'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 Rd file 'ADMM_EN2.Rd':
  ‘alpha’

Documented arguments not in \usage in Rd file 'ADMM_EN_SMW.Rd':
  ‘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 file 'testRmACD.Rd':
  ‘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 Rd file 'fitSnpNmfArray.Rd':
  ‘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.
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'd1.Rd':
  ‘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
'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 file 'asggm-internal.Rd':
  ‘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 Rd file 'print.aTest.Rd':
  ‘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 Rd file 'ae_count.Rd':
  ‘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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘rgdal’
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
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'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
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
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
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'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'gs.Rd':
  ‘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 file 'MLS.Rd':
  ‘MSE1’
'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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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 Rd file 'check_factors.Rd':
  ‘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 file 'rowVars.Rd':
  \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: \~
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'ggplot_gtable.Rd':
  ‘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 Rd file 'crawl_interpolation.Rd':
  ‘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
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'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 Rd file 'alternate.sol3.Rd':
  ‘lambda0’

Documented arguments not in \usage in Rd file 'check.group.Rd':
  ‘k’

Documented arguments not in \usage in Rd file 'getrow3.Rd':
  ‘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.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'apci.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.bar.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.plot.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.plot.heatmap.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.plot.hexagram.Rd':
  ‘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 file 'apci.plot.raw.Rd':
  ‘\dots’
Argument items with no description in Rd file 'cohortdeviation.Rd':
  ‘\dots’
Argument items with no description in Rd file 'compute_xcoordinate.Rd':
  ‘p’
Argument items with no description in Rd file 'compute_ycoordinate.Rd':
  ‘p’ ‘a’
Argument items with no description in Rd file 'maineffect.Rd':
  ‘\dots’
Argument items with no description in Rd file 'temp_model.Rd':
  ‘\dots’
Argument items with no description in Rd file 'tests.Rd':
  ‘\dots’
Documented arguments not in \usage in Rd file 'apercu.Rd':
  ‘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
Package required but not available: ‘bgw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following 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’
'LazyData' is specified without a 'data' directory
'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 file 'dynamac_pkg_bounds_test.Rd':
  ‘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
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Documented arguments not in \usage in Rd file 'allocateFromCdf.AromaUnitTabularBinaryFile.Rd':
  ‘path’ ‘tags’ ‘footer’

Documented arguments not in \usage in Rd file 'byChipType.DChipSnpInformation.Rd':
  ‘rootPath’ ‘pattern’ ‘verbose’

Documented arguments not in \usage in Rd file 'byChipType.UgpGenomeInformation.Rd':
  ‘version’

Documented arguments not in \usage in Rd file 'calculateResidualSet.FirmaModel.Rd':
  ‘verbose’

Documented arguments not in \usage in Rd file 'findByChipType.AromaChipTypeAnnotationFile.Rd':
  ‘chipType’ ‘tags’

Documented arguments not in \usage in Rd file 'fit.SmoothMultiarrayModel.Rd':
  ‘data’

Documented arguments not in \usage in Rd file 'getCellIndices.ExonChipEffectFile.Rd':
  ‘units’

Documented arguments not in \usage in Rd file 'getImage.AffymetrixCelFile.Rd':
  ‘palette’

Documented arguments not in \usage in Rd file 'getOutputDataSet.Transform.Rd':
  ‘force’

Documented arguments not in \usage in Rd file 'getUnitTypes.AffymetrixCdfFile.Rd':
  ‘map’

Documented arguments not in \usage in Rd file 'plotMvsX.AffymetrixCelFile.Rd':
  ‘xlim’ ‘xlab’

Documented arguments not in \usage in Rd file 'process.BackgroundCorrection.Rd':
  ‘force’ ‘verbose’

Documented arguments not in \usage in Rd file 'readUnits.CnagCfhFile.Rd':
  ‘cdf’

Documented arguments not in \usage in Rd file 'setArrays.ArrayExplorer.Rd':
  ‘arrays’

Documented arguments not in \usage in Rd file 'setRestructor.AffymetrixCdfFile.Rd':
  ‘units’

Documented arguments not in \usage in Rd file 'setupExampleData.Rd':
  ‘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 Rd file 'fitOne.MultiSourceCopyNumberNormalization.Rd':
  ‘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 Rd file 'fit.CopyNumberSegmentationModel.Rd':
  ‘chromosome’

Documented arguments not in \usage in Rd file 'getPath.Explorer.Rd':
  ‘create’

Documented arguments not in \usage in Rd file 'process.AromaTransform.Rd':
  ‘force’ ‘verbose’

Documented arguments not in \usage in Rd file 'process.ChromosomeExplorer.Rd':
  ‘chromosome’

Documented arguments not in \usage in Rd file 'process.Explorer.Rd':
  ‘arrays’ ‘verbose’

Documented arguments not in \usage in Rd file 'setArrays.Explorer.Rd':
  ‘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 Rd file 'RweaveAsciiSetup.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweaveOrg.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweavePandoc.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweaveReST.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweaveT2t.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweaveTextile.Rd':
  ‘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
Package which this enhances but not available for checking: ‘asreml’
Documented arguments not in \usage in Rd file 'check.args_.Rd':
  ‘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
Unknown packages ‘assertive.properties’, ‘assertive.types’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘asteRiskData’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Running examples in ‘astrochron-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: asm
> ### Title: Average Spectral Misfit
> ### Aliases: asm
> 
> ### ** Examples
> 
> ## These frequencies are from modelA (type '?astrochron' for more information). 
> ## They are for an 8 meter window, centered at 22 meters height. Units are cycles/m . 
> freq <- c(0.1599833,0.5332776,1.5998329,2.6797201,3.2796575,3.8795948,5.5194235,6.5459830)
> freq <- data.frame(freq)
> 
> ## Rayleigh frequency in cycles/m
> rayleigh <- 0.1245274
> 
> ## Nyquist frequency in cycles/m
> nyquist <- 6.66597
> 
> ## orbital target in 1/ky. Predicted periods for 94 Ma (see Meyers et al., 2012)
> target <- c(1/405.47,1/126.98,1/96.91,1/37.66,1/22.42,1/18.33)
> 
> ## percent uncertainty in orbital target
> fper=c(0.023,0.046,0.042,0.008,0.035,0.004)
> 
> asm(freq=freq,target=target,fper=fper,rayleigh=rayleigh,nyquist=nyquist,sedmin=0.5,sedmax=3,
+     numsed=100,linLog=1,iter=100000,output=FALSE)

----- PERFORMING AVERAGE SPECTRAL MISFIT ANALYSIS -----

 *** caught segfault ***
address 0x7ffe382f2a00, cause 'memory not mapped'

Traceback:
 1: asm1.8(freq[, 1], numfreq, target[, 1], numtarg, fper[, 1], rayleigh,     nyquist, sedmin, sedmax, numsed, linLog, ispecgen, irepl,     isetfreq, iter)
 2: asm(freq = freq, target = target, fper = fper, rayleigh = rayleigh,     nyquist = nyquist, sedmin = 0.5, sedmax = 3, numsed = 100,     linLog = 1, iter = 1e+05, output = FALSE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
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 3.7 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
'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 Rd file 'write.narrative.Rd':
  ‘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
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Auto-generated content requiring editing in Rd file 'BartMixVs-package.Rd':
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
Running ‘testthat.R’ [4s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(baseballDBR)
  > 
  > test_check("baseballDBR")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-check_urls.R:21:1'): (code run outside of `test_that()`) ─────
  urlExists("https://raw.githubusercontent.com/chadwickbureau/baseballdatabank/master/core/AllstarFull.csv") is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘rgdal’
'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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BayesFM.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘INLA’
Documented arguments not in \usage in Rd file 'Q_prime.Rd':
  ‘spdean’

Documented arguments not in \usage in Rd file 'neg_kappa_fn4.Rd':
  ‘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.
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
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 file 'hmmeantemp.Rd':
  ‘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 Rd file 'contour_ggplot_params.Rd':
  ‘pos_legend’

Documented arguments not in \usage in Rd file 'geom_quad_txt.Rd':
  ‘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 Rd file 'export.bce.Rd':
  ‘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
Found the following files/directories:
  ‘dump.txt’
Argument items with no description in Rd file 'bdw.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plot.bdw.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.bdw.Rd':
  ‘\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’
'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
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'print_summary_gibbs_psd_help.Rd':
  ‘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.
Package suggested but not available for checking: ‘SoDA’
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in Rd file 'getFpTransforms.Rd':
  ‘%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
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bgw.Rcheck/00install.out’ for details.
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 file 'h.pr.u.Rd':
  ‘z’ ‘ih’ ‘mu’ ‘sigma’ ‘pk’ ‘K’ ‘H’ ‘n’
Argument items with no description in Rd file 'hatpai.u.Rd':
  ‘z’ ‘hk1’ ‘hk0’ ‘ph1’ ‘ph0’ ‘sigma1’ ‘sigma0’ ‘mu1’ ‘mu0’ ‘pai’ ‘H’
  ‘n’
Argument items with no description in Rd file 'ind.u.Rd':
  ‘pr’
Argument items with no description in Rd file 'lambda.u.Rd':
  ‘nu’
Argument items with no description in Rd file 'mu.k.u.Rd':
  ‘k’ ‘ik’ ‘z’ ‘sigma’ ‘mu0’
Argument items with no description in Rd file 'nu.u.Rd':
  ‘ind’ ‘tau’ ‘H’
Argument items with no description in Rd file 'pai.u.Rd':
  ‘b’ ‘a.pai’ ‘b.pai’
Argument items with no description in Rd file 'sig.k.u.Rd':
  ‘k’ ‘ik’ ‘z’ ‘mu0’ ‘a0’ ‘b0’
Argument items with no description in Rd file 'z.pr.u.Rd':
  ‘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
Running examples in ‘bigalgebra-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dscal
> ### Title: Scales a vector by a constant.
> ### Aliases: dscal
> 
> ### ** Examples
> 
> set.seed(4669)
> A = big.matrix(3, 2, type="double", init=1, dimnames=list(NULL, 
+ c("alpha", "beta")), shared=FALSE)
> dscal(ALPHA=2,Y=A)
Error in .Call(`_dscal_wrapper`, N, as.double(ALPHA), Y, as.double(INCY),  : 
  WEIRD RETURN VALUE: 0x8
Calls: dscal
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’.
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
'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 Rd file 'select.cfs.Rd':
  ‘select.cfs’

S3 methods shown with full name in Rd file 'select.fast.filter.Rd':
  ‘select.fast.filter’

S3 methods shown with full name in Rd file 'select.forward.Corr.Rd':
  ‘select.forward.Corr’

S3 methods shown with full name in Rd file 'select.forward.wrapper.Rd':
  ‘select.forward.wrapper’

S3 methods shown with full name in Rd file 'select.inf.chi2.Rd':
  ‘select.inf.chi2’

S3 methods shown with full name in Rd file 'select.inf.gain.Rd':
  ‘select.inf.gain’

S3 methods shown with full name in Rd file 'select.inf.symm.Rd':
  ‘select.inf.symm’

S3 methods shown with full name in Rd file 'select.process.Rd':
  ‘select.process’

S3 methods shown with full name in Rd file 'select.relief.Rd':
  ‘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.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
Documented arguments not in \usage in Rd file 'predict2.em.Rd':
  ‘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.
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: \&
'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 file 'ONA_compiled.Rd':
  ‘ATN’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'export.dyadic.Rd':
  ‘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
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'id2rownum.Rd':
  ‘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.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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 Rd file 'check_inputs.Rd':
  ‘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 Rd file 'InternalFunctions.Rd':
  ‘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 Rd file 'info.Rd':
  ‘mod_spec’ ‘pkg_spec’

Documented arguments not in \usage in Rd file 'path.Rd':
  ‘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.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'b_samp.Rd':
  ‘Y’

Documented arguments not in \usage in Rd file 'betaBlock.Rd':
  ‘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 Rd file 'utils.Rd':
  ‘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 Rd file 'availability.int.Rd':
  ‘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 Rd file 'subset.int.Rd':
  ‘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
Package suggested but not available for checking: ‘cmdstanr’
Package suggested but not available for checking: ‘ggstats’
Package suggested but not available for checking: ‘glmmADMB’
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 Rd file 'table.Rd':
  ‘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 file 'plot.bshazard.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.bshazard.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.bshazard.Rd':
  ‘\dots’
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
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 Rd file 'count.Rd':
  ‘.data’

Documented arguments not in \usage in Rd file 'unite.Rd':
  ‘.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 Rd file 'calcIntegralSurv2_cpp.Rd':
  ‘dsurvival’

Documented arguments not in \usage in Rd file 'dot-calcIntegralCif_cpp.Rd':
  ‘cif’ ‘CIF_t’

Documented arguments not in \usage in Rd file 'validFCTs.Rd':
  ‘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
Package suggested but not available for checking: ‘ReGenesees’
Documented arguments not in \usage in Rd file 'get_result.Rd':
  ‘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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgdal’
Argument items with no description in Rd file 'makeEventHistory.Rd':
  ‘type’
Argument items with no description in Rd file 'plotSeqCount.Rd':
  ‘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: \$
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 Rd file 'validate_cover_cats.Rd':
  ‘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 Rd file 'add_catmaply_slider.Rd':
  ‘text_font_color’ ‘categorical_col’

Documented arguments not in \usage in Rd file 'add_catmaply_traces.Rd':
  ‘categorical_col’

Documented arguments not in \usage in Rd file 'catmaply_annotations.Rd':
  ‘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: \&
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
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 Rd file 'buildModel.Rd':
  ‘x’ ‘y’

Documented arguments not in \usage in Rd file 'modelKrigingInternalPredictor.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'selfAdapt.Rd':
  ‘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 Rd file 'evaluate_rule.Rd':
  ‘class’

Documented arguments not in \usage in Rd file 'tree_leaf_nodes.Rd':
  ‘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 file 'CensMFM-package.Rd':
  \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 Rd file 'blackboost_train.Rd':
  ‘x’ ‘y’

Documented arguments not in \usage in Rd file 'survival_prob_mboost.Rd':
  ‘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 file 'centralplot.Rd':
  ‘alpha’
'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.
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 Rd file 'create_epa.Rd':
  ‘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 Rd file 'select.cglasso.Rd':
  ‘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 Rd file 'influence-methods.Rd':
  ‘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 Rd file 'jumpointsVar-internal.Rd':
  ‘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 Rd file 'jumpointsVar-internal.Rd':
  ‘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 file 'ChangePointAnalyzer-package.Rd':
  \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 Rd file 'multiplierDSeqfun.Rd':
  ‘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.
'LazyData' is specified without 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’
Documented arguments not in \usage in Rd file 'dot-chkArgs.Rd':
  ‘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 file 'chngpt.test.Rd':
  ‘by.percentile’ ‘both’ ‘main’ ‘prec.weights’ ‘p.val.method’ ‘boot.B’
  ‘keep.fits’
Argument items with no description in Rd file 'convert.coef.Rd':
  ‘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 file 'double.hinge.Rd':
  ‘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 file 'hinge.test.Rd':
  ‘formula’ ‘cov.interest’ ‘family’ ‘data’ ‘verbose’
Argument items with no description in Rd file 'performance.unit.test.Rd':
  ‘formula.1’ ‘formula.2’ ‘family’ ‘data’ ‘B’ ‘I’
Argument items with no description in Rd file 'sim.chngpt.Rd':
  ‘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 file 'sim.hinge.Rd':
  ‘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 Rd file 'choplump-internal.Rd':
  ‘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 Rd file 'SearchEmptyClusters.Rd':
  ‘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
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
'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.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'clpm-internal.Rd':
  ‘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 Rd file 'auxiliary_functions.Rd':
  ‘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 Rd file 'clustEff-internal.Rd':
  ‘.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 Rd file 'calculate_connectivity.Rd':
  ‘datdf’

Documented arguments not in \usage in Rd file 'dunn_metric.Rd':
  ‘distance’ ‘method’

Documented arguments not in \usage in Rd file 'evaluate_all_column_dataset.Rd':
  ‘data’

Documented arguments not in \usage in Rd file 'information_external.Rd':
  ‘info’

Documented arguments not in \usage in Rd file 'information_internal.Rd':
  ‘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
'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
'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.
Package suggested but not available for checking: ‘PopGenome’
Documented arguments not in \usage in Rd file 'feat_sample.Rd':
  ‘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 Rd file 'get_superior.Rd':
  ‘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 Rd file 'lb_calculation.Rd':
  ‘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 Rd file 'cocorresp-internal.Rd':
  ‘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’
Package suggested but not available for checking: ‘bvpSolve’
'LazyData' is specified 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
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 file 'summary.CommunityClimateInput.Rd':
  ‘object’ ‘\dots’
Argument items with no description in Rd file 'summary.CommunityClimateStatistics.Rd':
  ‘object’ ‘\dots’
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
Objects in \usage without \alias in Rd file 'comf-internal.Rd':
  ‘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 Rd file 'CopulaSelection.Rd':
  ‘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 file 'concordancer-package.Rd':
  \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) 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 Rd file 'checkCountsWholeNumbers.Rd':
  ‘aggregated.samples’

Documented arguments not in \usage in Rd file 'getGlobalClusterMarkers.Rd':
  ‘min.percent.samples.expression’

Documented arguments not in \usage in Rd file 'getPercentGlobalClusters.Rd':
  ‘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 Rd file 'postProcessSys.Rd':
  ‘myFile’

Documented arguments not in \usage in Rd file 'theta_ll.Rd':
  ‘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 Rd file 'print_table.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond 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
Invalid package aliases in Rd file 'coopProductGame-package.Rd':
  ‘coopProducGame-package’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'ft.Rd':
  ‘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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'dCount_dePril_bi.Rd':
  ‘inheritParams’

Documented arguments not in \usage in Rd file 'dCount_naive_bi.Rd':
  ‘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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'pinvGamma.Rd':
  ‘logical;’

Documented arguments not in \usage in Rd file 'qinvGamma.Rd':
  ‘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
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgeos’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'tool.Rd':
  ‘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 Rd file 'ctqr-internal.Rd':
  ‘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 Rd file 'ctqr-internal.Rd':
  ‘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 Rd file 'chi2cub2cov.Rd':
  ‘covar’

Documented arguments not in \usage in Rd file 'cubpq.Rd':
  ‘summary’

Documented arguments not in \usage in Rd file 'cubshe.Rd':
  ‘makeplot’ ‘summary’

Documented arguments not in \usage in Rd file 'kkk.Rd':
  ‘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 Rd file 'cvRiskPlot.Rd':
  ‘estimator’

Documented arguments not in \usage in Rd file 'matrixMetrics.Rd':
  ‘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 Rd file 'compute_stat.Rd':
  ‘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 Rd file 'tree.filter.Rd':
  ‘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.
'LazyData' is specified without 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 Rd file 'mm_run_reg.Rd':
  ‘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
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'plotDataExplorer.single.Rd':
  ‘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 Rd file 'dotgetJSONValue.Rd':
  ‘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: ‘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
Specified C++11: please drop specification unless essential
S3 methods shown with full name in Rd file 'dbglm-internal.Rd':
  ‘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 Rd file 'a_dcc_mat_est.Rd':
  ‘param’

Documented arguments not in \usage in Rd file 'dcc_mat_est.Rd':
  ‘param’

Documented arguments not in \usage in Rd file 'deco_mat_est.Rd':
  ‘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.
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 file 'DDPNA-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
Argument items with no description in Rd file 'DEP_Mod_net_plot.Rd':
  ‘\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 Rd file 'getTriContextFraction.Rd':
  ‘trimer.counts.ref’

Documented arguments not in \usage in Rd file 'norm.it.Rd':
  ‘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 Rd file 'degreenet-internal.Rd':
  ‘range’ ‘lims’
Objects in \usage without \alias in Rd file 'degreenet-internal.Rd':
  ‘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 Rd file 'boot_f_cor.Rd':
  ‘fun’

Documented arguments not in \usage in Rd file 'boot_f_pcor.Rd':
  ‘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
Package required but not available: ‘signatureSearch’

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
'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
Documented arguments not in \usage in Rd file 'encode_unit.Rd':
  ‘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.
Package suggested but not available for checking: ‘rlibkriging’
'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 Rd file 'Nortonbass_startvalgen.Rd':
  ‘param’ ‘startvalgen’

Documented arguments not in \usage in Rd file 'seqdiffusion.Rd':
  ‘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’
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
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 Rd file 'internals.Rd':
  ‘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 Rd file 'internalmleHelpers.Rd':
  ‘validity.check’

Objects in \usage without \alias in Rd file 'internals.Rd':
  ‘.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 Rd file 'internalGenerics.Rd':
  x <- samplesize(object, value)

Documented arguments not in \usage in Rd file 'internals.Rd':
  ‘DClass’
Objects in \usage without \alias in Rd file 'internals.Rd':
  ‘.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 Rd file 'diveMove-internal.Rd':
  ‘.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’
Package suggested but not available for checking: ‘rgdal’
'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 file 'dml_bagging.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_boosting.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_ensemble_lm.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_ensemble_rf.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_neural_network.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_random_forest.Rd':
  ‘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 file 'dnapath2-package.Rd':
  \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 Rd file 'add.joint.mean.many.Rd':
  ‘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 file 'derivType.Rd':
  ‘L’ ‘mu’ ‘eps’
Argument items with no description in Rd file 'getNewParams.SC.Rd':
  ‘n.fft’
Argument items with no description in Rd file 'graph.CTMC.Rd':
  ‘\dots’
Argument items with no description in Rd file 'num.deriv.Rd':
  ‘\dots’
Argument items with no description in Rd file 'power.coef.one.Rd':
  ‘\dots’
Documented arguments not in \usage in Rd file 'concDict.Rd':
  ‘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 Rd file 'check_results.Rd':
  ‘error_on_failure’ ‘error_on_warning’

Documented arguments not in \usage in Rd file 'function_get_comments.Rd':
  ‘thresholds’

Documented arguments not in \usage in Rd file 'vignette_results_display.Rd':
  ‘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.
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’.
'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
Documented arguments not in \usage in Rd file 'show-dparserFunction-method.Rd':
  ‘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
Package suggested but not available for checking: ‘clustermq’
'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 Rd file 'forecastCovCompiled.Rd':
  ‘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
GNU make is a SystemRequirements.
Objects in \usage without \alias in Rd file 'd.spls.norm1.Rd':
  ‘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: ‘rgdal’
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
'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 file 'e.cluster.decision.Rd':
  ‘reg_data’ ‘log.lambda’
Argument items with no description in Rd file 'e.cluster.dendrogram.Rd':
  ‘echelon.obj’ ‘n.sim’ ‘cluster.legend.pos’ ‘cluster_reg’ ‘p_rank’
  ‘para’
Argument items with no description in Rd file 'e.cluster.map.Rd':
  ‘x’ ‘c_separates’ ‘locs’ ‘coo’ ‘rin’ ‘p_rank’ ‘cluster_reg’ ‘n.sim’
  ‘cluster.type’
Argument items with no description in Rd file 'e.dendrogram.Rd':
  ‘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 file 'e.dendrogram.axis.Rd':
  ‘main’ ‘ylab’ ‘yaxes’ ‘ylim’ ‘xaxes’ ‘xdper’ ‘dmai’ ‘peaks’ ‘x’
Argument items with no description in Rd file 'e.main.Rd':
  ‘x’ ‘rin’ ‘T’
Argument items with no description in Rd file 'e.monte.bin.Rd':
  ‘rin’ ‘cas’ ‘pop’ ‘n.sim’ ‘K’ ‘cluster.type’
Argument items with no description in Rd file 'e.monte.poi.Rd':
  ‘rin’ ‘cas’ ‘pop’ ‘ex’ ‘n.sim’ ‘K’ ‘cluster.type’
Argument items with no description in Rd file 'e.profile.Rd':
  ‘peaks’ ‘parents’ ‘separates’
Argument items with no description in Rd file 'e.scan.Rd':
  ‘x’ ‘locs’ ‘peaks’ ‘c_separates’ ‘parents’ ‘K’
Argument items with no description in Rd file 'e.scan.pop.Rd':
  ‘x’ ‘locs’ ‘peaks’ ‘c_separates’ ‘parents’ ‘K’ ‘pop’
Argument items with no description in Rd file 'nlimb.Rd':
  ‘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
Documented arguments not in \usage in Rd file 'fcf.env.Rd':
  ‘vars’

Documented arguments not in \usage in Rd file 'getlevels.Rd':
  ‘editarray’

Documented arguments not in \usage in Rd file 'parseCatEdit.Rd':
  ‘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 Rd file 'rotate_to_equilibrium.Rd':
  ‘xy_may’

Documented arguments not in \usage in Rd file 'wide.dyads.to.edgelist.Rd':
  ‘fist.var’

Documented arguments not in \usage in Rd file 'wide.to.long.Rd':
  ‘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’
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 Rd file 'colBoxplot4.Rd':
  ‘id’

Documented arguments not in \usage in Rd file 'elaborator_server.Rd':
  ‘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
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.
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)’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RStoolbox’
Documented arguments not in \usage in Rd file 'div_plot.Rd':
  ‘plot_cols’

Documented arguments not in \usage in Rd file 'seq_plot.Rd':
  ‘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 file 'EnviroPRA-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
'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 Rd file 'dots_to_charlist.Rd':
  ‘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 Rd file 'addDrug.Lexis.Rd':
  ‘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 Rd file 'subnetwork_templates.Rd':
  ‘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 Rd file 'call.ErgmTerm.Rd':
  ‘A’

Objects in \usage without \alias in Rd file 'ergm-defunct.Rd':
  ‘sociality’

Documented arguments not in \usage in Rd file 'ergm-deprecated.Rd':
  ‘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 Rd file 'ergm_state.Rd':
  ‘nw’

Documented arguments not in \usage in Rd file 'nodal_attributes-API.Rd':
  ‘l’

Documented arguments not in \usage in Rd file 'summary.ergm_model.Rd':
  ‘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 Rd file 'summary.error_interval.Rd':
  ‘summary.error_interval’

S3 methods shown with full name in Rd file 'summary.measure.Rd':
  ‘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 Rd file 'ETAS-internal.Rd':
  ‘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 Rd file 'poly_clip.Rd':
  ‘x’ ‘y’

Documented arguments not in \usage in Rd file 'setup_gpar.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'setup_grobs.Rd':
  ‘centers’

Documented arguments not in \usage in Rd file 'update_list.Rd':
  ‘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.
'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 Rd file 'doHttrRequest.Rd':
  ‘params’ ‘customConfig’

Documented arguments not in \usage in Rd file 'errorMessage.Rd':
  ‘test_me’

Documented arguments not in \usage in Rd file 'isError.Rd':
  ‘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 Rd file 'borrOrderingInternal.Rd':
  ‘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
'LazyData' is specified without a 'data' directory
Error: package or namespace load failed for ‘ExomeDepth’:
 .onLoad failed in loadNamespace() for 'Rsamtools', details:
  call: h(simpleError(msg, call))
  error: error in evaluating the argument 'x' in selecting a method for function 'levels': attempt to use zero-length variable name
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), do
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cec2013’
checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:29: Escaped LaTeX specials: \&
Argument items with no description in Rd file 'plot.expectreg.Rd':
  ‘\dots’
Argument items with no description in Rd file 'update.expectreg.Rd':
  ‘\dots’
'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 ‘associated_data.Rmd’ using rmarkdown
--- finished re-building ‘associated_data.Rmd’

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

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

Quitting from lines 165-175 [unnamed-chunk-9] (mining_accepted_genera.Rmd)
Error: processing vignette 'mining_accepted_genera.Rmd' failed with diagnostics:
Any genus in the provided genus vector might have a typo or is
                 not present in POWO.
 Please correct the following names in your genus vector
                 according to POWO:
 
 Bertholletia 
 
 Find help also at DBOSLab-UFBA:
 Debora Zuanny, deborazuanny@gmail.com
 Domingos Cardoso, cardosobot@gmail.com
--- failed re-building ‘mining_accepted_genera.Rmd’

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

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

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

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

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

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

Error: Vignette re-building failed.
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 file 'fbvpot.Rd':
  ‘cutoff’
checkRd: (-1) outlierPlot.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) outlierPlot.Rd:32: Escaped LaTeX specials: \$
Documented arguments not in \usage in Rd file 'getQQLimit.Rd':
  ‘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: \#
'LazyData' is specified 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
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'complete.log.likelihood_Sj.Rd':
  ‘z’
Auto-generated content requiring editing in Rd file 'getStuffForDIC.Rd':
  \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 significant warnings:
  Warning: file ‘print.FactoClass.R’ is invalid UTF-8
  Warning: file ‘ward.cluster.R’ is invalid UTF-8
  Warning: invalidly encoded .R file(s)
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/FactoClass.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 17.0.5 (1)’
* used C++ compiler: ‘Debian clang version 17.0.5 (1)’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    minor changes
Auto-generated content requiring editing in Rd file 'procrustes_switching.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'rsp_exact.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'rsp_full_sa.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'rsp_partial_sa.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'weighted_procrustes_switching.Rd':
  \details: ‘If necessary, more details than the description above.’
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'Factoshiny-package.Rd':
  \references: ‘~~ Literature or other references for background information ~~’
  \seealso: ‘~~ Optional links to other man pages, e.g. ~~’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'dot-get_default_sign_size.Rd':
  ‘outcome_type’

Documented arguments not in \usage in Rd file 'dot-get_iteration_data.Rd':
  ‘file_dir’

Documented arguments not in \usage in Rd file 'extract_model_vimp.Rd':
  ‘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 Rd file 'cache.Rd':
  ‘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 Rd file 'kkk.Rd':
  ‘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
Documented arguments not in \usage in Rd file 'Get_C_R_K_Q.Rd':
  ‘have_noise’

Documented arguments not in \usage in Rd file 'Sample_KF_post.Rd':
  ‘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
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
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 Rd file 'bin.Rd':
  ‘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 file 'getbasispenalty.Rd':
  ‘Lfdobj’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘vert.txt’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘treesAll.txt’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New Stuff
'LazyData' is specified without a 'data' directory
checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'checkStream.Rd':
  ‘skipChecks’

Documented arguments not in \usage in Rd file 'cpp_detectCUSUMMeanSinglePrechange.Rd':
  ‘BL’

Documented arguments not in \usage in Rd file 'cpp_detectEWMAMeanSinglePrechange.Rd':
  ‘BL’

Documented arguments not in \usage in Rd file 'makeStreamMeanChangeR.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'update_Omega.Rd':
  ‘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 Rd file 'recode_subquad.Rd':
  ‘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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 Rd file 'plot_data_type.Rd':
  ‘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
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 Rd file 'hl.factor.number.Rd':
  ‘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
Found the following significant warnings:

  Warning: 'Node$fieldsAll' is deprecated.
  Warning: 'Node$fieldsAll' is deprecated.
  Warning: 'Node$fieldsAll' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
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 Rd file 'assert.surface.Rd':
  ‘surf’

Documented arguments not in \usage in Rd file 'check.dtype.for.data.Rd':
  ‘silent’

Documented arguments not in \usage in Rd file 'fread3.Rd':
  ‘filehandle:’

Documented arguments not in \usage in Rd file 'fwrite3.Rd':
  ‘filehandle:’ ‘data:’

Documented arguments not in \usage in Rd file 'polygon.soup.to.indexed.mesh.Rd':
  ‘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 Rd file 'freqdom.transpose.Rd':
  ‘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 Rd file 'draw.colorbar.Rd':
  ‘coloredmesh’

Documented arguments not in \usage in Rd file 'extend_neighbors.Rd':
  ‘min_dotp_threshold’

Documented arguments not in \usage in Rd file 'surf.sphere.spatialfilter.Rd':
  ‘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 file 'fsdam.Rd':
  ‘verbose’ ‘which’
Argument items with no description in Rd file 'plot.classes.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.fsim.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.lm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.sfpl.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.sfplsim.FASSMR.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.summary.mfplsim.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘simulated.Rmd’ using rmarkdown
free(): invalid next size (normal)
Aborted
--- re-building ‘traffic.Rmd’ using rmarkdown
--- finished re-building ‘traffic.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Documented arguments not in \usage in Rd file 'imp_small_gaps_WMA.Rd':
  ‘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 Rd file 'funData-constructor.Rd':
  ‘funData’

Objects in \usage without \alias in Rd file 'irregFunData-constructor.Rd':
  ‘irregFunData’

Objects in \usage without \alias in Rd file 'multiFunData-constructor.Rd':
  ‘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 Rd file 'plot.funData.Rd':
  ‘plot.funData’

S3 methods shown with full name in Rd file 'plot.irregFunData.Rd':
  ‘plot.irregFunData’

S3 methods shown with full name in Rd file 'plot.multiFunData.Rd':
  ‘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 Rd file 'build_limits_lookup.Rd':
  ‘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 Rd file 'loggedOutput.Rd':
  ‘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 Rd file 'mandelbrot.Rd':
  ‘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
Invalid package aliases in Rd file 'GAabbreviate-internal.Rd':
  ‘GAabbreviation-package’
Documented arguments not in \usage in Rd file 'splitQTL_comment.Rd':
  ‘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 Rd file 'as.gapdata.Rd':
  ‘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 Rd file 'lrr_plot.Rd':
  ‘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 Rd file 'align_peaks.Rd':
  ‘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 Rd file 'geepack-internal.Rd':
  ‘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 file 'gemlog-package.Rd':
  \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
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 Rd file 'CirDisp.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'CirKurt.Rd':
  ‘x’ ‘na.rm’

Documented arguments not in \usage in Rd file 'CirSD.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'CirSkew.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'CirVar.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'MeanDir.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'impact.Rd':
  ‘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 Rd file 'expand.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'grapes-bq-grapes.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'grapes-bt-grapes.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'stftcalc.Rd':
  ‘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 suggested but not available for checking: ‘maptools’
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 Rd file 'generalizedwendland-internal.Rd':
  ‘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
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
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'variables_query-method.Rd':
  ‘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’.
Package suggested but not available for checking: ‘rgdal’
'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: ‘argon2’
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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 Rd file 'attract_by_distance.Rd':
  ‘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.
'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 Rd file 'labels.rpart.Rd':
  ‘pretty:’

Documented arguments not in \usage in Rd file 'rpart_labels.Rd':
  ‘model’ ‘...’

Documented arguments not in \usage in Rd file 'rpart_segments.Rd':
  ‘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 Rd file 'interpolateDataFrame.Rd':
  ‘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 file 'isADMG.Rd':
  ‘amat’
Argument items with no description in Rd file 'isAG.Rd':
  ‘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 Rd file 'operator.Rd':
  ‘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 Rd file 'ggplot_gtable.Rd':
  ‘plot’

Documented arguments not in \usage in Rd file 'undocumented.Rd':
  ‘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
Running examples in ‘ggthemes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: circlefill_shape_pal
> ### Title: Filled Circle Shape palette (discrete)
> ### Aliases: circlefill_shape_pal
> 
> ### ** Examples
> 
> library("ggplot2")
> 
> p <- ggplot(mtcars, aes(x = mpg, y = hp, shape = factor(cyl))) +
+  geom_point()
> 
> p + scale_shape_tremmel()
> p + scale_shape_circlefill()
Error in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) : 
  conversion failure on '●' in 'mbcsToSbcs': for ● (U+25CF)
Calls: <Anonymous> ... drawDetails -> drawDetails.points -> grid.Call.graphics
Execution halted
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 Rd file 'add_scale.Rd':
  ‘domain’

Documented arguments not in \usage in Rd file 'bin_vector.Rd':
  ‘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 file 'GLD.lm.full.surv.Rd':
  ‘maxit’
Argument items with no description in Rd file 'GLD.lm.surv.Rd':
  ‘maxit’
Documented arguments not in \usage in Rd file 'getBeta.Rd':
  ‘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 Rd file 'glmpathcr-internal.Rd':
  ‘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 Rd file 'fun.svd_1.Rd':
  ‘X’

Documented arguments not in \usage in Rd file 'fun.svd_2.Rd':
  ‘X’

Documented arguments not in \usage in Rd file 'fun.svd_3.Rd':
  ‘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
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
'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 Rd file 'doHttrRequest.Rd':
  ‘session’ ‘params’

Documented arguments not in \usage in Rd file 'get_google_token.Rd':
  ‘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.
Invalid package aliases in Rd file '00.GPArotateDF.Rd':
  ‘00.GPArotateDF-package’
Documented arguments not in \usage in Rd file 'estimate_noise_nn.Rd':
  ‘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
Package suggested but not available for checking: ‘maptools’
'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
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'HistPCA.Rd':
  ‘ggplot’
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 Rd file 'prCaSetRownames.Rd':
  ‘rownames.fn’

Documented arguments not in \usage in Rd file 'prClearPCAclass.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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 Rd file 'groc.fit.Rd':
  ‘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
'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 '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 Rd file 'GSA.internal.Rd':
  ‘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
Specified C++11: please drop specification unless essential
Running examples in ‘gtop-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hts
> ### Title: Prediction conciliation by ...n.
> ### Aliases: hts
> 
> ### ** Examples
> 
> K <- 5
> hts(preds_indiv = rep(0, K), 1)
Warning in cbind.Matrix(x, y, deparse.level = 0L) :
  number of rows of result is not a multiple of vector length
Error in utmat %*% fcasts : non-conformable arguments
Calls: hts ... combinef -> LU -> <Anonymous> -> .class1 -> %*% -> %*%
Execution halted
Package suggested but not available for checking: ‘ggstats’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RRprof.out’
'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 Rd file 'traits.Rd':
  ‘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.
'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: ‘rgeos’
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
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’
Argument items with no description in Rd file 'haplo.em.fitter.Rd':
  ‘random.start ’
Argument items with no description in Rd file 'haplo.model.frame.Rd':
  ‘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: \&
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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
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.
'LazyData' is specified without 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 Rd file 'check_arg_for_hyperslab_func.Rd':
  ‘cur_arg’

Documented arguments not in \usage in Rd file 'extract_dim.Rd':
  ‘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
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 Rd file 'compute_counts.Rd':
  ‘init’ ‘inflow’

Documented arguments not in \usage in Rd file 'compute_values.Rd':
  ‘counts’

Documented arguments not in \usage in Rd file 'create_demographic_table.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'eval_strategy_newdata.Rd':
  ‘model’

Documented arguments not in \usage in Rd file 'get_state_value_names.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond 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
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'check.Rd':
  ‘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 Rd file 'check_known_repos.Rd':
  ‘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 Rd file 'HH-defunct.Rd':
  ‘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 file 'residual.plots.lattice.Rd':
  ‘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
Package suggested but not available for checking: ‘INLA’
Argument items with no description in Rd file 'qcplate.Rd':
  ‘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
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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: ‘rgdal’
'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 file 'HistDAWass-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
Invalid package aliases in Rd file 'histogram-package.Rd':
  ‘histogramtools-package’
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
Documented arguments not in \usage in Rd file 'bootstrapfun.Rd':
  ‘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 file 'HMVD-package.Rd':
  \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 file 'bid2.Rd':
  ‘numattable1’ ‘playerseats1’ ‘blinds1’ ‘dealer1’ ‘b3’ ‘b4’ ‘round1’
  ‘ntable1’ ‘decision1’
Argument items with no description in Rd file 'calcwin1.Rd':
  ‘numattable1’ ‘playerseats1’ ‘b3’ ‘b7’
Argument items with no description in Rd file 'mycount1.Rd':
  ‘x’
Argument items with no description in Rd file 'mygraphics1.Rd':
  ‘numattable1’ ‘playerseats1’ ‘chips1’ ‘blinds1’ ‘dealer1’ ‘b3’ ‘b4’
  ‘b5’ ‘b6’ ‘b7’ ‘chips2’ ‘ntable1’ ‘myfast1’ ‘chipstart1’ ‘name1’
  ‘lowercut1’
Argument items with no description in Rd file 'nothing1.Rd':
  ‘x’
Argument items with no description in Rd file 'onepair1.Rd':
  ‘x’
Argument items with no description in Rd file 'straight1.Rd':
  ‘x’
Argument items with no description in Rd file 'straightdraw1.Rd':
  ‘x’
Argument items with no description in Rd file 'strflsh1.Rd':
  ‘x’ ‘y’
Argument items with no description in Rd file 'trip1.Rd':
  ‘x’
Argument items with no description in Rd file 'twopair1.Rd':
  ‘x’
Argument items with no description in Rd file 'writebets1.Rd':
  ‘b9’ ‘y1’ ‘numattable1’ ‘b3’ ‘playerseats1’ ‘chips1’ ‘chips2’ ‘over1’
  ‘myfast1’ ‘name1’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'plot.hopitCP.Rd':
  ‘plotf’

Documented arguments not in \usage in Rd file 'sigma.hopit.Rd':
  ‘model’

Documented arguments not in \usage in Rd file 'summary.hopit.Rd':
  ‘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 Rd file 'dot-E3.Rd':
  ‘i’ ‘M’

Documented arguments not in \usage in Rd file 'dot-E4.Rd':
  ‘i’ ‘M’

Documented arguments not in \usage in Rd file 'hrm.0w.2s.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.0w.3s.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.0w.4s.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.0w.5s.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.1f.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.1w.0f.Rd':
  ‘factor1’

Documented arguments not in \usage in Rd file 'hrm.2w.2f.Rd':
  ‘factor’

Documented arguments not in \usage in Rd file 'hrm.mv.1w.1f.Rd':
  ‘H’ ‘text’

Documented arguments not in \usage in Rd file 'hrm.mv.internal.Rd':
  ‘alpha’ ‘H’ ‘text’

Documented arguments not in \usage in Rd file 'hrm.test.1.none.Rd':
  ‘factor1’ ‘factor2’

Documented arguments not in \usage in Rd file 'hrm.test.1.one.Rd':
  ‘group’ ‘factor2’

Documented arguments not in \usage in Rd file 'hrm.test.2.one.Rd':
  ‘factor2’

Documented arguments not in \usage in Rd file 'hrm.test.2.two.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.test.3.three.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.test.4.four.Rd':
  ‘group’

Documented arguments not in \usage in Rd file 'hrm.test.5.five.Rd':
  ‘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 file 'imageplot.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'FramedHTML.Rd':
  ‘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 Rd file 'as-redactor.Rd':
  ‘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
'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’
'LazyData' is specified without a 'data' directory
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:7: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘rgeos’
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
Documented arguments not in \usage in Rd file 'read.txt.Witec.Rd':
  ‘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.
'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 Rd file 'btibgen.Rd':
  ‘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 file 'pairSum.Rd':
  ‘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 Rd file 'GetCustomKmerCounts.Rd':
  ‘custom.range’

Documented arguments not in \usage in Rd file 'GetMutationLoadsFromStrelkaIDVCFs.Rd':
  ‘list.of.vcfs’

Documented arguments not in \usage in Rd file 'GetMutationLoadsFromStrelkaSBSVCFs.Rd':
  ‘split.vcfs’

Documented arguments not in \usage in Rd file 'PlotPPM.Rd':
  ‘pwm’

Documented arguments not in \usage in Rd file 'PlotPPMToPdf.Rd':
  ‘list.of.pwm’

Documented arguments not in \usage in Rd file 'ReadStrelkaSBSVCF.Rd':
  ‘suppress.discarded.variants.warnings’

Documented arguments not in \usage in Rd file 'ReadVCF.Rd':
  ‘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: \$
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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 Rd file 'pkg-internal.Rd':
  ‘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 Rd file 'pkg-internal.Rd':
  ‘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’
'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 Rd file 'dot-compl.Rd':
  ‘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
Package suggested but not available for checking: ‘accdata’
Documented arguments not in \usage in Rd file 'new_impactr_peaks.Rd':
  ‘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
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’
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  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
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 file 'IntervalSurgeon-package.Rd':
  \seealso: ‘Optional links to other man pages’
  \examples: ‘## Optional simple examples of the most important functions ...’
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'selectRuleRRF.Rd':
  ‘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 Rd file 'rawAvgCost-deprecated.Rd':
  ‘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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'chars_collapse.Rd':
  ‘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 file 'mrbayes.Rd':
  ‘unlink’ ‘constraint’
Argument items with no description in Rd file 'mrbayes.lset.Rd':
  ‘partition’
Argument items with no description in Rd file 'multistate.Rd':
  ‘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
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Documented arguments not in \usage in Rd file 'print.cat_output.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'sub-subset-Itempool-numeric-missing-method.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'sub-subset-Response_set-numeric-missing-method.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'sub-subset-Testlet-numeric-missing-method.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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 Rd file 'print.Item.Rd':
  ‘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
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'islasso-internal.Rd':
  ‘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 Rd file 'dot-assignmentMaker.Rd':
  ‘.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’
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
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
'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 Rd file 'paste_coef.Rd':
  ‘parlemts’

Documented arguments not in \usage in Rd file 'paste_linpred.Rd':
  ‘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 file 'covQualNested.Rd':
  ‘covBet’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'bw.abram.temp.Rd':
  ‘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 Rd file 'calc_PGtheta_R.Rd':
  ‘model’ ‘iter’

Documented arguments not in \usage in Rd file 'make_wsz_cpp.Rd':
  ‘info’ ‘initialized’

Documented arguments not in \usage in Rd file 'read_dfm_cpp.Rd':
  ‘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 Rd file 'b_wincred_get.Rd':
  ‘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 Rd file 'unlist.constr.Rd':
  ‘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
Package suggested but not available for checking: ‘maptools’
'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’
'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
S3 methods shown with full name in Rd file 'stat.Rd':
  ‘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
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 Rd file 'latrend-generics.Rd':
  ‘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
Documented arguments not in \usage in Rd file 'moments2.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'skeleton.Rd':
  ‘endogeneous’ ‘...’

Documented arguments not in \usage in Rd file 'vcov2-internal.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
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 Rd file 'H_inv.Rd':
  ‘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 Rd file 'dot-choose_best_subjects.Rd':
  ‘best’ ‘candidate’

Documented arguments not in \usage in Rd file 'dot-normalize_props.Rd':
  ‘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 file 'top.topic.words.Rd':
  ‘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 Rd file 'backward_step.Rd':
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in Rd file 'backward_step_IM.Rd':
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in Rd file 'forward_step.Rd':
  ‘empty_start_dataset’ ‘fit’ ‘...’

