprod’ is not an exported object from ‘namespace:Matrix’
--- failed re-building ‘Intro_To_net4pg.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro_To_net4pg.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
‘:::’ 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: \_
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checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
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Argument items with no description in Rd object ‘print.networkDynamic’:
  ‘\dots’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map.png’ ‘maze.html’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘network-internal’:
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/neuralGAM.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
Missing or unexported object: ‘Matrix::tcrossprod’
Running examples in ‘newsmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: textmodel_newsmap
> ### Title: Semi-supervised Bayesian multinomial model for geographical
> ###   document classification
> ### Aliases: textmodel_newsmap
> 
> ### ** Examples
> 
> require(quanteda)
Loading required package: quanteda
Package version: 3.3.1
Unicode version: 15.0
ICU version: 72.1
Parallel computing: 3 of 32 threads used.
See https://quanteda.io for tutorials and examples.
> text_en <- c(text1 = "This is an article about Ireland.",
+              text2 = "The South Korean prime minister was re-elected.")
> 
> toks_en <- tokens(text_en)
> label_toks_en <- tokens_lookup(toks_en, data_dictionary_newsmap_en, levels = 3)
> label_dfm_en <- dfm(label_toks_en)
> 
> feat_dfm_en <- dfm(toks_en, tolower = FALSE)
> 
> model_en <- textmodel_newsmap(feat_dfm_en, label_dfm_en)
> predict(model_en)
Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
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
Invalid package aliases in Rd file ‘NH-MSAR-package.Rd’:
  ‘NH-MSAR-package’
Argument items with no description in Rd object ‘ENu_graph’:
  ‘N.s.data’
Argument items with no description in Rd object ‘Estep.MSAR.VM’:
  ‘verbose’
Auto-generated content requiring editing in Rd object ‘NH-MSAR-package’:
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Argument items with no description in Rd object ‘init.theta.MSAR (NH-MSAR)’:
  ‘\dots’
Argument items with no description in Rd object ‘init.theta.MSAR.VM’:
  ‘\dots’
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
Package required but not available: ‘geiger’

Package suggested but not available for checking: ‘phytools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
Objects in \usage without \alias in documentation object ‘getPossibleR’:
  ‘brkCalc’ ‘findPowerR’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘MLInterfaces’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Specified C++11: please drop specification unless essential
Packages which this enhances but not available for checking:
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checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
Documented arguments not in \usage in documentation object ‘nldoc_write_nldoc’:
  ‘number_ections’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) nltm.control.Rd:29: Escaped LaTeX specials: \$
Packages suggested but not available for checking:
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Package suggested but not available for checking: ‘mail’
Documented arguments not in \usage in documentation object ‘ccSpec’:
  ‘a’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘NMOF-internal’:
  ‘mRU’ ‘mRN’ ‘mcList’ ‘repair1c’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘logistf-package.Rd’:
  ‘logistf-package’ ‘{logistf}-package’
'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
Packages required but not available:
  'phangorn', 'DDD', 'geiger', 'babette', 'beastier', 'mauricer'

Packages suggested but not available for checking: 'TreeSim', 'RPANDA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Auto-generated content requiring editing in Rd object ‘noise-package’:
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘get_max_stat’:
  ‘statfunc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘StatQQVPC’:
  ‘mapping’ ‘data’ ‘geom’ ‘position’ ‘na.rm’ ‘show.legend’
  ‘inherit.aes’ ‘...’

Documented arguments not in \usage in documentation object ‘StatQQnorm’:
  ‘mapping’ ‘data’ ‘geom’ ‘position’ ‘na.rm’ ‘show.legend’
  ‘inherit.aes’ ‘...’

Documented arguments not in \usage in documentation object ‘StatQQrefline’:
  ‘mapping’ ‘data’ ‘geom’ ‘position’ ‘na.rm’ ‘show.legend’
  ‘inherit.aes’ ‘...’

Documented arguments not in \usage in documentation object ‘covload.sub.table’:
  ‘nrows’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Auto-generated content requiring editing in Rd object ‘nose-package’:
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Documented arguments not in \usage in documentation object ‘FunctionSanityChecks’:
  ‘structure’

Documented arguments not in \usage in documentation object ‘newLine’:
  ‘current.in’

Documented arguments not in \usage in documentation object ‘nosoiSimConstructor’:
  ‘pres.time’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘read’:
  ‘dots’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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.
Documented arguments not in \usage in documentation object ‘Create_P’:
  ‘y_zx_dependent’

