Packages required but not available: 'doParallel', 'uwot', 'torch'

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

Packages suggested but not available for checking:
  'biomaRt', 'KEGGREST', 'ontoProc', 'SingleCellSignalR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'strucchange', 'mirt'

Package suggested but not available for checking: ‘psychotree’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘buildtree.Rmd’
Package required but not available: ‘SCEPtER’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
prime.factor: no visible global function definition for ‘data’
prime.factor: no visible binding for global variable ‘primlist’
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘schoolmath/R/prime.factor.R’:
  data(primlist)
See section ‘Good practice’ in ‘?data’.
Package suggested but not available for checking: ‘ez’
Packages suggested but not available for checking: 'hexSticker', 'showtext'
Packages suggested but not available for checking: 'cobs', 'scam'
Error(s) in re-building vignettes:
  ...
--- re-building ‘schumaker.Rmd’ using rmarkdown
Quitting from lines 218-266 (schumaker.Rmd) 
Error: processing vignette ‘schumaker.Rmd’ failed with diagnostics:
there is no package called 'cobs'
--- failed re-building ‘schumaker.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyverse', 'readr', 'easypackages'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ComplexHeatmap', 'edgeR', 'sva', 'Rmisc', 'ggpubr', 'sccore', 'NMF'

Packages suggested but not available for checking:
  'simplifyEnrichment', 'WGCNA', 'AnnotationDbi', 'GO.db', 'conos',
  'pagoda2', 'betareg', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/scLink.Rcheck/00install.out’ for details.
Packages required but not available:
  'Seurat', 'GSVA', 'pcaMethods', 'gprofiler2', 'ADAPTS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'SingleCellExperiment', 'BiocSingular', 'SummarizedExperiment',
  'scater', 'scran', 'S4Vectors'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'alakazam', 'shazam', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'behavr', 'readr', 'RSQLite'

Packages suggested but not available for checking: 'ggetho', 'zeitgebr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'partykit', 'sqldf'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
score.GGUM: no visible global function definition for ‘dnorm’
score.GGUM: no visible global function definition for ‘hist’
score.GGUM: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  dnorm hist write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘EAP_est1.txt’
'LazyData' is specified without a 'data' directory
CreatePssm: no visible binding for global variable ‘training’
Undefined global functions or variables:
  training
Package required but not available: ‘msm’

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

Packages suggested but not available for checking:
  'Rmixmod', 'speedglm', 'plotly'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dynwrap', 'lmds'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'forecast'

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

Package suggested but not available for checking: ‘lme4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'CVXR', 'doRNG', 'doSNOW', 'Qtools'

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

Package which this enhances but not available for checking: ‘fields’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'RSQLite', 'oligoClasses'
Packages required but not available:
  'splatter', 'S4Vectors', 'SummarizedExperiment',
  'SingleCellExperiment', 'edgeR', 'Seurat', 'fitdistrplus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘RCy3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'Seurat', 'clustree'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ALL', 'ConsensusClusterPlus', 'edgeR', 'TPEA', 'Rmisc',
  'PerformanceAnalytics', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SCRSELECT.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘httptest’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'cvTools', 'furrr'

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

Package suggested but not available for checking: ‘irlba’

Package which this enhances but not available for checking: ‘glmGamPoi’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘survey’
Error(s) in re-building vignettes:
  ...
--- re-building ‘SDaA_using_survey.Rnw’ using Sweave

Error: processing vignette ‘SDaA_using_survey.Rnw’ failed with diagnostics:
 chunk 2 (label = loadPkg) 
Error in library(survey) : there is no package called ‘survey’

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

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'PrevMap', 'raster', 'spatstat', 'splancs', 'maptools', 'spacetime',
  'mapview', 'geoR', 'spatstat.geom'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘care’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sda.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sdcHierarchies.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘lfe’
Packages required but not available: 'car', 'haven', 'VIM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SDCNway.Rcheck/00install.out’ for details.
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sdcHierarchies', 'Rglpk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'magic', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'tseries'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘MC p-value.ps’ ‘Output.csv’ ‘Rh.ps’ ‘Th.ps’ ‘dataratio .Rdata’
  ‘featuresRmax.csv’ ‘featuresT.csv’
Package required but not available: ‘fda’