Documented arguments not in \usage in Rd file 'forward_step_IM.Rd':
  ‘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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘maptools’
'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 Rd file 'get_generic.Rd':
  ‘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
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 Rd file 'CoordInBounds.Rd':
  ‘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: \# \#
Specified C++11: please drop specification unless essential
S3 methods shown with full name in Rd file 'BIC.threshold.Rd':
  ‘BIC.threshold’

S3 methods shown with full name in Rd file 'BIC.threshold.ggm.Rd':
  ‘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 Rd file 'MassAcylCer.Rd':
  ‘glccer’

Documented arguments not in \usage in Rd file 'MassPEo.Rd':
  ‘PEp’

Documented arguments not in \usage in Rd file 'findMS2precursor.Rd':
  ‘minint’ ‘maxint’

Documented arguments not in \usage in Rd file 'joinAnnotationResults.Rd':
  ‘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 Rd file 'get_variable.Rd':
  ‘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
'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
'LazyData' is specified without a 'data' directory
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) ACS.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) EmployedACS.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSale.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleCA.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleCanton.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleNY.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:24: Escaped LaTeX specials: \$
checkRd: (-1) SalaryGender.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) SandP500.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) SandwichAnts.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) SandwichAnts2.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) TrafficFlow.Rd:18: Escaped LaTeX specials: \#
Invalid package aliases in Rd file 'Lock5Data-package.Rd':
  ‘Lock5Data-package’
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'spec.emb.Rd':
  ‘A’
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'dlogitnorm.Rd':
  ‘sigma’
Argument items with no description in Rd file 'invlogit.Rd':
  ‘q’ ‘\dots’
Argument items with no description in Rd file 'logit.Rd':
  ‘p’ ‘\dots’
Argument items with no description in Rd file 'plogitnorm.Rd':
  ‘sigma’ ‘\dots’
Argument items with no description in Rd file 'qlogitnorm.Rd':
  ‘sigma’ ‘\dots’
Argument items with no description in Rd file 'twCoefLogitnorm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'twCoefLogitnormE.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘apollo’
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
Argument items with no description in Rd file 'levopt.Rd':
  ‘x’ ‘alpha’ ‘fmax’ ‘tm’
Argument items with no description in Rd file 'pershow.Rd':
  ‘object’
Argument items with no description in Rd file 'norpt.Rd':
  ‘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’.
checkRd: (-1) butstrap.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.nri.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.s.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.s.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) nri.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) roc.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) roc.s.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.s.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'LoopAnalyst-package.Rd':
  \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 Rd file 'importance_sampling.array.Rd':
  ‘is_method’

Documented arguments not in \usage in Rd file 'importance_sampling.default.Rd':
  ‘is_method’

Documented arguments not in \usage in Rd file 'importance_sampling.matrix.Rd':
  ‘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 file 'LotkasXX.Rd':
  ‘Table’
Argument items with no description in Rd file 'LotkasXY.Rd':
  ‘Table’
'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
Argument items with no description in Rd file 'followx.Rd':
  ‘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: \&
checkRd: (-1) lpepa.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:90: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:65: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘kerdiest’
checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) spectral.density.Rd:55: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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Documented arguments not in \usage in Rd file 'setlogdata.Rd':
  ‘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 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'
Running examples in ‘magicaxis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: magplot
> ### Title: Magically pretty plots
> ### Aliases: magplot
> ### Keywords: plot axis log
> 
> ### ** Examples
> 
> x=10^{1:9}
> y=1:9
> magplot(log10(x),y,unlog='x')
> magplot(x,y,log='x')
> 
> #Not ideal to have two decades between major labels:
> 
> magplot(x,y,log='x',majorn=c(10,5))
> magplot(x,y,log='xy',majorn=c(10,5,5,5),side=1:4)
> 
> #Sometimes it is helpful to focus on where most of the data actually is.
> #Using a single value for xlim and ylim sigma clips the data to that range.
> #Here a value of 2 means we only show the inner 2-sigma (2% to 98%) range.
> #The 'auto' option allows magclip to dynamically estimate a clip value.
> 
> temp=cbind(rt(1e3,1.5),rt(1e3,1.5))
> magplot(temp)
> magplot(temp, xlim=2, ylim=2)
> magplot(temp, xlim='auto', ylim='auto')
> 
> #Some astronomy related examples (and how to display the solar symbol):
> 
> temp=cbind(runif(10,8,12),runif(10,0,5))
> 
> magplot(temp[,1:2], xlab=expression(M['\u0298']), ylab=expression(M['\u0298']/Yr), unlog='xy')
Warning in mtext(text = expression(M["ʘ"]), side = 1L, line = 2) :
  font metrics unknown for Unicode character U+0298
Warning in mtext(text = expression(M["ʘ"]), side = 1L, line = 2) :
  font metrics unknown for Unicode character U+0298
Warning in mtext(text = expression(M["ʘ"]), side = 1L, line = 2) :
  font metrics unknown for Unicode character U+0298
Warning in mtext(text = expression(M["ʘ"]), side = 1L, line = 2) :
  font metrics unknown for Unicode character U+0298
Error in mtext(text = expression(M["ʘ"]), side = 1L, line = 2) : 
  conversion failure on 'ʘ' in 'mbcsToSbcs': for ʘ (U+0298)
Calls: magplot ... plot -> plot.default -> magaxis -> do.call -> mtext
Execution halted
'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 file 'plot.magree.Rd':
  ‘xlab’ ‘ylab’ ‘main’ ‘\dots’
Argument items with no description in Rd file 'print.summary.magree.Rd':
  ‘x’ ‘\dots’
Argument items with no description in Rd file 'summary.magree.Rd':
  ‘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
Argument items with no description in Rd file 'alignPeaks.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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:
    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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) Interpolation-class.Rd:41: Escaped LaTeX specials: \#
checkRd: (-1) MareyMap-class.Rd:85: Escaped LaTeX specials: \_
checkRd: (-1) MareyMap-methods.Rd:11: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) MareyMap-methods.Rd:12: Escaped LaTeX specials: \_
checkRd: (-1) SpeciesMaps-methods.Rd:11: Escaped LaTeX specials: \_
checkRd: (-1) interpolation-methods.Rd:13: Escaped LaTeX specials: \_
Argument items with no description in Rd file 'bias.factor.Rd':
  ‘RRud’ ‘RReu’ ‘rr’ ‘s2’
'LazyData' is specified without a 'data' directory
checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'mark_my_dir.Rd':
  ‘mark_file’

Documented arguments not in \usage in Rd file 'path_type.Rd':
  ‘github_token’

Documented arguments not in \usage in Rd file 'read_assignment_yml.Rd':
  ‘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 Rd file 'utility_functions.Rd':
  ‘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: ‘wallace’
'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 file 'NewPackage-package.Rd':
  \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
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
'LazyData' is specified without 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 file 'mccca-package.Rd':
  \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: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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 Rd file 'geom_cp_density.Rd':
  ‘include’

Documented arguments not in \usage in Rd file 'get_simulate.Rd':
  ‘par_trials’ ‘pars_pop’ ‘pars_varying’

Documented arguments not in \usage in Rd file 'pp_eval.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond 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: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
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.
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 Rd file 'buildModelMatrix.Rd':
  ‘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
Invalid package aliases in Rd file 'taxa-package.Rd':
  ‘taxa-package’
Documented arguments not in \usage in Rd file 'limited_print.Rd':
  ‘trunc’

Documented arguments not in \usage in Rd file 'parse_heirarchies_to_taxonomy.Rd':
  ‘A’

Documented arguments not in \usage in Rd file 'parse_raw_heirarchies_to_taxonomy.Rd':
  ‘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 Rd file 'ClusterMF-deprecated.Rd':
  ‘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.
Packages suggested but not available for checking: 'Rcgmin', 'Rvmmin'
Unknown packages ‘Rcgmin’, ‘Rvmmin’ 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
Documented arguments not in \usage in Rd file 'plot.metaplot_gtable.Rd':
  ‘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.
Specified C++11: please drop specification unless essential
checkRd: (-1) cardiac.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) plvol.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) sbp.Rd:16: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'dot-gev.postpred.Rd':
  ‘vector’

Documented arguments not in \usage in Rd file 'dot-gpd_2D_fit.Rd':
  ‘...other’

Documented arguments not in \usage in Rd file 'dot-mvasym.check.Rd':
  ‘vector’

Documented arguments not in \usage in Rd file 'dot-rPexstud.Rd':
  ‘Sigma’

Documented arguments not in \usage in Rd file 'dot-rPsite.Rd':
  ‘index’ ‘param’

Documented arguments not in \usage in Rd file 'dot-rdirspec.Rd':
  ‘rho’

Documented arguments not in \usage in Rd file 'dot-rexstudspec.Rd':
  ‘index’ ‘Sigma’

Documented arguments not in \usage in Rd file 'dot-rhrspec.Rd':
  ‘index’

Documented arguments not in \usage in Rd file 'dot-rmevA1.Rd':
  ‘param’

Documented arguments not in \usage in Rd file 'dot-rmevA2.Rd':
  ‘param’

Documented arguments not in \usage in Rd file 'dot-rmevasy.Rd':
  ‘param’

Documented arguments not in \usage in Rd file 'dot-rmevspec_cpp.Rd':
  ‘param’

Documented arguments not in \usage in Rd file 'dot-wecdf.Rd':
  ‘ord’

Documented arguments not in \usage in Rd file 'tem.corr.Rd':
  ‘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 file 'predict.mfp.Rd':
  ‘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 file 'Rpackage-package.Rd':
  \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.
S3 methods shown with full name in Rd file 'complete.miceadds.Rd':
  ‘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
'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: ‘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 Rd file 'changeDevSettings.Rd':
  ‘defaultsSettings’

Documented arguments not in \usage in Rd file 'getResultPerScheme.Rd':
  ‘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 file 'micSimParallel.Rd':
  ‘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 file 'MIDASwrappeR-package.Rd':
  \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
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 Rd file 'getvol.Rd':
  ‘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
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 Rd file 'logAdd.Rd':
  ‘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.
Argument items with no description in Rd file 'randomizationTest.Rd':
  ‘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: \&
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Documented arguments not in \usage in Rd file 'mixAR-internal.Rd':
  ‘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 Rd file 'rigaussian.Rd':
  ‘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 Rd file 'Sn_A.Rd':
  ‘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
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    New .R files
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Auto-generated content requiring editing in Rd file 'mixl-package.Rd':
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  \seealso: ‘Optional links to other man pages’
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Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
Running examples in ‘mlr3pipelines-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mlr_pipeops_colroles
> ### Title: Change Column Roles of a Task
> ### Aliases: mlr_pipeops_colroles PipeOpColRoles
> 
> ### ** Examples
> 
> library("mlr3")
> 
> task = tsk("boston_housing")
> pop = po("colroles", param_vals = list(
+   new_role = list(cmedv = "order")
+ ))
> 
> pop$train(list(task))
Error: Cannot change the role of a target.
This happened PipeOp colroles's $train()
Execution halted
Documented arguments not in \usage in Rd file 'cpoTemplate.Rd':
  ‘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.
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Argument items with no description in Rd file 'mlVARsim0.Rd':
  ‘nPerson’ ‘nNode’ ‘nTime’ ‘sparsity’ ‘parRange’ ‘propPositive’
  ‘diagPositive’ ‘diagIncluded’ ‘sdRange’ ‘shrinkFactor’
  ‘residualStyle’ ‘residualShared’ ‘residualSDrange’ ‘verbose’
Problems with news in ‘NEWS.md’:
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Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.pdf’
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Rd files without \alias:
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Packages which this enhances but not available for checking:
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Documented arguments not in \usage in Rd file 'check_augment_data_specification.Rd':
  ‘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.
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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.
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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.
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  ‘curFile’

Documented arguments not in \usage in Rd file 'extractIndirect_section.Rd':
  ‘curFile’

Documented arguments not in \usage in Rd file 'graphModel.Rd':
  ‘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.
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‘gs+qpdf’ made some significant size reductions:
     compacted ‘mptinr_introduction.pdf’ from 580Kb to 330Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files,
  or build the source package with --compact-vignettes=both
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Objects in \usage without \alias in Rd file 'Mqrcm-internal.Rd':
  ‘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 file 'mrbsizer-package.Rd':
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  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
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  ‘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 Rd file 'popdynCPP.Rd':
  ‘SSBcurr’

Documented arguments not in \usage in Rd file 'popdynOneMICE.Rd':
  ‘nyears’

Documented arguments not in \usage in Rd file 'qestMICE.Rd':
  ‘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:
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  ‘Velocity.pdf’
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  ‘data’
Argument items with no description in Rd file 'Royston.test.Rd':
  ‘data’
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  ‘\dots’
Argument items with no description in Rd file 'larg.ellip.Rd':
  ‘n’ ‘box’ ‘add’ ‘xlim’ ‘ylim’ ‘zlim’ ‘xlab’ ‘ylab’ ‘zlab’ ‘col’
  ‘alpha’ ‘\dots’
Argument items with no description in Rd file 'prism.Rd':
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S3 methods shown with full name in Rd file 'data.visualisation.Rd':
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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.
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  ‘lwd’ ‘T.base’ ‘font.family’ ‘fig’ ‘mar’

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  ‘width’ ‘lwd’ ‘label.groups’ ‘T.base’ ‘orientation’

Documented arguments not in \usage in Rd file 'plotTs.Rd':
  ‘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
Package suggested but not available for checking: ‘powerplus’
Running examples in ‘MultiATSM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Reg_K1Q
> ### Title: Estimate the risk-neutral feedbak matrix K1Q using linear
> ###   regressions
> ### Aliases: Reg_K1Q
> 
> ### ** Examples
> 
> data(CM_Yields)
> 
> Y_China <- Yields[1:6,]
> Z_China <- Spanned_Factors(Y_China, Economies ="China", N=3)
> mat <-c(0.25 , 0.5 , 1, 3, 5, 10)
> dt <- 1/12
> type <- 'Jordan'
> Reg_K1Q(Y_China, mat, Z_China, dt, type)
Error in loadNamespace(x) : there is no package called ‘powerplus’
Calls: Reg_K1Q
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Paper-Replications.Rmd’ using rmarkdown
--- finished re-building ‘Paper-Replications.Rmd’

--- re-building ‘my-vignette.Rmd’ using rmarkdown

Quitting from lines 430-451 [unnamed-chunk-28] (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
there is no package called 'powerplus'
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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  ‘x’

Documented arguments not in \usage in Rd file 'iteraite_fun_Iter.Rd':
  ‘The’

Documented arguments not in \usage in Rd file 'prepare_data.Rd':
  ‘The’

Documented arguments not in \usage in Rd file 'project.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'select_initial_Iter.Rd':
  ‘X’ ‘parametrs’

Documented arguments not in \usage in Rd file 'similarity_function.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'similarity_noncum.Rd':
  ‘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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  ‘fix’

Documented arguments not in \usage in Rd file 'text_colour.Rd':
  ‘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.
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GNU make is a SystemRequirements.
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Argument items with no description in Rd file 'check_subject_pattern.Rd':
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Argument items with no description in Rd file 'names_or_error.Rd':
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Argument items with no description in Rd file 'only_captures.Rd':
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Argument items with no description in Rd file 'stop_for_names.Rd':
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Problems with news in ‘NEWS.md’:
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    Version (2018-01-22)
    Version  (2017-08-22)
    Version
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GNU make is a SystemRequirements.
Invalid package aliases in Rd file 'NBBttest-package.Rd':
  ‘NBBtatest-package’
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No news entries found.
Documented arguments not in \usage in Rd file 'Moth.Rd':
  ‘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’:
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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.
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':::' call which should be '::': ‘lhs:::maximinLHS’
  See the note in ?`:::` about the use of this operator.
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Argument items with no description in Rd file 'print.networkDynamic.Rd':
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  ‘map.png’ ‘maze.html’
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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.
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:
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Invalid package aliases in Rd file 'NH-MSAR-package.Rd':
  ‘NH-MSAR-package’
Argument items with no description in Rd file 'ENu_graph.Rd':
  ‘N.s.data’
Argument items with no description in Rd file 'Estep.MSAR.VM.Rd':
  ‘verbose’
Auto-generated content requiring editing in Rd file 'NH-MSAR-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Argument items with no description in Rd file 'init.theta.MSAR.Rd':
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Argument items with no description in Rd file 'init.theta.MSAR.VM.Rd':
  ‘\dots’
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
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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 Rd file 'internalRK.Rd':
  ‘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
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Documented arguments not in \usage in Rd file 'nldoc_write_nldoc.Rd':
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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.
checkRd: (-1) nltm.control.Rd:29: Escaped LaTeX specials: \$
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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
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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
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Auto-generated content requiring editing in Rd file 'noise-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
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'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get_max_stat.Rd':
  ‘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 Rd file 'StatQQVPC.Rd':
  ‘mapping’ ‘data’ ‘geom’ ‘position’ ‘na.rm’ ‘show.legend’
  ‘inherit.aes’ ‘...’

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

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

Documented arguments not in \usage in Rd file 'covload.sub.table.Rd':
  ‘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 file 'nose-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
Documented arguments not in \usage in Rd file 'FunctionSanityChecks.Rd':
  ‘structure’

Documented arguments not in \usage in Rd file 'newLine.Rd':
  ‘current.in’

Documented arguments not in \usage in Rd file 'nosoiSimConstructor.Rd':
  ‘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 Rd file 'read.Rd':
  ‘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
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'Create_P.Rd':
  ‘y_zx_dependent’

Documented arguments not in \usage in Rd file 'make_proposer.Rd':
  ‘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
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'exp_hclust.Rd':
  ‘df_allele’

Documented arguments not in \usage in Rd file 'log_mem.Rd':
  ‘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
'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
Argument items with no description in Rd file 'plot.comphat.Rd':
  ‘\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
Package suggested but not available for checking: ‘rgdal’
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 Rd file 'unary_ops.Rd':
  ‘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 Rd file 'clique_color_pals.Rd':
  ‘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 Rd file 'bertinBase.Rd':
  ‘x’ ‘ratings’ ‘trim’

Documented arguments not in \usage in Rd file 'biplot3dBase2.Rd':
  ‘ext.sphere’

Documented arguments not in \usage in Rd file 'convertImportObjectToRepGridObject.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'convertScivescoImportObjectToRepGridObject.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'mapCoordinatesToColor.Rd':
  ‘color’

Documented arguments not in \usage in Rd file 'quasiDistributionDistanceSlater.Rd':
  ‘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.
Packages suggested but not available for checking: 'maptools', 'rgeos'
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 file 'dsevdist.Rd':
  ‘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 Rd file 'distsuml2.Rd':
  ‘partial’

Documented arguments not in \usage in Rd file 'distsumlp.Rd':
  ‘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 Rd file 'dosepred.Rd':
  ‘w’

Documented arguments not in \usage in Rd file 'surv_dm_solver.Rd':
  ‘bw_optim’

Documented arguments not in \usage in Rd file 'surv_forward_solver.Rd':
  ‘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.
Running ‘testthat.R’ [46s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(outerbase)
  > 
  > test_check("outerbase")
  OMP: Warning #96: Cannot form a team with 32 threads, using 3 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 63 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-obombasic.R:72:3'): basic test ───────────────────────────────
  base mat agreement (`actual`) not equal to 0 (`expected`).
  
    `actual`: 2
  `expected`: 0
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 63 ]
  Error: Test failures
  Execution halted
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 Rd file 'prediction_regression.Rd':
  ‘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 file 'joint_estimate.rd':
  ‘\dots’
Argument items with no description in Rd file 'only_A_estimate.rd':
  ‘\dots’
Argument items with no description in Rd file 'only_F_estimate.rd':
  ‘\dots’
Argument items with no description in Rd file 'plot.Full_PAFit_result.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plot.PAFit_net.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plot.PAFit_result.rd':
  ‘\dots’
Argument items with no description in Rd file 'plot.PA_result.rd':
  ‘\dots’
Argument items with no description in Rd file 'print.CV_Result.rd':
  ‘\dots’
Argument items with no description in Rd file 'print.CV_data.rd':
  ‘\dots’
Argument items with no description in Rd file 'print.Full_PAFit_result.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.PAFit_data.rd':
  ‘\dots’
Argument items with no description in Rd file 'print.PAFit_net.rd':
  ‘\dots’
Argument items with no description in Rd file 'print.PAFit_result.rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.CV_Data.rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.CV_Result.rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.Full_PAFit_result.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.PAFit_data.rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.PAFit_net.rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.PAFit_result.rd':
  ‘\dots’
'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 Rd file 'other.Rd':
  ‘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 Rd file 'dplyr_verbs.Rd':
  ‘funs’ ‘.dots’ ‘keep_attributes’

Documented arguments not in \usage in Rd file 'nest_tdc.Rd':
  ‘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 Rd file 'pamr.internal.Rd':
  ‘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: \_
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 Rd file 'getOption2.Rd':
  ‘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.
Package suggested but not available for checking: ‘BayesFM’
'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
Package suggested but not available for checking: ‘rgdal’
Documented arguments not in \usage in Rd file 'expect_missing_argument.Rd':
  ‘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 Rd file 'as_partition.Rd':
  ‘.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 Rd file 'fixvar_of_red_mod.Rd':
  ‘data’

Documented arguments not in \usage in Rd file 'get_ndf.Rd':
  ‘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 Rd file 'vec_cast.partial_time.Rd':
  ‘vec_cast.partial_time’

S3 methods shown with full name in Rd file 'vec_cast.timespan.Rd':
  ‘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
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \# \# \#
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'markbouts.acclist.Rd':
  ‘extreme’
S3 methods shown with full name in Rd file 'ped.Rd':
  ‘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
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
GNU make is a SystemRequirements.
Objects in \usage without \alias in Rd file 'pch-internal.Rd':
  ‘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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'getResponse.Rd':
  ‘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 Rd file 'ODACATH.estimate.Rd':
  ‘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
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'PoissonLoss.Rd':
  ‘count’ ‘seg.mean’ ‘weight’
Argument items with no description in Rd file 'getPath.Rd':
  ‘A’
Argument items with no description in Rd file 'PoissonLoss.Rd':
  ‘count’ ‘seg.mean’ ‘weight’
Argument items with no description in Rd file 'featureMatrixJoint.Rd':
  ‘profile.list’
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'PoissonLoss.Rd':
  ‘count’ ‘seg.mean’ ‘weight’
Argument items with no description in Rd file 'oracleModelComplexity.Rd':
  ‘bases’ ‘segments’
S3 methods shown with full name in Rd file 'format.relation.Rd':
  ‘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’
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: \$ \$ \$
Specified C++11: please drop specification unless essential
checkRd: (-1) my.bspline.Rd:21: Escaped LaTeX specials: \$ \$ \$ \$ \$ \$
checkRd: (-1) my.bspline.Rd:27: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) pendensity.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:57: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:82: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:96: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:100: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:105: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'lmres.Rd':
  ‘\dots’
Argument items with no description in Rd file 'simpleSlope.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.lmres.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) chart.ECDF.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘DMwR’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dendextendRcpp’
Documented arguments not in \usage in Rd file 'allTrees.Rd':
  ‘dist’

Documented arguments not in \usage in Rd file 'getNode.Rd':
  ‘hc’ ‘pair’

Documented arguments not in \usage in Rd file 'switchEntries.Rd':
  ‘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: \&
'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
Invalid package aliases in Rd file 'perspective-package.Rd':
  ‘perspective-package’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown packages ‘maptools’, ‘rgdal’ in Rd xrefs
checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRD.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRDUS.Rd:4: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘animation.gif’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.pdf’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'process_season.Rd':
  ‘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 file 'phm-package.Rd':
  \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...’
Running examples in ‘phonTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: createtemplate
> ### Title: Create an LDA Template
> ### Aliases: createtemplate print.template plot.template territorialmap
> 
> ### ** Examples
> 
> data (pb52)            ## load the Peterson and Barney vowels.
> ## normalize them.
> normdvowels = normalize (pb52[,7:9], pb52$speaker, pb52$vowel)  
> formants = normdvowels[,1:3]
> vowels = pb52$vowel
> 
> ## create a vowel template with the normalized formant frequencies
> ## and information about the vowel category.
> template = createtemplate (formants, vowels)
> 
> ## and inspect with plot()
> plot (template, xsampa = TRUE)
Error in plot.xy(xy.coords(x, y), type = type, ...) : 
  conversion failure on 'ɝ' in 'mbcsToSbcs': for ɝ (U+025D)
Calls: plot ... plot.template -> points -> points.default -> plot.xy
Execution halted
checkRd: (-1) phylo4d-methods.Rd:209: Escaped LaTeX specials: \$
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Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
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Package suggested but not available for checking: ‘pinnacle.API’
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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 Rd file 'TungUbRF.Rd':
  ‘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.
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 Rd file 'make_pgk_cache_subdir_for_all_relative_files.Rd':
  ‘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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'sample_store.Rd':
  ‘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.
'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
Running examples in ‘poissonMT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: glmrobMT
> ### Title: Robust Fitting of Poisson Generalized Linear Models using MT
> ###   robust method
> ### Aliases: glmrobMT
> ### Keywords: robust regression nonlinear
> 
> ### ** Examples
> 
>   data(epilepsy)  
>   Efit1 <- glm(Ysum ~ Age10 + Base4*Trt, family=poisson, data=epilepsy)
> 
>   x <- model.matrix( ~ Age10 + Base4*Trt, data=epilepsy)
>   poissonMTsetwd(tempdir())   
>   Efit2 <- glmrobMT(x=x, y=epilepsy$Ysum) 
Computing initial estimate
Floating point exception
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
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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’.
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
Documented arguments not in \usage in Rd file 'genclone-method.Rd':
  ‘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
Package suggested but not available for checking: ‘ragt2ridges’
Unknown package ‘ragt2ridges’ in Rd xrefs
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: \$
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checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
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checkRd: (-1) med_pn.Rd:129: Escaped LaTeX specials: \&
Unknown package ‘advclust’ in Rd xrefs
Objects in \usage without \alias in Rd file 'ppmlasso-internal.Rd':
  ‘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
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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 Rd file 'local_test_setup.Rd':
  ‘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
Packages suggested but not available for checking: 'maptools', 'rgdal'
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
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
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
checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
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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 Rd file 'validate_inputs.Rd':
  ‘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 Rd file 'bitAND.Rd':
  ‘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 Rd file 'dot-marxan_data_reader.Rd':
  ‘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.
Invalid package aliases in Rd file 'granova-package.Rd':
  ‘granova-package’
Documented arguments not in \usage in Rd file 'estimateDeltaLOH.PairedPSCBS.Rd':
  ‘scale’

Documented arguments not in \usage in Rd file 'getLocusData.AbstractCBS.Rd':
  ‘splitters’

Documented arguments not in \usage in Rd file 'getSegments.AbstractCBS.Rd':
  ‘simplify’ ‘splitters’

Documented arguments not in \usage in Rd file 'mergeTwoSegments.AbstractCBS.Rd':
  ‘left’ ‘update’ ‘verbose’

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

Documented arguments not in \usage in Rd file 'updateMeansTogether.AbstractCBS.Rd':
  ‘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.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'kepner_robinson_test_internal.Rd':
  ‘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 Rd file 'pspline.sample.scalars.Rd':
  ‘time’

Documented arguments not in \usage in Rd file 'pspline.sample.timeseries.Rd':
  ‘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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'GetFitHReg.Rd':
  ‘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 Rd file 'assert_correct_attributes.Rd':
  ‘expected_colnames’

Documented arguments not in \usage in Rd file 'geopath_to_tibble.Rd':
  ‘route’

Documented arguments not in \usage in Rd file 'run_to_tibble.Rd':
  ‘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
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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: \#
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Documented arguments not in \usage in Rd file 'http_was_redirected.Rd':
  ‘response’

Documented arguments not in \usage in Rd file 'permutations.Rd':
  ‘nset’

Documented arguments not in \usage in Rd file 'pxweb_split_query.Rd':
  ‘pxweb_metadata’

Documented arguments not in \usage in Rd file 'split_dimensions_left_right.Rd':
  ‘pxq’

Documented arguments not in \usage in Rd file 'str_pad.Rd':
  ‘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 Rd file 'lagm.Rd':
  ‘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 Rd file 'get_names_MV.Rd':
  ‘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 Rd file 'Qest-internal.rd':
  ‘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 Rd file 'Qest-internal.rd':
  ‘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 file 'ad.simudata.Rd':
  ‘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.
Running examples in ‘qlcMatrix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sim.wordlist
> ### Title: Similarity matrices from wordlists
> ### Aliases: sim.wordlist sim.con sim.lang sim.graph
> 
> ### ** Examples
> 
> # ----- load data -----
> 
> # an example wordlist, see help(huber) for details
> data(huber)
> 
> # ----- similarity between languages -----
> 
> # most time is spend splitting the strings
> # the rest does not really influence the time needed
> system.time( sim <- sim.lang(huber, method = "p") )
Warning in split.default(yx, yj) :
  data length is not a multiple of split variable
Warning in split.default(yx, yj) :
  data length is not a multiple of split variable
Warning in match.fun(FUN)(x1, x2) :
  longer object length is not a multiple of shorter object length
Error in validObject(.Object) : 
  invalid class “dgCMatrix” object: 'i' and 'x' slots do not have equal length
Calls: system.time ... initialize -> callNextMethod -> .nextMethod -> validObject
Timing stopped at: 2.41 0.075 3.01
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in Rd file 'qrcmNP-internal.Rd':
  ‘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 Rd file 'qrcmNP-internal.Rd':
  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 Rd file 'qrcmNP-internal.Rd':
  ‘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 Rd file 'qrcm-internal.Rd':
  ‘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 Rd file 'qrcm-internal.Rd':
  ‘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 Rd file 'mmer_adapted.Rd':
  ‘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 Rd file 'export_responses_filedownload.Rd':
  ‘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 Rd file 'convert-wrappers.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'corpus-class.Rd':
  ‘if’

Documented arguments not in \usage in Rd file 'dfm-class.Rd':
  ‘drop_docid’

Documented arguments not in \usage in Rd file 'dictionary-class.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'matrix2fcm.Rd':
  ‘slots’

Documented arguments not in \usage in Rd file 'meta_system.Rd':
  ‘source’

Documented arguments not in \usage in Rd file 'search_index.Rd':
  ‘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 Rd file 'wordcloud_comparison.Rd':
  ‘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 file 'quhomology-package.Rd':
  \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
'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 Rd file 'bugs.inits.Rd':
  ‘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
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'print.ramchoiceRevealAtte.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.ramchoiceRevealPref.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.ramchoiceRevealPrefModel.Rd':
  ‘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’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'get_parameters.Rd':
  ‘parameters_def’

Documented arguments not in \usage in Rd file 'print.rapi_api.Rd':
  ‘...further’

Documented arguments not in \usage in Rd file 'print.rapi_operation.Rd':
  ‘...further’

Documented arguments not in \usage in Rd file 'print.rapi_schema_function.Rd':
  ‘...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 file 'RApiDatetime-package.Rd':
  \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
Package suggested but not available for checking: ‘gurobi’
Objects in \usage without \alias in Rd file 'cache.Rd':
  ‘\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 Rd file 'is.cached.Rd':
  ‘\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
Documented arguments not in \usage in Rd file 'mpaRaoS.Rd':
  ‘rasterm’

Objects in \usage without \alias in Rd file 'paRaoP.Rd':
  ‘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: \_
Package suggested but not available for checking: ‘clustermq’
'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 Rd file 'convert_to_native_raster.Rd':
  ‘ncol’ ‘nrow’

Documented arguments not in \usage in Rd file 'pad_to_fit.Rd':
  ‘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 Rd file 'onb_from_w.Rd':
  ‘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 Rd file 'init_time.Rd':
  ‘verbose’ ‘message’

Documented arguments not in \usage in Rd file 'print_time.Rd':
  ‘message’

Documented arguments not in \usage in Rd file 'process_point_series_1d.Rd':
  ‘points’

Documented arguments not in \usage in Rd file 'process_point_series_2d.Rd':
  ‘points’

Documented arguments not in \usage in Rd file 'tween.Rd':
  ‘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 Rd file 'gen_fractal_perlin.Rd':
  ‘image’

Documented arguments not in \usage in Rd file 'generate_base_shape.Rd':
  ‘image’

Documented arguments not in \usage in Rd file 'generate_cloud_layer.Rd':
  ‘image’

Documented arguments not in \usage in Rd file 'make_base_triangulated.Rd':
  ‘zscale’

Documented arguments not in \usage in Rd file 'raymarch_cloud_layer.Rd':
  ‘image’

Documented arguments not in \usage in Rd file 'render_snapshot_software.Rd':
  ‘ground_size’

Documented arguments not in \usage in Rd file 'transform_into_heightmap_coords.Rd':
  ‘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 Rd file 'generate_toon_outline.Rd':
  ‘angle’ ‘order_rotation’

Documented arguments not in \usage in Rd file 'init_time.Rd':
  ‘verbose’ ‘message’

Documented arguments not in \usage in Rd file 'merge_scene.Rd':
  ‘scene’

Documented arguments not in \usage in Rd file 'print_time.Rd':
  ‘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 Rd file 'Min_Max_Inverse_Scale_Vec.Rd':
  ‘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 Rd file 'export.default.Rd':
  ‘export.default’

S3 methods shown with full name in Rd file 'export.listpoly.Rd':
  ‘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.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.RData’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘data.csv’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'makeTitle.Rd':
  ‘string:’ ‘length:’ ‘prefix.length:’ ‘char:’

Documented arguments not in \usage in Rd file 'messageConsole.Rd':
  ‘message:’

Documented arguments not in \usage in Rd file 'tkEmptyLine.Rd':
  ‘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’
'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’
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 file 'RcppAnnoy-package.Rd':
  \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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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 file 'RcppSpdlog-package.Rd':
  \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
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'h_opt_density_res.Rd':
  ‘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 Rd file 'favicon.Rd':
  ‘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 file 'RDocumentation-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
'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
Documented arguments not in \usage in Rd file 'readAcquFile.Rd':
  ‘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 file 'readmnist-package.Rd':
  \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
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'add_docid.Rd':
  ‘impute_types’

Documented arguments not in \usage in Rd file 'texts.Rd':
  ‘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 Rd file 'rearrr_fn_.Rd':
  ‘overwrite’

Documented arguments not in \usage in Rd file 'rev_windows_rearranger_.Rd':
  ‘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 file 'recom-package.Rd':
  \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
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
Invalid package aliases in Rd file 'RED.Rd':
  ‘RED-package’
Auto-generated content requiring editing in Rd file 'referenceIntervals-package.Rd':
  \references: ‘~~ Literature or other references for background information ~~’
'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 Rd file 'Estep.Rd':
  ‘adaptive_quad’

Documented arguments not in \usage in Rd file 'd_bernoulli.Rd':
  ‘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
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ena.plot.group.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:46: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:38: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:42: Escaped LaTeX specials: \$
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PackageCites.bib’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'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
Documented arguments not in \usage in Rd file 'gaussian_process_cv.Rd':
  ‘ncomp’

Documented arguments not in \usage in Rd file 'get_samples_from_strata.Rd':
  ‘starta’

Documented arguments not in \usage in Rd file 'ith_subsets_ortho_diss.Rd':
  ‘remove’

Documented arguments not in \usage in Rd file 'pca_nipals.Rd':
  ‘Y’

Documented arguments not in \usage in Rd file 'predict_gaussian_process.Rd':
  ‘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.
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 Rd file 'get.V.Rd':
  ‘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
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 Rd file 'compareChecksum.GenericDataFile.Rd':
  ‘verbose’

Documented arguments not in \usage in Rd file 'dim.GenericTabularFile.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'dsApplyInPairs.GenericDataFileSet.Rd':
  ‘ds’

Documented arguments not in \usage in Rd file 'fromFile.GenericDataFile.Rd':
  ‘unknown’

Documented arguments not in \usage in Rd file 'gzip.GenericDataFile.Rd':
  ‘verbose’

Documented arguments not in \usage in Rd file 'readChecksum.ChecksumFile.Rd':
  ‘verbose’

Documented arguments not in \usage in Rd file 'writeChecksum.GenericDataFile.Rd':
  ‘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.
'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
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
Package suggested but not available for checking: ‘rgdal’
Documented arguments not in \usage in Rd file 'rgl.fns.Rd':
  ‘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
'LazyData' is specified without a 'data' directory
'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 Rd file 'dimnames.AbstractFileArray.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'length.AbstractFileArray.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'readContiguousValues.AbstractFileArray.Rd':
  ‘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
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 Rd file 'inner_t_index_calculation.Rd':
  ‘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
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: \$
'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
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
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
Documented arguments not in \usage in Rd file 'bind.Rd':
  ‘.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’.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rnaturalearthhires’
Malformed Title field: should not end in a period.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
'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: ‘rgdal’
Documented arguments not in \usage in Rd file 'SanitizeURL.Rd':
  ‘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.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'internal_plots.Rd':
  ‘panelFirst’

Documented arguments not in \usage in Rd file 'internals.Rd':
  ‘L2fam’
Objects in \usage without \alias in Rd file 'internals.Rd':
  ‘.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
Running examples in ‘robcbi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: QQline
> ### Title: Add a theoretical QQ-line in a plot
> ### Aliases: QQline
> ### Keywords: stats
> 
> ### ** Examples
> 
> library(robcbi)
> data(Finney)
> Vol  <- Finney$Vol; Rate <- Finney$Rate; Resp <- Finney$Resp
> lVol <-log(Vol); lRate <- log(Rate)
> z.cub <- glm(Resp~lVol+lRate,family=binomial,method="cubinf", ufact=3.2)
Floating point exception
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'internal-interpolate.Rd':
  ‘upRad.s’
Objects in \usage without \alias in Rd file 'internal-interpolate.Rd':
  ‘.getPsi.wL’ ‘.getPsi.P’

Objects in \usage without \alias in Rd file 'rescaleFunction-methods.Rd':
  ‘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 Rd file 'createITPSplineResult.Rd':
  ‘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 file 'nlrob.control.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'Sample.rgasp.Rd':
  ‘interval_data’

Objects in \usage without \alias in Rd file 'neg_log_marginal_post_approx_ref_ppgasp.Rd':
  ‘neg_log_marginal_post_approx_ref’

Objects in \usage without \alias in Rd file 'separable_multi_kernel.Rd':
  ‘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 file 'choose.test.Rd':
  ‘Xpaired’ ‘Ypaired’ ‘Xextra’ ‘Yextra’ ‘mc.rep’
Argument items with no description in Rd file 'multinom.test.Rd':
  ‘X’ ‘Y’ ‘alternative’ ‘correct’ ‘perm’ ‘mc.rep’ ‘method’ ‘verbose’
  ‘mode’ ‘useC’
Argument items with no description in Rd file 'mw.mw.2.perm.Rd':
  ‘X’ ‘Y’ ‘Xprime’ ‘Yprime’ ‘.corr’ ‘mc.rep’ ‘alternative’ ‘verbose’
Argument items with no description in Rd file 'pm.wilcox.test.Rd':
  ‘Xpaired’ ‘Ypaired’ ‘Xextra’ ‘Yextra’ ‘alternative’ ‘verbose’
Argument items with no description in Rd file 'sim.partially.matched.Rd':
  ‘meanRatio’ ‘sdRatio’ ‘within.sd’ ‘type’ ‘hyp’
Argument items with no description in Rd file 'wmw.paired.replicates.test.Rd':
  ‘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 Rd file 'gettptnfpfn-defunct.Rd':
  ‘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 Rd file 'add_matches_columns.Rd':
  ‘Matches’

Documented arguments not in \usage in Rd file 'run_checks_two.Rd':
  ‘lookback’ ‘standard_deviaion’ ‘match_on’ ‘model_type’

Documented arguments not in \usage in Rd file 'trim_pool.Rd':
  ‘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.
Auto-generated content requiring editing in Rd file 'roloc-package.Rd':
  \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 Rd file 'DOLLAR.Class.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'DOLLARLT_-.Class.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'getMethods.Class.Rd':
  ‘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 Rd file 'internal-interpolate.Rd':
  ‘upRad.s’ ‘withSmooth’
Assignments in \usage in Rd file 'internal-interpolate.Rd':
  .readGridFromCSV <- function(fromFileCSV) .generateInterpGrid(thGrid, 
      PFam, toFileCSV = "temp.csv", getFun = .getLMGrid, ..., modifyfct, 
      nameInSysdata, GridFileName, withPrint = TRUE, len = 13)

Objects in \usage without \alias in Rd file 'internalRobestHelpers.Rd':
  ‘.constructArg.list’ ‘.fix.in.defaults’ ‘.pretreat’ ‘.check.eps’
  ‘.isOKsteps’ ‘.isOKfsCor’

Documented arguments not in \usage in Rd file 'internal_Cniperplots.Rd':
  ‘origCl’

Objects in \usage without \alias in Rd file 'internals.Rd':
  ‘.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’
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'anova.phylopars.lm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'logLik.phylopars.Rd':
  ‘\dots’
Argument items with no description in Rd file 'logLik.phylopars.lm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.SSC.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.phylopars.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.phylopars.lm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.phylopars.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.phylopars.lm.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: 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 Rd file 'rrcov-utils.Rd':
  ‘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 file 'RNAPlot.Rd':
  ‘seqTF’
Argument items with no description in Rd file 'aptPlotCT.Rd':
  ‘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 Rd file '000-LB-.RspDocument.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'RspEvalDirective.Rd':
  ‘attributes’

Documented arguments not in \usage in Rd file 'RspExpression.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'RspIncludeDirective.Rd':
  ‘attributes’

Documented arguments not in \usage in Rd file 'buildNonSweaveVignette.Rd':
  ‘pathname’

Documented arguments not in \usage in Rd file 'buildNonSweaveVignettes.Rd':
  ‘path’ ‘pattern’

Documented arguments not in \usage in Rd file 'exprToCode.RspSourceCodeFactory.Rd':
  ‘expr’

Documented arguments not in \usage in Rd file 'getContent.RspText.Rd':
  ‘unescaped’

Documented arguments not in \usage in Rd file 'toSourceCode.RspSourceCodeFactory.Rd':
  ‘expr’

Documented arguments not in \usage in Rd file 'trim.RspDocument.Rd':
  ‘envir’

Documented arguments not in \usage in Rd file 'writeResponse.RspResponse.Rd':
  ‘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 Rd file 'rrum_helper.Rd':
  ‘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.
'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 17.0.5 (1)’
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 Rd file 'ApiRequest.Rd':
  ‘report.description’

Documented arguments not in \usage in Rd file 'BuildLineItemSegment.Rd':
  ‘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.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'SetHash.Rd':
  ‘\dots’
Invalid package aliases in Rd file 'Rstpm2-package.Rd':
  ‘Rstpm2-package’
Documented arguments not in \usage in Rd file 'calculate.var.np.Rd':
  ‘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 Rd file 'summary.trimbatch.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'trim_workhorse.Rd':
  ‘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’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'tidy_pi_traces.Rd':
  ‘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 Rd file 'MEM_MIDAS_lr_pred_no_skew.Rd':
  ‘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 Rd file 'printHTML.trackinfo.Rd':
  ‘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 Rd file 'dot-is_datetime_valid.Rd':
  ‘(`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
Running examples in ‘rusquant-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getSymbols.Moex
> ### Title: Get financial data from MOEX Exchange
> ### Aliases: getSymbols.Moex
> 
> ### ** Examples
> 
> data <- getSymbols.Moex('GAZP', from='2022-01-01', to='2022-01-10', period='day', auto.assign=FALSE)
Warning in open.connection(con, "rb") :
  URL 'https://iss.moex.com/iss/securities.json?q=GAZP': Timeout of 60 seconds was reached
Error in open.connection(con, "rb") : 
  cannot open the connection to 'https://iss.moex.com/iss/securities.json?q=GAZP'
Calls: getSymbols.Moex ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘glmmADMB’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gpuR’
Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'summary.rv.Rd':
  ‘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 Rd file 'matmult.Rd':
  ‘%*%.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 Rd file 'wind.fit_int.Rd':
  ‘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
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
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 Rd file 'LoadDataFile.Rd':
  ‘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 file 'predict.s2netR.Rd':
  ‘...’
Argument items with no description in Rd file 'print_misc.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'file_status.Rd':
  ‘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 file 'SAMM-package.Rd':
  \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
'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 file 'creer_graphe.Rd':
  ‘groupes’
Argument items with no description in Rd file 'fichiers.Rd':
  ‘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.
Package suggested but not available for checking: ‘rgdal’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 Rd file 'item_rm_recursive.Rd':
  ‘sb_id’

Documented arguments not in \usage in Rd file 'session_age.Rd':
  ‘sb_id’ ‘...’