Documented arguments not in \usage in documentation object ‘make_proposer’:
  ‘N’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
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
Package required but not available: ‘scistreer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘numOSL/libs/numOSL.so’:
  Found ‘_gfortran_arandom_r8’, possibly from ‘random_number’ (Fortran)
    Object: ‘diffev.o’
  Found ‘_gfortran_random_r8’, possibly from ‘random_number’ (Fortran)
    Objects: ‘mcCAM.o’, ‘mcFMM2.o’, ‘mcFMM3.o’, ‘mcFMM4.o’, ‘mcMam3.o’,
      ‘mcMam4.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Objects: ‘mcCAM.o’, ‘mcFMM2.o’, ‘mcFMM3.o’, ‘mcFMM4.o’, ‘mcMam3.o’,
      ‘mcMam4.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
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 required but not available: ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in documentation object ‘cust.colorbar’:
  ‘\code{input.mode}’ ‘\code{force.figdim.widget}’ ‘\code{xpos}’
  ‘region’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd object ‘plot.comphat’:
  ‘\dots’
Rd files without \alias:
  ‘odbc-package.Rd’
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
Packages required but not available: 'tigger', 'alakazam'

See section ‘The DESCRIPTION file’ 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
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Packages required but not available:
  'GenomicFeatures', 'TxDb.Hsapiens.UCSC.hg19.knownGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lfe’
Specified C++11: please drop specification unless essential
Rd files without \alias:
  ‘ontologyPlot-package.Rd’
'LazyData' is specified without 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.
'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘openNLPmodels.en’
Documented arguments not in \usage in documentation object ‘clique_color_pals’:
  ‘aplha’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘bertinBase’:
  ‘x’ ‘ratings’ ‘trim’

Documented arguments not in \usage in documentation object ‘biplot3dBase2’:
  ‘ext.sphere’

Documented arguments not in \usage in documentation object ‘convertImportObjectToRepGridObject’:
  ‘x’

Documented arguments not in \usage in documentation object ‘convertScivescoImportObjectToRepGridObject’:
  ‘x’

Documented arguments not in \usage in documentation object ‘mapCoordinatesToColor’:
  ‘color’

Documented arguments not in \usage in documentation object ‘quasiDistributionDistanceSlater’:
  ‘rep’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘assign_binIDs’:
  ‘id:’ ‘binID:’ ‘lastbit:’

Documented arguments not in \usage in documentation object ‘calcCatchmArea_assignNetID’:
  ‘netID’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages required but not available: 'geiger', 'paleotree', 'taxize'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Packages suggested but not available for checking: 'arm', '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
Argument items with no description in Rd object ‘dsevdist’:
  ‘x’ ‘sevdist’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘glmmTMB’
Running examples in ‘ordbetareg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pp_check_ordbeta
> ### Title: Accurate Posterior Predictive Plots for Ordbetareg Models
> ### Aliases: pp_check_ordbeta
> 
> ### ** Examples
> 
> 
> # need a fitted ordbetareg model
> 
> data("ord_fit_mean")
> 
> out_plots <- pp_check_ordbeta(ord_fit_mean)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.matrix': 'tcrossprod' is not an exported object from 'namespace:Matrix'
Error: Something went wrong (see the error message above). Perhaps you transformed numeric variables to factors or vice versa within the model formula? If yes, please convert your variables beforehand. Or did you use a grouping factor also for a different purpose? If yes, please make sure that its factor levels are correct also in the new data you may have provided.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘package_introduction.Rmd’ using rmarkdown

Quitting from lines 197-209 [post_predict] (package_introduction.Rmd)
Error: processing vignette ‘package_introduction.Rmd’ failed with diagnostics:
Something went wrong (see the error message above). Perhaps you transformed numeric variables to factors or vice versa within the model formula? If yes, please convert your variables beforehand. Or did you use a grouping factor also for a different purpose? If yes, please make sure that its factor levels are correct also in the new data you may have provided.
--- failed re-building ‘package_introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'DESeq2', 'SummarizedExperiment'

See section ‘The DESCRIPTION file’ 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:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
Documented arguments not in \usage in documentation object ‘distsuml2’:
  ‘partial’

Documented arguments not in \usage in documentation object ‘distsumlp’:
  ‘partial’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Documented arguments not in \usage in documentation object ‘dosepred’:
  ‘w’

Documented arguments not in \usage in documentation object ‘surv_dm_solver’:
  ‘bw_optim’

Documented arguments not in \usage in documentation object ‘surv_forward_solver’:
  ‘Phit’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Rd files without \alias:
  ‘otp-package.Rd’
'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
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'geiger', 'phytools', 'paleotree', 'phangorn'

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
Invalid package aliases in Rd file ‘packagetracker.Rd’:
  ‘packagetracker-package’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘IPDFileCheck’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Packages required but not available: 'genbankr', 'GenomicAlignments'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Argument items with no description in Rd object ‘joint_estimate’:
  ‘\dots’
Argument items with no description in Rd object ‘only_A_estimate’:
  ‘\dots’
Argument items with no description in Rd object ‘only_F_estimate’:
  ‘\dots’
Argument items with no description in Rd object ‘plot.Full_PAFit_result’:
  ‘\dots’
Argument items with no description in Rd object ‘plot.PAFit_net’:
  ‘\dots’
Argument items with no description in Rd object ‘plot.PAFit_result’:
  ‘\dots’
Argument items with no description in Rd object ‘plot.PA_result’:
  ‘\dots’
Argument items with no description in Rd object ‘print.CV_Result’:
  ‘\dots’
Argument items with no description in Rd object ‘print.CV_Data’:
  ‘\dots’
Argument items with no description in Rd object ‘print.Full_PAFit_result’:
  ‘\dots’
Argument items with no description in Rd object ‘print.PAFit_data’:
  ‘\dots’
Argument items with no description in Rd object ‘print.PAFit_net’:
  ‘\dots’
Argument items with no description in Rd object ‘print.PAFit_result’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.CV_Data’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.CV_Result’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.Full_PAFit_result’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.PAFit_data’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.PAFit_net’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.PAFit_result’:
  ‘\dots’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘phangorn’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'paleotree', 'phytools'
Running examples in ‘palaeoverse-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: phylo_check
> ### Title: Check phylogeny tip names
> ### Aliases: phylo_check
> 
> ### ** Examples
> 
> # track user par
> oldpar <- par(no.readonly = TRUE)
> #Read in example tree of ceratopsians from paleotree
> library(paleotree)
Error in library(paleotree) : there is no package called ‘paleotree’
Execution halted
Package which this enhances but not available for checking: ‘CorShrink’
Documented arguments not in \usage in documentation object ‘other’:
  ‘trial’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'phangorn', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in documentation object ‘dplyr_verbs’:
  ‘funs’ ‘.dots’ ‘keep_attributes’

Documented arguments not in \usage in documentation object ‘nest_tdc’:
  ‘vars’ ‘id’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘pamr-internal’:
  ‘print.nsc’ ‘print.nsccv’

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.
'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: \_
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PanelMatch.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MBESS’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘getOption2’:
  ‘envvar’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'EGAnet', 'glmmTMB', 'lfe', 'sparsepca'
'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
Documented arguments not in \usage in documentation object ‘expect_missing_argument’:
  ‘message’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Documented arguments not in \usage in documentation object ‘as_partition’:
  ‘.partition_step’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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’
Documented arguments not in \usage in documentation object ‘fixvar_of_red_mod’:
  ‘data’

Documented arguments not in \usage in documentation object ‘get_ndf’:
  ‘data’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘vec_cast.partial_time’:
  ‘vec_cast.partial_time’

S3 methods shown with full name in documentation object ‘vec_cast.timespan’:
  ‘vec_cast.timespan’

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
Documented arguments not in \usage in documentation object ‘help_console’:
  ‘which’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \# \# \#
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘anomalize’
Package required but not available: ‘Morpho’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Argument items with no description in Rd object ‘markbouts.acclist’:
  ‘extreme’
S3 methods shown with full name in documentation object ‘ped’:
  ‘ped.markerNames’

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.
Packages required but not available: 'DDD', 'phytools'

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
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
'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.
Objects in \usage without \alias in documentation object ‘internals’:
  ‘CumSum’ ‘myapply’ ‘makebreaks.ct’ ‘makebreaks.ic’ ‘pois.loglik’
  ‘icpch.loglik’ ‘convert.Surv’ ‘break.y’ ‘pois.fit’ ‘pch.fit.ct’
  ‘pch.fit.ic’ ‘newton’ ‘cleanlambda’ ‘predF.pch’ ‘predQ.pch’ ‘sim.pch’
  ‘build.splinex’ ‘predict.splinex’ ‘logLik.pch’ ‘nobs.pch’ ‘vcov.pch’
  ‘coef.pch’ ‘print.pch’ ‘summary.pch’ ‘print.summary.pch’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘phangorn’

Package suggested but not available for checking: ‘geiger’