Documented arguments not in \usage in Rd file 'session_expired.Rd':
  ‘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.
Running examples in ‘scales-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: label_dollar
> ### Title: Label currencies ($100, $2.50, etc)
> ### Aliases: label_dollar
> 
> ### ** Examples
> 
> demo_continuous(c(0, 1), labels = label_dollar())
scale_x_continuous(labels = label_dollar())
> demo_continuous(c(1, 100), labels = label_dollar())
scale_x_continuous(labels = label_dollar())
> 
> # Customise currency display with prefix and suffix
> demo_continuous(c(1, 100), labels = label_dollar(prefix = "USD "))
scale_x_continuous(labels = label_dollar(prefix = "USD "))
> euro <- label_dollar(
+   prefix = "",
+   suffix = "\u20ac",
+   big.mark = ".",
+   decimal.mark = ","
+ )
> demo_continuous(c(1000, 1100), labels = euro)
scale_x_continuous(labels = euro)
Error in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  : 
  conversion failure on '1.000€' in 'mbcsToSbcs': for € (U+20AC)
Calls: <Anonymous> ... <Anonymous> -> heightDetails -> heightDetails.text -> grid.Call
Execution halted
'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
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.
'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
S3 methods shown with full name in Rd file 'plot.Rd':
  ‘plot.discretization’

S3 methods shown with full name in Rd file 'predict.Rd':
  ‘predict.discretization’ ‘predict.reject_infered’

S3 methods shown with full name in Rd file 'summary.Rd':
  ‘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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘sdcLog-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sdc_descriptives
> ### Title: Disclosure control for descriptive statistics
> ### Aliases: sdc_descriptives
> 
> ### ** Examples
> 
> sdc_descriptives(
+   data = sdc_descriptives_DT,
+   id_var = "id",
+   val_var = "val_1"
+ )
Error in `[.data.table`(dt, id_na == TRUE, list(value_share_na = value_share),  : 
  'by' or 'keyby' must evaluate to a vector or a list of vectors (where 'list' includes data.table and data.frame which are lists, too)
Calls: sdc_descriptives -> check_dominance -> [ -> [.data.table
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘FAQ.Rmd’ using rmarkdown
--- finished re-building ‘FAQ.Rmd’

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

Quitting from lines 115-116 [descriptives_simple] (intro.Rmd)
Error: processing vignette 'intro.Rmd' failed with diagnostics:
'by' or 'keyby' must evaluate to a vector or a list of vectors (where 'list' includes data.table and data.frame which are lists, too)
--- failed re-building ‘intro.Rmd’

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

Quitting from lines 52-53 [example1_sdc.n_ids] (options.Rmd)
Error: processing vignette 'options.Rmd' failed with diagnostics:
'by' or 'keyby' must evaluate to a vector or a list of vectors (where 'list' includes data.table and data.frame which are lists, too)
--- failed re-building ‘options.Rmd’

SUMMARY: processing the following files failed:
  ‘intro.Rmd’ ‘options.Rmd’

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'rgdal', 'rgeos'
Packages suggested but not available for checking: 'maptools', 'rgdal'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'parse_search_analytics.Rd':
  ‘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 Rd file 'pipe.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond 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
Packages suggested but not available for checking: 'spgrass6', 'rgdal'
'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 Rd file 'min.abs.Rd':
  ‘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: \^
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Running examples in ‘SenSpe-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: snsp2mp
> ### Title: Two-biomarker paired comparison in specificity (or sensitivity)
> ###   at a controlled sensitivity (or specificity) level
> ### Aliases: snsp2mp
> 
> ### ** Examples
> 
> ## simulate paired biomarkers X and Y, with correlation 0.5, 100 cases and 100 controls
> n1 <- 100
> n0 <- 100
> rho <- 0.5
> mkx <- rnorm(n1+n0,0,1)
> mky <- rho*mkx + sqrt(1-rho^2)*rnorm(n1+n0,0,1)
> mkx <- mkx + c(rep(2,n1),rep(0,n0))
> mky <- mky + c(rep(1,n1),rep(0,n0))
> mk <- rbind(mkx,mky)
> 
> ## compare specificity at controlled 0.95 sensitivity
> est <- snsp2mp(mk, 100, 0.95)

 *** caught segfault ***
address 0x5648c57c6a70, cause 'memory not mapped'

Traceback:
 1: snsp2mp(mk, 100, 0.95)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
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 file 'seqCBS-package.Rd':
  \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 file 'sequential.design.Rd':
  ‘\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
Package suggested but not available for checking: ‘BPCells’
Packages suggested but not available for checking: 'BPCells', 'presto'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'jc_clc_perm_impl.Rd':
  ‘a’

Documented arguments not in \usage in Rd file 'local_g_spt.Rd':
  ‘n_sim’

Documented arguments not in \usage in Rd file 'permute_listw.Rd':
  ‘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
'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
'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
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
Package suggested but not available for checking: ‘uchardet’
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'shiny_models.Rd':
  ‘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
Package suggested but not available for checking: ‘uchardet’
'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 file 'estThetaRow.Rd':
  ‘theta’
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:
  ‘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 Rd file 'make_kernel_dist.Rd':
  ‘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’
Packages suggested but not available for checking: 'Rcgmin', 'Rvmmin'
Unknown packages ‘Rvmmin’, ‘Rcgmin’ in Rd xrefs
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
Packages suggested but not available for checking: 'rgdal', 'rgeos'
Documented arguments not in \usage in Rd file 'interval_labels.Rd':
  ‘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 file 'SimplifyStats-package.Rd':
  \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...’
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 Rd file 'sim_founderRVstatus.Rd':
  ‘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.
Package suggested but not available for checking: ‘INLA’
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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 file 'management.prob.Rd':
  ‘...’
Argument items with no description in Rd file 'mng.tree.removal.Rd':
  ‘\dots’
Argument items with no description in Rd file 'prep.common.vars.fun.Rd':
  ‘\dots’
Argument items with no description in Rd file 'recr.BBG2008.Rd':
  ‘common.vars’
Documented arguments not in \usage in Rd file 'to_shiny_tag.Rd':
  ‘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 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 Rd file 'calculate_gefficiency.Rd':
  ‘RunMatrix’

Documented arguments not in \usage in Rd file 'constructRunMatrix.Rd':
  ‘Levelvector’

Documented arguments not in \usage in Rd file 'effectpower.Rd':
  ‘X’

Documented arguments not in \usage in Rd file 'gen_momentsmatrix.Rd':
  ‘Levelvector’

Documented arguments not in \usage in Rd file 'generate_noise_block.Rd':
  ‘RunMatrix’

Documented arguments not in \usage in Rd file 'genhypmatrix.Rd':
  ‘Parameters’ ‘Levels’ ‘G’

Documented arguments not in \usage in Rd file 'genparammatrix.Rd':
  ‘Parameters’ ‘Levels’ ‘G’

Documented arguments not in \usage in Rd file 'priorlevels.Rd':
  ‘Levelvector’

Documented arguments not in \usage in Rd file 'reduceRunMatrix.Rd':
  ‘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
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’
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 file 'smallstuff-package.Rd':
  \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.
Package suggested but not available for checking: ‘rgdal’
'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: \$ \$
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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 Rd file 'aux_cs.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gauss.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gw.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_mat.Rd':
  ‘mat_list1’ ‘mat_list2’ ‘x’ ‘y’ ‘return_single’

Documented arguments not in \usage in Rd file 'aux_matern.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_pexp.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_spher.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_tapmat.Rd':
  ‘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 file 'smoke-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
'LazyData' is specified without a 'data' directory
checkRd: (-1) hoods2dsmooth.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dmeitsjer.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dsmooth.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) smoothie-package.Rd:42: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
Auto-generated content requiring editing in Rd file 'smotefamily-package.Rd':
  \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 Rd file 'sm-internal.Rd':
  ‘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
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 Rd file 'som.nn.do.train.Rd':
  ‘model’

Documented arguments not in \usage in Rd file 'som.nn.som.internal.Rd':
  ‘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 Rd file 'plot.predictions.Rd':
  ‘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 Rd file 'path2name.Rd':
  ‘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
'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’
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 Rd file 'logit.Rd':
  ‘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’
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'binarizer.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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.
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.
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 Rd file 'hazard.Rd':
  ‘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 Rd file 'grapes-matches-grapes.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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 Rd file 'changeDevSettings.Rd':
  ‘defaultsSettings’

Documented arguments not in \usage in Rd file 'checkMethod.Rd':
  ‘allowedMethod’

Documented arguments not in \usage in Rd file 'convertListToS4.Rd':
  ‘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 Rd file 'i_is_index.Rd':
  ‘max_length’

Documented arguments not in \usage in Rd file 'i_read_asd_spectra.Rd':
  ‘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 Rd file 'add_details.Rd':
  ‘\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’
Specified C++11: please drop specification unless essential
checkRd: (-1) PimaIndiansDiabetes_long.Rd:14: Escaped LaTeX specials: \^
checkRd: (-1) PimaIndiansDiabetes_wide.Rd:16: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'split_feasibility.Rd':
  ‘split_feasibility-package’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'obis_search.Rd':
  ‘scientificname’

Documented arguments not in \usage in Rd file 'spocc_objects.Rd':
  ‘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 Rd file 'basketball_center_circle_fill.Rd':
  ‘linethickness’

Documented arguments not in \usage in Rd file 'basketball_free_throw_circle_dash.Rd':
  ‘end_angleThe’

Documented arguments not in \usage in Rd file 'basketball_painted_area.Rd':
  ‘free_throw_lane_boundary_line_thickness’

Documented arguments not in \usage in Rd file 'curling_features_set_colors.Rd':
  ‘sheet’ ‘ring_1’ ‘ring_2’ ‘ring_3’

Documented arguments not in \usage in Rd file 'football_field_border.Rd':
  ‘boundary_thickness’

Documented arguments not in \usage in Rd file 'football_field_border_outline.Rd':
  ‘boundary_thickness’

Documented arguments not in \usage in Rd file 'hockey_features_set_colors.Rd':
  ‘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 Rd file 'lacrosse_off_field_officials_box.Rd':
  ‘feature_thickness’

Documented arguments not in \usage in Rd file 'lacrosse_penalty_box_outline.Rd':
  ‘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 Rd file 'checkFunEvalsDesignSize.Rd':
  ‘fun’ ‘upper’

Documented arguments not in \usage in Rd file 'print.spotBOModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotGaussianProcessModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotLOESS.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotLassoModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotLinearModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotRSM.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotRandomForest.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotRanger.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotSeverity.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'print.spotTreeModel.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'simulationSpectral.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond 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 file 'sim.kong.Rd':
  ‘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 Rd file 'sraAutoregTimeseries.Rd':
  ‘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 Rd file 'namesMultiple.Rd':
  ‘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 Rd file 'connect-report_mig-method.Rd':
  ‘h’ ‘...’

Documented arguments not in \usage in Rd file 'print-report_mig-method.Rd':
  ‘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 Rd file 'which_class.Rd':
  ‘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’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Documented arguments not in \usage in Rd file 'estEffsCPP.Rd':
  ‘y’ ‘w’ ‘x’ ‘ncores’

Documented arguments not in \usage in Rd file 'updateFA.Rd':
  ‘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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘imputeMissings’
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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 file 'd.sum.of.mixtures.EXPLN.Rd':
  ‘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 file 'strategicplayers-package.Rd':
  \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
Package suggested but not available for checking: ‘rgeos’
Specified C++11: please drop specification unless essential
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get_groups.Rd':
  ‘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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
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 Rd file 'size.penalize.Rd':
  ‘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
Package suggested but not available for checking: ‘maptools’
Documented arguments not in \usage in Rd file 'subsamp.Rd':
  ‘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 file 'supcluster-package.Rd':
  \references: ‘~~ Literature or other references for background information ~~’
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 Rd file 'check_package.Rd':
  ‘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
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘apollo’
Specified C++11: please drop specification unless essential
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
Package suggested but not available for checking: ‘INLA’
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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘swephRdata’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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
'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 Rd file 'table_params_circle.Rd':
  ‘d’

Documented arguments not in \usage in Rd file 'table_params_rect.Rd':
  ‘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 Rd file 'plot.prEntries.Rd':
  ‘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 Rd file 'designMatrices.Rd':
  ‘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
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘clustermq’
'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 Rd file 'default_db_ref.Rd':
  ‘name’ ‘url’ ‘desc’ ‘id_regex’

Documented arguments not in \usage in Rd file 'limited_print.Rd':
  ‘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
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'maptools', '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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgdal’
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
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
'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 Rd file 'CompileLatexDir.Rd':
  ‘engine:’ ‘compile.dir:’

Documented arguments not in \usage in Rd file 'GetLayerSampleIndexes.Rd':
  ‘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'
'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.
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in Rd file 'timeSeries.Rd':
  ‘tbind.timeSeries’

Objects in \usage without \alias in Rd file 'tis.Rd':
  ‘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
Documented arguments not in \usage in Rd file 'witcher.Rd':
  ‘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 Rd file 'poisson_likelihood.Rd':
  ‘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
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3dimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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
Documented arguments not in \usage in Rd file 'gate_interactive_chr_int.Rd':
  ‘gate_list’

Documented arguments not in \usage in Rd file 'gate_programmatic.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'gate_programmatic_chr_int.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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 Rd file 'deprecated-se.Rd':
  ‘expand_cols’

Documented arguments not in \usage in Rd file 'tidyr_legacy.Rd':
  ‘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 Rd file 'vars_select.Rd':
  ‘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
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 17.0.5 (1)’
Specified C++11: please drop specification unless essential
Auto-generated content requiring editing in Rd file 'timeperiodsR-package.Rd':
  \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’
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'LazyData' is specified without a 'data' directory
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'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 Rd file 'TNRS_core.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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: ‘corpus.JSS.papers’
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
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Package suggested but not available for checking: ‘toscaData’
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Problems with news in ‘NEWS.md’:
No news entries found.
Documented arguments not in \usage in Rd file 'createLink.Rd':
  ‘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 file 'abrams.Rd':
  ‘prior’ ‘change’
Argument items with no description in Rd file 'absoluteIncreaseALL.Rd':
  ‘storedev’ ‘\dots’
Argument items with no description in Rd file 'boundaryLineALL.Rd':
  ‘\dots’
Argument items with no description in Rd file 'growthAveragingALL.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plotFirstYears.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plotRelease.Rd':
  ‘\dots’
Argument items with no description in Rd file 'splechtnaALL.Rd':
  ‘\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 file 'seqimplic.Rd':
  ‘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 Rd file 'transport-internal.Rd':
  ‘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.
Package which this enhances but not available for checking: ‘fwelnet’
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Eunomia', 'CohortGenerator', 'CirceR'
Documented arguments not in \usage in Rd file 'clean_data.Rd':
  ‘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 Rd file 'correct_continuous.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'tc_correlation.Rd':
  ‘p’

Documented arguments not in \usage in Rd file 'tc_efunc.Rd':
  ‘p’

Documented arguments not in \usage in Rd file 'tc_mfunc.Rd':
  ‘p’

Documented arguments not in \usage in Rd file 'tc_response.Rd':
  ‘p’

Documented arguments not in \usage in Rd file 'truncate_input.Rd':
  ‘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
Auto-generated content requiring editing in Rd file 'treemisc-package.Rd':
  \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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
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Malformed Title field: should not end in a period.
'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:
    Changes
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
Documented arguments not in \usage in Rd file 'dvinecopula_objective.Rd':
  ‘udata’

Documented arguments not in \usage in Rd file 'wobjective.Rd':
  ‘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 Rd file 'nlar.struct.Rd':
  ‘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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in Rd file 'tsibble-vctrs.Rd':
  ‘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
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
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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
Package which this enhances but not available for checking: ‘sl3’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
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 file 'HC.Rd':
  ‘X’ ‘K’
Argument items with no description in Rd file 'KA.Rd':
  ‘X’ ‘K’ ‘distancemetric’
Argument items with no description in Rd file 'SOMs.Rd':
  ‘X’ ‘K’ ‘topo’ ‘rlen’ ‘alpha’ ‘n.hood’
Argument items with no description in Rd file 'binarise.Rd':
  ‘U’ ‘K’ ‘technique’ ‘parameter’
Argument items with no description in Rd file 'closestToSquareFactors.Rd':
  ‘n’
Argument items with no description in Rd file 'clustDist.Rd':
  ‘U1’ ‘U2’ ‘X’ ‘criterion’
Argument items with no description in Rd file 'clustVec2partMat.Rd':
  ‘C’
Argument items with no description in Rd file 'clusterDataset.Rd':
  ‘X’ ‘K’ ‘D’ ‘methods’
Argument items with no description in Rd file 'factors.Rd':
  ‘n’ ‘primeonly’
Argument items with no description in Rd file 'fixnans.Rd':
  ‘X’ ‘type’
Argument items with no description in Rd file 'fuzzystretch.Rd':
  ‘X’ ‘x0’
Argument items with no description in Rd file 'generateCoPaM.Rd':
  ‘U’ ‘relabel_technique’ ‘w’ ‘X’ ‘distCriterion’ ‘K’ ‘GDM’
Argument items with no description in Rd file 'isValidBPM.Rd':
  ‘U’
Argument items with no description in Rd file 'isempty.Rd':
  ‘X’
Argument items with no description in Rd file 'isnullorempty.Rd':
  ‘X’
Argument items with no description in Rd file 'kmeansKA.Rd':
  ‘X’ ‘K’ ‘distancemetric’ ‘iter.max’ ‘nstart’ ‘algorithm’ ‘trace’
Argument items with no description in Rd file 'mnplots.Rd':
  ‘Vmse’ ‘mseCache’ ‘subplotdim’ ‘subplotind’ ‘minimiseDistance’
Argument items with no description in Rd file 'mseclusters.Rd':
  ‘X’ ‘B’ ‘normalise’
Argument items with no description in Rd file 'normaliseMatrix.Rd':
  ‘X’ ‘type’
Argument items with no description in Rd file 'partMat2clustVec.rd':
  ‘U’ ‘skipValidity’
Argument items with no description in Rd file 'permutations.Rd':
  ‘n’
Argument items with no description in Rd file 'relabelClusts.Rd':
  ‘ref’ ‘input’ ‘technique’ ‘X’ ‘distCriterion’
Documented arguments not in \usage in Rd file 'sqrtm.Rd':
  ‘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 Rd file 'MortSmooth_tpower.Rd':
  ‘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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘USA.state.boundaries.data’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'use_course_details.Rd':
  ‘destdir’ ‘zipfile’

Documented arguments not in \usage in Rd file 'write-this.Rd':
  ‘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: \_ \_ \_
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checkRd: (-1) exec.pay.Rd:5: Escaped LaTeX specials: \$
checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
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Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'countDNAPatternInAlt.Rd':
  ‘trascriptsTable’

Documented arguments not in \usage in Rd file 'countDNAPatternInAltOneVariant.Rd':
  ‘trascriptsTable’

Documented arguments not in \usage in Rd file 'getAltSequence.Rd':
  ‘trascriptsTable’

Documented arguments not in \usage in Rd file 'getCodonInAlt.Rd':
  ‘trascriptsTable’ ‘codonPositionsColumnn’

Documented arguments not in \usage in Rd file 'getCodonInAltOneVariant.Rd':
  ‘trascriptsTable’ ‘codonPositionsColumnn’

Documented arguments not in \usage in Rd file 'getTSSKozakOneVariant.Rd':
  ‘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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
Documented arguments not in \usage in Rd file 'validate_extend.Rd':
  ‘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
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: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'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 Rd file 'syntab.Rd':
  ‘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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/vein.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Argument items with no description in Rd file 'learnPartitionWithLLR.Rd':
  ‘type’ ‘procedure’ ‘ql’ ‘qq’ ‘BinaryLearningProcedure’
Argument items with no description in Rd file 'plotClassifRule.Rd':
  ‘object’
Documented arguments not in \usage in Rd file 'boxplot_VICI.Rd':
  ‘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 Rd file 'draw_map_shiny.Rd':
  ‘rigth.lim’

Documented arguments not in \usage in Rd file 'map_summary.Rd':
  ‘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
'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 Rd file 'insert_preview.Rd':
  ‘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 Rd file 'cpp_vol2bird_version.Rd':
  ‘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 Rd file 'blendColor.Rd':
  ‘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: \&
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No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'get.wal.mipmap.heights.Rd':
  ‘height_mm’

Documented arguments not in \usage in Rd file 'get.wal.mipmap.widths.Rd':
  ‘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
Documented arguments not in \usage in Rd file 'WaveDjF.Rd':
  ‘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 file 'maxithresh.Rd':
  \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
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 Rd file 'train_spectra.Rd':
  ‘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.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'read_img.Rd':
  ‘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.
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 file 'zdifference_ordinal.Rd':
  ‘na.rm’
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'sampledHierarchicalConsensusModules.Rd':
  ‘consensusTOMFilePattern’
S3 methods shown with full name in Rd file 'QIC.gee.Rd':
  ‘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
Documented arguments not in \usage in Rd file 'remove_empty.Rd':
  ‘quiet’

Documented arguments not in \usage in Rd file 'undoHistory.Rd':
  ‘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
Package suggested but not available for checking: ‘rgdal’
Documented arguments not in \usage in Rd file 'displayDataTable.Rd':
  ‘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
Package suggested but not available for checking: ‘pageviews’
Package suggested but not available for checking: ‘pageviews’
'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.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'new_givens_path.Rd':
  ‘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 Rd file 'sample_me.Rd':
  ‘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 Rd file 'Cut.off.Rd':
  ‘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
'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
Package suggested but not available for checking: ‘rbokeh’
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 Rd file 'xpose.create.title.Rd':
  ‘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 Rd file 'check_problem.Rd':
  ‘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 file 'getCondition.Rd':
  ‘object’
Argument items with no description in Rd file 'screen.Rd':
  ‘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
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'IC.Rd':
  ‘\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 file 'ZIBseq-package.Rd':
  \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
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
Specified C++11: please drop specification unless essential
checkRd: (-1) abclass.Rd:133: Lost braces; missing escapes or markup?
   133 |     \code{abclass.control()} returns an object of class {abclass.control}
       |                                                         ^
checkRd: (-1) supclass.Rd:109: Lost braces; missing escapes or markup?
   109 | to solve the equivalent linear programming problem via the package {Rglpk}.
       |                                                                    ^
checkRd: (-1) supclass.Rd:110: Lost braces; missing escapes or markup?
   110 | It is recommended to use a recent version of {GLPK}.
       |                                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) abess.Rd:260: Lost braces in \itemize; meant \describe ?
checkRd: (-1) abess.Rd:261: Lost braces in \itemize; meant \describe ?
checkRd: (-1) abess.Rd:262: Lost braces in \itemize; meant \describe ?
checkRd: (-1) abess.Rd:263: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coef.abesspca.Rd:16: Lost braces; missing escapes or markup?
    16 | This parameter is omitted if {sparse.type = "kpc"}.}
       |                              ^
checkRd: (-1) coef.abesspca.Rd:22: Lost braces; missing escapes or markup?
    22 | This parameter is omitted if {sparse.type = "fpc"}.}
       |                              ^
checkRd: (-1) generate.data.Rd:51: Lost braces
    51 | code{cortype = 3} denotes the constant structure,
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_ex_data.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_ex_data.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_ex_data.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_ex_data.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_results.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_results.Rd:30: Lost braces in \itemize; meant \describe ?
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
checkRd: (-1) bind_tweets.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bind_tweets.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) accelimp.Rd:15: Lost braces
    15 | \item[]{...}
       |        ^
Found the following files/directories:
  ‘acceldata2.RData’
Documented arguments not in \usage in Rd file 'ADMM_EN2.Rd':
  ‘alpha’

Documented arguments not in \usage in Rd file 'ADMM_EN_SMW.Rd':
  ‘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 file 'testRmACD.Rd':
  ‘pStar’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) overstallwoods.Rd:184-185: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:186-187: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:188-189: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:190-191: Lost braces in \itemize; \value handles \item{}{} directly
'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 Rd file 'fitSnpNmfArray.Rd':
  ‘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
checkRd: (-1) Ehrenfest.Rd:19: Lost braces
    19 | In this experiment there are i balls in Urn I, and remaining 2n-i balls in Urn II. Then at any instance, the probability of selecting a ball from Urn I and placing it in Urn II is i/2n, and the other way of placing a ball from Urn II to Urn I is (2n-i)/2n. At each instant we let the number i of balls in the Urn I to be the state of the system. Thus, the state space is S = { 0, 1, 2, \ldots, 2n }. Then we can pass from state i only to either of the states i-1 or i+1.
       |                                                                                                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) Ehrenfest.Rd:20: Lost braces
    20 | Here, S = {0, 1, \ldots, 2n}. 
       |           ^
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 Rd file 'd1.Rd':
  ‘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
'LazyData' is specified without a 'data' directory
checkRd: (-1) add_predictions.Rd:38: Lost braces; missing escapes or markup?
    38 | "_{x}", where x = 1 to the number of values returned.
       |   ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
checkRd: (-1) est_S_Plus_Plus_MethodA.Rd:31: Lost braces; missing escapes or markup?
    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
checkRd: (-1) est_S_Plus_Plus_MethodB.Rd:31: Lost braces; missing escapes or markup?
    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method B}
       |                                                          ^
checkRd: (-1) est_S_Star_Plus_MethodA.Rd:29: Lost braces; missing escapes or markup?
    29 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
checkRd: (-1) est_S_Star_Plus_MethodB.Rd:29: Lost braces; missing escapes or markup?
    29 |   \item{trt_diff}{Estimate of treatment difference for S_{*+} using Method B}
       |                                                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) adana.Rd:25: Lost braces; missing escapes or markup?
    25 |   \item{gatype}{Type of GA. \itemize{\item{"gga": generational GA}  \item{"ssga": steady state GA} } {Default value is "gga"}}
       |                                                                                                      ^
checkRd: (-1) adana.Rd:26: Lost braces; missing escapes or markup?
    26 |   \item{objective}{Type of optimization. \itemize{\item{"min": minimization}  \item{"max": maximization} } {Default value is "max"}}
       |                                                                                                            ^
checkRd: (-1) adana.Rd:34: Lost braces; missing escapes or markup?
    34 |                  {Default value is "initbin"}}
       |                  ^
checkRd: (-1) adana.Rd:56: Lost braces; missing escapes or markup?
    56 |                \itemize{\item{"integer"}  \item{"real"} } {Default value is "real"}}
       |                                                           ^
checkRd: (-1) adana.Rd:185: Lost braces; missing escapes or markup?
   185 |     {Default value is "w"}
       |     ^
'LazyData' is specified without a 'data' directory
Invalid package aliases in Rd file 'AdaptGauss-package.Rd':
  ‘MultiModal-package’
checkRd: (-1) aslm-methods.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aslm-methods.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aslm-methods.Rd:13: Lost braces in \itemize; meant \describe ?
Invalid package aliases in Rd file 'aslm-package.Rd':
  ‘aslm-package’ ‘asggm-package’
Argument items with no description in Rd file 'asggm-internal.Rd':
  ‘ansL’ ‘kNodes’ ‘spP’
Specified C++11: please drop specification unless essential
Unknown packages ‘HI’, ‘MHadaptive’ in Rd xrefs
checkRd: (-1) adapt.Rd:46: Lost braces
    46 | \item{qvals}{a vector of values in [0, 1]U{Inf}. Q-values. See Details}
       |                                           ^
checkRd: (-1) corr_lfdr.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ctgm_lfdr.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ctgm_lfdr.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot_2d.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{plot_2d_lfdr} gives the contour plot of local FDR estimates when all p-values are equal to \code{targetp}. It is recommended to run \code{plot_2d_lfdr} for multiple \code{targetp}'s ranging from {0.001, 0.005, 0.01, 0.05}.
       |                                                                                                                                                                                                          ^
checkRd: (-1) SVMDECON.Rd:23: Lost braces; missing escapes or markup?
    23 | and the best result from three values of v = {0.25, 0.5, 0.75}
       |                                              ^
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
checkRd: (-1) additive.Rd:140: Lost braces
   140 | \item{gamma}{Increase this beyond 1 to produce smoother models. \code{gamma} multiplies the effective degrees of freedom in the GCV or UBRE/AIC. code{n/gamma} can be viewed as an effective sample size in the GCV score, and this also enables it to be used with REML/ML. Ignored with P-RE/ML or the \code{efs} optimizer. }
       |                                                                                                                                                      ^
Documented arguments not in \usage in Rd file 'print.aTest.Rd':
  ‘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
checkRd: (-1) varipart.Rd:19: Lost braces
    19 | \item{type}{a character specifying the algorithm which should be used to adjust R-squared (either \code{"simulated"} or \ code{"parametric"}).}
       |                                                                                                                               ^
checkRd: (-1) adeoptions.Rd:21-23: Lost braces
    21 |   \code{epsilon}{  the smallest significant distance between two points
       |                 ^
checkRd: (-1) adeoptions.Rd:25-27: Lost braces
    25 |   \code{shortprint}{  logical.  Defines whether special \code{show}
       |                    ^
Documented arguments not in \usage in Rd file 'ae_count.Rd':
  ‘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
checkRd: (-1) liquenes.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) liquenes.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) liquenes.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) liquenes.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) liquenes.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) liquenes.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) liquenes.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) liquenes.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) liquenes.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) liquenes.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) liquenes.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) liquenes.Rd:25: Lost braces in \itemize; meant \describe ?
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) med.groups.Rd:20: Lost braces; missing escapes or markup?
    20 | medication groups using the construction \emph{"{NAME}"}.
       |                                                 ^
checkRd: (-1) med.groups.Rd:26: Lost braces; missing escapes or markup?
    26 | Another example is "NotVita" defined as "(!{Vitamines})", which selects all
       |                                            ^
checkRd: (-1) adjClust.Rd:35-37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) adjClust.Rd:38-41: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Amatdual.Rd:15: Lost braces
    15 |   \item{removelist}{a vector of indices into env{X} of the lifted coefficients during the transform (in the order of removal). }
       |                                                 ^
checkRd: (-1) fwtnp.Rd:30: Lost braces
    30 | Given \eqn{n} points on a line, \env{input}, each with a corresponding env{f} value this algorithm computes a lifting transform of the (\env{input},\env{f}) data. If lengths are inputted (\env{inputtype="lengths"}), then the gridpoints are taken to be the left endpoints of the intervals defined by the lengths inputted. 
       |                                                                           ^
checkRd: (-1) joins.Rd:32: Lost braces; missing escapes or markup?
    32 | The \verb{*_join()} functions from {dplyr} without a warning on different attributes
       |                                    ^
checkRd: (-1) get_crpr_dataset.Rd:16: Lost braces; missing escapes or markup?
    16 | Some {admiralonco} function check that the in the source records CR is not
       |      ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) count_cases.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitaep.Rd:14: Lost braces
    14 | \item A sequence of goodness-of-fit measures consist of Akaike Information Criterion (\code{AIC}), Consistent Akaike Information Criterion (\code{CAIC}), Bayesian Information Criterion (\code{BIC}), Hannan-Quinn information criterion (\code{HQIC}), Anderson-Darling (\code{AD}), Cram\'{e}er-von Misses (\code{CVM}), Kolmogorov-Smirnov (\code{KS}), and log-likelihood (\code{log-likelihood}) statistics.
       |                                                                                                                                                                                                                                                                                              ^
Found the following files/directories:
  ‘table_AeRobiology’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) estimate.affinity.matrix.Rd:31: Lost braces; missing escapes or markup?
    31 | than \code{Y}, then those variables that appear in \code{X} but no in {Y}
       |                                                                       ^
checkRd: (-1) estimate.affinity.matrix.lowrank.Rd:36: Lost braces; missing escapes or markup?
    36 | \code{Y}, then those variables that appear in \code{X} but no in {Y} should
       |                                                                  ^
checkRd: (-1) show.correlations.Rd:47: Lost braces
    47 | code{ndims} dimensions. Defaults to all dimensions unless the latter are
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) gini.w.Rd:20: Lost braces; missing escapes or markup?
    20 | where \eqn{x_i,x_j} are incomes of individuals \eqn{i} and {j}, respectively, \eqn{n} is the number of individuals, \eqn{\mu_w} is the mean income. The Gini coefficient ranges between 1 (perfect equality) and 1 (perfect inequality).
       |                                                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) getNetworkGridLayout.Rd:6-11: Lost braces
     6 | getCoordinatesFromVertexId2<-function(AFMImage, vId) {
       |                                                      ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘rgdal’
checkRd: (-1) battese.survey.Rd:42: Lost braces
    42 |   emph{Journal of the American Statistical Association}, 83, 28-36.
       |       ^
checkRd: (-1) butron.maize.Rd:49: Lost braces
    49 |   Butron, A and Velasco, P and Ord{\'a}s, A and Malvar, RA (2004).
       |                                   ^
Package which this enhances but not available for checking: ‘asreml’
Specified C++11: please drop specification unless essential
checkRd: (-1) h2o_train.Rd:108: Lost braces
   108 | \item{mtries}{Number of variables randomly sampled as candidates at each split. If set to -1, defaults to sqrt{p} for
       |                                                                                                               ^
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) AEHMLE.Rd:42-45: Lost braces
    42 | \item{basehaz}{: {baseline hazard structure including baseline
       |                  ^
checkRd: (-1) AHMLE.Rd:41-43: Lost braces
    41 | \item{basehaz}{: {baseline hazard structure including baseline
       |                  ^
checkRd: (-1) CalOptimalDecision.Rd:45: Lost braces; missing escapes or markup?
    45 | A \code{data.frame} of (1) the probability that the optimal decision for each observation being d in {0,1,...,k}, (2) expected utility of binary version of judge's decision (g_d), (3) expected utility of binary DMF recommendation, and (4) the difference between (2) and (3). If \code{include.utility.diff.mcmc = TRUE}, returns a list of such \code{data.frame} and a \code{data.frame} that includes the result for mean and quantile of \code{Utility.diff.control.mcmc} and \code{Utility.diff.treated.mcmc} across mcmc samples.
       |                                                                                                      ^
checkRd: (-1) aimPlot.Rd:39: Lost braces; missing escapes or markup?
    39 |  \item \code{Variable} {1st column: The various aims to be completed}
       |                        ^
checkRd: (-1) aimPlot.Rd:40: Lost braces; missing escapes or markup?
    40 |  \item \code{Percentage} {2nd column: The percentage of completeness}
       |                          ^
Invalid package aliases in Rd file 'aire.zmvm-deprecated.Rd':
  ‘aire.zmvm-deprecated-package’
checkRd: (-1) CreateInputsPert.Rd:65: Lost braces
    65 | \emph{InputsPert}{[list] object of class \emph{InputsModel} containing the ensembles of perturbed model inputs required to perform data assimilation:}
       |                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) monitor_combine.Rd:14: Lost braces
    14 | \item{...}{Any number of valid emph{mts_monitor} objects or a list of objects.}
       |                                    ^
checkRd: (-1) monitor_leaflet.Rd:60: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) monitor_leaflet.Rd:61: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) monitor_leaflet.Rd:62: Lost braces in \enumerate; meant \describe ?
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checkRd: (-1) monitor_nowcast.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{\code{pm}}: {hours = 12, weight = 0.5}
       |                   ^
checkRd: (-1) monitor_nowcast.Rd:33: Lost braces; missing escapes or markup?
    33 | \item{\code{pmAsian}}: {hours = 3, weight = 0.1}
       |                        ^
checkRd: (-1) monitor_nowcast.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{\code{ozone}}: {hours = 8, weight = NA}
       |                      ^
checkRd: (-1) monitor_replaceValues.Rd:12: Lost braces
    12 | \item{filter}{\R{R} expression used to identify values for replacement.}
       |                 ^
checkRd: (-1) get_airnow_area.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{parameters}{Parameter(s) to return data for. Choices are PM_{2.5}
       |                                                                   ^
Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.dke.fun.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item{las}{ Numeric in {0,1,2,3}; the style of axis labels. 
       |                          ^
checkRd: (-1) interpp.Rd:119: Lost braces
   119 |   If \code{linear} is \\code{TRUE}, linear
       |                             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) buildPhylipLineage.Rd:61: Lost braces; missing escapes or markup?
    61 |                                      names with the format {"Inferred1", "Inferred2", ...}.
       |                                                            ^
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) APEXMS.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) APEXMS.Rd:15: Lost braces in \enumerate; meant \describe ?
'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
checkRd: (-1) amDataset.Rd:28: Lost braces
    28 | 		A code{matrix} or \code{data.frame} containing samples in rows and alleles in columns.\cr
       |                       ^
checkRd: (-1) ASBT.Rd:36-37: Lost braces
    36 | \item{method}{Method for aggregating across categories: {"none", "max",
       |                                                         ^
checkRd: (-1) Aggregator.Rd:26: Lost braces; missing escapes or markup?
    26 | {"none", "max", "sum"}. Default: "none".}
       | ^
checkRd: (-1) DGP.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DGP.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DGP.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DGP.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OLS.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OLS.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OLS.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OLS.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) allestimates.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allestimates.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allestimates.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allestimates.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_cohorts.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_cohorts.Rd:36: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'gs.Rd':
  ‘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.
checkRd: (-1) 6_ci.reg.Rd:23: Lost braces
    23 | Interval Estimation of E{Y_h}
       |                         ^
Argument items with no description in Rd file 'MLS.Rd':
  ‘MSE1’
'LazyData' is specified without a 'data' directory
checkRd: (-1) altopt.ic.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) convertCoord.Rd:32: Lost braces
    32 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) convertCoord.individual.Rd:33: Lost braces
    33 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) getCoord.Rd:39: Lost braces
    39 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) getCoord.individual.Rd:39: Lost braces
    39 | here{https://lbs.amap.com/faq/account/key/72}}
       |     ^
checkRd: (-1) getLocation.Rd:60: Lost braces; missing escapes or markup?
    60 | {https://lbs.amap.com/faq/account/key/72}}
       | ^
checkRd: (-1) getLocation.individual.Rd:60: Lost braces
    60 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
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
checkRd: (-1) aMNLFA.prune.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) AmpliconDuo-package.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:40-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:43-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:53-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:56-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diff.Rd:14: Lost braces
    14 | \item{x}{A track_xy{t}.}
       |                    ^
checkRd: (-1) nsd.Rd:22: Lost braces
    22 | \item{x}{A track_xy{t}.}
       |                    ^
Documented arguments not in \usage in Rd file 'check_factors.Rd':
  ‘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
'LazyData' is specified without a 'data' directory
Auto-generated content requiring editing in Rd file 'rowVars.Rd':
  \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: \~
checkRd: (-1) EKF_1d_interp_joint.Rd:55: Lost braces; missing escapes or markup?
    55 | Prior 1x1 covariance matrix for predicting x_t from x_{t-1}.
       |                                                       ^
checkRd: (-1) EKF_interp_joint.Rd:65: Lost braces; missing escapes or markup?
    65 | Prior 2x2 covariance matrix for predicting x_t from x_{t-1}.
       |                                                       ^
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) animate.Rd:625-627: Lost braces
   625 | group = function(...) {
       |                       ^
Documented arguments not in \usage in Rd file 'crawl_interpolation.Rd':
  ‘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) concat.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                     ^
checkRd: (-1) concat.Rd:35: Lost braces
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                               ^
checkRd: (-1) concat.Rd:35: Lost braces
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                                             ^
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
checkRd: (-1) backupStudy.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{extension}{Defaut is {.zip}.}
       |                            ^
checkRd: (-1) writeHydroValues.Rd:22-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeHydroValues.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeHydroValues.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeHydroValues.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeHydroValues.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeIniHydro.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeIniHydro.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeIniHydro.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeIniHydro.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeIniHydro.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeIniHydro.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeIniHydro.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeIniHydro.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeIniHydro.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeIniHydro.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeIniHydro.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeIniHydro.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeIniHydro.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeIniHydro.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) writeIniHydro.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregatate_mc_all.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregatate_mc_all.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregatate_mc_all.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PS-methods.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:65-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Sim-Functions.Rd:126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:127-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:138-140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:141-143: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) aic-class.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aic-class.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aic-class.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gof.Rd:32: Lost braces
    32 | Assuming that the data length is \eqn{N} and the number of the parameters in the model is \eqn{p}, eqn{D} and eqn{X^2} are compared to a chi-squared distribution with \eqn{N-p} degrees of freedom.
       |                                                                                                       ^
checkRd: (-1) gof.Rd:32: Lost braces
    32 | Assuming that the data length is \eqn{N} and the number of the parameters in the model is \eqn{p}, eqn{D} and eqn{X^2} are compared to a chi-squared distribution with \eqn{N-p} degrees of freedom.
       |                                                                                                                  ^
checkRd: (-1) iccbin.Rd:23: Lost braces
    23 |   \item{m}{A vector of the numbers of successes (proportions are eqn{y = m / n}).}
       |                                                                     ^
checkRd: (-1) varbin.Rd:22: Lost braces
    22 |   \item{m}{A vector of the numbers of successes (proportions are eqn{y = m / n}).}
       |                                                                     ^
Documented arguments not in \usage in Rd file 'alternate.sol3.Rd':
  ‘lambda0’

Documented arguments not in \usage in Rd file 'check.group.Rd':
  ‘k’

Documented arguments not in \usage in Rd file 'getrow3.Rd':
  ‘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.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'apci.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.bar.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.plot.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.plot.heatmap.Rd':
  ‘\dots’
Argument items with no description in Rd file 'apci.plot.hexagram.Rd':
  ‘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 file 'apci.plot.raw.Rd':
  ‘\dots’
Argument items with no description in Rd file 'cohortdeviation.Rd':
  ‘\dots’
Argument items with no description in Rd file 'compute_xcoordinate.Rd':
  ‘p’
Argument items with no description in Rd file 'compute_ycoordinate.Rd':
  ‘p’ ‘a’
Argument items with no description in Rd file 'maineffect.Rd':
  ‘\dots’
Argument items with no description in Rd file 'temp_model.Rd':
  ‘\dots’
Argument items with no description in Rd file 'tests.Rd':
  ‘\dots’
checkRd: (-1) apc.indiv.est.model.Rd:142: Lost braces
   142 | For model testing: \code{\link{apc.indiv.model.table}}, code{\link{apc.indiv.compare.direct}}, \code{\link{waldtest}}, \code{\link{linearHypothesis}}
       |                                                             ^
Documented arguments not in \usage in Rd file 'apercu.Rd':
  ‘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
checkRd: (-1) aphylo-class.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
checkRd: (-1) raphylo.Rd:33: Lost braces; missing escapes or markup?
    33 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
checkRd: (-1) sim_fun_on_tree.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
checkRd: (-1) predict_adjust.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iconplot.Rd:172: Lost braces
   172 |     the height of the area containing the panels and a margin of size code{100 * 0.1} 
       |                                                                           ^
'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’.
checkRd: (-1) apple_apps.Rd:22: Lost braces; missing escapes or markup?
    22 | with a corresponding ID that can be used in {appler} functions.
       |                                             ^
checkRd: (-1) get_apple_reviews.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_apple_reviews.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) itunes_artists.Rd:22: Lost braces; missing escapes or markup?
    22 | a corresponding ID that can be used in {appler} functions.
       |                                        ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘APBinary_PPV.csv’ ‘APBinary_TPF.csv’
  ‘APBinary_ap_summary(method=perturbation,B=1500).csv’
  ‘APBinary_auc_summary(method=perturbation,B=1500).csv’
  ‘APSurv_PPV.csv’ ‘APSurv_TPF.csv’
  ‘APSurv_ap_summary(method=bootstrap,B=500).csv’
  ‘APSurv_auc_summary(method=bootstrap,B=500).csv’
  ‘CompareAP_Binary_dap_summary(method=none).csv’
  ‘CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv’
checkRd: (-1) isolate.signal.Rd:79-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) isolate.signal.Rd:82-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) isolate.signal.Rd:87-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootstrapSoilTexture.Rd:20: Lost braces
    20 | \item{\code{samples}} - {\code{data.frame} of simulated sand, silt, clay values}
       |                         ^
checkRd: (-1) bootstrapSoilTexture.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{\code{mean}} - {compositional mean}
       |                      ^
checkRd: (-1) bootstrapSoilTexture.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{\code{var}} - {compositional variance-covariance matrix}
       |                     ^
checkRd: (-1) bootstrapSoilTexture.Rd:23: Lost braces
    23 | \item{\code{D.alpha}} - {(fitted) alpha parameters of the Dirichlet distribution, \code{NULL} when \code{method = 'normal'}}
       |                         ^
checkRd: (-1) colorQuantiles.Rd:26: Lost braces; missing escapes or markup?
    26 | Colors are converted from sRGB to CIELAB (D65 illuminant), marginal quantiles of L,A,B coordinates are estimated, and L1 median {L,A,B} is estimates. The closest Munsell chips (via Munsell/CIELAB lookup table provided by \code{munsell}) and R colors are determined by locating chips closest to the marginal quantiles and L1 median.
       |                                                                                                                                 ^
checkRd: (-1) colorQuantiles.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) colorQuantiles.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hzTransitionProbabilities.Rd:49: Lost braces; missing escapes or markup?
    49 | Convert a cross-tabulation: {original, genhz} to adjacency matrix.
       |                             ^
checkRd: (-1) mixMunsell.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixMunsell.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixMunsell.Rd:94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcEto.Rd:63-64: Lost braces
    63 | \code{ET.Daily:} {daily estimations of reference crop evapotranspiration
       |                  ^
checkRd: (-1) calcEto.Rd:66-67: Lost braces
    66 | \code{Ra.Daily:} {daily estimations of extraterristrial radiation
       |                  ^
checkRd: (-1) calcEto.Rd:69-70: Lost braces
    69 | \code{Slope.Daily:} {daily estimations of slope of vapour pressure curve
       |                     ^
checkRd: (-1) calcEto.Rd:72: Lost braces; missing escapes or markup?
    72 | \code{ET.type:} {type of the estimation obtained}
       |                 ^
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                              ^
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                                            ^
checkRd: (-1) MultiPhasesTransition.Rd:23: Lost braces
    23 | code{position_minimum}.}
       |     ^
checkRd: (-1) find_closer_points.Rd:41: Lost braces
    41 |   \item rows_closer_matrix, a matrix with ]code{npoints} rows  which are closer to each archetype
       |                                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) estimate_t0.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_t0.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_t0.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:75: Lost braces in \itemize; meant \describe ?
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 file 'dynamac_pkg_bounds_test.Rd':
  ‘obs’ ‘fstat’ ‘tstat’ ‘case’ ‘k’
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       | ^
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       |                                 ^
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       |                                                ^
checkRd: (-1) uecm.Rd:76: Lost braces; missing escapes or markup?
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |   ^
checkRd: (-1) uecm.Rd:76: Lost braces; missing escapes or markup?
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                  ^
checkRd: (-1) uecm.Rd:76-77: Lost braces
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
checkRd: (-1) CnPlm.Rd:83-84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SnpPlm.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAlleleProbePairs.AffymetrixCdfFile.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAlleleProbePairs.AffymetrixCdfFile.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAlleleProbePairs3.AffymetrixCdfFile.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAlleleProbePairs3.AffymetrixCdfFile.Rd:42: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'allocateFromCdf.AromaUnitTabularBinaryFile.Rd':
  ‘path’ ‘tags’ ‘footer’

Documented arguments not in \usage in Rd file 'byChipType.DChipSnpInformation.Rd':
  ‘rootPath’ ‘pattern’ ‘verbose’

Documented arguments not in \usage in Rd file 'byChipType.UgpGenomeInformation.Rd':
  ‘version’

Documented arguments not in \usage in Rd file 'calculateResidualSet.FirmaModel.Rd':
  ‘verbose’

Documented arguments not in \usage in Rd file 'findByChipType.AromaChipTypeAnnotationFile.Rd':
  ‘chipType’ ‘tags’

Documented arguments not in \usage in Rd file 'fit.SmoothMultiarrayModel.Rd':
  ‘data’

Documented arguments not in \usage in Rd file 'getCellIndices.ExonChipEffectFile.Rd':
  ‘units’

Documented arguments not in \usage in Rd file 'getImage.AffymetrixCelFile.Rd':
  ‘palette’

Documented arguments not in \usage in Rd file 'getOutputDataSet.Transform.Rd':
  ‘force’

Documented arguments not in \usage in Rd file 'getUnitTypes.AffymetrixCdfFile.Rd':
  ‘map’

Documented arguments not in \usage in Rd file 'plotMvsX.AffymetrixCelFile.Rd':
  ‘xlim’ ‘xlab’

Documented arguments not in \usage in Rd file 'process.BackgroundCorrection.Rd':
  ‘force’ ‘verbose’

Documented arguments not in \usage in Rd file 'readUnits.CnagCfhFile.Rd':
  ‘cdf’

Documented arguments not in \usage in Rd file 'setArrays.ArrayExplorer.Rd':
  ‘arrays’

Documented arguments not in \usage in Rd file 'setRestructor.AffymetrixCdfFile.Rd':
  ‘units’

Documented arguments not in \usage in Rd file 'setupExampleData.Rd':
  ‘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 Rd file 'fitOne.MultiSourceCopyNumberNormalization.Rd':
  ‘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'
checkRd: (-1) colBinnedSmoothing.matrix.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) colBinnedSmoothing.matrix.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) colBinnedSmoothing.matrix.Rd:66-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) colBinnedSmoothing.matrix.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'fit.CopyNumberSegmentationModel.Rd':
  ‘chromosome’

Documented arguments not in \usage in Rd file 'getPath.Explorer.Rd':
  ‘create’

Documented arguments not in \usage in Rd file 'process.AromaTransform.Rd':
  ‘force’ ‘verbose’

Documented arguments not in \usage in Rd file 'process.ChromosomeExplorer.Rd':
  ‘chromosome’

Documented arguments not in \usage in Rd file 'process.Explorer.Rd':
  ‘arrays’ ‘verbose’

Documented arguments not in \usage in Rd file 'setArrays.Explorer.Rd':
  ‘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) ars.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:29: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:30: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:31: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:32: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:36: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:37: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:38: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ars.Rd:39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) anolis.rd:10: Lost braces
    10 | lizard species {\emph{A. sargei} and \emph{A. distichus}}, branch height {high and low}, and branch size {small and large}.
       |                ^
checkRd: (-1) anolis.rd:10: Lost braces; missing escapes or markup?
    10 | lizard species {\emph{A. sargei} and \emph{A. distichus}}, branch height {high and low}, and branch size {small and large}.
       |                                                                          ^
checkRd: (-1) anolis.rd:10: Lost braces; missing escapes or markup?
    10 | lizard species {\emph{A. sargei} and \emph{A. distichus}}, branch height {high and low}, and branch size {small and large}.
       |                                                                                                          ^
checkRd: (-1) auc.rd:18: Lost braces; missing escapes or markup?
    18 | Dichotomous {0, 1} outcomes (i.e. response values for binomial GLM).
       |             ^
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'RweaveAsciiSetup.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweaveOrg.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweavePandoc.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweaveReST.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweaveT2t.Rd':
  ‘stylepath’

Documented arguments not in \usage in Rd file 'RweaveTextile.Rd':
  ‘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
checkRd: (-1) convertAlgoPerfToWideFormat.Rd:28: Lost braces
    28 | code{NA} means the performance value is not available, possibly because the algorithm run was aborted.
       |     ^
checkRd: (-1) parseASScenario.Rd:40: Lost braces
    40 |   code{NA} means the cost is not available, possibly because the feature computation was aborted.
       |       ^
checkRd: (-1) parseASScenario.Rd:47: Lost braces
    47 |   code{NA} means the cost is not available, possibly because the feature computation was aborted.
       |       ^
checkRd: (-1) parseASScenario.Rd:55: Lost braces
    55 |   code{NA} means the feature is not available, possibly because the feature computation was aborted.
       |       ^
checkRd: (-1) parseASScenario.Rd:62: Lost braces
    62 |   code{NA} means the feature is not available, possibly because the feature computation was aborted.
       |       ^
Package which this enhances but not available for checking: ‘asreml’
checkRd: (-1) G.tuneup.Rd:81-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) G.tuneup.Rd:89-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) G.tuneup.Rd:92-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) snp.pruning.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) snp.pruning.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) synthetic.cross.Rd:103-108: Lost braces
   103 | \item{If \code{na.action = "expected"},
       |      ^
Documented arguments not in \usage in Rd file 'check.args_.Rd':
  ‘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
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                    ^
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                                                                                                                 ^
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                                                                                                                          ^
Unknown packages ‘assertive.properties’, ‘assertive.types’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.AssetPricing.Rd:199-200: Lost braces
   199 |   yakka. (Note that \code{flap} stands for dQuote{function list
       |                                                  ^
Package suggested but not available for checking: ‘asteRiskData’
Specified C++11: please drop specification unless essential
checkRd: (-1) readOEM.Rd:34: Lost braces
    34 |   always, the identifier has the format YYYY-NNNP{PP}, where YYYY is the year
       |                                                  ^
checkRd: (-1) readOEM.Rd:36: Lost braces
    36 |   during year YYYY and P{PP} is a part specifier comprising 1 to 3 capital letters
       |                         ^
checkRd: (-1) readOEM.Rd:74-75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readOEM.Rd:76-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readOEM.Rd:80-86: Lost braces in \itemize; \value handles \item{}{} directly
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) gen.Rd:36: Lost braces; missing escapes or markup?
    36 | `gen({...}) returns an \link{iteror}.
       |      ^
checkRd: (-1) ataCoKriging.Rd:52: Lost braces; missing escapes or markup?
    52 | only one contrained condition for all points and all variables, \\sum_{i=1}^n\\lambda_i +\\sum_{j=1}^m\\beta_j =1, assuming expected means of variables known and constant with the study area.
       |                                                                       ^
checkRd: (-1) ataCoKriging.Rd:52: Lost braces; missing escapes or markup?
    52 | only one contrained condition for all points and all variables, \\sum_{i=1}^n\\lambda_i +\\sum_{j=1}^m\\beta_j =1, assuming expected means of variables known and constant with the study area.
       |                                                                                                ^
checkRd: (-1) simulation_dgp.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{x_discrete}{TRUE if the distribution of the covariate is uniform on {-3.0, -2.9, ..., 3.0} and
       |                                                                           ^
checkRd: (-1) simulation_dgp.Rd:23: Lost braces
    23 | \item{att_oracle}{the sample analog of E[D{Y(1) - Y(0)}|D=1]}
       |                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘snpar’ in Rd xrefs
checkRd: (-1) att_from_rmds.Rd:42: Lost braces; missing escapes or markup?
    42 | {knitr} and {rmarkdown} are added by default to allow building the vignettes
       | ^
checkRd: (-1) att_from_rmds.Rd:42: Lost braces; missing escapes or markup?
    42 | {knitr} and {rmarkdown} are added by default to allow building the vignettes
       |             ^
checkRd: (-1) create_renv_for_dev.Rd:6: Lost braces; missing escapes or markup?
     6 | \title{Create reproducible environments for your R projects with {renv}}
       |                                                                  ^
checkRd: (-1) create_renv_for_dev.Rd:60: Lost braces; missing escapes or markup?
    60 | Indeed, although packages like {attachment} or {pkgload} must be installed to develop,
       |                                ^
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    60 | Indeed, although packages like {attachment} or {pkgload} must be installed to develop,
       |                                                ^
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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.
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    50 | \item \code{covars_data}   {The \code{data.frame} that is filtered out of \code{df} with only the selected \code{covars}}. The values of the
       |                            ^
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    53 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
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    40 | \item \code{multiplicative_bias}{The absolute log of the multiplicative bias term for each of the auto-selected prioritised covariates}
       |                                 ^
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    34 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
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   197 | Defaults to `"^v(\\d+\\.){2}\\d+(\\.\\d+)?$"` to identify patterns of
       |                          ^
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    27 | code{\link{help}}
       |     ^
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    25 | code{\link{help}}
       |     ^
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    22 | code{\link{help}}
       |     ^
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    29 | code{\link{help}}
       |     ^
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    32 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    30 | code{\link{help}}
       |     ^
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    20 | \item{fit}{See glm {stats}.}
       |                    ^
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    21 | \item{fit}{See glm {stats}.}
       |                    ^
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    15 | {'poisson','geometric','nb','bb','bnb','normal','halfnormal','lognormal','exponential',
       | ^
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    18 | \item{dist}{The distribution used as the null hypothesis. Can be one of {'poisson', 'geometric',
       |                                                                         ^
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    18 | \item{dist}{The distribution used as the null hypothesis. Can be one of {'poisson', 'geometric',
       |                                                                         ^
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    29 |  be one of {'poisson', 'geometric', 'nb', 'nb1', 'bb', 'bb1', 'bnb', 'bnb1', 'normal', 'halfnormal',
       |            ^
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    15 | \item{dist}{The corresponding standard distribution. Can be one of {'poisson', 'geometric','nb','bb', 'bnb','normal', 'lognormal', 'halfnormal','exponential'}, which corresponds to Poisson, geometric, negative binomial, beta binomial, beta negative binomial, normal, log normal, hal fnormal, and exponential distributions respectively.}
       |                                                                    ^
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    15 | \item{dist}{The corresponding standard distribution. Can be one of {'poisson', 'geometric','nb','bb', 'bnb','normal', 'lognormal', 'halfnormal','exponential'}, which corresponds to Poisson, geometric, negative binomial, beta binomial, beta negative binomial, normal, log normal, hal fnormal, and exponential distributions respectively.}
       |                                                                    ^
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    32 | of {'poisson.zihmle', 'geometric.zihmle', 'nb.zihmle', 'nb1.zihmle', 'bb.zihmle', 'bb1.zihmle',
       |    ^
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    21 | \item{host}{For \code{cosmos_mongo_endpoint}, the URL of the Cosmos DB MongoDB endpoint. Usually of the form "https://{account-name}.mongo.cosmos.azure.com:443/".}
       |                                                                                                                       ^
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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.
GNU make is a SystemRequirements.
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   132 | \item Fn_rep_sim; Dataframe meant to mimic formatting of Fn_Estimates that is part of \\code{bakRFit(bakRData object)} output. Contains information
       |                                                                                             ^
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   129 | \item Fn_rep_sim; Dataframe meant to mimic formatting of Fn_Estimates that is part of \\code{bakRFit(bakRData object)} output. Contains information
       |                                                                                             ^
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    48 | Ignored if {show.data == FALSE}.}
       |            ^
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    51 | Ignored if {show.data == FALSE}.}
       |            ^
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   104 | \item{alpha}{significance level used in the test H_{0K}: expected log predictive density (elpd) for the fitted model with  K components >= elpd for the fitted model
       |                                                    ^
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   148 | H_{0K}: expected log predictive density (elpd) for the fitted model with  K components >= elpd for the fitted model
       |   ^
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   163 | The incremental fitting stops if  H_{0K} cannot be rejected
       |                                     ^
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    34 |          random values it uses the function code{\link[bamm]{permute_pam}}
       |                                                 ^
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    27 | read.dna() from package {ape} was used to obtain DNAbin object for unaligned non-coding barcodes.
       |                         ^
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    61 |     Argument to code{\link{hist}}.
       |                     ^
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Auto-generated content requiring editing in Rd file 'BartMixVs-package.Rd':
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
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   153 |    response, code{y.train}, is internally scaled to range from -0.5 to
       |                  ^
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   150 |    response, code{y.train}, is internally scaled to range from -0.5 to
       |                  ^
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   261 |    For \code{x.train}/{x.test} with missing data elements, \code{gbart}
       |                       ^
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    10 |   {y = f(x) + e}, where \eqn{\epsilon \sim N(0, 1)}{e ~ N(0, 1)}.\cr
       |   ^
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    10 |   {y = f(x) + e}, where \eqn{\epsilon \sim N(0, 1)}{e ~ N(0, 1)}.\cr
       |   ^
Running ‘testthat.R’ [2s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(baseballDBR)
  > 
  > test_check("baseballDBR")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-check_urls.R:21:1'): (code run outside of `test_that()`) ─────
  urlExists("https://raw.githubusercontent.com/chadwickbureau/baseballdatabank/master/core/AllstarFull.csv") is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]
  Error: Test failures
  Execution halted
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    30 | the {dplyr}'s verbs and thus use it in local memory completely.
       |     ^
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    52 | Writes a remote table to disk that was called via {bdplyr}.
       |                                                   ^
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     5 | \title{Compatibility with {dplyr} verbs without using SQL language}
       |                           ^
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    Earlier versions
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   659 | `function(v, cell) { if(isTRUE(v>0.8)) return("green") }`.\cr
       |                    ^
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   151 | The CSS style rule, e.g. { text-align: center; color: red; }
       |                          ^
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   172 | The CSS style rule, e.g. cell { text-align: center; color: red; }
       |                               ^
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   209 | The CSS style rule, e.g. { text-align: center; color: red; }
       |                          ^
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   232 | The CSS style rule, e.g. cell { text-align: center; color: red; }
       |                               ^
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    23 | code{(4)} the number of
       |     ^
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   109 | beta ~ C(0, sigma^2 alpha (X'X/n)^{-1}).}
       |                                   ^
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    14 |   \item{\code{algo.id} [\code{character(1)}]:}{algo.id}{Algorithm ID.}
       |                                                        ^
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    13 | \item{ids}{[code{integer}]\cr
       |                 ^
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    13 | \item{ids}{[code{integer}]\cr
       |                 ^
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    28 | Default is dQuote{<name of registry>_files} in current working directory.}
       |                  ^
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    41 |  \item{namespaces}{code{character} with required packages to load via \code{\link[base]{requireNamespace}}.}
       |                        ^
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    31 | Algorithms are functions which get the code{data} part as well as the problem instance (the return value of the
       |                                            ^
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    51 | When {penalty="elastic net"} (default), the elastic net penalty is adopted. If {penalty="lasso"}, the lasso penalty is used.
       |      ^
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    51 | When {penalty="elastic net"} (default), the elastic net penalty is adopted. If {penalty="lasso"}, the lasso penalty is used.
       |                                                                                ^
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    53 | When {sparse=TRUE} (default), spike--and--slab priors are imposed to identify important main and interaction effects. If {sparse=FALSE}, Laplacian shrinkage will be used.
       |      ^
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    53 | When {sparse=TRUE} (default), spike--and--slab priors are imposed to identify important main and interaction effects. If {sparse=FALSE}, Laplacian shrinkage will be used.
       |                                                                                                                          ^
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    55 | When {robust=TRUE} (default), the distribution of \eqn{\epsilon_{i}} is defined as a Laplace distribution with density
       |      ^
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    58 | }, (\eqn{i=1,\dots,n}), which leads to a Bayesian formulation of LAD regression. If {robust=FALSE}, \eqn{\epsilon_{i}} follows a normal distribution.
       |                                                                                     ^
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    32 | plot{...} functions are generated programmatically so the function calls in
       |     ^
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    48 | doi{10.1002/jae.3950090208} Griffiths, W.E., Hill, R.C., and Judge, G.G. (1993).
       |    ^
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    30 | variables. It was observed that there are only ten sets of values for the first three explanatory variables, so these sets served as conditions for controlled distillation. These conditions are listed in the variable \ code {batch}.
       |                                                                                                                                                                                                                                 ^
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    91 | \item{$H_n1 }{ Bayesian prediction of volatilities and co-volatilities for y_{n+1}.}
       |                                                                              ^
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    92 | \item{$R_n1 }{ Bayesian prediction of coditional correlation for y_{n+1}.}
       |                                                                    ^
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    53 | online trajectories related to the state parameter, the simulated BOLD responses, \mjseqn{\hat{Y}}{ascii}.
       |                                                                                                   ^
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  ‘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.
GNU make is a SystemRequirements.
checkRd: (-1) gMLE.bb.Rd:18: Lost braces
    18 |   \item{optim.method}{optimization method in \code{optim()}{stats}.}
       |                                                            ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) bma.bx.cy.Rd:69: Lost braces
    69 | the initial values for parameters in models. For example, inits<-function(){list(alpha=0,beta=0,c=0,var1=0.5,r=1,lamda=0.01)}.
       |                                                                            ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) DE.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DE.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DE.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DE.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.trajectories.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.trajectories.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.trajectories.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.trajectories.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.trajectories.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:34: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.bayeslm.fit.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{X         }{ If call \code{bayeslm} with matrices input \code{x} and {y} but not formula, pass new matrix to predict here. See example for details.}
       |                                                                              ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) bmr.Rd:172: Lost braces
   172 |    code{\link[stats]{formula}} interface instead, a regressor matrix may
       |        ^
checkRd: (-1) plot-traj.Rd:71: Lost braces; missing escapes or markup?
    71 | the plots are saved into directory {sim.dir}/predictions/migTrajectories.}
       |                                    ^
checkRd: (-1) insert_NAs.Rd:22: Lost braces; missing escapes or markup?
    22 | A data frame where new rows have been inserted to regularize the \code{date} column. This results in values provided for \code{id}, \code{date}, and {dt} while inserting NAs for all other columns. Additionally, observations with duplicate date-times are removed.
       |                                                                                                                                                      ^
checkRd: (-1) bayes_estimation.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bayes_estimation.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bayes_estimation.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bayes_estimation.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bayes_estimation.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bayes_mode.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bayes_mode.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bayes_mode.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bayes_mode.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bayes_mode.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bayes_mode.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bayes_mode.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bayes_mode.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) new_BayesMixture.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) new_BayesMixture.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) new_BayesMixture.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) new_BayesMixture.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) new_BayesMixture.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
'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.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'hmmeantemp.Rd':
  ‘dat’
checkRd: (-1) BayesTreePrior.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:41: Lost braces in \itemize; meant \describe ?
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
checkRd: (-1) runUI.Rd:11: Lost braces
    11 | Runs a \bold{Shiny} application. This function normally does not return; interrupt bold{R} to stop the application (usually by pressing Ctrl+C or Esc).
       |                                                                                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) getOperatingSystem.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:30: Lost braces in \itemize; meant \describe ?
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
checkRd: (-1) BayesT.Rd:18: Lost braces
    18 | discrepancy measure T(bm{y}, bm{Theta}) with following steps
       |                         ^
checkRd: (-1) BayesT.Rd:18: Lost braces
    18 | discrepancy measure T(bm{y}, bm{Theta}) with following steps
       |                                ^
checkRd: (-1) goftype1.Rd:4: Lost braces
     4 | \description{The goodness-of-fit (GOF) measures consist of Anderson-Darling (\code{AD}) and Cram\'{e}er-von Misses (\code{CVM}) statistics for progressive type-I interval censoring scheme are given, respectively, by
       |                                                                                                   ^
Found the following files/directories:
  ‘fabiabreast.txt’
Package suggested but not available for checking: ‘INLA’
Documented arguments not in \usage in Rd file 'contour_ggplot_params.Rd':
  ‘pos_legend’

Documented arguments not in \usage in Rd file 'geom_quad_txt.Rd':
  ‘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) BCE-1_5.Rd:175-197: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BCE-1_5.Rd:199-208: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BCE-1_5.Rd:210-212: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bce1.Rd:142-164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bce1.Rd:166-175: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bce1.Rd:177-179: Lost braces in \itemize; meant \describe ?
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 Rd file 'export.bce.Rd':
  ‘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) BchronDensity.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronRSL.Rd:34-41: Lost braces
    34 | itemize{
       |        ^
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) WindowSweep.Rd:32: Lost braces
    32 | `code{\link{GetVT}}`.   Otherwise, any column (e.g. \code{"Depth"}) in the 
       |      ^
checkRd: (-1) WindowSweep.Rd:36: Lost braces
    36 | \code{T.mid}  from the output of the `code{\link{GetVT}}`.}
       |                                           ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) gene_s.Rd:17: Lost braces; missing escapes or markup?
    17 | giving the virus access to the cell and thus facilitating the COVID-19 disease. The gene sequence is mapped to the alphabet {0,1,2,3} via the obvious map A->0, C->1, G->2, T->3.
       |                                                                                                                             ^
checkRd: (-1) sars_cov_2.Rd:16: Lost braces; missing escapes or markup?
    16 | It consists of n = 29903 base pairs. The gene sequence is mapped to the alphabet {0,1,2,3} via the obvious map A->0, C->1, G->2, T->3.
       |                                                                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bde.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:56: Lost braces in \itemize; meant \describe ?
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:
  ‘dump.txt’
Argument items with no description in Rd file 'bdw.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plot.bdw.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.bdw.Rd':
  ‘\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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) excess.Rd:20: Lost braces
    20 |       \link{dea}, \link{dea.direct}, link{sdea}, and \link{mea}. }
       |                                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) sockeye.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sockeye.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hill.Rd:39: Lost braces; missing escapes or markup?
    39 | \code{a} in {0, 1, 2} (see details))}
       |             ^
checkRd: (-1) read_ambi.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_ambi.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) headtail.Rd:28: Lost braces
    28 | Tries to find good methods of combining the two results according to {code{class(x)}}.
       |                                                                      ^
checkRd: (-1) headtail.Rd:28: Lost braces
    28 | Tries to find good methods of combining the two results according to {code{class(x)}}.
       |                                                                           ^
checkRd: (-1) logAxis.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{expr}{Expression drawing over the ablines, like (points(x,y). Can be code within {braces}.}
       |                                                                                        ^
checkRd: (-1) smallPlot.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{expr}{expression creating a plot. Can be code within {braces}.}
       |                                                            ^
Specified C++11: please drop specification unless essential
checkRd: (-1) gen.data.Rd:42: Lost braces
    42 | code{cortype = 2} denotes the constant structure, where the \eqn{(i,j)} entry of covariance
       |     ^
'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) BETSsearch.Rd:56: Lost braces
    56 |        \item{To exclude whole expressions from the search, surround them with code{' '} and insert a \code{~} before each of them.
       |                                                                                   ^
checkRd: (-1) dummy.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{date}{a \code{list}. The periods for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                               ^
checkRd: (-1) dummy.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{from}{An \code{integer vector} The starting period of a sequence of perids for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                                                                         ^
checkRd: (-1) dummy.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{to}{The ending period of a sequence of perids for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) bdp_dw_bayes_factor_k1.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Estimating the Bayes factor of hypothesis {k1 = 1}.}
       |                                                  ^
checkRd: (-1) bdp_dw_bayes_factor_k1.Rd:19: Lost braces; missing escapes or markup?
    19 | Estimating the Bayes factor of hypothesis {k1 = 1}.
       |                                           ^
checkRd: (-1) local_moving_FT_zigzag.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{thinning_factor}{Selected from {1, 2, 3}.}
       |                                      ^
Documented arguments not in \usage in Rd file 'print_summary_gibbs_psd_help.Rd':
  ‘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.
Package suggested but not available for checking: ‘SoDA’
Specified C++11: please drop specification unless essential
Objects in \usage without \alias in Rd file 'getFpTransforms.Rd':
  ‘%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.
checkRd: (-1) bggCollection.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggCollection.Rd:65-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggCollection.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggCollection.Rd:70-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggCollection.Rd:74-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggCollection.Rd:77-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggGames.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggGames.Rd:70-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggSearch.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggSearch.Rd:68-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bggSearch.Rd:72-73: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) sp_bgsmtr.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{c.star}{The threshold for computing posterior tail probabilities p_{ij} for Bayesian FDR as defined in Section 3.2 of  Song, Ge et al.(2019). If not specified the default is to set this threshold as the minimum posterior standard deviation, where the minimum is taken over all regression coefficients in the model.}
       |                                                                          ^
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
checkRd: (-1) fmridata.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fmridata.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fmridata.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fmridata.Rd:21: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'h.pr.u.Rd':
  ‘z’ ‘ih’ ‘mu’ ‘sigma’ ‘pk’ ‘K’ ‘H’ ‘n’
Argument items with no description in Rd file 'hatpai.u.Rd':
  ‘z’ ‘hk1’ ‘hk0’ ‘ph1’ ‘ph0’ ‘sigma1’ ‘sigma0’ ‘mu1’ ‘mu0’ ‘pai’ ‘H’
  ‘n’
Argument items with no description in Rd file 'ind.u.Rd':
  ‘pr’
Argument items with no description in Rd file 'lambda.u.Rd':
  ‘nu’
Argument items with no description in Rd file 'mu.k.u.Rd':
  ‘k’ ‘ik’ ‘z’ ‘sigma’ ‘mu0’
Argument items with no description in Rd file 'nu.u.Rd':
  ‘ind’ ‘tau’ ‘H’
Argument items with no description in Rd file 'pai.u.Rd':
  ‘b’ ‘a.pai’ ‘b.pai’
Argument items with no description in Rd file 'sig.k.u.Rd':
  ‘k’ ‘ik’ ‘z’ ‘mu0’ ‘a0’ ‘b0’
Argument items with no description in Rd file 'z.pr.u.Rd':
  ‘z’ ‘hk’ ‘mu’ ‘sigma’ ‘ph’ ‘H’ ‘n’
checkRd: (-1) module_calibrationfile_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_correctedplots_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_correctedstats_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_fileupload_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_info_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_log_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_modelselection_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_plotting_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_results_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_settings_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_statistics_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) couplingMap.Rd:42: Lost braces
    42 | using code{impact.measure = "global"}, the function uses the Normalized Global Citation Score to measure elements impact.}
       |           ^
checkRd: (-1) normalizeCitationScore.Rd:17: Lost braces
    17 | using code{impact.measure = "global"}, the function uses the Normalized Global Citation Score to measure elements impact.}
       |           ^
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) CausalGraphInferMainFunc.Rd:55: Lost braces; missing escapes or markup?
    55 | A framework to infer causality on binary data using techniques in frequent pattern mining and estimation statistics. Given a set of individual vectors S={x} where x(i) is a realization value of binary variable i, the framework infers empirical causal relations of binary variables i,j from S in a form of causal graph G=(V,E) where V is a set of nodes representing binary variables and there is an edge from i to j in E if the variable i causes j. The framework determines dependency among variables as well as analyzing confounding factors before deciding whether i causes j.
       |                                                                                                                                                          ^
Specified C++11: please drop specification unless essential
checkRd: (-1) BiDimRegression.Rd:29: Lost braces; missing escapes or markup?
    29 | \item \code{euclidean.df1, affine.df1} -  degrees of freedom of the nominator used for the F-statistics propagated by Nakaya (1997); df1 = p-2, with p is the number of elements  needed to calculate the referring model: p=4 for the Euclidean and p=6 for the affine geometry {Nakaya, 1997, Table 1}.
       |                                                                                                                                                                                                                                                                                  ^
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’.
checkRd: (-1) plotResponseSurface.Rd:60: Lost braces; missing escapes or markup?
    60 | {d2} columns is supplied, dose combinations from \code{colorBy} will be
       | ^
Specified C++14: please drop specification unless essential
checkRd: (-1) bdm.ptsne.Rd:47: Lost braces; missing escapes or markup?
    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                         ^
checkRd: (-1) bdm.ptsne.Rd:47: Lost braces; missing escapes or markup?
    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                                                                                   ^
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) attach.resource.Rd:21-23: Lost braces
    21 |  function (obj, ...){
       |                     ^
checkRd: (-1) pQF.Rd:30: Lost braces; missing escapes or markup?
    30 | When \code{M} is not square, a randomised estimator for the trace of \code{crossprod(M)^2} is used. This is the sample size. When \code{M} is of \code{"matrixfree"} and does not include the trace of {crossprod(M)} as a component, this sample size will also be used to compute that. See Hutchinson reference. }
       |                                                                                                                                                                                                        ^
checkRd: (-1) bqr_upload_data.Rd:112: Lost braces
   112 | url{https://cloud.google.com/bigquery/loading-data-post-request}
       |    ^
'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
checkRd: (-1) FBM-class.Rd:97: Lost braces; missing escapes or markup?
    97 | to be used by package {bigmemory}.
       |                       ^
checkRd: (-1) FBM-class.Rd:99: Lost braces; missing escapes or markup?
    99 | to be used by package {bigmemory}.
       |                       ^
checkRd: (-1) big_read.Rd:57: Lost braces; missing escapes or markup?
    57 | Read a file as a Filebacked Big Matrix by using package {bigreadr}.
       |                                                         ^
Specified C++11: please drop specification unless essential
checkRd: (-1) VARXFit.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXLagCons.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXLagCons.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) binom.confint.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:32-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:45: Lost braces in \itemize; meant \describe ?
'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
checkRd: (-1) aa.index.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:15: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:16: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:17: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:18: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:20-23: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) example.data.Rd:33-37: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) example.data.Rd:38-39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) example.data.Rd:40-41: Lost braces in \enumerate; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) CalcROC.Rd:47: Lost braces
    47 | The accuracy of the classifier is the mean value of dQuote{(optSn, optSp)} for two-class problem and the mean value of \dQuote{(optSn, optSp,optS3)} for three-class problem.
       |                                                           ^
S3 methods shown with full name in Rd file 'select.cfs.Rd':
  ‘select.cfs’

S3 methods shown with full name in Rd file 'select.fast.filter.Rd':
  ‘select.fast.filter’

S3 methods shown with full name in Rd file 'select.forward.Corr.Rd':
  ‘select.forward.Corr’

S3 methods shown with full name in Rd file 'select.forward.wrapper.Rd':
  ‘select.forward.wrapper’

S3 methods shown with full name in Rd file 'select.inf.chi2.Rd':
  ‘select.inf.chi2’

S3 methods shown with full name in Rd file 'select.inf.gain.Rd':
  ‘select.inf.gain’

S3 methods shown with full name in Rd file 'select.inf.symm.Rd':
  ‘select.inf.symm’

S3 methods shown with full name in Rd file 'select.process.Rd':
  ‘select.process’

S3 methods shown with full name in Rd file 'select.relief.Rd':
  ‘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.
checkRd: (-1) ringApply.Rd:9: Lost braces; missing escapes or markup?
     9 |   \item{lv}{{numeric} position, or {character} name, of an
       |                                    ^
checkRd: (-1) calc_ed.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_pi.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_si.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) cluster_reg_exp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) ROC.Rd:55: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:56: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:57: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:58: Lost braces in \enumerate; \value handles \item{}{} directly
Package which this enhances but not available for checking: ‘asreml’
Documented arguments not in \usage in Rd file 'predict2.em.Rd':
  ‘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.
checkRd: (-1) simulation.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:60-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dynamic_omes.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dynamic_omes.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dynamic_omes.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dynamic_omes.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dynamic_omes.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elsc.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elsc.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elsc.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mcbasc.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mcbasc.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mcbasc.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mcbasc.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mcbasc.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mcbasc.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) omes.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) omes.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) omes.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) omes.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) omes.Rd:41: Lost braces in \itemize; meant \describe ?
Invalid package aliases in Rd file 'bios2cor-package.Rd':
  ‘bios2cor-package’
checkRd: (-1) mmds.2D.multi.Rd:118: Lost braces
   118 |   a numeric value in inches indicating the height of graph outfile. Default differs by outfile.type. The resolution for tiff and png figures is 150 dpi. See \code{pdf}, code{tiff}, \code{png}, \code{postscript}.
       |                                                                                                                                                                              ^
checkRd: (-1) mmds.2D.plot.Rd:134: Lost braces
   134 |   a numeric value in inches indicating the height of graph outfile. Default differs by outfile.type. The resolution for tiff and png figures is 150 dpi. See \code{pdf}, code{tiff}, \code{png}, \code{postscript}.
       |                                                                                                                                                                              ^
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) versionlog.Rd:235: Lost braces
   235 | 	\item{new feature}{\code{\link{plotweb}}}{Named abundance-vector for each level can be used.}
       |                                                  ^
checkRd: (-1) wine.rd:81: Lost braces; missing escapes or markup?
    81 | This is WINE version 3.2, available also in Matlab and C++ at the certificate-blocked site ({https://hypatia.agricolas.upm.es/WINE/WINE.html}).
       |                                                                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) keypos.rd:27: Lost braces
    27 |   an integer vector of the same length as code{x} containing positions relativ to code{sort(unique(x), na.last=FALSE)}
       |                                               ^
checkRd: (-1) keypos.rd:27: Lost braces
    27 |   an integer vector of the same length as code{x} containing positions relativ to code{sort(unique(x), na.last=FALSE)}
       |                                                                                       ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bizdays.options.Rd:30-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) saveOldFile.Rd:19: Lost braces
    19 | This function copies the file named \dQuote{\emph{first names}}{\emph{.ext}} under a name created by inserting a string of the form \code{.old_}\eqn{n} between \dQuote{\emph{first names}} and \emph{.ext}, where \eqn{n} is one more than the highest value for any file, matching the first names and extension, already in the current directory, and 0 if no file matches. For example, if \code{filename} is \code{my.beautiful.pdf}, it is copied as \code{my.beautiful.old_0.pdf} if no \code{my.beautiful.old_}\eqn{n}\code{.pdf} file exists, and is is copied as \code{my.beautiful.old_4.pdf} if \code{my.beautiful.old_3.pdf} (and any lower \eqn{n}) file exists.
       |                                                                ^
Argument items with no description in Rd file 'ONA_compiled.Rd':
  ‘ATN’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Argument items with no description in Rd file 'export.dyadic.Rd':
  ‘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: \&
checkRd: (-1) RLdata500.Rd:8: Lost braces
     8 | A data frame with five variables: \code{fname_c1},\code{lname_c1},  \code{by}, code{bm}, \code{bd}.
       |                                                                                    ^
checkRd: (-1) identity.RLdata500.Rd:15: Lost braces
    15 | format A vector that contains the code{id}
       |                                       ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) durban.Rd:16: Lost braces; missing escapes or markup?
    16 | This data set was obtained from the durban.rowcol {agridat} example in package 'agridat' 
       |                                                   ^
checkRd: (-1) fraction.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fraction.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fraction.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_density.Rd:25: Lost braces; missing escapes or markup?
    25 | evenly spaced points between \code{min} and {max}.
       |                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bluebike.Rd:17: Lost braces
    17 | \item{\code{import_month_data}}\cr {Takes in numeric year/month values and imports data from \href{https://www.bluebikes.com/system-data}{Blue Bikes System Data} for the specified time}
       |                                    ^
checkRd: (-1) bluebike.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{\code{station_distance}}\cr {Returns stations with distance in ascending order given the user's current location}
       |                                   ^
checkRd: (-1) bluebike.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{\code{station_radius}}\cr {Plots the position of the stations within walking distance (500 m), and present the basic information about the stations via leaflet}
       |                                 ^
checkRd: (-1) bluebike.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{\code{trip_distance}}\cr {Computes the geographical distance between the start and end stations}
       |                                ^
checkRd: (-1) bluebike.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{\code{trip_history_sample}} \cr {A sample of 1000 trip data entries from February 2022}
       |                                       ^
checkRd: (-1) bluebike.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{\code{station_data}} \cr {A dataset that includes identification, position, and other basic information about bluebike stations}
       |                                ^
Specified C++11: please drop specification unless essential
checkRd: (-1) dot-pred_array_to_df.Rd:20: Lost braces; missing escapes or markup?
    20 | Helper function for as.data.frame.{fitted, forecast}. Converts predictive array to data.frame.
       |                                   ^
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'id2rownum.Rd':
  ‘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.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BMRMM.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BMRMM.Rd:93-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BMRMM.Rd:95-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.BMRMM.Rd:38-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.BMRMM.Rd:44-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BMSC_pareto_k_table.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:57-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:60-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:64-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:67-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) autoplot.tsregime.Rd:20: Lost braces
    20 | Graph for the stochastic processes of the object \ dQuote {\ code {tsregime}} for: Output process and if they exist for: Threshold process and Covariates process. In the case that there are missing data, a red line is drawn at the indicated time.
       |                                                           ^
checkRd: (-1) autoplot.tsregime.Rd:20: Lost braces; missing escapes or markup?
    20 | Graph for the stochastic processes of the object \ dQuote {\ code {tsregime}} for: Output process and if they exist for: Threshold process and Covariates process. In the case that there are missing data, a red line is drawn at the indicated time.
       |                                                                   ^
checkRd: (-1) cpquery.Rd:129: Lost braces; missing escapes or markup?
   129 |   {cpquery} does that automatically when computing the final conditional
       |   ^
checkRd: (-1) gRain.Rd:34: Lost braces
    34 |   converted to $m$ code{grain} objects by replacing the missing conditional
       |                        ^
checkRd: (-1) MvInv.Rd:23-35: Lost braces
    23 | function(eps, u = 0.5, alpha = 1, kappa = 1, gama = 1 / 2, N = 3001) {
       |                                                                      ^
checkRd: (-1) dt_.Rd:19-21: Lost braces
    19 | function(x, df, mean, sd) {
       |                           ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) InferenceEngine-class.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) InferenceEngine-class.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) InferenceEngine-class.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) InferenceEngine-class.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) add.observations-set.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) add.observations-set.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) interventions-set.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) interventions-set.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) interventions.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) interventions.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) observations-set.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) observations-set.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) observations.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) observations.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:152: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |               ^
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |                                             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) refAnnots.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) refAnnots.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:19: Lost braces in \itemize; meant \describe ?
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
checkRd: (-1) shrinkage.regression.Rd:122-126: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) spike.slab.prior.base.Rd:73-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) spike.slab.prior.base.Rd:76-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) spike.slab.prior.base.Rd:79-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) spike.slab.prior.base.Rd:82-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary.logit.spike.Rd:98-100: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) select_Uc.Rd:16: Lost braces
    16 | function /code{ppBS_srs()}.
       |               ^
checkRd: (-1) bootSVD.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{Y}{initial data sample, which can be either a matrix or a \code{\link{ff}} matrix. \code{Y} can be either tall (\eqn{p} by \eqn{n}) or wide (\eqn{n} by \eqn{p}). If \code{Y} is entered and \code{V}, \code{d} and \code{U} (see definitions below) are not entered, then \code{bootSVD} will also compute the SVD of \code{Y}. In this case where the SVD is computed, \code{bootSVD} will assume that the larger dimension of \code{Y} is \eqn{p}, and the smaller dimension of code {Y} is \eqn{n} (i.e. \code{bootSVD} assumes that (\eqn{p>n}). This assumption can be overriden by manually entering \code{V}, \code{U} and \code{d}.\cr
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               ^
Documented arguments not in \usage in Rd file 'check_inputs.Rd':
  ‘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 Rd file 'InternalFunctions.Rd':
  ‘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
checkRd: (-1) boxplotcluster.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotcluster.Rd:93-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotcluster.Rd:96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotcluster.Rd:97: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'info.Rd':
  ‘mod_spec’ ‘pkg_spec’

Documented arguments not in \usage in Rd file 'path.Rd':
  ‘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.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'b_samp.Rd':
  ‘Y’

Documented arguments not in \usage in Rd file 'betaBlock.Rd':
  ‘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: \&
checkRd: (-1) bp_sv.Rd:75: Lost braces; missing escapes or markup?
    75 | $$SV = sqrt(sum(x_{i+1} - x_i)^2/n-1)$$
       |                   ^
checkRd: (-1) bp_sv.Rd:80: Lost braces; missing escapes or markup?
    80 | $$SD = sqrt(sum(x_{i+1} - xbar)^2/n-1)$$
       |                   ^
checkRd: (-1) sv.Rd:78: Lost braces; missing escapes or markup?
    78 | $$SV = sqrt(sum(x_{i+1} - x_i)^2/n-1)$$
       |                   ^
checkRd: (-1) sv.Rd:82: Lost braces; missing escapes or markup?
    82 | $$SD = sqrt(sum(x_{i+1} - xbar)^2/n-1)$$
       |                   ^
Specified C++11: please drop specification unless essential
checkRd: (-1) little.ana.bc.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) little.ana.bc.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) little.ana.bc.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) little.ana.bc.Rd:22-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) little.ana.bc.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) little.ana.bc.Rd:34: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
checkRd: (-1) utils.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) utils.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) utils.Rd:60: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'utils.Rd':
  ‘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
checkRd: (-1) breakfast.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) breakfast.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) breakfast.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) breakfast.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) breakfast.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) breakfast.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) breakfast.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) breakfast.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) model.lp.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model.lp.Rd:24: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) t50_bluck_coward.Rd:15: Lost braces; missing escapes or markup?
    15 | Time where value is 1/2 of the maximum, i.e. t_{50} or t_{1/2} in minutes; 
       |                                                ^
checkRd: (-1) t50_bluck_coward.Rd:15: Lost braces; missing escapes or markup?
    15 | Time where value is 1/2 of the maximum, i.e. t_{50} or t_{1/2} in minutes; 
       |                                                          ^
checkRd: (-1) t50_bluck_coward.Rd:16: Lost braces; missing escapes or markup?
    16 | in the publication by Bluck et al, the parameter is called t_{1/2(in)}.
       |                                                              ^
GNU make is a SystemRequirements.
Documented arguments not in \usage in Rd file 'availability.int.Rd':
  ‘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 Rd file 'subset.int.Rd':
  ‘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.
checkRd: (-1) brew.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brew.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brew.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brew.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brew.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brew.Rd:76-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:173: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:174: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:175-176: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:177-178: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:179-180: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:181-182: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:183-184: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) printHands.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) printHands.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) printHands.Rd:42: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) assertall.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) assertall.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) assertall.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) assertall.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brmsmargins.Rd:129: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brmsmargins.Rd:130: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brmsmargins.Rd:131: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brmsmargins.Rd:132: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) builders.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:55: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘cmdstanr’
checkRd: (-1) gp.Rd:93-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) select_helpers.Rd:43: Lost braces; missing escapes or markup?
    43 | Set of functions to supplement the {tidyselect} set of
       |                                    ^
Package suggested but not available for checking: ‘glmmADMB’
checkRd: (-1) tidy.varFunc.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy.varFunc.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy.varFunc.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy.varFunc.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brsim.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brsim.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brsim.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brsim.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brsim.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brsim.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brsim.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brsim.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
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 Rd file 'table.Rd':
  ‘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.
checkRd: (-1) bsaqdpm.Rd:166: Lost braces
   166 | MacEachern, S. N. and M{\"u}ller, P. (1998) Estimating mixture of Dirichlet process models.
       |                        ^
checkRd: (-1) bsardpm.Rd:165: Lost braces
   165 | MacEachern, S. N. and M{\"u}ller, P. (1998) Estimating mixture of Dirichlet process models.
       |                        ^
Argument items with no description in Rd file 'plot.bshazard.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.bshazard.Rd':
  ‘\dots’
Argument items with no description in Rd file 'summary.bshazard.Rd':
  ‘\dots’
checkRd: (-1) bscontrol.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{opt.solver}{a character string in the set {'enum', 'enum_c', 'gurobi', 'cplex', 'lpSolve', 'greedy'} indicating the optimization solver to be used in the program. The choice of 'cplex' requires the package \code{cplexAPI}, 'gurobi' requires the package \code{gurobi}, and 'lpSolve' requires the package \code{lpSolve}. These solver options are only available in the full version at \url{https://github.com/profyliu/bsnsing/}. The default (and the best) is 'enum_c'.}
       |                                                 ^
checkRd: (-1) bscontrol.Rd:45: Lost braces; missing escapes or markup?
    45 | \item{opt.model}{a character string in the set {'gini','error'} indicating the optimization model to solve in the program. The default is 'gini'. The 'error' option is not available in the current version.}
       |                                                ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) bsc.Rd:51: Lost braces; missing escapes or markup?
    51 | {splines::bs()}, {splines2::bSpline()}
       |                  ^
checkRd: (-1) bsp.Rd:37: Lost braces; missing escapes or markup?
    37 | {bsc}, {par2bsp}
       |        ^
checkRd: (-1) bspline.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bspline.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bspline.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bspline.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bspline.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bspline.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bspline.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bspline.Rd:30: Lost braces in \itemize; meant \describe ?
'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) gof-statistics.Rd:192: Lost braces
   192 | Users can create their own statistics for use with the code{gof} methods. To
       |                                                            ^
Package suggested but not available for checking: ‘gvcm.cat’
Specified C++11: please drop specification unless essential
Unknown package ‘gvcm.cat’ in Rd xrefs
checkRd: (-1) terms.BTM.Rd:23-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) terms.BTM.Rd:26-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) terms.data.frame.Rd:25-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) terms.data.frame.Rd:32-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pnbd.mcmc.DrawParameters.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pnbd.mcmc.DrawParameters.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) bubbleHMLegends.Rd:42: Lost braces; missing escapes or markup?
    42 | function. If {sizeBreaks} vector is supplied then this will be ignored and
       |              ^
checkRd: (-1) bubbleHeatmap.Rd:96: Lost braces; missing escapes or markup?
    96 | function. If {sizeBreaks} vector is supplied then this will be ignored and
       |              ^
checkRd: (-1) multiPlotInput.Rd:117: Lost braces; missing escapes or markup?
   117 | \code{unitBase}. This will be supplied to pretty function. If {sizeBreaks} is
       |                                                               ^
'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 Rd file 'count.Rd':
  ‘.data’