See section ‘The DESCRIPTION file’ 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
Documented arguments not in \usage in documentation object ‘getResponse’:
  ‘model’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘ODACATH.estimate’:
  ‘ODACAT.estimate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pdynmc.Rcheck/00install.out’ for details.
Package required but not available: ‘stevemisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘PoissonLoss’:
  ‘count’ ‘seg.mean’ ‘weight’
Argument items with no description in Rd object ‘getPath’:
  ‘A’
Argument items with no description in Rd object ‘PoissonLoss’:
  ‘count’ ‘seg.mean’ ‘weight’
Argument items with no description in Rd object ‘featureMatrixJoint’:
  ‘profile.list’
Specified C++11: please drop specification unless essential
Argument items with no description in Rd object ‘PoissonLoss’:
  ‘count’ ‘seg.mean’ ‘weight’
Argument items with no description in Rd object ‘oracleModelComplexity’:
  ‘bases’ ‘segments’
S3 methods shown with full name in documentation object ‘format.relation’:
  ‘format.relation’

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.
Missing or unexported object: ‘Matrix::crossprod’
Running examples in ‘pedigreeTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getA
> ### Title: Additive relationship matrix
> ### Aliases: getA
> 
> ### ** Examples
> 
> ped <- pedigree(sire = c(NA, NA, 1,  1, 4, 5),
+                 dam =  c(NA, NA, 2, NA, 3, 2),
+                 label = 1:6)
> (A <- getA(ped))
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Package suggested but not available for checking: ‘georob’
Invalid package aliases in Rd file ‘pedSimulte-package.Rd’:
  ‘pedSimulte-package’
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) breslow.Rd:27: Escaped LaTeX specials: \# \#
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PenCoxFrail.Rcheck/00install.out’ for details.
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro-to-penppml.Rmd’ using rmarkdown

Quitting from lines 140-155 [plot regularization path] (intro-to-penppml.Rmd)
Error: processing vignette ‘intro-to-penppml.Rmd’ failed with diagnostics:
object ‘last.bumpup’ not found
--- failed re-building ‘intro-to-penppml.Rmd’

SUMMARY: processing the following file failed:
  ‘intro-to-penppml.Rmd’

Error: Vignette re-building failed.
Execution halted
Argument items with no description in Rd object ‘lmres’:
  ‘\dots’
Argument items with no description in Rd object ‘simpleSlope’:
  ‘\dots’
Argument items with no description in Rd object ‘summary.lmres’:
  ‘\dots’
Package required but not available: ‘phytools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Documented arguments not in \usage in documentation object ‘getNode’:
  ‘hc’ ‘pair’

Documented arguments not in \usage in documentation object ‘switchEntries’:
  ‘pair’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘glmmTMB’
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘perspective-package.Rd’:
  ‘perspective-package’
'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
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'LazyData' is specified without a 'data' directory
Package required but not available: ‘phytools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Invalid package aliases in Rd file ‘00_PH1XBAR-package.Rd’:
  ‘00_PH1XBAR-package’
'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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.pdf’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘process_season’:
  ‘d’ ‘options_season’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
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Auto-generated content requiring editing in Rd object ‘phm-package’:
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  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
Documented arguments not in \usage in documentation object ‘adaptive_smoothing’:
  ‘smooth.limt’ ‘smooth.thershold’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) phylo4d-methods.Rd:209: Escaped LaTeX specials: \$
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Packages suggested but not available for checking: 'phytools', 'TreeSim'
Missing or unexported object: ‘Matrix::tcrossprod’
Note: skipping ‘tutorial.Rmd’ due to unavailable dependencies: 'TreeSim'
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Package required but not available: ‘phangorn’

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

Packages suggested but not available for checking:
  'semPlot', 'phytools', 'Rphylopars'

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

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

Package suggested but not available for checking: ‘geiger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
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Packages required but not available: 'alakazam', 'tigger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Invalid package aliases in Rd file ‘pipegs.Rd’:
  ‘pipegs-package’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in documentation object ‘TungUbRF’:
  ‘feature_num_tree’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages required but not available:
  'babette', 'beastier', 'DDD', 'mauricer', 'mcbette', 'nodeSub',
  'phangorn', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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: \$
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Documented arguments not in \usage in documentation object ‘make_pgk_cache_subdir_for_all_relative_files’:
  ‘relative_filenames’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in documentation object ‘imports_env’:
  ‘path’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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: ‘PLMIX’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PlackettLuce.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RStoolbox’
'LazyData' is specified without a 'data' directory
Missing or unexported object: ‘Matrix::tcrossprod’
Running examples in ‘plantTracker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aggregateByGenet
> ### Title: aggregateByGenet
> ### Aliases: aggregateByGenet
> 
> ### ** Examples
> 
> dat <- grasslandData[grasslandData$Site == c("AZ") &
+  grasslandData$Species %in% c("Bouteloua rothrockii", "Calliandra eriophylla" ),]
> names(dat)[1] <- "speciesName"
> inv <- grasslandInventory[unique(dat$Quad)]
> outDat <- trackSpp(dat = dat,
+  inv = inv,
+  dorm = 1,
+  buff = .05,
+  buffGenet = 0.005,
+  clonal = data.frame("Species" = unique(dat$speciesName),
+  "clonal" = c(TRUE,FALSE)),
+  species = "speciesName",
+  aggByGenet = FALSE
+  )
Site: AZ