Documented arguments not in \usage in Rd file 'unite.Rd':
  ‘.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
checkRd: (-1) depreciation-class.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) depreciation-class.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) depreciation-class.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) depreciation-class.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loan-class.Rd:46-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loan-class.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loan-class.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model2df-methods.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model2df-methods.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model2df-methods.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model2df-methods.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BuyseTest.Rd:144: Lost braces
   144 | To export the classification of each pair set the argument code{keep.pairScore} to \code{TRUE} and call the function \code{getPairScore} on the result of the \code{BuyseTest} function. \cr \cr \cr
       |                                                                ^
Documented arguments not in \usage in Rd file 'calcIntegralSurv2_cpp.Rd':
  ‘dsurvival’

Documented arguments not in \usage in Rd file 'dot-calcIntegralCif_cpp.Rd':
  ‘cif’ ‘CIF_t’

Documented arguments not in \usage in Rd file 'validFCTs.Rd':
  ‘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
checkRd: (-1) calcUnique.Rd:24: Lost braces
    24 | functions, and often the /code{cut()} function are relatively slow when working with tens of millions of rows or more.
       |                               ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
checkRd: (-1) calibration_bands.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{y}{response variable (in {0,1}).}
       |                                ^
Documented arguments not in \usage in Rd file 'get_result.Rd':
  ‘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
checkRd: (-1) heage.Rd:18: Lost braces
    18 | B{\"o}hning, D.  and Schlattmann, P. and Lindsay, B. (1992). \dQuote{Computer-Assisted Analysis of Mixtures (C.A.MAN): Statistical Algorithms}. \emph{Biometrics}. \bold{48}, 283--303.
       |  ^
checkRd: (-1) hepab.Rd:5: Lost braces
     5 | Hepatitis B data from Schlattmann and B{\"o}hning (1993).
       |                                        ^
checkRd: (-1) hepab.Rd:19: Lost braces
    19 | Schlattmann, P. and B{\"o}hning, D. (1993). \dQuote{Mixture models and disease mapping}. \emph{Statistics in Medicine}. \bold{12}, 1943--1950.
       |                      ^
checkRd: (-1) mixalg.Rd:117: Lost braces
   117 | D. B{\"o}hning, P. Schlattmann, B.G. Lindsay: C.A.MAN - Computer Assisted
       |     ^
checkRd: (-1) thai_cohort.Rd:19: Lost braces
    19 | Schelp, F., P. Vivatanasept, P. Sitaputra, S. Sornmani, P. Pongpaew, N. Vudhivai, S. Egormaiphol, and D. B{\"o}hning.  \dQuote{Relationship of the morbidity of under-fives to anthropometric measurements and community health intervention.} \emph{Trop Med Parasitol}, 1990, 41(2), 121--126.
       |                                                                                                           ^
checkRd: (-1) Recording.Rd:112: Lost braces; missing escapes or markup?
   112 | Stop recording images with {camcorder}.
       |                            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgdal’
checkRd: (-1) get_census.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{resolution}{Resolution of the geographic data. {cancensus} will download simplified geometries by default. For lower level geometries like DB or DA this will be very close to the high resolution data.
       |                                                      ^
Argument items with no description in Rd file 'makeEventHistory.Rd':
  ‘type’
Argument items with no description in Rd file 'plotSeqCount.Rd':
  ‘segColors’
Found the following files/directories:
  ‘MDA231_tree.pdf’
checkRd: (-1) macrocaic.Rd:31: Lost braces; missing escapes or markup?
    31 |      {RRD = ln(N_1/N_2)}
       |      ^
checkRd: (-1) macrocaic.Rd:34: Lost braces; missing escapes or markup?
    34 |      {PDI = (N_1/(N_1 + N_2))-0.5}
       |      ^
checkRd: (-1) pd.calc.Rd:33: Lost braces
    33 |   \item{Length of tip branch lengths (TIPS)}{Length of tip branch lengths (TIPS)}{Unlike UEH, this measure does not use the unique paths to each tips on the \strong{subtree} and instead gives the sum of the unique branches leading to the tips on the \strong{complete tree}.}
       |                                                                                  ^
'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) plot.ca.rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ca.rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ca.rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ca.rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) fitweibull.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitweibull.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitweibull.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) zipcode.Rd:14: Lost braces; missing escapes or markup?
    14 | This is a dataset from the archived/orphaned {zipcode} package.
       |                                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) NEWS.Rd:96: Lost braces
    96 |     \item code{train} now removes duplicate models in the tuning grid. Duplicates could occur for models with discrete parameters.
       |               ^
checkRd: (-1) calibration.Rd:46: Lost braces; missing escapes or markup?
    46 | formula. This argument is not used for \code{xyplot.calibration}. For {ggplot.calibration}, \code{data}
       |                                                                       ^
checkRd: (-1) build_for_cran.Rd:13: Lost braces
    13 | The exit status code{R CMD build}, invisibly.
       |                     ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) compareCoefs.Rd:30: Lost braces
    30 | \item{pvals}{If code{TRUE} (the default is \code{FALSE}), print two-sided p-values
       |                     ^
checkRd: (-1) mcPlots.Rd:38: Lost braces; missing escapes or markup?
    38 |   axis.  To plot against a factor, you need to specify the full name of one of the indicator variables that define the factor.  For example, for a factor called \code{type} with levels \code{A}, \code{B} and {C}, using the usual drop-first level parameterization of the factor, the regressors for \code{type} would be \code{typeB} or \code{typeC}.  Similarly, to plot against the regressor \code{log(X4)}, you must specify \code{"log((X4)"}, not \code{"X4"}.
       |                                                                                                                                                                                                                 ^
checkRd: (-1) scatterplot.Rd:137: Lost braces
   137 | For  \code{style="filled"} several subarguments modify the appearance of the region:  code{alpha} is a number between 0 and 1 that specifies opacity with defualt 0.15, \code{border}, \code{TRUE} or \code{FALSE} specifies a border for the envelope, and \code{vertical} either \code{TRUE} or \code{FALSE}, modifies the behavior of the envelope at the edges of the graph.
       |                                                                                           ^
checkRd: (-1) cartogramR_options.Rd:22: Lost braces; missing escapes or markup?
    22 | max_{polygons} |area_on_cartogram - target_area| <= abserror
       |     ^
checkRd: (-1) cartogramR_options.Rd:25: Lost braces; missing escapes or markup?
    25 | max_{polygons} |area(i) - area(i-1)|
       |     ^
checkRd: (-1) cartogramR_options.Rd:29: Lost braces; missing escapes or markup?
    29 | max_{polygons} |area_on_cartogram / target_area - 1| <= relerror
       |     ^
checkRd: (-1) cartogramR_options.Rd:32: Lost braces; missing escapes or markup?
    32 | max_{polygons} abs((area(i) - area(i-1))/area(i-1)
       |     ^
GNU make is a SystemRequirements.
checkRd: (-1) influences.RH.Rd:17: Lost braces
    17 |   provided. Default is code{FALSE}.}
       |                            ^
'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 Rd file 'validate_cover_cats.Rd':
  ‘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.
checkRd: (-1) evaluateClusterQuality.Rd:13: Lost braces
    13 | assessors, \code{J} products, code{M} attributes where CATA data have values 
       |                                   ^
checkRd: (-1) homogeneity.Rd:12: Lost braces
    12 | assessors, \code{J} products, code{M} attributes where CATA data have values 
       |                                   ^
checkRd: (-1) inspect.Rd:12: Lost braces
    12 | assessors, \code{J} products, code{M} attributes where CATA data have values 
       |                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) gen.sim.data.Rd:73: Lost braces; missing escapes or markup?
    73 | Y = X_0 Beta_0^T + X_1 Beta_1^T + Z Gamma^T + E Sigma^{1/2},
       |                                                       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) slpDGCM.Rd:130-133: Lost braces
   130 | \code{x1, x2, x3, \dots}- {input to the model, there must be one column
       |                           ^
Documented arguments not in \usage in Rd file 'add_catmaply_slider.Rd':
  ‘text_font_color’ ‘categorical_col’

Documented arguments not in \usage in Rd file 'add_catmaply_traces.Rd':
  ‘categorical_col’

Documented arguments not in \usage in Rd file 'catmaply_annotations.Rd':
  ‘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.
checkRd: (-1) catmapdata.Rd:9-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:20-21: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
checkRd: (-1) colAUC.Rd:79: Lost braces
    79 |      Meteorol. Soc. textbf{30} 291-303. 
       |                           ^
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: \&
checkRd: (-1) as.mbsts.Rd:71: Lost braces; missing escapes or markup?
    71 |   \item{states.samples}{(\code{niter}- \code{burn}) draws from p(alpha_t | Y_{1:T}).}
       |                                                                              ^
checkRd: (-1) mcmc.Rd:61: Lost braces; missing escapes or markup?
    61 |   \item{states.samples}{(\code{niter}- \code{burn}) draws from p(alpha_t | Y_{1:T}).}
       |                                                                              ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) cbc_design.Rd:160: Lost braces; missing escapes or markup?
   160 | see \code{?DoE.base::fac.design} as well as the JSS article on the {DoE.base}
       |                                                                    ^
checkRd: (-1) cbc_design.Rd:174: Lost braces; missing escapes or markup?
   174 | well as the JSS article on the {DoE.base} package (Grömping, 2018).
       |                                ^
checkRd: (-1) cbc_design.Rd:197: Lost braces; missing escapes or markup?
   197 | {idefix} package (Traets et al, 2020).
       | ^
checkRd: (-1) cbc_power.Rd:70: Lost braces; missing escapes or markup?
    70 | estimation. See the {logitr} documentation for details about other
       |                     ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) CUR.Rd:25: Lost braces; missing escapes or markup?
    25 | The number of low-dimension of C (J1 < {N,M}).
       |                                        ^
checkRd: (-1) CUR.Rd:29: Lost braces; missing escapes or markup?
    29 | The number of low-dimension of R (J2 < {N,M}).
       |                                        ^
checkRd: (-1) CX.Rd:23: Lost braces; missing escapes or markup?
    23 | The number of low-dimension (J < {N,M}).
       |                                  ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hotcold.csv’
checkRd: (-1) cdnet.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdnet.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdnet.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdnet.Rd:93: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Packages which this enhances but not available for checking:
  'CirceR', 'Capr'
checkRd: (-1) data.dtmr.Rd:57: Lost braces; missing escapes or markup?
    57 | \code{RU}: {Referent units}
       |            ^
checkRd: (-1) data.dtmr.Rd:59: Lost braces; missing escapes or markup?
    59 | \code{PI}: {Partitioning and iterating attribute}
       |            ^
checkRd: (-1) data.dtmr.Rd:61: Lost braces; missing escapes or markup?
    61 | \code{APP}: {Appropriateness attribute}
       |             ^
checkRd: (-1) data.dtmr.Rd:63: Lost braces; missing escapes or markup?
    63 | \code{MC}: {Multiplicative Comparison attribute}
       |            ^
Specified C++11: please drop specification unless essential
checkRd: (-1) cec.Rd:164-165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cec.Rd:166-168: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cec.Rd:169-172: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cec.Rd:173-175: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cec.Rd:176-177: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cec.Rd:178-180: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cec.Rd:181-182: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.centers.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) init.centers.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) optimMIES.Rd:62: Lost braces; missing escapes or markup?
    62 | Note, that a more simple bound constraint method is used. Instead of the Transformation T_{a,b}(x) 
       |                                                                                           ^
Documented arguments not in \usage in Rd file 'buildModel.Rd':
  ‘x’ ‘y’

Documented arguments not in \usage in Rd file 'modelKrigingInternalPredictor.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'selfAdapt.Rd':
  ‘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 Rd file 'evaluate_rule.Rd':
  ‘class’

Documented arguments not in \usage in Rd file 'tree_leaf_nodes.Rd':
  ‘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
checkRd: (-1) aggregate.tracks.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregate.tracks.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregate.tracks.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregate.tracks.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregate.tracks.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregate.tracks.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregate.tracks.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repairGaps.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repairGaps.Rd:16-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repairGaps.Rd:20-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rMMSN.contour.Rd:20: Lost braces
    20 |  is an object resultant from the code{\link{fit.FMMSNC}} function.
       |                                      ^
Auto-generated content requiring editing in Rd file 'CensMFM-package.Rd':
  \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 Rd file 'blackboost_train.Rd':
  ‘x’ ‘y’

Documented arguments not in \usage in Rd file 'survival_prob_mboost.Rd':
  ‘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) listCensusApis.Rd:10: Lost braces; missing escapes or markup?
    10 | Scrapes {https://api.census.gov/data.json} and returns a dataframe
       |         ^
checkRd: (-1) call_api_once.Rd:36: Lost braces
    36 | A code{data.frame} with the requested variables at the requested
       |       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) centroid.Rd:22: Lost braces; missing escapes or markup?
    22 | Centroid value C_{cen}(v) for node v defined as:
       |                  ^
checkRd: (-1) clusterrank.Rd:23: Lost braces; missing escapes or markup?
    23 | where the term f(c_{i}) accounts for the effect of i's local clustering and the term '+1' results from the contribution of \eqn{j}{j} itself. \cr
       |                    ^
Argument items with no description in Rd file 'centralplot.Rd':
  ‘alpha’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cequre.Rd:31: Lost braces; missing escapes or markup?
    31 |   {epsi}^{# regression coefficients} times the initial value,
       |   ^
checkRd: (-1) cequre.Rd:31: Lost braces; missing escapes or markup?
    31 |   {epsi}^{# regression coefficients} times the initial value,
       |          ^
checkRd: (-1) cities.Rd:8: Lost braces; missing escapes or markup?
     8 | Dataset from package {maps}.
       |                      ^
Specified C++11: please drop specification unless essential
checkRd: (-1) performParallelNLMERun.Rd:22: Lost braces
    22 | \item{partialJob}{is /code{TRUE} if it is not required to stop the job
       |                           ^
checkRd: (-1) performParallelNLMERun.Rd:25: Lost braces
    25 | \item{allowIntermediateResults}{is /code{TRUE} if intermediate results
       |                                         ^
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
checkRd: (-1) helpers_pbp.Rd:336: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:337: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:338: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:339: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:340: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:341: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:390: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:391: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:392: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:393: Lost braces in \itemize; meant \describe ?
checkRd: (-1) helpers_pbp.Rd:394: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_cfb_db.Rd:46-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_cfb_db.Rd:49-52: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'create_epa.Rd':
  ‘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.
checkRd: (-1) cfc.tbasis.Rd:23: Lost braces
    23 | Assuming one-dimensional \code{p1} and \code{p2} for clarity, the algorithm calculates cumulative incidence function for cuase 1 using a recursive formula: \code{ci1[n+1] = ci1[n] + dci1[n]}, where \code{dci1[n] = 0.5*(p2[n] + p2[n+1])*(p1[n] - p1[n+1])}. The increment in cumulative incidence function for cause 2 is similarly calculated, \code{dci2[n] = 0.5*(p1[n] + p1[n+1])*(p2[n] - p2[n+1])}. These equations guarantee that \code{dci1[n] + dci2[n] = p1[n]*p2[n] - p1[n+1]*p2[n+1]}. Event-free probability is simply calculated as code{efp[n] = p1[n]*p2[n]}. Taken together, this numerical integration ensures that \code{efp[n+1] - efp[n] + dci1[n] + dci2[n] = 0}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           ^
'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
checkRd: (-1) CGGP_internal_calcpw.Rd:22: Lost braces; missing escapes or markup?
    22 | Predictive weights are Sigma^{-1}*y in standard GP.
       |                              ^
S3 methods shown with full name in Rd file 'select.cglasso.Rd':
  ‘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
checkRd: (-1) comparisonsTable.cgOneFactorFit.Rd:47: Lost braces
    47 | 	call (see {\dots } section below.)
       |                   ^
checkRd: (-1) InfluenceMap.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) InfluenceMap.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) InfluenceMap.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) InfluenceMap.Rd:57: Lost braces in \itemize; meant \describe ?
Objects in \usage without \alias in Rd file 'influence-methods.Rd':
  ‘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.
checkRd: (-1) ftse100.Rd:8: Lost braces; missing escapes or markup?
     8 |  This dataset gives the daily returns (c_{t+1}/c_t -1) of the UK FTSE 100 index from 2nd April 1984 until the 13th September 2012.
       |                                          ^
checkRd: (-1) Hausdorff.dist.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{vec1}{A \code{integer} vector forms a subset of {1, 2, ..., n}.}
       |                                                       ^
checkRd: (-1) Hausdorff.dist.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{vec2}{A \code{integer} vector forms a subset of {1, 2, ..., n}.}
       |                                                       ^
checkRd: (-1) online.univar.multi.Rd:47-57: Lost braces
    47 | online.univar.one2 = function(y_vec, gamma, tau_gamma, ...){
       |                                                            ^
checkRd: (-1) online.univar.multi.Rd:50-55: Lost braces
    50 |   while(FLAG == 0 & t <= length(y_vec)){
       |                                        ^
checkRd: (-1) online.univar.multi.Rd:71-89: Lost braces
    71 | online.univar.one3 = function(y_vec, tau_vec, ...){
       |                                                   ^
checkRd: (-1) online.univar.multi.Rd:72-74: Lost braces
    72 |   if(length(y_vec) != length(tau_vec)){
       |                                       ^
checkRd: (-1) online.univar.multi.Rd:77-87: Lost braces
    77 |   while(FLAG == 0 & t <= length(y_vec)){
       |                                        ^
checkRd: (-1) online.univar.multi.Rd:81-86: Lost braces
    81 |     while(j < J & FLAG == 0){
       |                             ^
Invalid package aliases in Rd file 'jumpointsVar-package.Rd':
  ‘jumpointsVar-package’
Objects in \usage without \alias in Rd file 'jumpointsVar-internal.Rd':
  ‘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 Rd file 'jumpointsVar-internal.Rd':
  ‘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 file 'ChangePointAnalyzer-package.Rd':
  \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 Rd file 'multiplierDSeqfun.Rd':
  ‘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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cql.Rd:28: Lost braces; missing escapes or markup?
    28 | {X} \code{<x_var>, <(x_facet)>}: \tab\tab\tab\tab  X-axis variable. May include a second categorical\cr
       | ^
checkRd: (-1) cql.Rd:30: Lost braces; missing escapes or markup?
    30 | {Y} \code{<y_var>}: \tab\tab\tab\tab Y-axis variable. *Not used for \code{hist}.\cr
       | ^
checkRd: (-1) cql.Rd:38: Lost braces; missing escapes or markup?
    38 | {Y_label} \code{'<ylab>'}: \tab\tab\tab\tab  Y-axis custom label. Defaults to <y_var>\cr
       | ^
checkRd: (-1) cql.Rd:39: Lost braces; missing escapes or markup?
    39 | {Legend} \code{'<legend>'}: \tab\tab\tab\tab  Legend custom label. Defaults to <x_category>\cr
       | ^
checkRd: (-1) cql.Rd:40: Lost braces; missing escapes or markup?
    40 | {Colorset} \code{'<clist>'}: \tab\tab\tab\tab  Custom set of colors for <x_category> levels.\cr
       | ^
checkRd: (-1) cql.Rd:42: Lost braces; missing escapes or markup?
    42 | {AggFunc} \code{'<func>'}: \tab\tab\tab\tab Summary function for \code{bar} type.\cr
       | ^
checkRd: (-1) cql.Rd:45: Lost braces; missing escapes or markup?
    45 | {Fit} \code{'<show_se>'}: \tab\tab\tab\tab Valid types: \code{true|false}. Fit quadratic line.\cr
       | ^
checkRd: (-1) cql.Rd:47: Lost braces; missing escapes or markup?
    47 | {ConfInt} \code{'<interval>'}: \tab\tab\tab\tab  Show error bars. Value is confidence interval value. E.g. '.95'
       | ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) create_unit_tests.Rd:17: Lost braces; missing escapes or markup?
    17 | Create `{testthat}` test cases for the code.
       |         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) as.data.frame.checkglobals.Rd:43: Lost braces; missing escapes or markup?
    43 | \item \code{type}, the type of the detected entity, either \code{"global"} or {"import"}.
       |                                                                               ^
checkRd: (-1) as.matrix.checkglobals.Rd:32: Lost braces; missing escapes or markup?
    32 | \item \code{type}, the type of the detected entity, either \code{"global"} or {"import"}.
       |                                                                               ^
Package suggested but not available for checking: ‘darts’
checkRd: (-1) LoadCollection.Rd:7: Lost braces
     7 | for loading and saving code{CommunityCollection} objects to text files.
       |                            ^
checkRd: (-1) ShortestPaths.Rd:25: Lost braces
    25 | \references{Williams, R.J. and Berlow, E.L. and Dunne, J.A. and Barab{\'a}si, 
       |                                                                      ^
checkRd: (-1) YthanEstuary.Rd:19: Lost braces
    19 | Read G., St\"{o}hr S., Walter T.C., Costello M.J. Editors. (2012) World 
       |              ^
checkRd: (-1) calc_metrics.Rd:22-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:26-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:30-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:34-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:38-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:45-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:49-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:53-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:56-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:59-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calc_metrics.Rd:62-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) files2SpectraObject.Rd:142: Lost braces
   142 | (in code{matrix2SpectraObject}) is done one at
       |         ^
checkRd: (-1) check4Gaps.Rd:31: Lost braces; missing escapes or markup?
    31 | Also a plot if {y} is provided.  In the event there are no gaps found,
       |                ^
Documented arguments not in \usage in Rd file 'dot-chkArgs.Rd':
  ‘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
checkRd: (-1) C316.amp.Rd:28-32: Lost braces
    28 |     40 x {
       |          ^
checkRd: (-1) C317.amp.Rd:28-32: Lost braces
    28 |     40 x {
       |          ^
checkRd: (-1) C60.amp.Rd:63-67: Lost braces
    63 |     40 x {
       |          ^
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 file 'chngpt.test.Rd':
  ‘by.percentile’ ‘both’ ‘main’ ‘prec.weights’ ‘p.val.method’ ‘boot.B’
  ‘keep.fits’
Argument items with no description in Rd file 'convert.coef.Rd':
  ‘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 file 'double.hinge.Rd':
  ‘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 file 'hinge.test.Rd':
  ‘formula’ ‘cov.interest’ ‘family’ ‘data’ ‘verbose’
Argument items with no description in Rd file 'performance.unit.test.Rd':
  ‘formula.1’ ‘formula.2’ ‘family’ ‘data’ ‘B’ ‘I’
Argument items with no description in Rd file 'sim.chngpt.Rd':
  ‘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 file 'sim.hinge.Rd':
  ‘threshold.type’ ‘family’ ‘thres’ ‘X.ditr’ ‘mu.X’ ‘coef.X’ ‘cov.X’
  ‘eps.sd’ ‘seed’ ‘n’
checkRd: (-1) logB.to.OBIGT.Rd:39: Lost braces
    39 | To avoid overfitting, only the first three parameters (code{G}, \code{S}, and \code{c1}) are used by default.
       |                                                            ^
checkRd: (-1) util.fasta.Rd:39: Lost braces; missing escapes or markup?
    39 | If {id} is not given, and a UniProt FASTA header is detected (regular expression \code{"\\|......\\|.*_"}), information there (accession, name, organism) is split into the \code{protein}, \code{abbrv}, and {organism} columns of the resulting data frame.
       |    ^
checkRd: (-1) util.fasta.Rd:39: Lost braces; missing escapes or markup?
    39 | If {id} is not given, and a UniProt FASTA header is detected (regular expression \code{"\\|......\\|.*_"}), information there (accession, name, organism) is split into the \code{protein}, \code{abbrv}, and {organism} columns of the resulting data frame.
       |                                                                                                                                                                                                               ^
Problems with news in ‘NEWS.md’:
No news entries found.
Objects in \usage without \alias in Rd file 'choplump-internal.Rd':
  ‘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
checkRd: (-1) chunker-methods.Rd:63: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:64: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:70: Lost braces in \enumerate; meant \describe ?
Documented arguments not in \usage in Rd file 'SearchEmptyClusters.Rd':
  ‘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
checkRd: (-1) ec.datalag.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{prepares Dy y_1 Dy_1 ... Dy_{nlag-1} for estimation}
       |                                    ^
checkRd: (-1) ec.datalag.Rd:15: Lost braces
    15 | ymat contains the folloiwing columns {Dy y_1 Dy_1 ... Dy_{nlag-1}}
       |                                      ^
checkRd: (-1) ec.datalag.Rd:15: Lost braces; missing escapes or markup?
    15 | ymat contains the folloiwing columns {Dy y_1 Dy_1 ... Dy_{nlag-1}}
       |                                                          ^
checkRd: (-1) lagn.Rd:21: Lost braces; missing escapes or markup?
    21 |              REM: alternative to "lead-lag" {dplyr} which applies to vector y
       |                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) interpolation_function.Rd:28: Lost braces; missing escapes or markup?
    28 |   defined by \code{x} and \code{y} to new values of {x}.
       |                                                     ^
Package suggested but not available for checking: ‘userfriendlyscience’
checkRd: (-1) CIplot.Rd:58: Lost braces; missing escapes or markup?
    58 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.
       |                       ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) rstable.Rd:42: Lost braces
    42 | Lo\"{g}ae\"{v}e, M. (1977). Probability Theory I. (fourth edition) Springer-Verlag, New York.
       |     ^
checkRd: (-1) rstable.Rd:42: Lost braces
    42 | Lo\"{g}ae\"{v}e, M. (1977). Probability Theory I. (fourth edition) Springer-Verlag, New York.
       |            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) doseFind.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) doseFind.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) doseFind.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) data_generator.Rd:93: Lost braces; missing escapes or markup?
    93 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                     ^
checkRd: (-1) data_generator.Rd:93: Lost braces; missing escapes or markup?
    93 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                             ^
checkRd: (-1) data_generator.Rd:95: Lost braces; missing escapes or markup?
    95 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++}, S_{*+}
       |                                                                 ^
checkRd: (-1) data_generator.Rd:95: Lost braces; missing escapes or markup?
    95 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++}, S_{*+}
       |                                                                         ^
checkRd: (-1) data_generator_loop.Rd:96: Lost braces; missing escapes or markup?
    96 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                     ^
checkRd: (-1) data_generator_loop.Rd:96: Lost braces; missing escapes or markup?
    96 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                             ^
checkRd: (-1) data_generator_loop.Rd:98: Lost braces; missing escapes or markup?
    98 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++},
       |                                                                 ^
checkRd: (-1) data_generator_loop.Rd:99: Lost braces; missing escapes or markup?
    99 |   S_{*+} and PP estimands}
       |     ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ciu.ggplot.col.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
checkRd: (-1) ciu.meta.explain.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
checkRd: (-1) ciu.meta.result.new.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
checkRd: (-1) ciu.textual.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
'LazyData' is specified without 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) get_langs.Rd:13: Lost braces
    13 | character vector listing all the languages that tag API call supports. See \code{\link{tag_images}} and code{\link{tag_image_urls}}
       |                                                                                                             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) cd01-0-distanceMatrix.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd01-0-distanceMatrix.Rd:40-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd01-0-distanceMatrix.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd01-0-distanceMatrix.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd01-0-distanceMatrix.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd01-0-distanceMatrix.Rd:51-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd02-1-cluster3.Rd:25: Lost braces
    25 |   Kevin R. Coombes email{krc@silicovore.com}
       |                         ^
checkRd: (-1) cd03-0-ClusterTest-class.Rd:70: Lost braces
    70 |   Kevin R. Coombes email{krc@silicovore.com}
       |                         ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) clean.Rd:136: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:141: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:142: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) cf_save_kml.Rd:68: Lost braces
    68 | \code{\link{cf_find_station}} and code{vignette("choose-station")} for
       |                                       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) clinsig.Rd:129: Lost braces
   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                   ^
checkRd: (-1) clinsig.Rd:129: Lost braces
   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) print.clogitL1.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.clogitL1.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.clogitL1.Rd:23: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) cb_participant_count.Rd:13: Lost braces
    13 | \item{query}{A phenotype query defined using the code{\link{phenotype}} function and logic operators (see example below)}
       |                                                      ^
checkRd: (-1) phenotype.Rd:10: Lost braces
    10 | \item{id}{A single phenotype id. Possible phenotyoes can be explored using the code{\link{cb_search_phenotypes}} function}
       |                                                                                    ^
Objects in \usage without \alias in Rd file 'clpm-internal.Rd':
  ‘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.
checkRd: (-1) clr.Rd:24: Lost braces
    24 | the sense that its Karhunen-Lo\`{e}ve decomposition has qx terms only.}
       |                                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) impute_covariance_matrix.Rd:74-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_covariance_matrix.Rd:80-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_covariance_matrix.Rd:88-98: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) estimate_H_fractions.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Estimates |H_i|/|H_{i+1}| for the first r rows}
       |                           ^
Documented arguments not in \usage in Rd file 'auxiliary_functions.Rd':
  ‘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 Rd file 'clustEff-internal.Rd':
  ‘.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
checkRd: (-1) HTKmeans.Rd:62: Lost braces
    62 | \item{centers }{A matrix of cluster centres.}
       |      ^
checkRd: (-1) HTKmeans.Rd:62: Lost braces
    62 | \item{centers }{A matrix of cluster centres.}
       |                ^
checkRd: (-1) HTKmeans.Rd:63: Lost braces
    63 | \item{cluster }{A vector of integers (from 1:\code{k}) indicating the cluster to which each point is allocated.}
       |      ^
checkRd: (-1) HTKmeans.Rd:63: Lost braces
    63 | \item{cluster }{A vector of integers (from 1:\code{k}) indicating the cluster to which each point is allocated.}
       |                ^
checkRd: (-1) HTKmeans.Rd:64: Lost braces
    64 | \item{itnb }{The number of iterations executed until convergence}
       |      ^
checkRd: (-1) HTKmeans.Rd:64: Lost braces
    64 | \item{itnb }{The number of iterations executed until convergence}
       |             ^
checkRd: (-1) HTKmeans.Rd:65: Lost braces
    65 | \item{converged }{Whether the algorithm stopped by converging or through reaching the maximum number of itertions.}
       |      ^
checkRd: (-1) HTKmeans.Rd:65: Lost braces
    65 | \item{converged }{Whether the algorithm stopped by converging or through reaching the maximum number of itertions.}
       |                  ^
Documented arguments not in \usage in Rd file 'calculate_connectivity.Rd':
  ‘datdf’

Documented arguments not in \usage in Rd file 'dunn_metric.Rd':
  ‘distance’ ‘method’

Documented arguments not in \usage in Rd file 'evaluate_all_column_dataset.Rd':
  ‘data’

Documented arguments not in \usage in Rd file 'information_external.Rd':
  ‘info’

Documented arguments not in \usage in Rd file 'information_internal.Rd':
  ‘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
'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) cluster.Gen.rd:82: Lost braces
    82 | Steinley, D., Henson, R. (2005), \emph{OCLUS: an analytic method for generating clusters with known overlap}, "Journal of Classification", vol. 22, 221-250. Available at: \\doi{10.1007/s00357-005-0015-6}.
       |                                                                                                                                                                                 ^
checkRd: (-1) index.DB.rd:23: Lost braces; missing escapes or markup?
    23 | \item{R}{R matrix $(S_r+S_s)/d_{rs}$}
       |                                ^
checkRd: (-1) index.GAP.rd:12: Lost braces; missing escapes or markup?
    12 | "pc" - generate the reference variables from a uniform distribution over a box aligned with the principal components of the data. In detail, if $X=\{x_{ij}\}$  is our   n x m data matrix, assume that the columns have mean 0 and compute the singular value decomposition $X=UDV^T$. We transform via $X'=XV$ and then draw uniform features Z'  over the ranges of the columns of X' , as in method a) above. Finally we back-transform via $Z=Z'V^T$   to give reference data Z 
       |                                                                                                                                                        ^
checkRd: (-1) pattern.GDM1.rd:77: Lost braces
    77 | Jajuga, K., Walesiak, M., Bak, A. (2003), \emph{On the general distance measure}, In: M. Schwaiger, O. Opitz (Eds.), Exploratory data analysis in empirical research, Springer-Verlag, Berlin, Heidelberg, 104-109. Available at: doi{10.1007/978-3-642-55721-7_12}.
       |                                                                                                                                                                                                                                      ^
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) kproto_gower.Rd:42: Lost braces
    42 | \item{lambda}{Distance parameter lambda. For \code{code}{type = "gower"} only a vector of variable specific weights is possible.}
       |                                                         ^
checkRd: (-1) validation_kproto.Rd:57-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) validation_kproto.Rd:63-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) validation_kproto.Rd:68-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) validation_kproto.Rd:74-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) validation_kproto.Rd:80-84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) validation_kproto.Rd:85-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) validation_kproto.Rd:93-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) validation_kproto.Rd:98-107: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CMAPSS.Rd:10: Lost braces
    10 | \item \code{train}{ a list of class "hhsmm.data" as the train dataset}
       |                   ^
checkRd: (-1) CMAPSS.Rd:11: Lost braces
    11 | \item \code{test}{ a list of class "hhsmm.data" as the test dataset}
       |                  ^
checkRd: (-1) CMAPSS.Rd:12: Lost braces
    12 | \item \code{subsets}{ a matrix containig the number of units in each subset of the CMAPSS data set (FD001-FD004) for the train and test datasets}
       |                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) cmb.search.Rd:50: Lost braces; missing escapes or markup?
    50 |   \item{order}{applied conditioning order {length p}}
       |                                           ^
checkRd: (-1) gp.realize.Rd:20: Lost braces; missing escapes or markup?
    20 | The list \code{l.v} is created by \code{makedistlist()} from a {n x p} design matrix on which to generate the unconditional GP realization.  The correlation parameters take on values in \code{(0,1)} and use the Gaussian correlation model, calculated as \code{rho^d(xi,xj)^2}.  This helper function is used to create the demonstration data used in the example for \code{calibrate()}.
       |                                                                ^
'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) bvp.Rd:24: Lost braces
    24 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
checkRd: (-1) ivp.Rd:38: Lost braces
    38 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
checkRd: (-1) ivpsys.Rd:29: Lost braces
    29 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
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: \#
checkRd: (-1) quicklook.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quicklook.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quicklook.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quicklook.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quicklook.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quicklook.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quicklook.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quicklook.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quicklook.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quicklook.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quicklook.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quicklook.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quicklook.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quicklook.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quicklook.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quicklook.Rd:75: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tobit1’
'LazyData' is specified without a 'data' directory
checkRd: (-1) cnlt.reg.Rd:43: Lost braces
    43 | \emph{Technometrics}, bold{60} (1), 48-60, DOI 10.1080/00401706.2017.1281846.\cr\cr
       |                           ^
checkRd: (-1) fwtnppermC.Rd:35: Lost braces
    35 | Given \eqn{n} points on a line, \env{x}, each with a corresponding env{f} value this function computes
       |                                                                       ^
Specified C++11: please drop specification unless essential
checkRd: (-1) conversion.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conversion.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conversion.Rd:70-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conversion.Rd:72-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conversion.Rd:75-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:103-104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:105-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:109-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:112-113: Lost braces in \itemize; meant \describe ?
'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 Rd file 'feat_sample.Rd':
  ‘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 Rd file 'get_superior.Rd':
  ‘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 Rd file 'lb_calculation.Rd':
  ‘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 Rd file 'cocorresp-internal.Rd':
  ‘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’
checkRd: (-1) educFM.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:28: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘userfriendlyscience’
checkRd: (-1) cb_add_col_attributes.Rd:41-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cb_add_col_attributes.Rd:52-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cb_add_col_attributes.Rd:62-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cb_add_col_attributes.Rd:96-131: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cb_add_col_attributes.Rd:132-141: Lost braces in \itemize; meant \describe ?
checkRd: (-1) asVarName.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) asVarName.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) asVarName.Rd:28-30: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
Package suggested but not available for checking: ‘bvpSolve’
'LazyData' is specified 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) kprime.Rd:36: Lost braces; missing escapes or markup?
    36 | kprime is a {p,d,q} set of functions that compute the K-prime distribution. This distribution has many applications,
       |             ^
checkRd: (-1) lsecond.Rd:37: Lost braces; missing escapes or markup?
    37 | lsecond are {p,d,q} functions that compute the Lambda-second (L") distribution. This
       |             ^
checkRd: (-1) pilsecond.Rd:39: Lost braces; missing escapes or markup?
    39 | pilsecond are {p,d,q} functions that compute the prior-informed Lambda-second (L") distribution. This
       |               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) getHistList.Rd:32: Lost braces; missing escapes or markup?
    32 | ({FALSE})? If a bin is empty, the center of the bin is returned as the
       |  ^
checkRd: (-1) imageClusterPipeline.Rd:82: Lost braces; missing escapes or markup?
    82 | of the bin ({FALSE})? If a bin is empty, the center of the bin is returned
       |             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a '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’.
checkRd: (-1) colour_values.Rd:143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values.Rd:144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values_rgb.Rd:143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values_rgb.Rd:144: Lost braces in \itemize; meant \describe ?
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.
checkRd: (-1) xsimplex.Rd:6: Lost braces; missing escapes or markup?
     6 |              Generates all points on a {p,n} simplex lattice (i.e. a p-part
       |                                        ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sum_every_n.Rd:15: Lost braces; missing escapes or markup?
    15 | \code{sum_every_n} returns a vector of sums of every \code{n}^{th} element of the vector \code{x}.
       |                                                               ^
checkRd: (-1) sum_every_n1.Rd:15: Lost braces; missing escapes or markup?
    15 | \code{sum_every_n1} returns a vector of sums of every \code{n}^{th} element of the vector \code{x}, plus 1.
       |                                                                ^
Argument items with no description in Rd file 'summary.CommunityClimateInput.Rd':
  ‘object’ ‘\dots’
Argument items with no description in Rd file 'summary.CommunityClimateStatistics.Rd':
  ‘object’ ‘\dots’
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
checkRd: (-1) calcHbExSteady.Rd:57-103: Lost braces
    57 | Returns a data.frame with the following columns \cr{
       |                                                    ^
checkRd: (-1) calcIso7933.Rd:71-100: Lost braces
    71 | \code{calcISO7933} returns a data.frame with the following items: \cr{
       |                                                                      ^
checkRd: (-1) calcdTNZ.Rd:53-57: Lost braces
    53 | \code{calcdTNZ} returns a dataframe with the columns dTNZ, dTNZTs, dTNZTa. Thereby \cr{
       |                                                                                       ^
Objects in \usage without \alias in Rd file 'comf-internal.Rd':
  ‘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.
checkRd: (-1) BMD.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add.risk.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add.risk.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) count_pairs.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) score_log_nonparam.Rd:36: Lost braces; missing escapes or markup?
    36 | {0, 1}.
       | ^
checkRd: (-1) score_log_semiparam.Rd:40: Lost braces; missing escapes or markup?
    40 | values in {0, 1}.
       |           ^
checkRd: (-1) sort_pairs.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) hmm.Rd:47-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:56-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:63-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:71-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:79-84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:85-89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:95-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:104-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:108-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:112-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:119-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:130-133: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) GIC.FuncompCGL.Rd:94: Lost braces
    94 | Tune the grid values of the penalty parameter code{lam} and the degrees of freedom of
       |                                                   ^
checkRd: (-1) GIC.compCL.Rd:37: Lost braces
    37 | Tune the penalty parameter code{lam} in the \code{compCGL} model by GIC, BIC, or AIC. This
       |                                ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘CAM’
checkRd: (-1) ARE_tte.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{case}{integer parameter in {1,2,3,4}
       |                                  ^
checkRd: (-1) effectsize_tte.Rd:37: Lost braces; missing escapes or markup?
    37 | \item{case}{integer parameter in {1,2,3,4}
       |                                  ^
checkRd: (-1) plot_tte.Rd:37: Lost braces; missing escapes or markup?
    37 | \item{case}{integer parameter in {1,2,3,4}
       |                                  ^
checkRd: (-1) samplesize_tte.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{case}{integer parameter in {1,2,3,4}
       |                                  ^
checkRd: (-1) simula_tte.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{case}{integer parameter in {1,2,3,4}
       |                                  ^
checkRd: (-1) surv_tte.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{case}{integer parameter in {1,2,3,4}
       |                                  ^
Documented arguments not in \usage in Rd file 'CopulaSelection.Rd':
  ‘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.
checkRd: (-1) glass.Rd:10: Lost braces
    10 | \item{item}{factor}{200 levels - which item the measurements came from}
       |                    ^
checkRd: (-1) glass.Rd:11-12: Lost braces
    11 | \item{fragment}{factor}{4 levels - which of the four fragments from each item the observations were made
       |                        ^
checkRd: (-1) glass.Rd:13: Lost braces
    13 | \item{logNaO}{numeric}{log of sodium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:14: Lost braces
    14 | \item{logMgO}{numeric}{log of magnesium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:15: Lost braces
    15 | \item{logAlO}{numeric}{log of aluminium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:16: Lost braces
    16 | \item{logSiO}{numeric}{log of silicon concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:17: Lost braces
    17 | \item{logKO}{numeric}{log of potassium concentration to oxygen concentration}
       |                      ^
checkRd: (-1) glass.Rd:18: Lost braces
    18 | \item{logCaO}{numeric}{log of calcium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:19: Lost braces
    19 | \item{logFeO}{numeric}{log of iron concentration to oxygen concentration}
       |                       ^
checkRd: (-1) atomdeps.Rd:9: Lost braces
     9 |  \item{"tangle"}: {Dihedral angle defined by atoms A-B-C-D as described below. \code{NA}'s represent the free side chain dihedral angles \emph{chi} for that amino acid.}
       |                   ^
checkRd: (-1) atomdeps.Rd:10: Lost braces; missing escapes or markup?
    10 |  \item{"names"}: {The component atoms of the amino acid side chain.  Represents atom D in the dihedral.}
       |                  ^
checkRd: (-1) atomdeps.Rd:11: Lost braces; missing escapes or markup?
    11 |  \item{"matx"}: {The names of atoms A,B,C in the dihedral, with rows corresponding to the atoms in "names".}
       |                 ^
checkRd: (-1) atomdeps.Rd:12: Lost braces; missing escapes or markup?
    12 |  \item{"bangle"}: {Planar bond angle formed between B-C-D}
       |                   ^
checkRd: (-1) atomdeps.Rd:13: Lost braces; missing escapes or markup?
    13 |  \item{"blength"}: {Bond length between C-D}
       |                    ^
checkRd: (-1) keener.Rd:82: Lost braces; missing escapes or markup?
    82 | a_{ij} = (S_ij + 1) / (S_ij + S_ji + 2). This step should make comparing
       |   ^
checkRd: (-1) CuHallData.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CuHallData.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CuHallData.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CuHallData.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CuHallData.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CuHallData.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CuHallData.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CuHallData.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CuHallData.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CuHallData.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CuHallData.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CuHallData.Rd:43: Lost braces in \itemize; meant \describe ?
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 file 'concordancer-package.Rd':
  \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...’
checkRd: (-1) concstats_hhi.Rd:13: Lost braces; missing escapes or markup?
    13 | value is required. Ranges from {0, 1} and often used for comparison over
       |                                ^
checkRd: (-1) KCI.Rd:44: Lost braces
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                ^
checkRd: (-1) KCI.Rd:44: Lost braces
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                      ^
checkRd: (-1) KCI.Rd:44: Lost braces; missing escapes or markup?
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                                    ^
'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
checkRd: (-1) mya.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
'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
checkRd: (-1) coversim.Rd:103: Lost braces; missing escapes or markup?
   103 | \item{xlas}{numeric in {0, 1, 2, 3} specifying the style of axis labels (see \code{las} in \code{\link{par}},
       |                        ^
checkRd: (-1) coversim.Rd:106: Lost braces; missing escapes or markup?
   106 | \item{ylas}{numeric in {0, 1, 2, 3} specifying the style of axis labels (see \code{las} in \code{\link{par}},
       |                        ^
checkRd: (-1) crplot.Rd:77: Lost braces; missing escapes or markup?
    77 | \item{xlas}{numeric in {0, 1, 2, 3} specifying the style of axis labels (see \code{las} in \code{\link{par}}).}
       |                        ^
checkRd: (-1) crplot.Rd:79: Lost braces; missing escapes or markup?
    79 | \item{ylas}{numeric in {0, 1, 2, 3} specifying the style of axis labels (see \code{las} in \code{\link{par}}).}
       |                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) binary_class_cm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) clResults.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clResults.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clResults.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clResults.Rd:62-63: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) NetStats.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
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 Rd file 'checkCountsWholeNumbers.Rd':
  ‘aggregated.samples’

Documented arguments not in \usage in Rd file 'getGlobalClusterMarkers.Rd':
  ‘min.percent.samples.expression’

Documented arguments not in \usage in Rd file 'getPercentGlobalClusters.Rd':
  ‘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.
checkRd: (-1) genResponses.Rd:34: Lost braces
    34 | perturbation is applied (double in{0 < x < 1}),
       |                                   ^
checkRd: (-1) genResponses.Rd:36: Lost braces; missing escapes or markup?
    36 | (double - when in {0 < x < 100} probs remain positively
       |                   ^
checkRd: (-1) genResponses.Rd:38: Lost braces
    38 | when in{100 < x < Inf} probs are negatively correlated with theta).
       |        ^
checkRd: (-1) plotMCC.Rd:20: Lost braces
    20 | \item{bins}{If _e\\emph{linetype} is "bins", how many bins should be used to chunk the empirical lines?
       |                        ^
Documented arguments not in \usage in Rd file 'postProcessSys.Rd':
  ‘myFile’