-- Quadrat: SG2

Error: 'tcrossprod' is not an exported object from 'namespace:Matrix'
Execution halted
Packages required but not available:
  'VariantAnnotation', 'rtracklayer', 'SummarizedExperiment'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'VariantAnnotation', 'rtracklayer', 'SummarizedExperiment'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
'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
Running examples in ‘pliman-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: efourier
> ### Title: Elliptical Fourier Analysis
> ### Aliases: efourier
> 
> ### ** Examples
> 
> library(pliman)
> leaf1 <- contours[[4]]
> plot_polygon(leaf1)
> 
> #### default options
> # 10 harmonics (default)
> # without alignment
> 
> ef <- efourier(leaf1)
> efourier_coefs(ef)
           an           bn          cn           dn
1  21.1298663 -382.7540180 -364.126202 -21.29189747
2   1.6804167  151.6255507  -40.467153  10.80476561
3   4.3779839   -0.9870311 -129.212508   3.20445130
4  -3.1329537  -46.3028113  -26.380285  -4.12257511
5  -1.6548827    3.6997248   19.343685  -3.32106033
6   4.9296483   39.2656639  -15.461424   0.48631684
7   1.2043295    0.5415148  -15.556049   0.96104147
8   0.5959547  -13.0422412  -18.885184   1.42268431
9  -0.8187422    3.9795071   -4.368973   0.04457129
10 -0.3849895   -5.7461417   -2.553430  -1.11528942
> 
> # object is aligned along the major caliper with `poly_align()`
> # object is centered on the origin with `poly_center()`
> # using a list of object coordinates
> ef2 <- efourier(contours, align = TRUE, center = TRUE)
Error in eval(substitute(list(...)), `_data`, parent.frame()) : 
  object 'X1' not found
Calls: efourier ... transform.default -> transform.data.frame -> eval -> eval
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘PlackettLuce’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lfe’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘arm’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘plsgenomics-deprecated.Rd’:
  ‘plsgenomics-deprecated-package’
Invalid package aliases in Rd file ‘plsgenomics-internal.Rd’:
  ‘plsgenomics-internal-package’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘eval.quoted’:
  ‘expr’

Documented arguments not in \usage in documentation object ‘indexed_df’:
  ‘env’

Documented arguments not in \usage in documentation object ‘list_to_dataframe’:
  ‘idname’

Documented arguments not in \usage in documentation object ‘split_indices’:
  ‘index’

Documented arguments not in \usage in documentation object ‘split_labels’:
  ‘list’ ‘whether’

Documented arguments not in \usage in documentation object ‘tryapply’:
  ‘f’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages required but not available: 'geiger', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MSnbase’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘sample_store’:
  ‘subjects_ids’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Objects in \usage without \alias in documentation object ‘PMwR-internal’:
  ‘.timestamp<-’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘pollimetrydata’
Running examples in ‘pollimetry-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bodysize
> ### Title: Converts the intertegular distance (IT) and co-variates to body
> ###   size in dry weight (mg) for bees or hoverflies.
> ### Aliases: bodysize
> 
> ### ** Examples
> 
> example=cbind.data.frame(IT=c(1.3,2.3),
+                          Sex=c("Female","Male"), 
+                          Subfamily=c("Syrphinae","Eristalinae"),
+                          Region=c("Australasia","Europe"),
+                          Species=c("Sphaerophoria_macrogaster","Myathropa_florea"))
> bodysize(x=example,taxa="hov",type="taxo")
Loading required namespace: pollimetrydata
Failed with error:  ‘there is no package called ‘pollimetrydata’’
Downloading data from: https://github.com/liamkendall/pollimetrydata/raw/master/data/hov_tax_mod.rdata 

SHA-1 hash of the downloaded data file is:
8fabe989dfed6c91d8e5834ad224ff4865b76b7f
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.matrix': 'tcrossprod' is not an exported object from 'namespace:Matrix'
Error: Something went wrong (see the error message above). Perhaps you transformed numeric variables to factors or vice versa within the model formula? If yes, please convert your variables beforehand. Or did you use a grouping factor also for a different purpose? If yes, please make sure that its factor levels are correct also in the new data you may have provided.
Execution halted
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gpclib’
Unknown package ‘gpclib’ in Rd xrefs
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:
  'VariantAnnotation', 'SummarizedExperiment', 'GenomicFeatures'
Packages unavailable to check Rd xrefs: ‘BSgenome’, ‘GenomicFeatures’, ‘VariantAnnotation’
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pomdp.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘pomdp’
Package required but not available: ‘phangorn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
Documented arguments not in \usage in documentation object ‘initialize,genclone-method’:
  ‘gen’ ‘loc’ ‘treatOther’ ‘quiet’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘popsom/libs/popsom.so’:
  Found ‘_gfortran_random_r4’, possibly from ‘random_number’ (Fortran)
    Object: ‘vsom.o’
  Found ‘_gfortran_random_seed_i4’, possibly from ‘random_seed’
    (Fortran)
    Object: ‘vsom.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.
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
Package required but not available: ‘refund’

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
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
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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
Objects in \usage without \alias in documentation object ‘ppmlasso-internal’:
  ‘spatRes’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
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
Packages required but not available: 'Seurat', 'scater', 'DR.SC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in documentation object ‘local_test_setup’:
  ‘use_precommmit’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package required but not available: ‘MBESS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘ffbase’
Unknown package ‘ffbase’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Missing or unexported object: ‘Matrix::tcrossprod’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
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: 'gurobi', 'rcbc'
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Missing or unexported objects:
  ‘Matrix::crossprod’ ‘Matrix::tcrossprod’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'DR.SC', 'PRECAST', 'Seurat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘validate_inputs’:
  ‘required_vars’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cin’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘bitAND’:
  ‘a’ ‘b’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘proDA’
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’
Documented arguments not in \usage in documentation object ‘.marxan_data_reader’:
  ‘parameter’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Package required but not available: ‘Morpho’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid package aliases in Rd file ‘granova-package.Rd’:
  ‘granova-package’
Documented arguments not in \usage in documentation object ‘estimateDeltaLOH.PairedPSCBS’:
  ‘scale’

Documented arguments not in \usage in documentation object ‘getLocusData.AbstractCBS’:
  ‘splitters’

Documented arguments not in \usage in documentation object ‘getSegments.AbstractCBS’:
  ‘simplify’ ‘splitters’

Documented arguments not in \usage in documentation object ‘mergeTwoSegments.AbstractCBS’:
  ‘left’ ‘update’ ‘verbose’

Documented arguments not in \usage in documentation object ‘plotTracks.PairedPSCBS’:
  ‘x’ ‘tracks’ ‘scatter’ ‘calls’ ‘pch’ ‘col’ ‘cex’ ‘changepoints’
  ‘grid’ ‘quantiles’ ‘xlim’ ‘Clim’ ‘Blim’ ‘xScale’ ‘add’ ‘subplots’
  ‘verbose’

Documented arguments not in \usage in documentation object ‘updateMeansTogether.AbstractCBS’:
  ‘idxList’ ‘verbose’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘kepner_robinson_test_internal’:
  ‘group’ ‘alternative’ ‘trend’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pspatreg.Rcheck/00install.out’ for details.
Documented arguments not in \usage in documentation object ‘pspline.sample.scalars’:
  ‘time’

Documented arguments not in \usage in documentation object ‘pspline.sample.timeseries’:
  ‘time’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'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
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘semPlot’
Invalid package aliases in Rd file ‘00.psych-package.Rd’:
  ‘00.psych-package’
Package suggested but not available for checking: ‘semPlot’
Documented arguments not in \usage in documentation object ‘GetFitHReg’:
  ‘z’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid package aliases in Rd file ‘package-ptf.Rd’:
  ‘package-ptf-package’
Documented arguments not in \usage in documentation object ‘assert_correct_attributes’:
  ‘expected_colnames’

Documented arguments not in \usage in documentation object ‘geopath_to_tibble’:
  ‘route’

Documented arguments not in \usage in documentation object ‘run_to_tibble’:
  ‘route’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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: ‘bibliometrix’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'SummarizedExperiment', 'GenomicFeatures', 'GenomicAlignments'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file ‘PVAClone-package.Rd’:
  ‘PVA-package’ ‘pva-package’ ‘Pva-package’
Package required but not available: ‘bibliometrix’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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: \&
Documented arguments not in \usage in documentation object ‘http_was_redirected’:
  ‘response’

Documented arguments not in \usage in documentation object ‘permutations’:
  ‘nset’

Documented arguments not in \usage in documentation object ‘pxweb_split_query’:
  ‘pxweb_metadata’

Documented arguments not in \usage in documentation object ‘split_dimensions_left_right’:
  ‘pxq’