Documented arguments not in \usage in Rd file 'theta_ll.Rd':
  ‘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.
checkRd: (-1) Univranks.Rd:69: Lost braces; missing escapes or markup?
    69 | To obtain the preference rankings from the paired comparisons the procedure has been the following: the first row of the raw data is [1  3  2   1   2   1  1  2  1   1   1   2   1    1   2]. London is preferred to Paris, St. Gallen, Barcelona Stockholm (LP, LM, LSg, LB and LSt are always equal to 1), and there is no preference between London and Milan (they are tied); Milan is preferred to Paris (PM = 2), St. Gallen, Barcelona and Stockholm; and so on. The first ordering is then <{L M} Sg St B P> corresponding to a ranking [1,5,1,2,4,3], where the columns indicate L  P  M Sg  B St.  
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) getConvexHull.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getConvexHull.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getConvexHull.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cf_grid.Rd:38: Lost braces; missing escapes or markup?
    38 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
checkRd: (-1) cf_highdim.Rd:58: Lost braces; missing escapes or markup?
    58 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
checkRd: (-1) gcf_grid.Rd:51: Lost braces; missing escapes or markup?
    51 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) set_seed.Rd:15: Lost braces
    15 | a code{\link{DISTRIBUTION}} object of the same class
       |       ^
Documented arguments not in \usage in Rd file 'print_table.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their 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) smoo_dataset.Rd:20: Lost braces; missing escapes or markup?
    20 | The smoother substitutes an original raw value $y_{m,i,t}$ of country $m$
       |                                                   ^
checkRd: (-1) smoo_dataset.Rd:22: Lost braces
    22 | $$\\check{y_{m,i,t}} = y_{m,i,t-1} ~ (1-w)/2   +w ~y_{m,i,t} +y_{m,i,t+1} ~(1-w)/2$$,
       |          ^
checkRd: (-1) smoo_dataset.Rd:22: Lost braces; missing escapes or markup?
    22 | $$\\check{y_{m,i,t}} = y_{m,i,t-1} ~ (1-w)/2   +w ~y_{m,i,t} +y_{m,i,t+1} ~(1-w)/2$$,
       |             ^
checkRd: (-1) smoo_dataset.Rd:22: Lost braces; missing escapes or markup?
    22 | $$\\check{y_{m,i,t}} = y_{m,i,t-1} ~ (1-w)/2   +w ~y_{m,i,t} +y_{m,i,t+1} ~(1-w)/2$$,
       |                          ^
checkRd: (-1) smoo_dataset.Rd:22: Lost braces; missing escapes or markup?
    22 | $$\\check{y_{m,i,t}} = y_{m,i,t-1} ~ (1-w)/2   +w ~y_{m,i,t} +y_{m,i,t+1} ~(1-w)/2$$,
       |                                                      ^
checkRd: (-1) smoo_dataset.Rd:22: Lost braces; missing escapes or markup?
    22 | $$\\check{y_{m,i,t}} = y_{m,i,t-1} ~ (1-w)/2   +w ~y_{m,i,t} +y_{m,i,t+1} ~(1-w)/2$$,
       |                                                                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CovrgPlot.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{plotCI}{a vector of up to 4 numbers out of the set {1,2,3,4}, corresponding to which
       |                                                          ^
Specified C++11: please drop specification unless essential
Invalid package aliases in Rd file 'coopProductGame-package.Rd':
  ‘coopProducGame-package’
checkRd: (-1) copCAR.Rd:40: Lost braces
    40 |        item{\code{maxit}}{the maximum number of iterations to be used by \code{\link{optim}} when optimizing the objective function. Defaults to \code{1000}.}
       |            ^
checkRd: (-1) copCAR.Rd:40: Lost braces
    40 |        item{\code{maxit}}{the maximum number of iterations to be used by \code{\link{optim}} when optimizing the objective function. Defaults to \code{1000}.}
       |                          ^
checkRd: (-1) condQestCopC.Rd:45: Lost braces; missing escapes or markup?
    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                          ^
checkRd: (-1) condQestCopC.Rd:45: Lost braces; missing escapes or markup?
    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                                      ^
checkRd: (-1) condQestCopC.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                  ^
checkRd: (-1) condQestCopC.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                              ^
checkRd: (-1) ComputeCope.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:57-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DrawContour.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Draws the contour {f=c}.}
       |                          ^
checkRd: (-1) DrawContour.Rd:20: Lost braces; missing escapes or markup?
    20 | Draws the contour {f=c}.
       |                   ^
checkRd: (-1) cope.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:35: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) cdtamodel.Rd:15-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:26-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:36-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:42-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cdtamodel.Rd:48: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'ft.Rd':
  ‘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
checkRd: (-1) NEWS.Rd:20: Lost braces; missing escapes or markup?
    20 |       \item Fix non-UTF-8 accents in C code {WARN on CRAN}.
       |                                             ^
checkRd: (-1) Stirling.Rd:36: Lost braces; missing escapes or markup?
    36 |   s(n,k) = (-1)^{n-k} times
       |                 ^
checkRd: (-1) fitMvdc.Rd:13: Lost braces; missing escapes or markup?
    13 |   If you assume {non parametric} margins, in other words, take the
       |                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) CopulaREMADA.Rd:17: Lost braces; missing escapes or markup?
    17 | {gl$nodes} and weights {gl$weights}.
       | ^
checkRd: (-1) CopulaREMADA.Rd:17: Lost braces; missing escapes or markup?
    17 | {gl$nodes} and weights {gl$weights}.
       |                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) getSurface.Rd:22: Lost braces
    22 | value \code{getSurface} shortens the output of \code{conv} to remove artificial surface layers. The output is thus a subset of the input, and identical in structure to the /code{conv} output.
       |                                                                                                                                                                                  ^
checkRd: (-1) cvGen.Rd:29: Lost braces
    29 | The function code{gatherFromList} returns a list with components containing elements of the same name.
       |                  ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) CorMID.Rd:54: Lost braces; missing escapes or markup?
    54 |  individual compound containing 2 carbons and observe a vector of {978,22,0}.
       |                                                                   ^
checkRd: (-1) CorMID.Rd:58: Lost braces; missing escapes or markup?
    58 |  The equivalent corMID vector would be {1,0,0}, indicating that the non-labeled
       |                                        ^
checkRd: (-1) carstats.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:14: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_policy_scores.Rd:63: Lost braces
    63 | \code{low_estimate}\\code{high_estimate} columns. The \code{SD_estimate} column has the standard deviation of the
       |                          ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) jointprobs.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) jointprobs.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) jointprobs.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) jointprobs.Rd:21: Lost braces; missing escapes or markup?
    21 | \eqn{K+1} categories the arrays will have either \eqn{K+1} or {K} dimensions, depending on whether 
       |                                                               ^
checkRd: (-1) multinom.gen.Rd:46: Lost braces
    46 | For a \emph{K}-variate multinomial, the matrix{m} should have \emph{K-1} columns
       |                                               ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) HeartAttack.Rd:25: Lost braces
    25 | \references{Saporta, G. (1990) Probabilit\'{e}s analyse des donn\'{e}es et statistique. Paris,\'{E}ditions technip}
       |                                            ^
checkRd: (-1) HeartAttack.Rd:25: Lost braces
    25 | \references{Saporta, G. (1990) Probabilit\'{e}s analyse des donn\'{e}es et statistique. Paris,\'{E}ditions technip}
       |                                                                   ^
checkRd: (-1) HeartAttack.Rd:25: Lost braces
    25 | \references{Saporta, G. (1990) Probabilit\'{e}s analyse des donn\'{e}es et statistique. Paris,\'{E}ditions technip}
       |                                                                                                 ^
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) summary_fitlist.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fasttrakg.Rd:18: Lost braces
    18 |     \item{\code{killip}}{Killip level of cardiac event severity (1-4)age75}{1= Age>75; 0=Age<=75}
       |                                                                            ^
Documented arguments not in \usage in Rd file 'dCount_dePril_bi.Rd':
  ‘inheritParams’

Documented arguments not in \usage in Rd file 'dCount_naive_bi.Rd':
  ‘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
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) coxphw-package.Rd:65: Lost braces
    65 |         {Maintainer: \email{daniela.dunkler@meduniwien.ac.at}} }
       |         ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) gen_data.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gen_data.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gen_data.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) coxph.RT.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) coxph.RT.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) coxph.RT.Rd:59-71: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) Sample.data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:21: Lost braces in \itemize; meant \describe ?
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:
checkRd: (-1) trimmed_quantile.Rd:21: Lost braces; missing escapes or markup?
    21 | the quantiles for a trimmed data set, e.g., X \ {x(1), x(r)} (trim = 1), or 
       |                                                 ^
checkRd: (-1) trimmed_quantile.Rd:22: Lost braces; missing escapes or markup?
    22 | X \ {x(1), x(2), x(r-1), x(r)} (trim = 2).
       |     ^
Specified C++11: please drop specification unless essential
checkRd: (-1) sharedat.Rd:23: Lost braces
    23 | \doi{10.7910/DVN/YXMQZM}{Harvard dataverse}
       |                         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) update_PACKAGES.Rd:35: Lost braces; missing escapes or markup?
    35 |     Type of packages: currently source \file{.tar.{gz,bz2,xz}} archives,
       |                                                   ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) crwPredict.Rd:54-68: Lost braces
    54 | \item("predTime"){
       |                  ^
checkRd: (-1) crwPredict.Rd:59: Lost braces
    59 |  no longer the default (see \item{return.type}). If the original data were 
       |                                  ^
checkRd: (-1) make_style.Rd:51: Lost braces
    51 | The style (the code{...} argument) can be anything of the
       |                    ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) generate_cre_dataset.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{n_rules}{The number of causal rules. (default: 2, range: {1,2,3,4}).}
       |                                                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) normFit.Rd:39: Lost braces; missing escapes or markup?
    39 | {analytes}}
       | ^
checkRd: (-1) normPred.Rd:27: Lost braces
    27 | ode{standards}, \code{analytes}}
       |    ^
checkRd: (-1) DualEndpointOld-class.Rd:21: Lost braces; missing escapes or markup?
    21 | contain a vector with elements \code{a} and {b} for the inverse-gamma prior
       |                                             ^
checkRd: (-1) DualEndpointRW-class.Rd:39: Lost braces; missing escapes or markup?
    39 | contain a vector with elements \code{a} and {b} for the inverse-gamma prior
       |                                             ^
checkRd: (-1) simulate-DualResponsesSamplesDesign-method.Rd:45: Lost braces
    45 | \item{trueNu}{(not with code{\linkS4class{EffFlexi}}) the precision, the inverse of the 
       |                             ^
checkRd: (-1) simulate-DualResponsesSamplesDesign-method.Rd:48: Lost braces
    48 | \item{trueSigma2}{(only with code{\linkS4class{EffFlexi}}) the true variance of the efficacy 
       |                                  ^
checkRd: (-1) simulate-DualResponsesSamplesDesign-method.Rd:51: Lost braces
    51 | \item{trueSigma2betaW}{(only with code{\linkS4class{EffFlexi}}) the true variance for the 
       |                                       ^
Documented arguments not in \usage in Rd file 'pinvGamma.Rd':
  ‘logical;’

Documented arguments not in \usage in Rd file 'qinvGamma.Rd':
  ‘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
checkRd: (-1) confRegCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                                                                                    ^
checkRd: (-1) confRegCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                                                                                      ^
checkRd: (-1) confRegUCRandUCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) cruts-package.Rd:21: Lost braces
    21 | section{Dependencies}{
       |        ^
checkRd: (-1) cruts-package.Rd:21-24: Lost braces
    21 | section{Dependencies}{
       |                      ^
checkRd: (-1) cruts-package.Rd:26: Lost braces
    26 | section{Citation}{
       |        ^
checkRd: (-1) cruts-package.Rd:26-28: Lost braces
    26 | section{Citation}{
       |                  ^
checkRd: (-1) cruts-package.Rd:30-32: Lost braces
    30 | references{
       |           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) calculate_cell_volume.Rd:16: Lost braces; missing escapes or markup?
    16 | V A real number. The volume (in angstroms^3 or angstroms^{-3})
       |                                                          ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rgeos’
checkRd: (-1) calculateEffects.Rd:24: Lost braces; missing escapes or markup?
    24 | equals (I-B)^{-1}Gamma. The indirect effect equals the difference between
       |              ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ch_tr_sign.Rd:15: Lost braces; missing escapes or markup?
    15 | {x} {an array of indices 1, 2, 3}
       |     ^
checkRd: (-1) ch_tr_signif.Rd:15: Lost braces; missing escapes or markup?
    15 | {x} {an array of indices 1 and 2, where 1 is NS and 2 is significant}
       |     ^
checkRd: (-1) lmranks.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lmranks.Rd:63: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'tool.Rd':
  ‘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.
checkRd: (-1) csvy.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) csvy.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) csvy.Rd:60: Lost braces in \itemize; meant \describe ?
'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) gm.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gm.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gm.Rd:32-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gm.Rd:35-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gm.Rd:38-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gm.Rd:41-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gm.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gm.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gm.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gm.Rd:53-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gm.Rd:56-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gm.Rd:59-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gmci.Rd:21-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gmci.Rd:24-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gmci.Rd:27-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mcmc.fmove.Rd:81: Lost braces; missing escapes or markup?
    81 |   beta ~ N( 0 , tau^2 * QQ^{-1} )
       |                            ^
'LazyData' is specified without a 'data' directory
Objects in \usage without \alias in Rd file 'ctqr-internal.Rd':
  ‘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 Rd file 'ctqr-internal.Rd':
  ‘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’
checkRd: (-1) cubintegrate.Rd:67: Lost braces; missing escapes or markup?
    67 | evaluated} - {returnCode}{the actual integer return code
       |              ^
checkRd: (-1) cubintegrate.Rd:67-69: Lost braces
    67 | evaluated} - {returnCode}{the actual integer return code
       |                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) chi2cub1cov.Rd:18-19: Lost braces
    18 | \item{gama}{gama}{Vector of parameters for the feeling component, with length equal to 2
       |                  ^
Documented arguments not in \usage in Rd file 'chi2cub2cov.Rd':
  ‘covar’

Documented arguments not in \usage in Rd file 'cubpq.Rd':
  ‘summary’

Documented arguments not in \usage in Rd file 'cubshe.Rd':
  ‘makeplot’ ‘summary’

Documented arguments not in \usage in Rd file 'kkk.Rd':
  ‘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: \_ \_ \_
checkRd: (-1) bandingEst.Rd:21: Lost braces; missing escapes or markup?
    21 | that are far removed from one another. The {i, j} entry of the estimated
       |                                            ^
checkRd: (-1) bandingEst.Rd:22: Lost braces; missing escapes or markup?
    22 | covariance matrix will be zero if the absolute value of {i - j} is greater
       |                                                         ^
checkRd: (-1) taperingEst.Rd:29: Lost braces; missing escapes or markup?
    29 | \code{abs(i - j) <= k / 2}, then entry {i, j} in the weight matrix is equal
       |                                        ^
checkRd: (-1) taperingEst.Rd:30: Lost braces; missing escapes or markup?
    30 | to 1. If \code{k / 2 < abs(i - j) < k}, then entry {i, j} is equal to
       |                                                    ^
checkRd: (-1) taperingEst.Rd:31: Lost braces; missing escapes or markup?
    31 | \code{2 - 2 * abs(i - j) / k}. Otherwise, entry {i, j} is equal to 0.
       |                                                 ^
Documented arguments not in \usage in Rd file 'cvRiskPlot.Rd':
  ‘estimator’

Documented arguments not in \usage in Rd file 'matrixMetrics.Rd':
  ‘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 Rd file 'compute_stat.Rd':
  ‘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
checkRd: (-1) render_toc.Rd:49: Lost braces; missing escapes or markup?
    49 |     ```{r echo=FALSE}
       |        ^
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.
checkRd: (-1) fit.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.Rd:39: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) CytofTree.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RetrievePops.Rd:20-21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RetrievePops.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) czso_get_catalogue.Rd:14: Lost braces; missing escapes or markup?
    14 | \item the \code{spatial} columns contains an IRI ending in the pattern {unit_type}/{unit_code}.
       |                                                                        ^
checkRd: (-1) czso_get_catalogue.Rd:14: Lost braces; missing escapes or markup?
    14 | \item the \code{spatial} columns contains an IRI ending in the pattern {unit_type}/{unit_code}.
       |                                                                                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'tree.filter.Rd':
  ‘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.
checkRd: (-1) D4TAlinkTask.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bestsetNoise.Rd:128-129: Lost braces
   128 |   \code{tcrit}{For each model, the minimum of the absolute values of
       |               ^
checkRd: (-1) bestsetNoise.Rd:130: Lost braces
   130 |   \code{regsubsets_obj}{The object returned by the call to \code{regsubsets}.}
       |                        ^
checkRd: (-1) plotSimScat.Rd:30: Lost braces; missing escapes or markup?
    30 | Specify \code{points} or {residuals}.
       |                          ^
checkRd: (-1) print.sumry.glm.Rd:34: Lost braces; missing escapes or markup?
    34 |   \item{show.iter}{\code{NULL} or {integer}. If \code{NULL}, or if
       |                                   ^
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{  A small, positive scalar that determines when iterations
       |               ^
checkRd: (-1) fpiter.Rd:60-61: Lost braces
    60 |     \code{maxiter}{  An integer denoting the maximum limit on the number of
       |                   ^
checkRd: (-1) fpiter.Rd:63-65: Lost braces
    63 |     \code{trace}{  A logical variable denoting whether some of the intermediate
       |                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exp249.munit.des.Rd:10: Lost braces
    10 | \source{Coombes, N. E. (2009) code{Digger}\emph{: design search tool in R}. {URL:} {\url{http://nswdpibiom.org/austatgen/software/}},
       |                                   ^
checkRd: (-1) get.daeTolerance.Rd:3: Lost braces; missing escapes or markup?
     3 | \title{Gets the value of {daeTolerance} for the package dae}
       |                          ^
checkRd: (-1) get.daeTolerance.Rd:7: Lost braces; missing escapes or markup?
     7 | \value{The \code{vector} of two values for {daeTolerance}, one named \code{element.tol} 
       |                                            ^
checkRd: (-1) set.daeTolerance.Rd:21: Lost braces; missing escapes or markup?
    21 | \value{The \code{vector} {daeTolerance} is returned invisibly.}
       |                          ^
checkRd: (-1) formatScientificTeX.Rd:33: Lost braces; missing escapes or markup?
    33 | function will return  " 3.0\\\\times 10^{2}"
       |                                         ^
checkRd: (-1) canonicalize.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) canonicalize.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) canonicalize.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) edges.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) edges.Rd:16-17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) edges.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) edges.Rd:19-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) edges.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getExample.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getExample.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getExample.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getExample.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getExample.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getExample.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getExample.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getExample.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getExample.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getExample.Rd:22: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'mm_run_reg.Rd':
  ‘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
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
checkRd: (-1) gl.filter.maf.Rd:7: Lost braces; missing escapes or markup?
     7 |  {adegenet} object}
       |  ^
checkRd: (-1) gl.pcoa.Rd:68: Lost braces; missing escapes or markup?
    68 | The function is essentially a wrapper for glPca {adegenet} or pcoa \{ape\}
       |                                                 ^
checkRd: (-1) gl.play.history.Rd:17: Lost braces
    17 | code{x2@other$history[c(1,4,5)]}). [optional].}
       |     ^
checkRd: (-1) utils.jackknife.Rd:49: Lost braces
    49 | bold{Note} that when n is very small, jackknife resampling is not recommended.
       |     ^
checkRd: (-1) utils.jackknife.Rd:51: Lost braces
    51 | Parallel computation is implemented. The argument code{n.cores} indicates the 
       |                                                       ^
GNU make is a SystemRequirements.
checkRd: (-1) StartEnd.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) StartEnd.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processFlow.Rd:14: Lost braces
    14 | \item{roundDigits}{Integer. If NA, numerics are not rounded before comparison. If /code{roundDigits} is specified, numerics are 
       |                                                                                        ^
checkRd: (-1) processFlow.Rd:15: Lost braces
    15 | rounded to /code{roundDigits} decimal places using \link[base]{round}.}
       |                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) data_edit.Rd:137: Lost braces
   137 | code{data_edit} is a shiny application built on \code{rhandsontable} that is
       |     ^
Documented arguments not in \usage in Rd file 'plotDataExplorer.single.Rd':
  ‘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
checkRd: (-1) number_of_rows.Rd:30-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) number_of_rows.Rd:33-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_methods.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_methods.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_methods.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_methods.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_source.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_source.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) special_simulation.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) special_simulation.Rd:40-43: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) defaultFactorSummaries.Rd:29: Lost braces
    29 | code{\link{variableType}}, \code{\link{countMissing}}, \code{\link{uniqueValues}},
       |     ^
Found the following files/directories:
  ‘my new data set.rds’
'LazyData' is specified without a 'data' directory
checkRd: (-1) build_date_factor.Rd:15: Lost braces; missing escapes or markup?
    15 | Map a vector of dates to a factor at one of these levels {"yearmonth", "yearquarter", "quarter", "month"}
       |                                                          ^
checkRd: (-1) build_date_factor.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{type}{One of {"year", "yearquarter", "yearmonth", "quarter", "month"}}
       |                    ^
checkRd: (-1) defaultFactorSummaries.Rd:29: Lost braces
    29 | code{\link{variableType}}, \code{\link{countMissing}}, \code{\link{uniqueValues}},
       |     ^
checkRd: (-1) readNWISuse.Rd:21: Lost braces
    21 | numeric (id), or code{NULL}, which will
       |                      ^
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 Rd file 'dotgetJSONValue.Rd':
  ‘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) is_datelife_query.Rd:17: Lost braces; missing escapes or markup?
    17 | First, that \code{input} is of class {datelifeQuery}.
       |                                      ^
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
checkRd: (-1) plot.mleBb.Rd:48: Lost braces
    48 |   \ code{size} is extracted from argument \code{x}.
       |         ^
checkRd: (-1) value_missing_table.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) value_missing_table.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dblog’
'LazyData' is specified without a 'data' directory
checkRd: (-1) CI_mc.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{i}{the row index of the interest entry X_{i,j}}
       |                                                ^
checkRd: (-1) CI_mc.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{j}{the row index of the interest entry X_{i,j}}
       |                                                ^
checkRd: (-1) is.wmppp.Rd:7: Lost braces; missing escapes or markup?
     7 |   Check whether its argument is an object of class {"wmppp"} (\code{\link{wmppp.object}}).
       |                                                    ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) Velocity.Rd:9: Lost braces; missing escapes or markup?
     9 | \item{probs}{the weight of each value {-1,0,1}. They define the probability that each of them will be picked}
       |                                       ^
checkRd: (-1) cte_times_vel_cpp.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{abs_op}{the final number of {1,-1} operations}
       |                                   ^
checkRd: (-1) natVelocity.Rd:15: Lost braces; missing escapes or markup?
    15 | \item{probs}{the weight of each value {-1,0,1}. They define the probability that each of them will be picked}
       |                                       ^
checkRd: (-1) nat_cte_times_vel_cpp.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{abs_op}{the final number of {1,-1} operations}
       |                                   ^
checkRd: (-1) nat_vel_plus_vel_cpp.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{abs_op1}{the number of {1,-1} operations in the first velocity}
       |                              ^
checkRd: (-1) nat_vel_plus_vel_cpp.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{abs_op2}{the number of {1,-1} operations in the second velocity}
       |                              ^
checkRd: (-1) randomize_vl_cpp.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{probs}{the probabilities of each value in the set {-1,0,1}}
       |                                                         ^
checkRd: (-1) vel_plus_vel_cpp.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{abs_op}{the final number of {1,-1} operations}
       |                                   ^
Specified C++11: please drop specification unless essential
S3 methods shown with full name in Rd file 'dbglm-internal.Rd':
  ‘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 Rd file 'a_dcc_mat_est.Rd':
  ‘param’

Documented arguments not in \usage in Rd file 'dcc_mat_est.Rd':
  ‘param’

Documented arguments not in \usage in Rd file 'deco_mat_est.Rd':
  ‘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.
checkRd: (-1) data.Rd:11: Lost braces
    11 | \doi{10.1007/s40258-021-00647-3}{DOI}
       |                                 ^
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘INLA’
checkRd: (-1) CalcStatClusterGivenCenter.Rd:36: Lost braces; missing escapes or markup?
    36 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) CalcStatClusterGivenCenter.Rd:37: Lost braces; missing escapes or markup?
    37 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) CalcStatsAllClusters.Rd:49: Lost braces; missing escapes or markup?
    49 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) CalcStatsAllClusters.Rd:50: Lost braces; missing escapes or markup?
    50 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) DetectClustersModel.Rd:60: Lost braces; missing escapes or markup?
    60 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) DetectClustersModel.Rd:61: Lost braces; missing escapes or markup?
    61 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) glmAndZIP.iscluster.Rd:34: Lost braces; missing escapes or markup?
    34 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) glmAndZIP.iscluster.Rd:35: Lost braces; missing escapes or markup?
    35 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) DCluster.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DCluster.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DCluster.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DCluster.Rd:134: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DCluster.Rd:136: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DCluster.Rd:138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DCluster.Rd:140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DCluster.Rd:142: Lost braces in \itemize; meant \describe ?
'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
checkRd: (-1) kernel.assign.Rd:27: Lost braces; missing escapes or markup?
    27 |  {q = [0, 1]}. Kernels are of the Müller-Wang type ("MW"), Müller type ("M")
       |  ^
checkRd: (-1) dNMF.Rd:76: Lost braces; missing escapes or markup?
    76 | The number of low-dimension (J < {N, M}, Default: 3)
       |                                  ^
checkRd: (-1) dNMF.Rd:103: Lost braces; missing escapes or markup?
   103 |   U : A matrix which has N-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) dNMF.Rd:104: Lost braces; missing escapes or markup?
   104 |   V : A matrix which has M-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) dPLS.Rd:53: Lost braces; missing escapes or markup?
    53 | The number of low-dimension (J < {N, M}, Default: 3)
       |                                  ^
checkRd: (-1) dPLS.Rd:74: Lost braces; missing escapes or markup?
    74 |   U : A matrix which has N-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) dPLS.Rd:75: Lost braces; missing escapes or markup?
    75 |   V : A matrix which has M-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) dSVD.Rd:60: Lost braces; missing escapes or markup?
    60 | The number of low-dimension (J < {N, M}, Default: 3)
       |                                  ^
checkRd: (-1) dSVD.Rd:81: Lost braces; missing escapes or markup?
    81 |   U : A matrix which has N-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) dSVD.Rd:82: Lost braces; missing escapes or markup?
    82 |   V : A matrix which has M-rows and J-columns (J < {N, M}).
       |                                                    ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) L2metric.Rd:10: Lost braces; missing escapes or markup?
    10 | is the number of the equi-distant points {1,...,d} in the domain of the data [1,d] at which the functional
       |                                          ^
checkRd: (-1) L2metric.Rd:15: Lost braces; missing escapes or markup?
    15 | is the number of the equi-distant points {1,...,d} in the domain of the data [1,d] at which the functional
       |                                          ^
checkRd: (-1) L2metric.Rd:27: Lost braces; missing escapes or markup?
    27 | represented by matrices of their functional values on the common domain {1,...,d}, 
       |                                                                         ^
checkRd: (-1) detectAgeInterval.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Age}, or code{age}.}
       |                                                                              ^
checkRd: (-1) detectSex.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Sex}, or code{sex}.}
       |                                                                              ^
checkRd: (-1) ggbgetAgesFit.Rd:28: Lost braces
    28 | code{\link{ggbChooseAges}}
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.ddpcr_plate.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ddpcr_plate.Rd:138-139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ddpcr_plate.Rd:140-141: Lost braces in \itemize; meant \describe ?
Auto-generated content requiring editing in Rd file 'DDPNA-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
Argument items with no description in Rd file 'DEP_Mod_net_plot.Rd':
  ‘\dots’
Specified C++11: please drop specification unless essential
checkRd: (-1) ddsPLS.Rd:81: Lost braces; missing escapes or markup?
    81 |   \item \code{$U_star}: Loadings for \code{X} in original base: $U_star=U(P'U)^{-1}$.
       |                                                                                ^
checkRd: (-1) modelddsPLSCpp_Rcpp.Rd:38: Lost braces; missing escapes or markup?
    38 |   \item \code{$U_star}: Loadings for \code{X} in original base: $U_star=U(P'U)^{-1}$.
       |                                                                                ^
checkRd: (-1) predict.ddsPLS.Rd:89-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.ddsPLS.Rd:92-93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.ddsPLS.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.ddsPLS.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly
'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 Rd file 'getTriContextFraction.Rd':
  ‘trimer.counts.ref’

Documented arguments not in \usage in Rd file 'norm.it.Rd':
  ‘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.
checkRd: (-1) deconv.Rd:85: Lost braces; missing escapes or markup?
    85 |     \code{tg}, std. error of \eqn{g}, \eqn{G} (the cdf of {g}),
       |                                                           ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) deepNN-package.Rd:18: Lost braces
    18 | section{Dependencies}{
       |        ^
checkRd: (-1) deepNN-package.Rd:18-21: Lost braces
    18 | section{Dependencies}{
       |                      ^
checkRd: (-1) deepNN-package.Rd:23: Lost braces
    23 | section{Citation}{
       |        ^
checkRd: (-1) deepNN-package.Rd:23-25: Lost braces
    23 | section{Citation}{
       |                  ^
checkRd: (-1) deepNN-package.Rd:27-38: Lost braces
    27 | references{
       |           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) defm_terms.Rd:69: Lost braces; missing escapes or markup?
    69 | \item Intercept effect: {...} No transition, only including the current state.
       |                         ^
checkRd: (-1) defm_terms.Rd:70: Lost braces; missing escapes or markup?
    70 | \item Transition effect: {...} > {...} Includes current and previous states.
       |                          ^
checkRd: (-1) defm_terms.Rd:70: Lost braces; missing escapes or markup?
    70 | \item Transition effect: {...} > {...} Includes current and previous states.
       |                                  ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'degreenet-internal.Rd':
  ‘range’ ‘lims’
Objects in \usage without \alias in Rd file 'degreenet-internal.Rd':
  ‘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.
checkRd: (-1) deltaPlot.Rd:28: Lost braces
    28 |  \item{purify}{logical: should item purification be performed? (Default is code{FALSE}). See \bold{Details}.}
       |                                                                                ^
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'LazyData' is specified without a 'data' directory
checkRd: (-1) deming.Rd:71: Lost braces
    71 | on whether the code{cv} option is TRUE or FALSE, respectively.
       |                    ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘smd_table.docx’
checkRd: (-1) pval_shapiro.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pval_shapiro.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pval_shapiro.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pval_shapiro.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pval_shapiro.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kin.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:53-61: Lost braces
    53 | {\itemize{
       | ^
checkRd: (-1) kin.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:59-67: Lost braces
    59 | {\itemize{
       | ^
checkRd: (-1) kin2sex.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) conifersIP.Rd:9: Lost braces; missing escapes or markup?
     9 | \code{conifersIP} {has following variables:}
       |                   ^
checkRd: (-1) conifersIP.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sync.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
Documented arguments not in \usage in Rd file 'boot_f_cor.Rd':
  ‘fun’

Documented arguments not in \usage in Rd file 'boot_f_pcor.Rd':
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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.
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Rd files without \alias:
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  ‘exportClasses’
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DESCRIPTION Depends or Imports field contains ‘methods’.
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    68 | 	response.  See code{\link{makeDepmix}} for an example of how to use
       |                            ^
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    34 | system, crs) of DeponsRaster and DeponsTrack objects. For {sp} objects the
       |                                                           ^
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    33 | guessed either from\ code{names(formals(f))} (if \code{f} is a function)
       |                          ^
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     7 | Computes a matrix of weighted correlations between the columns of \code{x} and the columns of {y}. This can be Pearson, Spearman or Kendall correlation.
       |                                                                                               ^
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     7 | Computes a matrix of weighted covariances between the columns of \code{x} and the columns of {y}.
       |                                                                                              ^
There are ::: calls to the package's namespace in its code. A package
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  ‘.factorQ3’ ‘.factormax’ ‘.factormean’ ‘.factormedian’ ‘.factormin’
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    21 | \item{r}{vector for the proportion for each sub-population, r_1 is 1, r_i>r_{i+1}}
       |                                                                             ^
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    25 | \item{r_set}{the matrix of proportion for each sub-population, r_1 is 1, r_i>r_{i+1}}
       |                                                                                ^
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    21 | \item{r}{vector for the proportion for each sub-population, r_1is 1, r_i>r_{i+1}}
       |                                                                            ^
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    26 | \item{expr}{an expression that generates a {detourr} widget}
       |                                            ^
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    80 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
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    67 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
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    65 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
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    76 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
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    11 | Variables are evaluated using {tidyselect} syntax.}
       |                               ^
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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    27 |   \item{s_1}{A function depending on the number of patients included used for adaptive randomization in plateau determination, only used if the estimation method chosen is "MTA-RA". The default function is function(n_cur,n){0.2}.}
       |                                                                                                                                                                                                                                ^
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    30 |   \item{s_1}{A function depending on the number of patients included used for adaptive randomization in plateau determination, only used if the estimation method chosen is "MTA-RA". The default function is function(n_cur){0.2}.}
       |                                                                                                                                                                                                                              ^
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    47 | \item{comp}{the measures of model complexity used to compute the measure of goodness-of-fit. It is equal to \code{npar} when code{complexity = "df"};}
       |                                                                                                                                  ^
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   258 | 		\item{\code{7}}{maximum number of solution points ('code{np}') reached.}
       |                                                                         ^
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    32 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
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    36 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
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    36 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
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    84 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
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    88 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
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    88 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
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   124 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
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   128 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
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   128 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
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    44 | pkg{htmlwidgets}.
       |    ^
Documented arguments not in \usage in Rd file 'encode_unit.Rd':
  ‘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.
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    40 |  {Paul Schneider <paul.schneider@usi.ch>}{}
       |  ^
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    74 | form average treatment effects for groups of {it}.
       |                                              ^
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    25 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
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    25 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
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    22 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
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  ‘param’ ‘startvalgen’

Documented arguments not in \usage in Rd file 'seqdiffusion.Rd':
  ‘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.
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    72 |   {The Sharma-Song test} {\code{\link[DiffXTables]{sharma.song.test}}}
       |   ^
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    74 |   {The comparative chi-squared test} {\code{\link[DiffXTables]{cp.chisq.test}}}
       |   ^
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    76 |   {The heterogeneity test} {\code{\link[DiffXTables]{heterogeneity.test}}}
       |   ^
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   185 |  \code{\link[deltaPlotR]{deltaPlot}}, code{\link[deltaPlotR]{diagPlot}}, \code{\link{dichoDif}}
       |                                           ^
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   272 | \item{name}{the name of the model {"GNG", "iNUDGE","NUDGE"} where
       |                                   ^
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    79 | n^{1/3} up to sacrificing some accuracy, for details see
       |   ^
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    11 | 'RStudio', use \code{startup}{restart} instead.
       |                              ^
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    10 | \item{input, output, session}{Internal parameters for `{shiny}`.
       |                                                        ^
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Unknown package ‘discreteMTP’ in Rd xrefs
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  ‘RV-package’
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    52 | P\'{a}ez, A. (2013). Mapping travelers’ attitudes: does space matter?. Journal of Transport Geography, 26, 117-125. (https://doi.org/10.1016/j.jtrangeo.2012.09.002)
       |    ^
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    49 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
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    74 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
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    87 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
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    50 | Lavery, T., P\'{a}ez, A., & Kanaroglou, P.S. (2013). Driving out of choices: An investigation of transport modality in a university sample. Transportation Research Part A: Policy and Practice, 57:37-46 (https://doi.org/10.1016/j.tra.2013.09.010)
       |                ^
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    32 | [a_{q-1}, a_q) are available.
       |    ^
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    31 | [a_{q-1}, a_q) are available.
       |    ^
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    23 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
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    24 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
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    23 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
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    24 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
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    21 | [a_0, a_1), [a_1, a_2), ..., [a_{q-1}, a_q) ("character vector")}
       |                                 ^
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    56 | strings, and you are encouraged to use {fasttime} to convert the strings to
       |                                        ^
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    10 | \item{.f}{a normal function or purrr syntax function i.e. `~{ ...code...}`}
       |                                                             ^
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    28 | Elith J., M. Kearney M., and S. Phillips, 2010. The art of modelling range-shifting species. \doi{10.1111/j.2041-210X.2010.00036.x}{Methods in Ecology and Evolution 1:330-342}.
       |                                                                                                                                    ^
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    89 | link{read_from_DB} function. Those parameters define rows and columns that will be returned.
       |     ^
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    46 | \code{data1.shared.var} and {data2.shared.var} must contain unique values within its own data frame.
       |                             ^
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    27 | udf <- function(x){
       |                   ^
Documented arguments not in \usage in Rd file 'internals.Rd':
  ‘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.
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    18 | the {ggdist} package to produce your own distribution plots. You can learn
       |     ^
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    19 | more about how this plot can be produced using {ggdist} here:
       |                                                ^
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    31 | \strong{Support}: {x in [0, \eqn{\infty})}
       |                   ^
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    37 |   {M(theta)=-(log(y_1-y_0)+log(y_2-y_1)+...+log(y_m-y_m-1))}
       |   ^
Documented arguments not in \usage in Rd file 'internalmleHelpers.Rd':
  ‘validity.check’

Objects in \usage without \alias in Rd file 'internals.Rd':
  ‘.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 Rd file 'internalGenerics.Rd':
  x <- samplesize(object, value)

Documented arguments not in \usage in Rd file 'internals.Rd':
  ‘DClass’
Objects in \usage without \alias in Rd file 'internals.Rd':
  ‘.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
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    30 | \item{diffbin}{\code{(logical)}: Difference-based duration for discreet time (only applicabble to cases when \code{bin} is provided). If set to \code{TRUE}, single-interval taxa will \code{0} durations. Setting this argument to \code{FALSE} will add code{1} to the durations of all taxa.}
       |                                                                                                                                                                                                                                                               ^
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    27 | Due to stratigraphic constraints, we can only process deep time data, when it is sliced to discrete bins. It is suggested that you do this separately for most of your analyses. This function is also used by the code{\link{divDyn}} function when \code{age} entries are provided.
       |                                                                                                                                                                                                                        ^
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    31 | Setting both \code{bin} If \code{bin=NULL} and code{tax=NULL}, will run \code{FUN} on the entire dataset (no effect). Providing either \code{bin} or \code{tax} and keeping the other \code{NULL} will iterate \code{FUN} for every \code{bin} or \code{tax} entry (whichever is presented).
       |                                                    ^
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Objects in \usage without \alias in Rd file 'diveMove-internal.Rd':
  ‘.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.
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    85 |     \item \code{root.p}{Vector of probabilities/weights to use when
       |                        ^
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    59 |     \code{make.x}, for tree type {x}.  The MuSSE simulator automatically
       |                                  ^
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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:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
checkRd: (-1) plot.compare_category.Rd:31: Lost braces; missing escapes or markup?
    31 | However, it only support las parameter. las is numeric in {0,1}; the style of axis labels.
       |                                                           ^
Invalid package aliases in Rd file 'dmaiIntro.Rd':
  ‘dmaiIntro-package’
'LazyData' is specified without a 'data' directory
checkRd: (-1) dma.Rd:47: Lost braces; missing escapes or markup?
    47 | When y_t is controlled, only y_{t-delay-1} and before 
       |                                ^
checkRd: (-1) dma.Rd:64: Lost braces; missing escapes or markup?
    64 | 		 estimate of theta_{j-1} for model k at t}
       |                                    ^
checkRd: (-1) dma.Rd:66: Lost braces; missing escapes or markup?
    66 | 		 variance of theta_{j-1} for model k at t}
       |                                    ^
checkRd: (-1) dma.Rd:68: Lost braces; missing escapes or markup?
    68 | 		 estimate of theta_{j-1} at t}
       |                                    ^
checkRd: (-1) dma.Rd:70: Lost braces; missing escapes or markup?
    70 | 		 variance of thetahat_{j-1} at t}
       |                                       ^
checkRd: (-1) dmbc-package.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dmbc-package.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dmbc-package.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dmbc-package.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dmbc-package.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dmbc-package.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dmbc-package.Rd:59-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dmbc-package.Rd:65-69: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Argument items with no description in Rd file 'dml_bagging.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_boosting.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_ensemble_lm.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_ensemble_rf.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_neural_network.Rd':
  ‘y,x,d,data,sed’
Argument items with no description in Rd file 'dml_random_forest.Rd':
  ‘y,x,d,data,sed’
checkRd: (-1) dca.Rd:24: Lost braces; missing escapes or markup?
    24 | \eqn{neglinks_{ij} = 1} means chunklet \code{i} and chunklet {j}
       |                                                              ^
checkRd: (-1) dca.Rd:26: Lost braces; missing escapes or markup?
    26 | \eqn{neglinks_{ij} = 0} means chunklet \code{i} and chunklet {j}
       |                                                              ^
checkRd: (-1) rca.Rd:57: Lost braces; missing escapes or markup?
    57 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |            ^
checkRd: (-1) rca.Rd:57: Lost braces; missing escapes or markup?
    57 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |                          ^
checkRd: (-1) condense.dmmblockarray.Rd:7: Lost braces
     7 | An object of class \code{dmmblockarray} is a list containing two items called \code{array} and \code{blocks}. Item \code{array} is an array of objects of type \code{dmm}, with each array element representing the reult of a \code{dmm()} analysis for one pair of blocks of traits. The function \code{condense.dmmarray} will recombine these results into a single object of class \code{dmm} with the variance component and genetic parameter estimates matrices being for all traits, and other elements of the \ code{dmm} object being appropriately pooled. Item \code{blocks} is a list, each element of which is a list of the traits present in each block.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               ^
checkRd: (-1) scale_color_dMod.Rd:10: Lost braces
    10 | \item{...}{arguments goint to code{scale_color_manual()}}
       |                                   ^
checkRd: (-1) scale_fill_dMod.Rd:10: Lost braces
    10 | \item{...}{arguments goint to code{scale_color_manual()}}
       |                                   ^
checkRd: (-1) trust.Rd:103: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:104: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:107-108: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:109-110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:111-112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:113-114: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:115-122: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:123-126: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:127: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:128-131: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:132-133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:134-135: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:136-138: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:139-141: Lost braces in \itemize; \value handles \item{}{} directly
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                 ^
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                             ^
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                                             ^
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                                                         ^
checkRd: (-1) outliers.ranking.Rd:143: Lost braces; missing escapes or markup?
   143 |   where g_{y,i} and g_{x,i} are the two groups involved in the merge at
       |           ^
checkRd: (-1) outliers.ranking.Rd:143: Lost braces; missing escapes or markup?
   143 |   where g_{y,i} and g_{x,i} are the two groups involved in the merge at
       |                       ^
checkRd: (-1) outliers.ranking.Rd:144: Lost braces; missing escapes or markup?
   144 |   step i, and g_{x,i} is the group which X belongs to. Note that if X
       |                 ^
checkRd: (-1) setCPT.O.Rd:85: Lost braces; missing escapes or markup?
    85 | statespace {0,1,2}, which this is *not* checked anywhere. Thus, if
       |            ^
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 file 'dnapath2-package.Rd':
  \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 Rd file 'add.joint.mean.many.Rd':
  ‘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 file 'derivType.Rd':
  ‘L’ ‘mu’ ‘eps’
Argument items with no description in Rd file 'getNewParams.SC.Rd':
  ‘n.fft’
Argument items with no description in Rd file 'graph.CTMC.Rd':
  ‘\dots’
Argument items with no description in Rd file 'num.deriv.Rd':
  ‘\dots’
Argument items with no description in Rd file 'power.coef.one.Rd':
  ‘\dots’
checkRd: (-1) beetle.Rd:13: Lost braces; missing escapes or markup?
    13 |     \item{\code{x}}{dose (log base 10 CS2mgl^{-1})}
       |                                              ^
Documented arguments not in \usage in Rd file 'concDict.Rd':
  ‘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 Rd file 'check_results.Rd':
  ‘error_on_failure’ ‘error_on_warning’

Documented arguments not in \usage in Rd file 'function_get_comments.Rd':
  ‘thresholds’

Documented arguments not in \usage in Rd file 'vignette_results_display.Rd':
  ‘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
checkRd: (-1) compare_heaps.Rd:11: Lost braces
    11 | sub-sample selected with code{dodgr_sample})}
       |                              ^
checkRd: (-1) dodgr_save_streetnet.Rd:24: Lost braces
    24 | result of a link{weight_streetnet} call can be rapidly loaded into a
       |                 ^
checkRd: (-1) weight_railway.Rd:23: Lost braces
    23 | \item{id_col}{Specify column of the code{sf} \code{data.frame} object which
       |                                         ^
checkRd: (-1) weight_streetnet.Rd:85: Lost braces
    85 | \item{id_col}{For \code{sf}-formatted data only: Specify column of the code{sf}
       |                                                                            ^
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘gurobi’
checkRd: (-1) rsmformula.Rd:96: Lost braces
    96 |       URL{http://www.jstatsoft.org/v32/i07/}.
       |          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) py_select_interpreter.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Tell {reticulate} to use Python Conda version available on Domino Data Lab.}
       |             ^
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
checkRd: (-1) redisWorker.Rd:56: Lost braces; missing escapes or markup?
    56 | You can increase it by including a {timeout=n} argument value.
       |                                    ^
checkRd: (-1) startLocalWorkers.Rd:54: Lost braces; missing escapes or markup?
    54 | You can increase it by including a {timeout=n} argument value.
       |                                    ^
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’.
checkRd: (-1) dot.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
'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
checkRd: (-1) PMLE.Weibull.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
checkRd: (-1) PMLE.Weibull.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
checkRd: (-1) PMLE.loglogistic.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
checkRd: (-1) PMLE.loglogistic.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
checkRd: (-1) PMLE.lognormal.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
checkRd: (-1) PMLE.lognormal.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) downscale.Rd:9: Lost braces; missing escapes or markup?
     9 | \item{occupancies}{Either a data frame containing two columns or an object of class \code{"upgrain"} from the \code{\link{upgrain}} function. If using a data frame the first column must be the grain sizes (cell area in squared units e.g. km^{2}). The second column is the proportion of occupancies at each grain size.}
       |                                                                                                                                                                                                                                                  ^
checkRd: (-1) ensemble.downscale.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
checkRd: (-1) hui.downscale.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{new.areas}{vector of grain sizes as cell area (in same units as cell.width but squared e.g. km^{2}) at fine scales for model prediction.}
       |                                                                                                      ^
checkRd: (-1) predict.downscale.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
checkRd: (-1) dparser-package.Rd:159-281: Lost braces
   159 | \itemize{\item  Terminal modifiers}{
       |                                    ^
checkRd: (-1) dparser-package.Rd:172: Lost braces; missing escapes or markup?
   172 | It is now possible to use $0.symbol == ${string parameter_comma} to differentiate ParseNode ($0) between
       |                                         ^
checkRd: (-1) dparser-package.Rd:277: Lost braces; missing escapes or markup?
   277 | ${declare longest_match ...}.  If global longest match
       |  ^
checkRd: (-1) dparser-package.Rd:278-279: Lost braces
   278 | disambiguation is \bold{ON}, it can be locally disabled with {$declare
       |                                                              ^
checkRd: (-1) mkdparse.Rd:202-324: Lost braces
   202 | \itemize{\item  Terminal modifiers}{
       |                                    ^
checkRd: (-1) mkdparse.Rd:215: Lost braces; missing escapes or markup?
   215 | It is now possible to use $0.symbol == ${string parameter_comma} to differentiate ParseNode ($0) between
       |                                         ^
checkRd: (-1) mkdparse.Rd:320: Lost braces; missing escapes or markup?
   320 | ${declare longest_match ...}.  If global longest match
       |  ^
checkRd: (-1) mkdparse.Rd:321-322: Lost braces
   321 | disambiguation is \bold{ON}, it can be locally disabled with {$declare
       |                                                              ^
Documented arguments not in \usage in Rd file 'show-dparserFunction-method.Rd':
  ‘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) detrend.series.Rd:91: Lost braces
    91 |   stiffness of 50 (code{\var{nyrs}=50}). See \code{\link{ads}}. If some of the fitted 
       |                        ^
'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) module_atemp_pl_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_completeness_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_config_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_dashboard_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_descriptive_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_log_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_mdr_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_report_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_uniq_plaus_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
'LazyData' is specified without a 'data' directory
checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gompertz.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) hatvalues.drc.Rd:43: Lost braces
    43 |   emph{Generalized Linear Models}, 
       |       ^
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: \&
checkRd: (-1) excalibur.Rd:18: Lost braces; missing escapes or markup?
    18 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
checkRd: (-1) festuca.Rd:16: Lost braces; missing escapes or markup?
    16 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
checkRd: (-1) logistic2_fn.Rd:34: Lost braces; missing escapes or markup?
    34 | This function allows values other than {0, 1, -1} for \code{alpha} and \code{delta} but
       |                                        ^
checkRd: (-1) loglogistic2_fn.Rd:35: Lost braces; missing escapes or markup?
    35 | This function allows values other than {0, 1, -1} for \code{alpha} and \code{delta} but
       |                                        ^
checkRd: (-1) generate_individual_graphs.Rd:11: Lost braces
    11 | code{\link[DrDimont]{compute_correlation_matrices}}}
       |     ^
checkRd: (-1) dreamerplot.Rd:53: Lost braces; missing escapes or markup?
    53 | a dose returns the plot of pr(trt_dose - trt_{reference_dose} | data).}
       |                                              ^
checkRd: (-1) posterior.Rd:70: Lost braces; missing escapes or markup?
    70 | a dose returns the plot of pr(trt_dose - trt_{reference_dose} | data).}
       |                                              ^
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.drf.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:44: Lost braces in \itemize; meant \describe ?
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.
checkRd: (-1) popsize.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
'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 Rd file 'forecastCovCompiled.Rd':
  ‘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.
checkRd: (-1) read_mnist.Rd:24-25: Lost braces
    24 | \item{keep.files}{A logical. If \code{TRUE} the downloaded files will be saved in \code{destdir}. If \code{FALSE} the entire directory is erased. This argument is ignored if \code{download} is \code{FALSE}.){
       |                                                                                                                                                                                                                ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘dsBaseClient’
checkRd: (-1) dsm_varprop.Rd:67: Lost braces
    67 | parameter uncertainty. See Wood, Pya & S{\"a}fken (2016) for more
       |                                         ^
checkRd: (-1) dsm_varprop.Rd:100: Lost braces
   100 | Wood, S.N., Pya, N. and S{\"a}fken, B. (2016) Smoothing parameter and model
       |                          ^
'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) pv.prev.Rd:24: Lost braces; missing escapes or markup?
    24 |   - PPV = 1 / {1 + (1 / pi - 1) / pDLR}
       |               ^
checkRd: (-1) pv.prev.Rd:25: Lost braces; missing escapes or markup?
    25 |   - NPV = 1 / {1 + (1 / (1 / pi - 1)) / nDLR}. 
       |               ^
checkRd: (-1) DTDAcif.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) DTDAcif.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) efron.petrosian.Rd:22: Lost braces
    22 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
checkRd: (-1) lynden.Rd:21: Lost braces
    21 |    \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                                ^
checkRd: (-1) shen.Rd:24: Lost braces
    24 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) extract-methods.Rd:105: Lost braces
   105 |   argument \code{what}.  For code{"["} the cutted object.
       |                                  ^
checkRd: (-1) applied_crm.Rd:64: Lost braces; missing escapes or markup?
    64 | The empiric model is specified as F(d, beta) = d^{exp(beta)}. The logistic model is
       |                                                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Mena.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) count_subgroup.Rd:29: Lost braces; missing escapes or markup?
    29 | {.subgroup} for the subgroup column name and \{.name\} for the subgroup
       | ^
checkRd: (-1) p_count_subgroup.Rd:29: Lost braces; missing escapes or markup?
    29 | {.subgroup} for the subgroup column name and \{.name\} for the subgroup
       | ^
GNU make is a SystemRequirements.
checkRd: (-1) DTWUMI_1gap_imputation.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTWUMI_1gap_imputation.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTWUMI_1gap_imputation.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTWUMI_1gap_imputation.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTWUMI_1gap_imputation.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
Objects in \usage without \alias in Rd file 'd.spls.norm1.Rd':
  ‘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: ‘rgdal’
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.
checkRd: (-1) dyadic_similarity.Rd:27: Lost braces; missing escapes or markup?
    27 |      For example, the order {a, b, c} implies that a > b, a  > c, and b > c.
       |                             ^
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.dynaTree.Rd:107: Lost braces
   107 |   For \code{coef} a new \R{XXc} field is created so as not to trample
       |                           ^
'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
checkRd: (-1) generate_kinetics.Rd:57: Lost braces; missing escapes or markup?
    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                          ^
checkRd: (-1) generate_kinetics.Rd:57: Lost braces; missing escapes or markup?
    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                                                     ^
checkRd: (-1) new_log_level.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{log_style}{is a {crayon::style()} that will colorize
       |                       ^
checkRd: (-1) new_log_level.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{msg_style}{is a {crayon::style()} style that will gray scale the
       |                       ^
checkRd: (-1) sys_context.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{"sysname"} : {The operating system name.}
       |                    ^
checkRd: (-1) sys_context.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{"release"} : {The OS release.}
       |                    ^
checkRd: (-1) sys_context.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{"version"} : {The OS version.}
       |                    ^
checkRd: (-1) sys_context.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{"nodename"} : {A name by which the machine is known on the network (if any).}
       |                     ^
checkRd: (-1) sys_context.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{"machine"} : {A concise description of the hardware, often the CPU type.}
       |                    ^
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    27 | \item{"login"} : {The user's login name, or "unknown" if it cannot be ascertained.}
       |                  ^
checkRd: (-1) sys_context.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{"user"} : {The name of the real user ID, or "unknown" if it cannot be ascertained.}
       |                 ^
checkRd: (-1) sys_context.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{"r-ver"} : {R Version in (major).(minor) format.}
       |                  ^
checkRd: (-1) Produc.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:14: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) Produc.Rd:16: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) Produc.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:22: Lost braces in \itemize; meant \describe ?
'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
checkRd: (-1) dynsim.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:57-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) earl.Rd:78: Lost braces; missing escapes or markup?
    78 | must be one of {linear, poly, radial}}
       |                ^
checkRd: (-1) estimator.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{dens}{If IQ-Learning, one of {norm, nonpar}}
       |                                    ^
checkRd: (-1) internal-owl-methods.Rd:34: Lost braces
    34 | code{.objFn} is not allowed for OWL with multiple radial kernels
       |     ^
checkRd: (-1) internal-owl-methods.Rd:36: Lost braces
    36 | code{.dobjFn} is not allowed for OWL with multiple radial kernels
       |     ^
checkRd: (-1) owl.Rd:57: Lost braces; missing escapes or markup?
    57 | must be one of {linear, poly, radial}}
       |                ^
checkRd: (-1) rwl.Rd:69: Lost braces; missing escapes or markup?
    69 | must be one of {linear, poly, radial}}
       |                ^
Specified C++11: please drop specification unless essential
checkRd: (-1) monitor_long_1d.Rd:33: Lost braces
    33 | If \code{side="upward"}{apply control charts that aim to detect upward shifts.} \cr
       |                        ^
checkRd: (-1) monitor_long_1d.Rd:34: Lost braces
    34 | If \code{side="downward"}{apply control charts that aim to detect downward shifts.} \cr
       |                          ^
checkRd: (-1) monitor_long_1d.Rd:35: Lost braces
    35 | If \code{side="both"}{apply control charts that aim to detect shifts in both sides}}
       |                      ^
checkRd: (-1) monitor_long_1d.Rd:38: Lost braces
    38 | If \code{chart="CUSUM"}{apply CUSUM charts.} \cr
       |                        ^
checkRd: (-1) monitor_long_1d.Rd:39: Lost braces
    39 | If \code{chart="EWMA"}{apply EWMA charts.}}
       |                       ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) AM.Rd:95-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:99-102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:123-125: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:126-133: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:134-135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:163-165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:166-173: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:174-176: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:177-178: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:179-180: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:55-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:75: Lost braces; missing escapes or markup?
    75 | From the initial values, \code{B0} and {S0}, \code{\link{MHLS}} draws \code{beta} and \code{subgrad} samples.
       |                                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
    34 | if (require(incidence)) {
       |                         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) surrogates_ews.Rd:31: Lost braces
    31 | \item{span}{parameter that controls the degree of smoothing (numeric between 0 and 100, Default 25). see more on loess{stats}}
       |                                                                                                                       ^
checkRd: (-1) surrogates_ews.Rd:33: Lost braces
    33 | \item{degree}{the degree of polynomial to be used for when loess fitting is applied, normally 1 or 2 (Default). see more on loess{stats}}
       |                                                                                                                                  ^
checkRd: (-1) varmod.Rd:99-101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) varmod.Rd:102-104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) varmod.Rd:105-108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) varmod.Rd:109-112: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘example_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’
checkRd: (-1) ArrayToNc.Rd:30-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ArrayToNc.Rd:39-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ArrayToNc.Rd:51-76: Lost braces in \itemize; meant \describe ?
'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’
checkRd: (-1) write_spss.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:35-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:46: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
checkRd: (-1) OCC1950.Rd:64: Lost braces
    64 |     \doi{10.18128/D010.V10.0}{IPUMS USA: Version 10.0 [dataset]. Minneapolis, MN: IPUMS}. 
       |                              ^
checkRd: (-1) Oil.Rd:45: Lost braces
    45 |       code{pt-pt-1} on a constant
       |           ^
checkRd: (-1) breaches.Rd:70-74: Lost braces
    70 |     \code{breach_end}{
       |                      ^
checkRd: (-1) breaches.Rd:75-78: Lost braces
    75 |     \code{year}{
       |                ^
checkRd: (-1) nuclearWeaponStates.Rd:82-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:93-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:104-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:128-140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:141-150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:151-161: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:162-172: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:173-191: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:192-219: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) ecd-class.Rd:43: Lost braces
    43 | \code{long_name.skew}, code{long_name},
       |                            ^
checkRd: (-1) BoxCox.Rd:266-269: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BoxCox.Rd:270-275: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BoxCox.Rd:276-284: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BoxCox.Rd:285-293: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Newdata.Rd:88-91: Lost braces
    88 |   {replace \code{newDat[, x2]}:  
       |   ^
checkRd: (-1) interpPairs.Rd:120: Lost braces
   120 |     environment / list to use with code{object},
       |                                        ^
checkRd: (-1) matchQuote.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) matchQuote.Rd:75-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) matchQuote.Rd:81-88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) matchQuote.Rd:89-94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simulate.bic.glm.Rd:81-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.bic.glm.Rd:92-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.bic.glm.Rd:104-108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.glm.Rd:79-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.glm.Rd:84-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.glm.Rd:96-100: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) e_pictorial.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) e_pictorial.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nesting.Rd:48: Lost braces
    48 | `{itemStyle: {color: 'red', fontBold: 'bold'}}`.
       |  ^
checkRd: (-1) nesting.Rd:48: Lost braces; missing escapes or markup?
    48 | `{itemStyle: {color: 'red', fontBold: 'bold'}}`.
       |              ^
checkRd: (-1) nesting.Rd:51: Lost braces; missing escapes or markup?
    51 | `{symbolSize: 4}`.
       |  ^
Argument items with no description in Rd file 'e.cluster.decision.Rd':
  ‘reg_data’ ‘log.lambda’
Argument items with no description in Rd file 'e.cluster.dendrogram.Rd':
  ‘echelon.obj’ ‘n.sim’ ‘cluster.legend.pos’ ‘cluster_reg’ ‘p_rank’
  ‘para’
Argument items with no description in Rd file 'e.cluster.map.Rd':
  ‘x’ ‘c_separates’ ‘locs’ ‘coo’ ‘rin’ ‘p_rank’ ‘cluster_reg’ ‘n.sim’
  ‘cluster.type’
Argument items with no description in Rd file 'e.dendrogram.Rd':
  ‘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 file 'e.dendrogram.axis.Rd':
  ‘main’ ‘ylab’ ‘yaxes’ ‘ylim’ ‘xaxes’ ‘xdper’ ‘dmai’ ‘peaks’ ‘x’
Argument items with no description in Rd file 'e.main.Rd':
  ‘x’ ‘rin’ ‘T’
Argument items with no description in Rd file 'e.monte.bin.Rd':
  ‘rin’ ‘cas’ ‘pop’ ‘n.sim’ ‘K’ ‘cluster.type’
Argument items with no description in Rd file 'e.monte.poi.Rd':
  ‘rin’ ‘cas’ ‘pop’ ‘ex’ ‘n.sim’ ‘K’ ‘cluster.type’
Argument items with no description in Rd file 'e.profile.Rd':
  ‘peaks’ ‘parents’ ‘separates’
Argument items with no description in Rd file 'e.scan.Rd':
  ‘x’ ‘locs’ ‘peaks’ ‘c_separates’ ‘parents’ ‘K’
Argument items with no description in Rd file 'e.scan.pop.Rd':
  ‘x’ ‘locs’ ‘peaks’ ‘c_separates’ ‘parents’ ‘K’ ‘pop’
Argument items with no description in Rd file 'nlimb.Rd':
  ‘x’ ‘k2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ecolRxC.Rd:161-166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:167-175: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:176-178: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:179-185: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:186-192: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:193-201: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:202-208: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:209-216: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:217-221: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) transformFitness.Rd:25: Lost braces; missing escapes or markup?
    25 | minimization (most others). This function computes a factor from {-1, 1} for
       |                                                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sd_map.Rd:33-34: Lost braces
    33 | the map. \itemize{ \item{\code{elem} {displays elementary and unified
       |                                      ^
checkRd: (-1) sd_map.Rd:34: Lost braces; missing escapes or markup?
    34 | districts}} \item{\code{secon} {displays secondary and unified districts}}}
       |                                ^
checkRd: (-1) read.edf.Rd:30: Lost braces
    30 | Kemp B., V\"{a}rri, A., Rosa, A.C., Nielsen, K.D. and Gade, J. (1992).
       |             ^
'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
checkRd: (-1) parseMix.Rd:15: Lost braces
    15 | list with categorical expression (\code{cat}), which is normalized,  a numerical expression (code{nums}) 
       |                                                                                                  ^
checkRd: (-1) parseMix.Rd:16: Lost braces
    16 | and a negated version of this  expression (code{negNums})
       |                                                ^
Documented arguments not in \usage in Rd file 'fcf.env.Rd':
  ‘vars’

Documented arguments not in \usage in Rd file 'getlevels.Rd':
  ‘editarray’

Documented arguments not in \usage in Rd file 'parseCatEdit.Rd':
  ‘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
checkRd: (-1) edm2psd.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{D}{A matrix in the set D_{n}^{-}.}
       |                                ^
checkRd: (-1) edm2psd.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{D}{A matrix in the set D_{n}^{-}.}
       |                                    ^
checkRd: (-1) items_ordered_eclsk_atl.Rd:23: Lost braces; missing escapes or markup?
    23 | \item \code{P4SRS10}: Keep working at something until {he/she} is finished?
       |                                                       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) eesim.Rd:148-151: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) eesim.Rd:152-155: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) eesim.Rd:156-158: Lost braces in \itemize; \value handles \item{}{} directly
'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 Rd file 'rotate_to_equilibrium.Rd':
  ‘xy_may’

Documented arguments not in \usage in Rd file 'wide.dyads.to.edgelist.Rd':
  ‘fist.var’

Documented arguments not in \usage in Rd file 'wide.to.long.Rd':
  ‘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.
checkRd: (-1) Constants.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Constants.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Constants.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxConcMonth.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{las}{numeric in {0,1,2,3}; the style of axis labels, see ?par}
       |                       ^
checkRd: (-1) boxQTwice.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{las}{numeric in {0,1,2,3}; the style of axis labels, see ?par}
       |                       ^
checkRd: (-1) boxResidMonth.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{las}{numeric in {0,1,2,3}; the style of axis labels}
       |                       ^
checkRd: (-1) aftreg.Rd:102: Lost braces; missing escapes or markup?
   102 | {S(t; a, b, beta, z) =  S_0((t/exp(b - z beta))^exp(a))}
       | ^
Invalid package aliases in Rd file 'HOF-package.Rd':
  ‘HOF-package’
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
checkRd: (-1) colBoxplot4.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{id}{Internal parameters for {shiny}.}
       |                                   ^
checkRd: (-1) elaborator_server.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{id, input, output, session}{Internal parameters for {shiny}.}
       |                                                           ^
Documented arguments not in \usage in Rd file 'colBoxplot4.Rd':
  ‘id’

Documented arguments not in \usage in Rd file 'elaborator_server.Rd':
  ‘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
checkRd: (-1) fit_mean.Rd:54: Lost braces
    54 | \code{t_optims}{optimal parametrizations}
       |                ^
checkRd: (-1) fit_mean.Rd:55: Lost braces
    55 | \code{G_optims}{optimal rotations}
       |                ^
checkRd: (-1) fit_mean.Rd:56: Lost braces
    56 | \code{b_optims}{optimal scalings}
       |                ^
checkRd: (-1) fit_mean.Rd:57: Lost braces
    57 | \code{n_optims}{optimal re-normalization}
       |                ^
checkRd: (-1) fit_mean.Rd:58: Lost braces
    58 | \code{n_iter}{number of iterations until convergence}
       |              ^
checkRd: (-1) docs_delete_by_query.Rd:47: Lost braces; missing escapes or markup?
    47 | as a document at .tasks/task/${taskId}. This is yours to keep or remove
       |                               ^
checkRd: (-1) docs_update_by_query.Rd:48: Lost braces; missing escapes or markup?
    48 | as a document at .tasks/task/${taskId}. This is yours to keep or remove
       |                               ^
'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
checkRd: (-1) electData.Rd:16: Lost braces; missing escapes or markup?
    16 | Variables: \code{id}  = {identification number},
       |                         ^
checkRd: (-1) electData.Rd:17: Lost braces; missing escapes or markup?
    17 | \code{state} = {state}, \code{age} = age in years on a shifted scale (current age minus 70),
       |                ^
checkRd: (-1) summary.elect.Rd:25: Lost braces; missing escapes or markup?
    25 |  TRUE for output on start-state totals e_{r.} (for \code{S}>0)
       |                                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) prepareInitsLM.Rd:21-23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) elliptic-package.Rd:92: Lost braces
    92 |     J. Kotus and M. Urb\'{a}nski 2003.  \emph{Hausdorff dimension and Hausdorff
       |                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) elo.run.Rd:80: Lost braces
    80 | \code{\link{score}}, \link{elo.run.helpers}{elo.run helpers}, \code{\link{elo.calc}},
       |                                            ^
GNU make is a SystemRequirements.
checkRd: (-1) Emas.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NEWS.Rd:194: Lost braces; missing escapes or markup?
   194 | 	    \item added {d,r}betabinom
       |                         ^
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 13.2.0-5) 13.2.0’
License stub is invalid DCF.
Specified C++11: please drop specification unless essential
checkRd: (-1) minimize.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EmiStatR-methods.Rd:86: Lost braces; missing escapes or markup?
    86 | execute {EmiStatR} function
       |         ^
checkRd: (-1) input-class.Rd:136: Lost braces; missing escapes or markup?
   136 |     \item{EmiStatR}{\code{signature(x = "input")}: execute {EmiStatR} function }
       |                                                            ^
'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’.
checkRd: (-1) macacaModels.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) macacaModels.Rd:10-11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) medal.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) medal.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) medal.Rd:23: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) WRegTest.Rd:43: Lost braces
    43 | For ordinary least squares estimator, \code{psifun} should be the identity function psifun <- function(t){t}.
       |                                                                                                          ^
Specified C++11: please drop specification unless essential
checkRd: (-1) em.Rd:25: Lost braces
    25 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.clogit.Rd:65: Lost braces
    65 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.default.Rd:65: Lost braces
    65 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.fitdist.Rd:49: Lost braces
    49 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.glmerMod.Rd:50: Lost braces
    50 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.panelmodel.Rd:49: Lost braces
    49 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) EMSC.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EMSC.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EMSC.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EMSC.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) droso.Rd:8: Lost braces; missing escapes or markup?
     8 | The dataset contains 400 true donor sites, 400 false donor sites and 50 false sites as test set. Each sequence is of 40 nucleotides long. The conserved di-nucleotides GT are present at $21^{st}$ and $22^{nd}$ positions respectively.
       |                                                                                                                                                                                              ^
checkRd: (-1) droso.Rd:8: Lost braces; missing escapes or markup?
     8 | The dataset contains 400 true donor sites, 400 false donor sites and 50 false sites as test set. Each sequence is of 40 nucleotides long. The conserved di-nucleotides GT are present at $21^{st}$ and $22^{nd}$ positions respectively.
       |                                                                                                                                                                                                            ^
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)’
checkRd: (-1) enetLTS-package.Rd:41: Lost braces; missing escapes or markup?
    41 |   \code{family="binomial"} should be a factor with two levels which is coded as \code{0} and {1}.
       |                                                                                              ^
checkRd: (-1) CTN.Rd:22: Lost braces; missing escapes or markup?
    22 | less memory. Genetic data consists of nucleotide data {A,T,C,G} and are usually saved
       |                                                       ^
checkRd: (-1) ALL.Regression.Config-class.Rd:39: Lost braces
    39 |     \item{code{shrinkage}:}{Object of class \code{"numeric"}, defining the shrinkage parameter applied to each tree in expansion.}
       |               ^
checkRd: (-1) entropy.Dirichlet.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:42: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RStoolbox’
Documented arguments not in \usage in Rd file 'div_plot.Rd':
  ‘plot_cols’

Documented arguments not in \usage in Rd file 'seq_plot.Rd':
  ‘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.
checkRd: (-1) HIdermal.Rd:35: Lost braces; missing escapes or markup?
    35 | AD {EnviroPRA}
       |    ^
checkRd: (-1) HIinhal.Rd:32: Lost braces; missing escapes or markup?
    32 | AIR {EnviroPRA}
       |     ^
checkRd: (-1) RISKdermal.Rd:34: Lost braces; missing escapes or markup?
    34 | AD {EnviroPRA}
       |    ^
Auto-generated content requiring editing in Rd file 'EnviroPRA-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
checkRd: (-1) metrics.Rd:124: Lost braces
   124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
       |                                  ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Olympic.NH4.df.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Olympic.NH4.df.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) eqpois.Rd:200: Lost braces
   200 |   \code{\link{epois}}, \link[stats]{Poisson}, code{\link{estimate.object}}.
       |                                                   ^
checkRd: (-1) plotPredIntLnormAltSimultaneousTestPowerCurve.Rd:77: Lost braces
    77 |   positive integer between \code{1} and code{r} specifying the number of future 
       |                                             ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
checkRd: (-1) misClustRate.Rd:18: Lost braces; missing escapes or markup?
    18 | Compute the empirical MCR, assuming that #{cluster} = #{block},
       |                                           ^
checkRd: (-1) misClustRate.Rd:18: Lost braces; missing escapes or markup?
    18 | Compute the empirical MCR, assuming that #{cluster} = #{block},
       |                                                        ^
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: \$
checkRd: (-1) estimate_R.Rd:59-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:64-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:70-72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:76-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:79-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:84-86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:48-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:56-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EpiForsk-package.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiForsk-package.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiForsk-package.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiForsk-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EpiForsk-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) charlson_score.Rd:65-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) charlson_score.Rd:69-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) charlson_score.Rd:74-77: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘epidict’
Documented arguments not in \usage in Rd file 'dots_to_charlist.Rd':
  ‘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.
checkRd: (-1) runSim.Rd:111: Lost braces
   111 | \ifelse{html}{\out{<i>r</i><sub>1</sub> = 1}}{{\eqn{r_1 = 1}}{r_1 = 1}} while the individual with the lowest phenotypic value
       |                                                              ^
checkRd: (-1) runSim.Rd:112: Lost braces
   112 | is given the rank \ifelse{html}{\out{<i>r<sub>n</sub></i> = <i>n</i>}}{{\eqn{r_n = n}}{r_n = n}}), the probability of an individual
       |                                                                                       ^
checkRd: (-1) runSim.Rd:120-122: Lost braces
   120 | }{
       |  ^
GNU make is a SystemRequirements.
checkRd: (-1) LCa.fit.Rd:151: Lost braces
   151 |   \code{pi} (\code{p}eriod code{i}nteraction) refers to \eqn{b_p(a)}{b_p(a)}
       |                                ^
checkRd: (-1) lls.Rd:30: Lost braces
    30 | code{name},
       |     ^
checkRd: (-1) lls.Rd:31: Lost braces
    31 | code{mode},
       |     ^
checkRd: (-1) lls.Rd:32: Lost braces
    32 | code{class} and
       |     ^
checkRd: (-1) lls.Rd:33: Lost braces
    33 | code{size} and one row per object in the workspace (if \code{pos=1}).
       |     ^
checkRd: (-1) plotCIF.Rd:79: Lost braces
    79 | \author{Esa L{\"a}{\"a}r{\"a}, \email{esa.laara@oulu.fi}
       |              ^
checkRd: (-1) plotCIF.Rd:79: Lost braces
    79 | \author{Esa L{\"a}{\"a}r{\"a}, \email{esa.laara@oulu.fi}
       |                   ^
checkRd: (-1) plotCIF.Rd:79: Lost braces
    79 | \author{Esa L{\"a}{\"a}r{\"a}, \email{esa.laara@oulu.fi}
       |                         ^
S3 methods shown with full name in Rd file 'addDrug.Lexis.Rd':
  ‘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.
checkRd: (-1) getAgeGender.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAgeGender.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAgeGender.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAgeGender.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getMap.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getMap.Rd:46-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getMap.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTableByMS.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTableByMS.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTableByMS.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTrend.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTrend.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAgeGender.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAgeGender.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAgeGender.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTS12MAvg.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTS12MAvg.Rd:28: Lost braces in \itemize; meant \describe ?
'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’
checkRd: (-1) addLegend.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) addLegend.Rd:99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) addLegend.Rd:100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) addLegend.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gridMetrics.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:55-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:64-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gridMetrics.Rd:76-77: Lost braces in \itemize; meant \describe ?
'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
checkRd: (-1) Tm.Rd:46-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:49-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:52-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:55-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:58-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:36-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:40-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:43-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:47-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:57-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:60-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:63-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:66-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:69-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:75-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evReturn.Rd:34: Lost braces
    34 |   \item{daEst }{  data used to estimate the market model for the last firm as specified in code{firm}.}
       |                                                                                                ^
checkRd: (-1) evRisk.Rd:19: Lost braces
    19 |   \item{daEst }{  data used to estimate CAPM for the last firm as specified in code{firm}.}
       |                                                                                    ^
checkRd: (-1) Lazega.Rd:58: Lost braces; missing escapes or markup?
    58 | \item{\code{friendship}}{(logical) whether \eqn{i} considers {j} a friend outside of work.}
       |                                                              ^
Documented arguments not in \usage in Rd file 'subnetwork_templates.Rd':
  ‘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.
checkRd: (-1) ergm.rank-package.Rd:42: Lost braces
    42 | 1100-1128. c("\\Sexpr[results=rd,stage=build]{tools:::Rd_expr_doi(\"#1\")}",
       |                                              ^
Documented arguments not in \usage in Rd file 'call.ErgmTerm.Rd':
  ‘A’

Objects in \usage without \alias in Rd file 'ergm-defunct.Rd':
  ‘sociality’

Documented arguments not in \usage in Rd file 'ergm-deprecated.Rd':
  ‘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 Rd file 'ergm_state.Rd':
  ‘nw’

Documented arguments not in \usage in Rd file 'nodal_attributes-API.Rd':
  ‘l’

Documented arguments not in \usage in Rd file 'summary.ergm_model.Rd':
  ‘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.
checkRd: (-1) ifa.Rd:16: Lost braces; missing escapes or markup?
    16 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then Sigma^{-1} 
       |                                                                         ^
checkRd: (-1) ifa.Rd:17: Lost braces; missing escapes or markup?
    17 | has the corresponding q-factor decomposition Sigma^{-1}=diag(phi)(I-theta theta')diag(phi), where theta is a mxq matrix and phi the vector of 
       |                                                    ^
checkRd: (-1) ifa.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{iSB}{m x q matrix (diag(Psi)+BB')^{-1}B.}
       |                                         ^
checkRd: (-1) isqrtfa.Rd:15: Lost braces; missing escapes or markup?
    15 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then the function returns a matrix Omega such that Sigma^{-1} = Omega Omega'. Equivalently,
       |                                                                                                                       ^
checkRd: (-1) best_distribution.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) best_distribution.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) best_distribution.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) best_distribution.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) best_distribution.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) best_distribution.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) best_distribution.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_distributions.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_distributions.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_distributions.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_distributions.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_distributions.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_distributions.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_distributions.Rd:42: Lost braces in \itemize; meant \describe ?
S3 methods shown with full name in Rd file 'summary.error_interval.Rd':
  ‘summary.error_interval’

S3 methods shown with full name in Rd file 'summary.measure.Rd':
  ‘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’
checkRd: (-1) enp.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enp.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evolat.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evolat.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psns.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psns.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) festRidge.Rd:80: Lost braces; missing escapes or markup?
    80 | \item{XtXlamIinv}{explicit value of (X'X + diag(penalty))^{-1}.  Useful
       |                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) USA_state_N.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) USA_state_N.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) confirmed.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) confirmed.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) death.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) death.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recovered.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recovered.Rd:11: Lost braces in \itemize; meant \describe ?
'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) momento.central.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{orden}{Es un valor numérico que representa el orden del momento central (orden = {1,2,3,4,...})}
       |                                                                                        ^
'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
checkRd: (-1) integration.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) integration.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) integration.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) integration.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loess.options.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loess.options.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maxlogLreg.Rd:138: Lost braces; missing escapes or markup?
   138 | $j^{th}$ for all the observations.
       |    ^
Specified C++11: please drop specification unless essential
checkRd: (-1) lm_lin.Rd:99: Lost braces
    99 | and \code{scaled_center}{the means of each of the covariates used for centering them}
       |                         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) etas.Rd:136: Lost braces; missing escapes or markup?
   136 |   uses the {C++} code implemented using the \pkg{Rcpp} package,
       |            ^
checkRd: (-1) etas.Rd:142: Lost braces; missing escapes or markup?
   142 |   {C++} code carries out the computations.
       |   ^
S3 methods shown with full name in Rd file 'ETAS-internal.Rd':
  ‘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.
checkRd: (-1) ETC-package.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ETC-package.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ETC-package.Rd:32: Lost braces in \itemize; meant \describe ?
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) data_cls.Rd:24: Lost braces
    24 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability 0.10 for
       |                    ^
checkRd: (-1) data_cls.Rd:24: Lost braces
    24 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability 0.10 for
       |                            ^
checkRd: (-1) data_reg.Rd:21: Lost braces
    21 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability given by
       |                    ^
checkRd: (-1) data_reg.Rd:21: Lost braces
    21 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability given by
       |                            ^
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Documented arguments not in \usage in Rd file 'poly_clip.Rd':
  ‘x’ ‘y’

Documented arguments not in \usage in Rd file 'setup_gpar.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'setup_grobs.Rd':
  ‘centers’

Documented arguments not in \usage in Rd file 'update_list.Rd':
  ‘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.
checkRd: (-1) FuzzyCluster.Rd:15: Lost braces; missing escapes or markup?
    15 | A list of cluster labels and a R object of class "fcm {ppclust}"
       |                                                       ^
checkRd: (-1) pamCluster.Rd:15: Lost braces; missing escapes or markup?
    15 | A list of cluster labels and a R object of class "pam {cluster}"
       |                                                       ^
checkRd: (-1) dist.evaluate.core.Rd:26: Lost braces; missing escapes or markup?
    26 | the \code{names} column in {data} as labels. If \code{NULL} (default),
       |                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) uccle.Rd:23: Lost braces
    23 |   L'intensit\'{e} maximale des pr\'{e}cipitations en Belgique.
       |               ^
checkRd: (-1) uccle.Rd:23: Lost braces
    23 |   L'intensit\'{e} maximale des pr\'{e}cipitations en Belgique.
       |                                    ^
checkRd: (-1) uccle.Rd:24: Lost braces
    24 |   \emph{Inst. Royal M\'{e}t\'{e}or. Belgique, B} \bold{86}.
       |                        ^
checkRd: (-1) uccle.Rd:24: Lost braces
    24 |   \emph{Inst. Royal M\'{e}t\'{e}or. Belgique, B} \bold{86}.
       |                              ^
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'doHttrRequest.Rd':
  ‘params’ ‘customConfig’

Documented arguments not in \usage in Rd file 'errorMessage.Rd':
  ‘test_me’

Documented arguments not in \usage in Rd file 'isError.Rd':
  ‘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) colplot.Rd:52: Lost braces
    52 | \item{legend}{should a legend be added? Defaults to code{FALSE}}
       |                                                         ^
checkRd: (-1) colplot.Rd:56: Lost braces
    56 | \item{legend.pretty}{logical: should the legend values produced by \[base]{pretty}? Othewrwise they are exact. Defaults to \code{TRUE}}
       |                                                                           ^
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) glr.Rd:5: Lost braces
     5 |   Conducts a generalized likelihood ratio test testing whether {\eqn{\beta \in}  (-\code{c},\code{c})}. Covariates can be accommodated.
       |                                                                ^
checkRd: (-1) glr.Rd:34: Lost braces
    34 |   This is a similar function to the main function \code{evian}. Instead of testing H0: \eqn{\beta}=0, it tests for whether H0:{\eqn{\beta \in} (-\code{c},\code{c})}.
       |                                                                                                                               ^
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) fmgammagpd.Rd:183: Lost braces; missing escapes or markup?
   183 |  \item {nlumgammagpd} and {proflumgammagpd} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], sigmau, xi)}
       |                           ^
checkRd: (-1) fmgammagpdcon.Rd:181: Lost braces; missing escapes or markup?
   181 |  \item {nlumgammagpdcon} and {proflumgammagpdcon} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], xi)}
       |                              ^
checkRd: (-1) kernels.Rd:87: Lost braces
    87 | code{\link[evmix:kernels]{kd*}}  and \code{\link[evmix:kernels]{kp*}} give the
       |     ^
Found the following files/directories:
  ‘sample .nwk’
checkRd: (-1) ShapeDist.Rd:18: Lost braces; missing escapes or markup?
    18 | Procrustes distance provides a measure of coincidence of two point sets {xi} and {yi}, i=1..N. For this purpose the variance of point deviations is calculated at the optimal superposition of the sets. It allows to characterize the shape proximity of a given simplex to shape of a reference one.
       |                                                                         ^
checkRd: (-1) ShapeDist.Rd:18: Lost braces; missing escapes or markup?
    18 | Procrustes distance provides a measure of coincidence of two point sets {xi} and {yi}, i=1..N. For this purpose the variance of point deviations is calculated at the optimal superposition of the sets. It allows to characterize the shape proximity of a given simplex to shape of a reference one.
       |                                                                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) stop_rule.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stop_rule.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stop_rule.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stop_rule.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'borrOrderingInternal.Rd':
  ‘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’
checkRd: (-1) uccle.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) uccle.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) uccle.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) uccle.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) uccle.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) uccle720.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) uccle720.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) uccle720.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) uccle720.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) uccle720.Rd:15-16: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error: package or namespace load failed for ‘ExomeDepth’:
 .onLoad failed in loadNamespace() for 'Rsamtools', details:
  call: h(simpleError(msg, call))
  error: error in evaluating the argument 'x' in selecting a method for function 'levels': attempt to use zero-length variable name
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), do
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cec2013’
checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:42: Lost braces
    42 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
checkRd: (-1) ccF.Rd:41: Lost braces
    41 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
Argument items with no description in Rd file 'plot.expectreg.Rd':
  ‘\dots’
Argument items with no description in Rd file 'update.expectreg.Rd':
  ‘\dots’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) Normatiza.Rd:60: Lost braces
    60 | /code{/link{gray_scale}/}
       |      ^
checkRd: (-1) Normatiza.Rd:60: Lost braces
    60 | /code{/link{gray_scale}/}
       |            ^
checkRd: (-1) get_wcs_limit.Rd:55: Lost braces; missing escapes or markup?
    55 |   difference(s) between \code{rl} and {sl}, if \code{xform[2] != "no"} on
       |                                       ^
checkRd: (-1) get_wcs_limit.Rd:58: Lost braces; missing escapes or markup?
    58 |   difference(s) between \code{rl} and {sl} on the original scale.}
       |                                       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) expm.Higham08.Rd:26: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) expm.Higham08.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) expm.Higham08.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) expm.Higham08.Rd:29: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) expm.Higham08.Rd:30: Lost braces in \enumerate; meant \describe ?
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) MatIn.Rd:6: Lost braces
     6 | Computation of aggregation matrices for generalized interactions that are used in code{\link{extRC}} to estimate extended RC models.
       |                                                                                       ^
checkRd: (-1) plot.Rd:5: Lost braces
     5 | \description{It plots the output of code{\link{extRC}} function for a vector of lambda values.}
       |                                         ^
checkRd: (-1) print.Rd:5: Lost braces
     5 | \description{Given the output of code{\link{extRC}} function, it is written in a readable form.}
       |                                      ^
checkRd: (-1) summary.Rd:5: Lost braces
     5 | \description{Summary method for the output of code{\link{extRC}} function.}
       |                                                   ^
Argument items with no description in Rd file 'fbvpot.Rd':
  ‘cutoff’
checkRd: (-1) outlierPlot.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) outlierPlot.Rd:32: Escaped LaTeX specials: \$
Documented arguments not in \usage in Rd file 'getQQLimit.Rd':
  ‘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’
checkRd: (-1) make_exvadec.Rd:21: Lost braces
    21 | (e.g., \code{"USA"}, code{"NAFTA"}, etc.). The default \code{"all"}
       |                          ^
checkRd: (-1) read_edf.Rd:32: Lost braces
    32 | code{TRUE}}
       |     ^
checkRd: (-1) read_edf.Rd:35: Lost braces
    35 | code{TRUE}}
       |     ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) va.Rd:80: Lost braces
    80 | \doi{10.1016/s0002-9394(02)01825-1}{Beck et al.}, and
       |                                    ^
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
checkRd: (-1) EEzGP_fit.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EEzGP_fit.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EEzGP_predict.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EEzGP_predict.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_fit.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_fit.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_predict.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_predict.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LEzGP_fit.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LEzGP_fit.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LLF_gradients.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LLF_gradients.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) ez-package.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:33: Lost braces in \itemize; meant \describe ?
'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
checkRd: (-1) getStuffForDIC.Rd:49: Lost braces
    49 | 	The information criteria are saved to the \code{informationCriteria_map_model.txt} file in the code{outputFolder}. 
       |                                                                                                            ^
Argument items with no description in Rd file 'complete.log.likelihood_Sj.Rd':
  ‘z’
Auto-generated content requiring editing in Rd file 'getStuffForDIC.Rd':
  \details: ‘If necessary, more details than the description above’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fmCov.Rd:37: Lost braces; missing escapes or markup?
    37 | where, \code{alpha(i)} is the intercept, \code{f(t)} is a {K x 1} vector of 
       |                                                           ^
checkRd: (-1) plot.ffm.Rd:82: Lost braces; missing escapes or markup?
    82 | \item{las}{one of {0, 1, 2, 3} to set the direction of axis labels, same as
       |                   ^
checkRd: (-1) summary.ffm.Rd:39: Lost braces; missing escapes or markup?
    39 | Returned object is of class {summary.ffm}.
       |                             ^
Found the following significant warnings:
  Warning: file ‘print.FactoClass.R’ is invalid UTF-8
  Warning: file ‘ward.cluster.R’ is invalid UTF-8
  Warning: invalidly encoded .R file(s)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FactoClass.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-5) 13.2.0’
* used C++ compiler: ‘g++-13 (Debian 13.2.0-5) 13.2.0’
checkRd: (-1) fviz_nbclust.Rd:75: Lost braces; missing escapes or markup?
    75 | (2001) proposed: "the smallest k such that gap(k) >= gap(k+1) - s_{k+1}". 
       |                                                                   ^
checkRd: (-1) fviz_nbclust.Rd:77: Lost braces; missing escapes or markup?
    77 | SE.factor*s_{k+1}" where SE.factor is a numeric value which can be 1
       |             ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    minor changes
Auto-generated content requiring editing in Rd file 'procrustes_switching.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'rsp_exact.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'rsp_full_sa.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'rsp_partial_sa.Rd':
  \details: ‘If necessary, more details than the description above.’
Auto-generated content requiring editing in Rd file 'weighted_procrustes_switching.Rd':
  \details: ‘If necessary, more details than the description above.’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) FADPclust.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) happy.Rd:14: Lost braces
    14 |                  code{Pretty happy} <  \code{Very happy}}
       |                      ^
checkRd: (-1) fra_sf.Rd:22: Lost braces; missing escapes or markup?
    22 | A map of France as {sf} object. Can be used as dataset or for maps
       |                    ^
Documented arguments not in \usage in Rd file 'dot-get_default_sign_size.Rd':
  ‘outcome_type’

Documented arguments not in \usage in Rd file 'dot-get_iteration_data.Rd':
  ‘file_dir’

Documented arguments not in \usage in Rd file 'extract_model_vimp.Rd':
  ‘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.
checkRd: (-1) Multistate.Rd:16: Lost braces
    16 | item{S}{the multistate survival function (S) and multistate transition probabilities (P)}
       |     ^
checkRd: (-1) Multistate.Rd:16: Lost braces
    16 | item{S}{the multistate survival function (S) and multistate transition probabilities (P)}
       |        ^
checkRd: (-1) Multistate.Rd:17: Lost braces
    17 | item{mslt}{other measures of the multistate life table: person-years (L); expectation at birth of sojourn times in the various states (e0); expectation at age x of the remaining expected sojourn times in the various states: population-based measures (e.p); expectation at age x of the remaining expected sojourn times in the various states: status-based measures (e.p)}
       |     ^
checkRd: (-1) Multistate.Rd:17: Lost braces
    17 | item{mslt}{other measures of the multistate life table: person-years (L); expectation at birth of sojourn times in the various states (e0); expectation at age x of the remaining expected sojourn times in the various states: population-based measures (e.p); expectation at age x of the remaining expected sojourn times in the various states: status-based measures (e.p)}
       |           ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) pi0FAMT.Rd:18: Lost braces
    18 | \code{pi0}{The estimated proportion \code{pi0} of null hypotheses.}}
       |           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) download_faostat_bulk.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) download_faostat_bulk.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) download_faostat_bulk.Rd:51-55: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'cache.Rd':
  ‘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
checkRd: (-1) auc.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{response}{Responses coded as logical or {0, 1}.}
       |                                               ^
checkRd: (-1) confusion_stats.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{response}{Responses coded as logical or {0, 1}.}
       |                                               ^
checkRd: (-1) confusion_stats.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{predicted}{Predicted value coded as {0, 1}}
       |                                           ^
checkRd: (-1) ndcg.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{response}{Responses coded as logical or {0, 1}.}
       |                                               ^
checkRd: (-1) roc.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{response}{Responses coded as logical or {0, 1}.}
       |                                               ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) icevision_IAAAffine.Rd:50: Lost braces; missing escapes or markup?
    50 | via affine transformations. Note: This class introduce interpolation artifacts to mask if it has values other than {0;1}
       |                                                                                                                    ^
checkRd: (-1) icevision_IAAPerspective.Rd:30: Lost braces; missing escapes or markup?
    30 | Note: This class introduce interpolation artifacts to mask if it has values other than {0;1}
       |                                                                                        ^
checkRd: (-1) icevision_IAAPiecewiseAffine.Rd:42: Lost braces; missing escapes or markup?
    42 | via affine transformations. Note: This class introduce interpolation artifacts to mask if it has values other than {0;1}
       |                                                                                                                    ^
'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 Rd file 'kkk.Rd':
  ‘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
checkRd: (-1) show.fgasp.Rd:13: Lost braces
    13 | Function to print the code{fgasp} object. 
       |                           ^
Documented arguments not in \usage in Rd file 'Get_C_R_K_Q.Rd':
  ‘have_noise’