Documented arguments not in \usage in documentation object ‘str_pad’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ 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
Documented arguments not in \usage in documentation object ‘lagm’:
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘get_names_MV’:
  ‘path_matrix’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in documentation object ‘internals’:
  ‘expit’ ‘logit’ ‘pmax0’ ‘num.fun’ ‘format.perc’ ‘Ltau’ ‘minabs’
  ‘invJ’ ‘tensorX’ ‘buildTau’ ‘callwtau’ ‘callQ’ ‘start.Qest’
  ‘start.Qest.family’ ‘rq.fit.br2’ ‘Qest.sgs.internal’
  ‘Qest.gs.internal’ ‘Qest.gs’ ‘Qest.newton’ ‘Qlm.bfun’ ‘start.Qlm’
  ‘scalevars.Qlm’ ‘descalecoef.Qlm’ ‘Qlm.sgs.internal’
  ‘Qlm.gs.internal’ ‘Qlm.gs’ ‘Qlm.newton’ ‘plfcox’ ‘scalevars.Qcoxph’
  ‘descalecoef.Qcoxph’ ‘check.singularities’ ‘starting.points.Qcox’
  ‘adjust.coef’ ‘agsurv.Qcoxph’ ‘coxsurv.fit.Qcoxph’ ‘seg.lm.fit1’ ‘gs’
  ‘myg’ ‘dlist’ ‘omega’ ‘choose_eps’ ‘derQtheta’ ‘der2Qtheta’ ‘intA’
  ‘findp’ ‘findAp’ ‘A_beta_fun’ ‘A_gamma_fun’ ‘A_beta_beta_fun’
  ‘A_gamma_gamma_mix_fun’ ‘A_gamma_gamma_fun’ ‘A_beta_gamma_fun’
  ‘coxBB’ ‘derQtheta.gamma’ ‘der2Qtheta.gamma’ ‘findAp.gamma’
  ‘QestGamma.ee.u’ ‘QestGamma.ee.c’ ‘QestGamma.ee.ct’ ‘tau.pois’
  ‘ppoisC’ ‘dpoisC’ ‘qpoisC.955’ ‘qpoisC.me’ ‘qpoisC.bisec’ ‘qpoisC’
  ‘derQtheta.pois’ ‘der2Qtheta.pois’ ‘findp.pois’ ‘findAp.pois’
  ‘QestPois.ee.u’ ‘QestUnif.ee.u’ ‘QestNorm.ee.u’ ‘QestNorm.ee.c’
  ‘QestNorm.ee.ct’ ‘Qest.ee.u’ ‘Qest.ee.c’ ‘Qest.ee.ct’ ‘QCox.ee.c’
  ‘QCox.ee.ct’ ‘Qlm.ee.u’ ‘Qest.covar’ ‘Qcox.covar’ ‘Qlm.covar’ ‘Loss’
  ‘coxLoss’ ‘qlmLoss’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘internals’:
  ‘format.perc’

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.
'LazyData' is specified without 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 required but not available: 'qgcomp', 'arm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spDataLarge’
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd object ‘ad.simudata’:
  ‘SimuNum’
'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
Package suggested but not available for checking: ‘glmmTMB’
Objects in \usage without \alias in documentation object ‘internals’:
  ‘Q’ ‘funQ1’ ‘check.fun’ ‘boot’ ‘predBeta’ ‘grad3’ ‘grad2’ ‘num.int’
  ‘integr’ ‘bisec’ ‘Bfun’ ‘bfun’ ‘funGrad’ ‘Fun’ ‘armijo’ ‘check.in.2’
  ‘check.out.2’ ‘piqr.newton’ ‘piqr.ee’ ‘pciqr.ee’ ‘pctiqr.ee’
  ‘plotCoef’ ‘nonzeroCoef’ ‘cov.theta.2’ ‘plot.piqr2’
  ‘divide.et.impera.2’ ‘print.niqr’ ‘print.summary.niqr’ ‘print.piqr’
  ‘print.summary.piqr’ ‘terms.piqr’ ‘coef.piqr’ ‘model.matrix.piqr’
  ‘nobs.piqr’
Assignments in \usage in documentation object ‘internals’:
  start.theta.niqr <- function(fun, x0, X, y, control = list()) piqr.internal(mf, 
      cl, formula.p, tol = 1e-06, maxit = 100, s, segno = 1, lambda = 0, 
      check = FALSE, A, st.theta = FALSE, theta0)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘internals’:
  ‘plot.piqr2’