Documented arguments not in \usage in Rd file 'Sample_KF_post.Rd':
  ‘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’
checkRd: (-1) KITdesign.Rd:36: Lost braces; missing escapes or markup?
    36 |  \item{trait}{One of {'c','d','s',NULL} indicating the type
       |                      ^
checkRd: (-1) KITkernel.Rd:51: Lost braces; missing escapes or markup?
    51 |  \item{trait}{One of {'c','d','s',NULL} indicating the type
       |                      ^
checkRd: (-1) geno.Rd:19: Lost braces; missing escapes or markup?
    19 |                 Must be one of {'ibs', 'linear', 'quadratic'}.
       |                                ^
checkRd: (-1) geno.Rd:31: Lost braces; missing escapes or markup?
    31 |                      {'add', 'dom', 'rec'} indicating additive,
       |                      ^
checkRd: (-1) nongeno.Rd:14: Lost braces; missing escapes or markup?
    14 |                 Must be one of {'interactive', 'linear', 'quadratic'}.
       |                                ^
checkRd: (-1) eigen_compute_single_entry_of_diagonal_matrix.Rd:17: Lost braces; missing escapes or markup?
    17 | The value of m^{-1}_{j,j}
       |                ^
checkRd: (-1) eigen_compute_single_entry_of_diagonal_matrix.Rd:17: Lost braces; missing escapes or markup?
    17 | The value of m^{-1}_{j,j}
       |                     ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:24: Lost braces
    24 | item{best}{The index of the observations with outlyingness smaller than the rejection threshold after C-steps are taken.}
       |     ^
checkRd: (-1) FastPCS.Rd:24: Lost braces
    24 | item{best}{The index of the observations with outlyingness smaller than the rejection threshold after C-steps are taken.}
       |           ^
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
Rd files without \alias:
  ‘FastPCS-package.Rd’
Specified C++11: please drop specification unless essential
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’
checkRd: (-1) update_nhl_db.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_nhl_db.Rd:54-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_phf_db.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_phf_db.Rd:54-57: Lost braces in \itemize; meant \describe ?
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 Rd file 'bin.Rd':
  ‘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.
checkRd: (-1) Error-Classes.Rd:107-119: Lost braces
   107 |   \item \code{do_verbose(response, template)} {
       |                                               ^
checkRd: (-1) Error.Rd:33-45: Lost braces
    33 |   \item \code{do(response, mssg)} {
       |                                   ^
checkRd: (-1) fh_bounds.Rd:14: Lost braces
    14 | \item{params1}{Arguments to pass to the r{dist} function for distribution 1}
       |                                          ^
checkRd: (-1) fh_bounds.Rd:16: Lost braces
    16 | \item{params2}{Arguments to pass to the r{dist} function for distribution 2}
       |                                          ^
checkRd: (-1) FBN.histogramMaxima.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:40: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) fbad_copy_ad.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_ad.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) fbad_copy_adset.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_adset.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) fbad_copy_campaign.Rd:31: Lost braces; missing escapes or markup?
    31 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_campaign.Rd:33: Lost braces; missing escapes or markup?
    33 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) plot.fbroc.conf.Rd:5: Lost braces
     5 | \title{Plots function for object of class{fbroc.conf}}
       |                                          ^
checkRd: (-1) fcaR_options.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fcaR_options.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fcaR_options.Rd:21: Lost braces in \itemize; meant \describe ?
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’
checkRd: (-1) fcr-package.Rd:15: Lost braces; missing escapes or markup?
    15 | Let $y_{ij}$ denote some outcome measured at
       |        ^
checkRd: (-1) fcr-package.Rd:16: Lost braces; missing escapes or markup?
    16 | $t_{ij}$ on the functional domain (e.g. time) for subject $i$ at observation
       |    ^
checkRd: (-1) fcr-package.Rd:29: Lost braces; missing escapes or markup?
    29 | Initially, a model is fit without $b_i(t_{ij})$. Using the residuals from this initial fit,
       |                                          ^
checkRd: (-1) fcr.Rd:13: Lost braces; missing escapes or markup?
    13 | The formula should only include terms not associated with the random function intercept b_i(t_{ij}). See Examples.}
       |                                                                                               ^
checkRd: (-1) fcs.Rd:36: Lost braces; missing escapes or markup?
    36 | The argument nPoints must be smaller than the total number of temporal observations N, it is recommended to set nPoints = 2^n, with n = {2, ..., infinity}.
       |                                                                                                                                         ^
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.
checkRd: (-1) simulation_model9.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                              ^
checkRd: (-1) simulation_model9.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                                           ^
checkRd: (-1) MakeGPFunctionalData.Rd:33: Lost braces; missing escapes or markup?
    33 | Y: X(t_{j}), Yn: noisy observations
       |        ^
checkRd: (-1) NormCurvToArea.Rd:20: Lost braces
    20 | Normalise a curve such that \\int{yNew}dx = area (according to trapezoid integration)
       |                                  ^
checkRd: (-1) NormCurvToArea.Rd:17: Lost braces
    17 | yNew values of curve at times x such that [\\int{yNew}dx = area]
       |                                                 ^
GNU make is a SystemRequirements.
Argument items with no description in Rd file 'getbasispenalty.Rd':
  ‘Lfdobj’
checkRd: (-1) NASAtemp.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NASAtemp.Rd:15: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) plot.dma.Rd:46: Lost braces; missing escapes or markup?
    46 | If {x} comes from estimation of Dynamic Model Selection (DMS) or Median Probability Model (MED), after executing \code{plot} the User is asked to choose
       |    ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘vert.txt’
checkRd: (-1) p.fdr.Rd:30: Lost braces
    30 | \item{adjust.method}{A string used to identify the p-value and false discovery rate adjustment method. Defaults to \code{BH}. Options are \code{BH}, \code{BY}, code{Bon},\code{Holm}, \code{Hoch}, and \code{Sidak}.}
       |                                                                                                                                                                     ^
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
checkRd: (-1) mutlicol_terminator.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutlicol_terminator.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rfeTerminator.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New Stuff
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'checkStream.Rd':
  ‘skipChecks’

Documented arguments not in \usage in Rd file 'cpp_detectCUSUMMeanSinglePrechange.Rd':
  ‘BL’

Documented arguments not in \usage in Rd file 'cpp_detectEWMAMeanSinglePrechange.Rd':
  ‘BL’

Documented arguments not in \usage in Rd file 'makeStreamMeanChangeR.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'update_Omega.Rd':
  ‘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 Rd file 'recode_subquad.Rd':
  ‘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
checkRd: (-1) contemParametros.Rd:19: Lost braces
    19 | \item{exclui3pontos}{verify por ... ? in f<-function(a, ...){ }}
       |                                                             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) fhir_cast.Rd:28: Lost braces; missing escapes or markup?
    28 | with {.} as a separator, e.g. \code{code.coding.system}. These names are produced automatically by \code{\link[=fhir_crack]{fhir_crack()}}
       |      ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘MicrobeDS’
checkRd: (-1) FORTRAN.internal.Rd:50: Lost braces
    50 | \item{evlpoly}{evaluates a univariate polynomial. See code{fields.evlpoly}}
       |                                                           ^
checkRd: (-1) FORTRAN.internal.Rd:51: Lost braces
    51 | \item{evlpoly2}{ evaluates a multivariate polynomial. See code{fields.evlpoly2}}
       |                                                               ^
checkRd: (-1) registeredC.Rd:77: Lost braces
    77 | \item{addToDiagC}{ adds diagonal elements to a matrix. See code{mKrig}.}
       |                                                                ^
checkRd: (-1) sim.Krig.Rd:200-221: Lost braces
   200 | \code{simLocal.spatialProcess}{This function is
       |                               ^
checkRd: (-1) tim.colors.Rd:96: Lost braces
    96 | \item{\dots}{Additional plotting arguments to code{image.plot}}
       |                                                   ^
'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
checkRd: (-1) read-links.Rd:72: Lost braces; missing escapes or markup?
    72 |     \code{\link{read.lines}} which wraps the function {readLines}
       |                                                       ^
checkRd: (-1) read-lynx.Rd:76: Lost braces; missing escapes or markup?
    76 |     \code{\link{read.lines}} which wraps the function {readLines}
       |                                                       ^
checkRd: (-1) read-w3m.Rd:74: Lost braces; missing escapes or markup?
    74 |     \code{\link{read.lines}} which wraps the function {readLines}
       |                                                       ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: \&
checkRd: (-1) fun-igraph_financial.Rd:34: Lost braces; missing escapes or markup?
    34 | The same result for both \code{igraph} and {igraph_financial} objects
       |                                            ^
checkRd: (-1) igraph_E_iterators.Rd:31: Lost braces; missing escapes or markup?
    31 | The same result for both \code{igraph} and {igraph_financial} objects
       |                                            ^
checkRd: (-1) igraph_v_iterators.Rd:29: Lost braces; missing escapes or markup?
    29 | The same result for both \code{igraph} and {igraph_financial} objects
       |                                            ^
checkRd: (-1) plot_igraph-methods.Rd:22: Lost braces
    22 | Methods to extend code{igraph}'s plotting functions to \code{igraph_financial} objects
       |                       ^
checkRd: (-1) plot_igraph-methods.Rd:19: Lost braces; missing escapes or markup?
    19 | For both \code{igraph} and {igraph_financial} objects, returns NULL invisibly. It is called to print the graph to any R device. (see method and \href{https://rdrr.io/cran/igraph/man/plot.igraph.html}{igraph::plot.igraph})
       |                            ^
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
checkRd: (-1) FiSh-package.Rd:19: Lost braces
    19 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
checkRd: (-1) FiSh-package.Rd:32: Lost braces
    32 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
checkRd: (-1) SEP_FIM.Rd:46: Lost braces
    46 | \doi{10.3389/feart.2020.00255}{Frontiers in Earth Science, 8:255}.
       |                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Documented arguments not in \usage in Rd file 'plot_data_type.Rd':
  ‘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) fitConic.Rd:66-73: Lost braces
    66 | \code{parA }{vector of the six "ABCDEF" coefficients
       |             ^
checkRd: (-1) fitConic.Rd:67: Lost braces
    67 | \code{RSS }{'root sum square' figure of merit describing the relative fit quality}
       |            ^
checkRd: (-1) fitConic.Rd:68: Lost braces
    68 | \code{iters }{number of iterations at convergence}
       |              ^
checkRd: (-1) fitConic.Rd:69-71: Lost braces
    69 | \code{exitCode }{1 means ellipse, 2 means hyperbola, 3 means parabola.
       |                 ^
checkRd: (-1) rotateA.Rd:59: Lost braces; missing escapes or markup?
    59 | For \code{xyrot} {a Nx2 array of the x,y coordinates of the rotated data set. }
       |                  ^
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) fitDist.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitDist.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitDist.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitDist.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitDist.Rd:51-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitDist.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitZIDist.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitZIDist.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitZIDist.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitZIDist.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitZIDist.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitZIDist.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitZIDist.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readData.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readData.Rd:25-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readData.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly
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’
checkRd: (-1) food_world_cup.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:75: Lost braces in \itemize; meant \describe ?
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
checkRd: (-1) distribution_vector.Rd:14: Lost braces; missing escapes or markup?
    14 | All standard distributions from {stats} package are covered. For a list
       |                                 ^
'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) convertInitDesignToGrid.Rd:11: Lost braces; missing escapes or markup?
    11 | The initial design, consisting of \code{d + 1} columns ({d} dimensions and
       |                                                         ^
Specified C++11: please drop specification unless essential
checkRd: (-1) ModelMixHMM-class.Rd:31: Lost braces; missing escapes or markup?
    31 |         \code{smoothed} of class {StatMixHMM}).
       |                                  ^
checkRd: (-1) ModelMixHMMR-class.Rd:31: Lost braces; missing escapes or markup?
    31 |         \code{smoothed} of class {StatMixHMMR}).
       |                                  ^
checkRd: (-1) summary.flamcv.rd:8: Lost braces
     8 | This function summarizes a call to code{\link{flamCV}} and identifies the tuning parameter chosen by cross-validation.
       |                                        ^
'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: \&
checkRd: (-1) flashlight.Rd:53: Lost braces; missing escapes or markup?
    53 | like those in package {MetricsWeighted}.}
       |                       ^
checkRd: (-1) grouped_stats.Rd:49: Lost braces; missing escapes or markup?
    49 | {MetricsWeighted}.}
       | ^
checkRd: (-1) plot_counts.Rd:45: Lost braces; missing escapes or markup?
    45 | Experimental. Uses package {ggpubr} to rearrange the figure.
       |                            ^
'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: \&
checkRd: (-1) flex_dashboard.Rd:96: Lost braces; missing escapes or markup?
    96 | the `{.storyboard}` attribute to individual pages rather than using the
       |      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) fmp.Rd:45: Lost braces; missing escapes or markup?
    45 | If k = 0: (xi_1, ..., x_{C_i - 1}, omega)
       |                         ^
checkRd: (-1) fmp.Rd:47: Lost braces; missing escapes or markup?
    47 | If k = 1: (xi_1, ..., x_{C_i - 1}, omega, alpha1, tau1)
       |                         ^
checkRd: (-1) fmp.Rd:49: Lost braces; missing escapes or markup?
    49 | If k = 2: (xi_1, ..., x_{C_i - 1}, omega, alpha1, tau1, alpha2, tau2)
       |                         ^
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘FPCEnv’
checkRd: (-1) FlexParamCurve-package.Rd:91: Lost braces
    91 |     4) Plot your curves using eqn{posnegRichards.eqn} specifying the appropriate model number and list of parameters/options.
       |                                  ^
checkRd: (-1) SSposnegRichards.Rd:397: Lost braces
   397 |      twocomponent.x = # (where # is the x of intersection). Whne \{code{\link{modpar}}
       |                                                                        ^
checkRd: (-1) modpar.Rd:331: Lost braces
   331 | the specified model in subsequent eqn{SSposnegRichards}, model selection or ploting calls
       |                                      ^
GNU make is a SystemRequirements.
checkRd: (-1) bootci.fmsm.Rd:24: Lost braces
    24 | \item{fn}{Function to bootstrap the results of.  It must have an argument named `code{x} giving a fitted flexsurv model object.  This may return a value with any format, e.g. list, matrix or vector, as long as it can be converted to a numeric vector with \code{unlist}.   See the example below.}
       |                                                                                      ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) flow_embed.Rd:30: Lost braces; missing escapes or markup?
    30 | \item Don't forget to add {flow} to Suggests in your DESCRIPTION file.
       |                           ^
checkRd: (-1) flowdata.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{Flow}{Water flow, in m^{3}/s}
       |                              ^
checkRd: (-1) to_flow.Rd:110-117: Lost braces
   110 | \strong{Behaviour:}{
       |                    ^
checkRd: (-1) to_flowdef.Rd:111-115: Lost braces
   111 | {
       | ^
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
checkRd: (-1) FMP.Rd:30: Lost braces; missing escapes or markup?
    30 | \eqn{m(\theta) = b_0 + b_1 \theta + b_2 \theta^2 + b_3 \theta^3}. Acceptable values of k = {0,1,2,3}. According to 
       |                                                                                            ^
checkRd: (-1) autoFMradio.Rd:46: Lost braces; missing escapes or markup?
    46 | Step 1 (regularized correlation matrix estimation) is performed using the \code{X}, \code{t}, and {fold} arguments.
       |                                                                                                   ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) GompertzMakeham.Rd:13: Lost braces
    13 |  \item{A}{The parameter A of the Gompertz-Makeham model u(t)=A*exp{B*t}+C.}
       |                                                                   ^
checkRd: (-1) GompertzMakeham.Rd:14: Lost braces
    14 |  \item{B}{The parameter B of the Gompertz-Makeham model u(t)=A*exp{B*t}+C.}
       |                                                                   ^
checkRd: (-1) GompertzMakeham.Rd:15: Lost braces
    15 |  \item{C}{The parameter C of the Gompertz-Makeham model u(t)=A*exp{B*t}+C.}
       |                                                                   ^
checkRd: (-1) truemedian.Rd:6: Lost braces; missing escapes or markup?
     6 |   exactly same.  For example, median of {3, 3, 4, 4, 4} will be 4.
       |                                         ^
checkRd: (-1) truemedian.Rd:9-10: Lost braces
     9 |   the previous data can be treated as rounded values of {2.75, 3.25,
       |                                                         ^
checkRd: (-1) truemedian.Rd:10: Lost braces; missing escapes or markup?
    10 |   11/3, 4, 13/3}.  From this viewpoint, true median of {3, 3, 4, 4, 4}
       |                                                        ^
checkRd: (-1) Estable.Rd:40: Lost braces
    40 |   \code{dEstable}{ gives the density function;}
       |                  ^
checkRd: (-1) Estable.Rd:41: Lost braces
    41 |   \code{pEstable}{ gives the distribution function or its complement;}
       |                  ^
checkRd: (-1) Estable.Rd:42: Lost braces
    42 |   \code{qEstable}{ gives quantiles;}
       |                  ^
checkRd: (-1) Estable.Rd:43-56: Lost braces
    43 |   \code{tailsEstable}{ returns a list with the following components
       |                      ^
checkRd: (-1) FMstable.Rd:50: Lost braces
    50 |   \code{dFMstable}{ gives the density function;}
       |                   ^
checkRd: (-1) FMstable.Rd:51: Lost braces
    51 |   \code{pFMstable}{ gives the distribution function or its complement;}
       |                   ^
checkRd: (-1) FMstable.Rd:52: Lost braces
    52 |   \code{qFMstable}{ gives quantiles;}
       |                   ^
checkRd: (-1) FMstable.Rd:53-66: Lost braces
    53 |   \code{tailsFMstable}{  returns a list with the following components
       |                       ^
Documented arguments not in \usage in Rd file 'hl.factor.number.Rd':
  ‘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
checkRd: (-1) cran_details.Rd:69-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cran_details.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cran_details.Rd:74-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cran_results.Rd:64-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cran_results.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cran_results.Rd:69-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) navbar_page.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) navbar_page.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) navbar_page.Rd:38: Lost braces in \itemize; meant \describe ?
'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
checkRd: (-1) foreca.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:78-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:84-87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:88-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:91-92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) foreca.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) initialize_weightvector.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initialize_weightvector.Rd:64-65: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) errorMetricFunctions.Rd:48: Lost braces
    48 | 	The metric MdAE is obtained using code{type = "AE"} and  \code{statistic = "Md"}
       |                                               ^
'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)
checkRd: (-1) species_bw.Rd:23: Lost braces
    23 | between trees." \doi{10.1371/journal.pone.0229930}{PLOS One 15: e0229930}.
       |                                                   ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) forest_theme.Rd:161: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forest_theme.Rd:162: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forest_theme.Rd:163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forest_theme.Rd:164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forest_theme.Rd:165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forest_theme.Rd:166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forest_theme.Rd:167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forest_theme.Rd:168: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forest_theme.Rd:169: Lost braces in \itemize; meant \describe ?
checkRd: (-1) process_pcl.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{pavd}{logical input to include Plant Area Volume Density Plot from {plot_pavd},
       |                                                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) depth.Rd:17: Lost braces; missing escapes or markup?
    17 |   \item {file} : {filename}
       |                  ^
checkRd: (-1) depth.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item {z_depth} : {measured focus range depth (z)}}
       |                     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) correlations.Rd:97: Lost braces
    97 |           for same named columns of \code{k.tree.plot} in code{\link{simulations}} \sQuote{Value}.
       |                                                               ^
checkRd: (-1) FGf.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FourgameteP.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:38: Lost braces in \itemize; meant \describe ?
'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) cgrestandard.Rd:83: Lost braces
    83 |   \code{\link{valstat.object}}, \code{\link{clusterbenchstats}}, \code{\link{stupidkcentroids}}, \code{\link{stupidknn}}, \\code{\link{stupidkfn}}, \code{\link{stupidkaven}}, code{\link{clustatsum}}
       |                                                                                                                                 ^
checkRd: (-1) cgrestandard.Rd:83: Lost braces
    83 |   \code{\link{valstat.object}}, \code{\link{clusterbenchstats}}, \code{\link{stupidkcentroids}}, \code{\link{stupidknn}}, \\code{\link{stupidkfn}}, \code{\link{stupidkaven}}, code{\link{clustatsum}}
       |                                                                                                                                                                                    ^
checkRd: (-1) ridgeline.Rd:6: Lost braces; missing escapes or markup?
     6 |   Computes (alpha*Sigma1^{-1}+(1-alpha)*Sigma2^{-1})^{-1}* 
       |                          ^
checkRd: (-1) ridgeline.Rd:6: Lost braces; missing escapes or markup?
     6 |   Computes (alpha*Sigma1^{-1}+(1-alpha)*Sigma2^{-1})^{-1}* 
       |                                                ^
checkRd: (-1) ridgeline.Rd:6: Lost braces; missing escapes or markup?
     6 |   Computes (alpha*Sigma1^{-1}+(1-alpha)*Sigma2^{-1})^{-1}* 
       |                                                      ^
checkRd: (-1) ridgeline.Rd:7: Lost braces; missing escapes or markup?
     7 |   alpha*(Sigma1^{-1}*mu1)+(1-alpha)*(Sigma2^{-1}*mu2)) as required for the
       |                 ^
checkRd: (-1) ridgeline.Rd:7: Lost braces; missing escapes or markup?
     7 |   alpha*(Sigma1^{-1}*mu1)+(1-alpha)*(Sigma2^{-1}*mu2)) as required for the
       |                                             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot_lines.Rd:66: Lost braces
    66 | moderator. By default it is equal to \8code{c(19, 17, 15, 8, 5, 4, 3, 1)}.}
       |                                            ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |     ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                        ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                              ^
checkRd: (-1) Fpop.Rd:9: Lost braces; missing escapes or markup?
     9 | m_{i+1}), where the indicator function I counts the number of
       |   ^
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
checkRd: (-1) emfrail_control.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:55-57: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) summary.frbs.Rd:32: Lost braces
    32 |                           \code{"GAUSSIAN"}, code{"TRIANGLE"}, \code{"TRAPEZOID"}, \code{"SIGMOID"}, and \code{"BELL"}.
       |                                                  ^
checkRd: (-1) summary.frbs.Rd:60: Lost braces; missing escapes or markup?
    60 |          {4.0, 0.23, 0.43, 0.53, 0.73} on its column. It means that the label a.2 of variable v.1 
       |          ^
checkRd: (-1) grade.Rd:57: Lost braces
    57 |   \code{freealg} object comprising terms of grade code{n}.
       |                                                       ^
checkRd: (-1) print.Rd:14: Lost braces
    14 |   \item{latex}{Boolean, with code{TRUE} meaning to print latex-friendly
       |                                  ^
Specified C++11: please drop specification unless essential
Documented arguments not in \usage in Rd file 'assert.surface.Rd':
  ‘surf’

Documented arguments not in \usage in Rd file 'check.dtype.for.data.Rd':
  ‘silent’

Documented arguments not in \usage in Rd file 'fread3.Rd':
  ‘filehandle:’

Documented arguments not in \usage in Rd file 'fwrite3.Rd':
  ‘filehandle:’ ‘data:’

Documented arguments not in \usage in Rd file 'polygon.soup.to.indexed.mesh.Rd':
  ‘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 Rd file 'freqdom.transpose.Rd':
  ‘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
checkRd: (-1) jaccardMatrix.Rd:20: Lost braces; missing escapes or markup?
    20 | This function will compute the Jaccard Index Matrix: ((A==i) and (B==j))/((A==i) or (B==j)) for all {i,j} possible label pairs presenet in A and B
       |                                                                                                     ^
Specified C++11: please drop specification unless essential
checkRd: (-1) maximin.Rd:197: Lost braces
   197 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
checkRd: (-1) adminlte_color.Rd:64: Lost braces; missing escapes or markup?
    64 |  defaults colors in {shinydashboard}.
       |                     ^
checkRd: (-1) adminlte_global.Rd:21: Lost braces; missing escapes or markup?
    21 |  global settings in {shinydashboard}.
       |                     ^
checkRd: (-1) adminlte_sidebar.Rd:61: Lost braces; missing escapes or markup?
    61 |  the sidebar in {shinydashboard}.
       |                 ^
checkRd: (-1) search_vars_adminlte2.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_adminlte2.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_bs.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_bs.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_bs4dash.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_bs4dash.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_bs4dash.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'dggrids', 'INLA'
'LazyData' is specified without a 'data' directory
checkRd: (-1) export.Rd:60: Lost braces; missing escapes or markup?
    60 | magick image instance or named list, depending on the value of 'img_only'. If the latter, the list contains the fields 'rev_vl', 'rev_cb', and 'rev_ex', which are the return values of the functions \code{vislayout.from.coloredmeshes}, \code{coloredmesh.plot.colorbar.separate}, and {combine.colorbar.with.brainview.image}, respectively.
       |                                                                                                                                                                                                                                                                                           ^
checkRd: (-1) vis.export.from.coloredmeshes.Rd:57: Lost braces; missing escapes or markup?
    57 | magick image instance or named list, depending on the value of 'img_only'. If the latter, the list contains the fields 'rev_vl', 'rev_cb', and 'rev_ex', which are the return values of the functions \code{vislayout.from.coloredmeshes}, \code{coloredmesh.plot.colorbar.separate}, and {combine.colorbar.with.brainview.image}, respectively.
       |                                                                                                                                                                                                                                                                                           ^
Documented arguments not in \usage in Rd file 'draw.colorbar.Rd':
  ‘coloredmesh’

Documented arguments not in \usage in Rd file 'extend_neighbors.Rd':
  ‘min_dotp_threshold’

Documented arguments not in \usage in Rd file 'surf.sphere.spatialfilter.Rd':
  ‘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 file 'fsdam.Rd':
  ‘verbose’ ‘which’
checkRd: (-1) FSelector-package.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-information_gain.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-information_gain.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) information_gain.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) information_gain.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
Argument items with no description in Rd file 'plot.classes.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.fsim.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.lm.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.sfpl.Rd':
  ‘\dots’
Argument items with no description in Rd file 'predict.sfplsim.FASSMR.Rd':
  ‘\dots’
Argument items with no description in Rd file 'print.summary.mfplsim.Rd':
  ‘\dots’
checkRd: (-1) report.Rd:18: Lost braces; missing escapes or markup?
    18 | 	\item{las}{numeric in {0,1,2,3}; the style of axis labels (see \code{\link{par}}).}
       |                               ^
Specified C++11: please drop specification unless essential
checkRd: (-1) fsl_cluster.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fsl_cluster.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fsl_cluster.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fsl_cluster.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fsl_cluster.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fsl_cluster.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fsl_cluster.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fsl_cluster.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rpi_orient.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rpi_orient.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rpi_orient.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fsEnsemble.Rd:17-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsEnsemble.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:25-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:27: Lost braces
    27 |  \item{\strong{"distance"}}{ - distance-based feature selection.
       |       ^
checkRd: (-1) fsMTS.Rd:27-31: Lost braces
    27 |  \item{\strong{"distance"}}{ - distance-based feature selection.
       |                            ^
checkRd: (-1) fsMTS.Rd:32: Lost braces
    32 |  \item{\strong{"CCF"}}{ - cross-correlation-based. The method returns values of Pearson's correlation coefficient between every MTS component
       |       ^
checkRd: (-1) fsMTS.Rd:32-33: Lost braces
    32 |  \item{\strong{"CCF"}}{ - cross-correlation-based. The method returns values of Pearson's correlation coefficient between every MTS component
       |                       ^
checkRd: (-1) fsMTS.Rd:35-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:39-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:44-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:48-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:70-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:73-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsMTS.Rd:76-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsSimilarity.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsSimilarity.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fsSimilarity.Rd:30: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'imp_small_gaps_WMA.Rd':
  ‘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) T_stationary.Rd:40: Lost braces
    40 | A. Aue, G. Rice, O. S\"{o}nmez (2018) "Detecting and dating structural breaks in functional data without dimension reduction", \emph{Journal of the Royal Statistical Society: Series B}, \bold{80}(3), 509-529.
       |                        ^
checkRd: (-1) facf.Rd:24: Lost braces
    24 | L. Horv\'{a}th, G. Rice and S. Whipple (2016) Adaptive bandwidth selection in the long run covariance estimator of functional time series, \emph{Computational Statistics and Data Analysis}, \bold{100}, 676-693.
       |          ^
checkRd: (-1) farforecast.Rd:43: Lost braces
    43 | J. Klepsch, C. Kl\"{u}ppelberg and T. Wei (2017) "Prediction of functional ARMA processes with an application to traffic data", \emph{Econometrics and Statistics}, \bold{1}, 128-149.
       |                    ^
checkRd: (-1) fplsr.Rd:122: Lost braces
   122 | M. Febrero-Bande, P. Galeano, W. Gonz\'{a}lez-Manteiga (2017), "Functional principal component regression and functional partial least-squares regression: An overview and a comparative study", \emph{International Statistical Review}, \bold{85}(1), 61-83.
       |                                        ^
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
checkRd: (-1) control_charts_sof_pc.Rd:39: Lost braces
    39 | and code{y},
       |         ^
Malformed Description field: should contain one or more complete sentences.
Objects in \usage without \alias in Rd file 'funData-constructor.Rd':
  ‘funData’

Objects in \usage without \alias in Rd file 'irregFunData-constructor.Rd':
  ‘irregFunData’

Objects in \usage without \alias in Rd file 'multiFunData-constructor.Rd':
  ‘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 Rd file 'plot.funData.Rd':
  ‘plot.funData’

S3 methods shown with full name in Rd file 'plot.irregFunData.Rd':
  ‘plot.irregFunData’

S3 methods shown with full name in Rd file 'plot.multiFunData.Rd':
  ‘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.
checkRd: (-1) SchmidLeiman.Rd:142: Lost braces
   142 |   \item{strong{HeywoodFlag}}(Integer) An integer indicating whether one or more 
       |               ^
checkRd: (-1) summary.monte.Rd:34: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:35: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:36: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:38: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:39: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:40: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:41: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:42: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:43: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:44: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:45: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:46: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) summary.monte.Rd:47: Lost braces in \enumerate; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.fd.Rd:69-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.fd.Rd:72-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funnel_plot.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funnel_plot.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funnel_plot.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funnel_plot.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funnel_plot.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funnel_plot.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funnel_plot.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) funnel_plot.Rd:57: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'build_limits_lookup.Rd':
  ‘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
checkRd: (-1) bpp.Rd:31: Lost braces
    31 | The BPP algorithm calculates the sum{K=0,k, 1/(b^K) * FracSum} , where FracSum is defined by the sum(M=1,m, A[M]/(m*K + M)^s) .  This means that the number of elements of \code{A} must equal \code{m}. Zero values are legal and are used to reject fractions not wanted in the inner sum. 
       |                                     ^
checkRd: (-1) add_flat_template.Rd:81: Lost braces; missing escapes or markup?
    81 | \item "minimal_package": Minimal template to start a new package when you already know {fusen}, along with the "dev_history" template. Note that this is called "minimal" in \code{create_fusen()}.
       |                                                                                        ^
checkRd: (-1) init_share_on_github.Rd:17: Lost braces; missing escapes or markup?
    17 | This uses {pkgdown} to share the documentation of the package through GitHub Actions.
       |           ^
checkRd: (-1) init_share_on_github.Rd:36: Lost braces; missing escapes or markup?
    36 | \item Init continuous deployment (CD) of the {pkgdown} website documentation
       |                                              ^
'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 Rd file 'loggedOutput.Rd':
  ‘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.
checkRd: (-1) plan.Rd:59-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plan.Rd:63-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plan.Rd:68-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plan.Rd:75-80: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'mandelbrot.Rd':
  ‘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
checkRd: (-1) misspellings.Rd:18: Lost braces
    18 | This is a code{tbl_df} mapping misspellings of their words, compiled by
       |               ^
checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                             ^
checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                                                     ^
checkRd: (-1) genmf.Rd:26: Lost braces; missing escapes or markup?
    26 | \item 'gbellmf' is c(\code{a, b, c}), where \code{a} denotes the width, \code{b} is usually positive and {c} locates the center of the curve.
       |                                                                                                          ^
checkRd: (-1) multTSA.Rd:40: Lost braces
    40 | deprecated argument; link{type} should now be used instead, although (at least for the timebeing) this argument will still be accepted (with Favourability=TRUE internally resulting in type="F") for back-compatibility.
       |                          ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) GAabbreviate.Rd:53: Lost braces; missing escapes or markup?
    53 | where \eqn{I} represents a user-specified fixed item cost, \eqn{k} represents the number of items retained by the GA (in any given iteration), \eqn{s} is the number of subscales in the measure, \eqn{w_i} are the weights (by default {w_i = 1} for any \eqn{i}) associated with each subscale (if there are any subsets to be retained), and \eqn{R_i^2} is the amount of variance in the ith subscale that can be explained by a linear combination of individual item scores. Adjusting the value of \eqn{I} low or high yields longer or shorter measures respectively. When the cost of each individual item retained in each generation outweighs the cost of a loss in explained variance, the GA yields a relatively brief measure. When the cost is low, the GA yields a relatively longer measure maximizing explained variance (Yarkoni, 2010).  
       |                                                                                                                                                                                                                                         ^
Invalid package aliases in Rd file 'GAabbreviate-internal.Rd':
  ‘GAabbreviation-package’
checkRd: (-1) cpp_multinomial_gaga.Rd:44: Lost braces; missing escapes or markup?
    44 | Coefficient matrix with K-1 columns beta_1,...,beta_{K-1} where K is the class number.
       |                                                     ^
checkRd: (-1) multinomial_GAGA.Rd:44: Lost braces; missing escapes or markup?
    44 | Coefficient matrix with K-1 columns beta_1,...,beta_{K-1} where K is the class number.
       |                                                     ^
checkRd: (-1) min_hpd_inc_area_df.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) min_hpd_inc_area_df.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) min_hpd_inc_area_df.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) vza_mean_and_var_rasters.Rd:20: Lost braces
    20 | of the paper on Wilson's warbler, this function computes $tilde{T}^{(mu)}$ (returned as
       |                                                                ^
checkRd: (-1) vza_mean_and_var_rasters.Rd:20: Lost braces; missing escapes or markup?
    20 | of the paper on Wilson's warbler, this function computes $tilde{T}^{(mu)}$ (returned as
       |                                                                    ^
checkRd: (-1) vza_mean_and_var_rasters.Rd:21: Lost braces; missing escapes or markup?
    21 | list component \code{mean.raster}) and $R^{(sigma^2)}$ (returned as list component
       |                                           ^
checkRd: (-1) QTLmarkers.Rd:30: Lost braces
    30 | (\doi{10.1093/jas/sky382}{PubMed})
       |                          ^
checkRd: (-1) QTLwindows.Rd:31: Lost braces
    31 | (\doi{10.1093/jas/sky382}{PubMed})
       |                          ^
Documented arguments not in \usage in Rd file 'splitQTL_comment.Rd':
  ‘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.
checkRd: (-1) stabsel.mboostLSS.Rd:44: Lost braces
    44 |     always use code{"none"}.}
       |                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) naref.Rd:13: Lost braces
    13 | \details{ For every \code{factor} or \code{character} column in \code{x}, \code{naref} sets \code{NA} as the reference level for a \code{factor} variable. Columns coded as \code{character} class are first converted to factors via \R{factor(x)}.  If \code{impute=TRUE} then the numeric columns are converted to two columns, one appended \code{.x} that contains imputed values and another appended \code{.miss} which is a binary variable indicating whether the original value was missing.  Numeric columns are returned without change if \code{impute=FALSE} or if they do not contain any missing values.  
       |                                                                                                                                                                                                                                         ^
checkRd: (-1) plotNN.Rd:20: Lost braces
    20 |   \item{nid}{logical value indicating if neural interpretation diagram is plotted, default is  code{TRUE}}
       |                                                                                                    ^
'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: \_
checkRd: (-1) brownfat.Rd:35: Lost braces
    35 | \references{ Routhier-Labadie, A., Ouellet, V.,  Bellemare, W., Richard, D., Lakhal-Chaieb, L., Turcotte, E., and Carpentier, A. C. (2011), Outdoor Temperature, Age, Sex, Body Mass Index, and Diabetic Status Determine the Prevalence, Mass, and Glucose-Uptake Activity of 18{F}-{FDG}-Detected {BAT} in Humans.\emph{The Journal of Clinical Endocrinology and Metabolism}, 	Volume \bold{96}, number 1, pp 192-199.
       |                                                                                                                                                                                                                                                                                  ^
checkRd: (-1) pc.Rd:17: Lost braces
    17 | The functions \code{gamlss.pcr()} and \code{gamlss.pc()} are supporting functions. The  are not intended to be called directly by users. The function \code{gamlss.pc()} is using the linear model function \code{lm()} to fit the first principal components while the function code{gamlss.pcr()} uses \code{fitPCR()}.
       |                                                                                                                                                                                                                                                                                      ^
checkRd: (-1) term.plotZadj.Rd:6: Lost braces
     6 |  \ This is a wrapper to function \code{\link[gamlss]{term.plot}}. code{term.plotZadj} produces term plots for a specified parameter from a    
       |                                                                       ^
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: \_
checkRd: (-1) Gapfill.Rd:66-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:69-70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:71-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Gapfill.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ndvi.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ndvi.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ndvi.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ndvi.Rd:13: Lost braces in \itemize; meant \describe ?
Documented arguments not in \usage in Rd file 'as.gapdata.Rd':
  ‘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.
checkRd: (-1) gaControl.Rd:20-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gaControl.Rd:28-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gaControl.Rd:36-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gaControl.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) glag.Rd:7: Lost braces; missing escapes or markup?
     7 | Similar to the \code{\link{lag}} function from the \code{stats} package, but \code{glag} enables padding (e.g. {NA}s or 0s) of the lost entries. Contrary to the \code{\link{lag}} function in the stats package, however, the default in \code{glag} is to pad (with \code{NA}s). The \code{glag} is particularly suited for \code{\link{zoo}} objects, since their indexing is retained
       |                                                                                                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) read.ctable.Rd:19: Lost braces; missing escapes or markup?
    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                      ^
checkRd: (-1) read.ctable.Rd:19: Lost braces; missing escapes or markup?
    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                                      ^
checkRd: (-1) read.ctable.Rd:29: Lost braces; missing escapes or markup?
    29 | output array, {row,col}.names are not necessary \code{dimnames[[1]]} and
       |               ^
checkRd: (-1) simulate_gastempt.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{tempt_mean, tempt_std}{Mean and between record standard deviation of parameter $t_{empt}$, typically in minutes.}
       |                                                                                         ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) logistic.mm.aireml.Rd:33: Lost braces; missing escapes or markup?
    33 |   {logit P(Y=1|X,omega_1,...,omega_k)  = X beta  + omega_1 + ... + omega_k}
       |   ^
Documented arguments not in \usage in Rd file 'lrr_plot.Rd':
  ‘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.
checkRd: (-1) summary.GauPro.Rd:5-35: Lost braces
     5 | \title{if (F) {
       |               ^
checkRd: (-1) summary.GauPro.Rd:20-22: Lost braces
    20 |   #' if (requireNamespace("MASS", quietly = TRUE)) {
       |                                                    ^
checkRd: (-1) summary.GauPro.Rd:24-34: Lost braces
    24 |   plot.GauPro <- function(x,  ...) {
       |                                    ^
checkRd: (-1) summary.GauPro.Rd:26-28: Lost braces
    26 |     # if (x$D == 1) {
       |                     ^
checkRd: (-1) summary.GauPro.Rd:28-30: Lost braces
    28 |     # } else if (x$D == 2) {
       |                            ^
checkRd: (-1) summary.GauPro.Rd:30-33: Lost braces
    30 |     # } else {
       |              ^
checkRd: (-1) summary.GauPro.Rd:49-79: Lost braces
    49 | if (F) {
       |        ^
checkRd: (-1) summary.GauPro.Rd:64-66: Lost braces
    64 |   #' if (requireNamespace("MASS", quietly = TRUE)) {
       |                                                    ^
checkRd: (-1) summary.GauPro.Rd:68-78: Lost braces
    68 |   plot.GauPro <- function(x,  ...) {
       |                                    ^
checkRd: (-1) summary.GauPro.Rd:70-72: Lost braces
    70 |     # if (x$D == 1) {
       |                     ^
checkRd: (-1) summary.GauPro.Rd:72-74: Lost braces
    72 |     # } else if (x$D == 2) {
       |                            ^
checkRd: (-1) summary.GauPro.Rd:74-77: Lost braces
    74 |     # } else {
       |              ^
checkRd: (-1) Sim.Markov.Chain.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{eta0}{inital value in {1,...,r}.}
       |                             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) CompoundDensPlot.Rd:18: Lost braces
    18 |   \item{shape1, scale ,shape2, shape3}{numeric; positive parameters of the GB2 distribution. On the plot they are denotes as \code{a}, code{b}, \code{p}, \code{q} and \code{pl0} respectively.}
       |                                                                                                                                            ^
checkRd: (-1) CompoundVarest.Rd:58: Lost braces
    58 | \code{scoreU.cgb2} returns a \eqn{N \times (L-1)} matrix of scores <code{U}.
       |                                                                         ^
checkRd: (-1) Fisk.Rd:26: Lost braces
    26 | \value{\code{fisk} and \code{fiskh} return vectors of length 4 containing the estimated parameters \eqn{a}, eqn{b}, as well as \eqn{p=1} and \eqn{q=1}. 
       |                                                                                                                ^
checkRd: (-1) MLfullGB2.Rd:23: Lost braces
    23 |   \item{method}{numeric; the method to be used by \code{optim}. By default, code{method = }1 and the used method is BFGS. If \code{method = }2, method L-BFGS-B is used.}
       |                                                                                 ^
checkRd: (-1) MLprofGB2.Rd:16: Lost braces
    16 |   \item{method}{numeric; the method to be used by \code{optim}. By default, code{method = }1 and the used method is BFGS. If \code{method = }2, method L-BFGS-B is used.}
       |                                                                                 ^
checkRd: (-1) gbfs.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gbfs.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gbfs.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gbfs.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gbfs.Rd:43-44: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘checkdata.csv’ ‘gbmforest.sas’
checkRd: (-1) gbm.auto.Rd:208: Lost braces; missing escapes or markup?
   208 | \item Error in if (n.trees > x$n.trees) { : argument is of length zero}. LR or BF probably too low
       |                                         ^
checkRd: (-1) gbm.Rd:85: Lost braces; missing escapes or markup?
    85 | targets {0,1} are expected for \code{map} and \code{mrr}. For \code{ndcg}
       |         ^
checkRd: (-1) gbm.Rd:319: Lost braces
   319 | url{https://dl.acm.org/citation.cfm?id=1354603}.
       |    ^
checkRd: (-1) gbm.fit.Rd:96: Lost braces; missing escapes or markup?
    96 | targets {0,1} are expected for \code{map} and \code{mrr}. For \code{ndcg}
       |         ^
checkRd: (-1) gbm.fit.Rd:215: Lost braces
   215 | url{https://dl.acm.org/citation.cfm?id=1354603}.
       |    ^
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 Rd file 'align_peaks.Rd':
  ‘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
checkRd: (-1) listInverseBlocks.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                           ^
checkRd: (-1) listInverseBlocks.Rd:17: Lost braces; missing escapes or markup?
    17 | List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) matern.cormat.Rd:17: Lost braces; missing escapes or markup?
    17 | value of the shape parameter of the Matern correlation class. The default {alpha = 0.5} corresponds to an exponential correlation model. 
       |                                                                           ^
checkRd: (-1) gconsensus.Rd:48-54: Lost braces
    48 | {\code{display.signif.digits} an integer representing the number of significant digits to be obtained in the adaptative approach of the Monte Carlo simulation,
       | ^
Specified C++11: please drop specification unless essential
checkRd: (-1) GCTF.Rd:56: Lost braces; missing escapes or markup?
    56 |   U : A matrix which has N-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) GCTF.Rd:57: Lost braces; missing escapes or markup?
    57 |   V : A matrix which has M-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) GCTF.Rd:58: Lost braces; missing escapes or markup?
    58 |   J : The number of dimension (J < {N, M}).
       |                                    ^
checkRd: (-1) nearblack.Rd:30: Lost braces
    30 | code{infile=}, indicating that the input file should be
       |     ^
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’.
checkRd: (-1) is.what.Rd:23-24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) is.what.Rd:25: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) is.what.Rd:26-27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GMSCDM.Rd:25: Lost braces; missing escapes or markup?
    25 | representing restricted GMS-DINA and GMS-DINO models where delta_{jm1} are equal for all strategies. Note that only a single model can be used
       |                                                                  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) GDSARM.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) GDSARM.Rd:10: Lost braces
    10 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
checkRd: (-1) GDS_givencols.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) GDS_givencols.Rd:10: Lost braces
    10 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
checkRd: (-1) dantzig.delta.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) dantzigS.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) dataCompoundExt.Rd:6: Lost braces
     6 | \title{Compound Extraction experiment of Dopico-Garc{\' i}a et al. (2007)}
       |                                                     ^
checkRd: (-1) dataCompoundExt.Rd:35: Lost braces
    35 | An analytical experiment conducted by Dopico-Garc{\' i}a et al. (2007) to
       |                                                  ^
checkRd: (-1) dataCompoundExt.Rd:22: Lost braces
    22 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
checkRd: (-1) EWmortality.Rd:10: Lost braces
    10 |   {\code{Exposure} is a mid-year estimate of the population exposed to risk.}}
       |   ^
Objects in \usage without \alias in Rd file 'geepack-internal.Rd':
  ‘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.
checkRd: (-1) dental.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geexex.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gelnet.logreg.obj.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{y}{n-by-1 binary response vector sampled from {0,1}}
       |                                                     ^
checkRd: (-1) ReadGem.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:79-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ReadGem.Rd:81-82: Lost braces in \itemize; \value handles \item{}{} directly
Auto-generated content requiring editing in Rd file 'gemlog-package.Rd':
  \details: ‘...the package, including the most important ~~ ~~ functions ~~’
'LazyData' is specified without a 'data' directory
checkRd: (-1) parkinson.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parkinson.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parkinson.Rd:11: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'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 Rd file 'CirDisp.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'CirKurt.Rd':
  ‘x’ ‘na.rm’

Documented arguments not in \usage in Rd file 'CirSD.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'CirSkew.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'CirVar.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'MeanDir.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'impact.Rd':
  ‘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 Rd file 'expand.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'grapes-bq-grapes.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'grapes-bt-grapes.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'stftcalc.Rd':
  ‘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.