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.
Objects in \usage without \alias in documentation object ‘internals’:
  ‘check.in.iqr’ ‘check.in0.iqrL’ ‘check.in.iqrL’ ‘check.out’
  ‘start.iqr’ ‘start.iqrL’ ‘ctiqr.internal’ ‘iqrL.internal’ ‘iqrL.fit’
  ‘iqr.ee’ ‘ciqr.ee’ ‘ctiqr.ee’ ‘iobjfun’ ‘iobjfun.ct’ ‘cov.fun.iqr’
  ‘iqrL.ee’ ‘cov.fun.iqrL’ ‘iqr.newton’ ‘divide.et.impera’
  ‘iqrL.newton’ ‘pmax0’ ‘maxind’ ‘num.fun’ ‘make.bfun’ ‘apply_bfun’
  ‘p.bisec’ ‘p.bisec.internal’ ‘slp.basis’ ‘is.slp’ ‘safesolve’
  ‘iqr.waldtest’ ‘extract.p’ ‘pred.beta’ ‘km’ ‘alpha’ ‘test.unif.ct’
  ‘findagoodestimator’ ‘quickpred’ ‘trans’ ‘alpha.bisec’
  ‘alpha.bisec.out’ ‘ks’ ‘print.iqr’ ‘print.summary.iqr’ ‘terms.iqr’
  ‘model.matrix.iqr’ ‘vcov.iqr’ ‘nobs.iqr’ ‘predict.iqrL.internal’
  ‘print.iqrL’ ‘print.summary.iqrL’ ‘terms.iqrL’ ‘model.matrix.iqrL’
  ‘vcov.iqrL’ ‘nobs.iqrL’ ‘qc.penalty’ ‘fixqc’ ‘print.qc.iqr’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object ‘internals’:
  ‘predict.iqrL.internal’

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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) NEWS.Rd:15: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sem’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in documentation object ‘mmer_adapted’:
  ‘void’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in documentation object ‘export_responses_filedownload’:
  ‘requestID’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Missing or unexported object: ‘Matrix::crossprod’
Documented arguments not in \usage in documentation object ‘convert-wrappers’:
  ‘...’

Documented arguments not in \usage in documentation object ‘corpus-class’:
  ‘if’

Documented arguments not in \usage in documentation object ‘dfm-class’:
  ‘drop_docid’

Documented arguments not in \usage in documentation object ‘dictionary2-class’:
  ‘object’

Documented arguments not in \usage in documentation object ‘matrix2fcm’:
  ‘slots’

Documented arguments not in \usage in documentation object ‘meta_system’:
  ‘source’

Documented arguments not in \usage in documentation object ‘search_index’:
  ‘regex’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘quanteda-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dfm_compress
> ### Title: Recombine a dfm or fcm by combining identical dimension elements
> ### Aliases: dfm_compress fcm_compress
> 
> ### ** Examples
> 
> # dfm_compress examples
> dfmat <- rbind(dfm(tokens(c("b A A", "C C a b B")), tolower = FALSE),
+                dfm(tokens("A C C C C C"), tolower = FALSE))
> colnames(dfmat) <- char_tolower(featnames(dfmat))
> dfmat
Document-feature matrix of: 3 documents, 5 features (46.67% sparse) and 0 docvars.
         features
docs      b a c a b
  text1.1 1 2 0 0 0
  text2.1 1 0 2 1 1
  text1.2 0 1 5 0 0
> dfm_compress(dfmat, margin = "documents")
Document-feature matrix of: 2 documents, 5 features (30.00% sparse) and 0 docvars.
       features
docs    b a c a b
  text1 1 3 5 0 0
  text2 1 0 2 1 1
> dfm_compress(dfmat, margin = "features")
Document-feature matrix of: 3 documents, 3 features (22.22% sparse) and 0 docvars.
         features
docs      b a c
  text1.1 1 2 0
  text2.1 2 1 2
  text1.2 0 1 5
> dfm_compress(dfmat)
Document-feature matrix of: 2 documents, 3 features (0.00% sparse) and 0 docvars.
       features
docs    b a c
  text1 1 3 5
  text2 2 1 2
> 
> # no effect if no compression needed
> dfmatsubset <- dfm(tokens(data_corpus_inaugural[1:5]))
> dim(dfmatsubset)
[1]    5 1948
> dim(dfm_compress(dfmatsubset))
[1]    5 1948
> 
> # compress an fcm
> fcmat1 <- fcm(tokens("A D a C E a d F e B A C E D"),
+              context = "window", window = 3)
> ## this will produce an error:
> # fcm_compress(fcmat1)
> 
> txt <- c("The fox JUMPED over the dog.",
+          "The dog jumped over the fox.")
> toks <- tokens(txt, remove_punct = TRUE)
> fcmat2 <- fcm(toks, context = "document")
Error: 'crossprod' is not an exported object from 'namespace:Matrix'
Execution halted