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

Packages suggested but not available for checking:
  'rgdal', 'automap', 'future.apply', 'blockCV', 'dismo', 'SSDM',
  'ggcorrplot', 'haven', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'dismo'

Packages suggested but not available for checking: 'maptools', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R.utils', 'raster', 'rgdal'

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

Packages suggested but not available for checking: 'R.rsp', 'dismo'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dismo', 'maxnet', 'raster'

Packages suggested but not available for checking:
  'plotROC', 'rasterVis', 'rgdal'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GB2', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sdpt3r.Rcheck/00install.out’ for details.
Packages required but not available:
  'rgdal', 'rgeos', 'rasterVis', 'raster', 'dismo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SEAGLE.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sealasso.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'doParallel', 'KScorrect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'createTree.Rd':
  \usage lines wider than 90 characters:
     createTree(data, treeType = "quad", dataType = "point", columns = if (dataType=="point") 1:2 else 1:4, ...)

These lines will be truncated in the PDF manual.
adx: no visible global function definition for ‘abline’
adx: no visible global function definition for ‘legend’
dx: no visible global function definition for ‘abline’
dx: no visible global function definition for ‘legend’
maxd: no visible global function definition for ‘abline’
maxd: no visible global function definition for ‘legend’
pc: no visible global function definition for ‘rainbow’
pc: no visible global function definition for ‘abline’
pc: no visible global function definition for ‘legend’
pc: no visible global function definition for ‘points’
pcu: no visible global function definition for ‘rainbow’
pcu: no visible global function definition for ‘abline’
pcu: no visible global function definition for ‘legend’
pcu: no visible global function definition for ‘points’
rmsd: no visible global function definition for ‘abline’
rmsd: no visible global function definition for ‘legend’
rsd: no visible global function definition for ‘abline’
rsd: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "points")
to your NAMESPACE file.
Package required but not available: ‘TTR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantmod', 'dygraphs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘seasonalview’
Packages required but not available: 'dygraphs', 'xts'

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

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

Package suggested but not available for checking: ‘waterData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'optimization'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SECP.Rcheck/00install.out’ for details.
Package required but not available: ‘secr’

Package suggested but not available for checking: ‘secrlinear’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'secr', 'maptools', 'rgdal'

Packages suggested but not available for checking: 'rgeos', 'secrdesign'

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

Packages suggested but not available for checking: 'gdistance', 'spsurvey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DDD', 'doParallel', 'apTreeshape', 'phylobase', 'geiger'

Packages suggested but not available for checking:
  'diversitree', 'phytools'

Package which this enhances but not available for checking: ‘doMC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'haven', 'readr'

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

Package suggested but not available for checking: ‘tidyverse’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'quanteda.textmodels', 'topicmodels'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/seededlda.Rcheck/00install.out’ for details.
Packages required but not available: 'drc', 'car', 'multcomp', 'hnp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'R.utils'

Package suggested but not available for checking: ‘rsbml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'demography', 'RSQLite', 'labelled', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'brms', 'factoextra', 'ggraph', 'ggrepel', 'ggside', 'glmmTMB',
  'lme4', 'metafor', 'nFactors', 'qqplotr', 'rstanarm'
Packages required but not available: 'maptools', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forecast', 'forecTheta', 'furrr', 'tsfeatures'

Packages suggested but not available for checking:
  'repmis', 'Mcomp', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dygraphs', 'xts', 'leaflet', 'adehabitatLT', 'depmixS4', 'moveHMM',
  'move', 'devtools'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SegCorr.Rcheck/00install.out’ for details.
Packages required but not available: 'rgdal', 'rgeos', 'spdep', 'OasisR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/segmented.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Package suggested but not available for checking: ‘doParallel’
Running ‘testthat.R’ [18s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(segmentr)
  > 
  > test_check("segmentr")
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 46 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-exactalg.R:28:3): works with cluster ────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'doParallel'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-exactalg.R:28:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test-hieralg.R:24:3): works with a cluster as well ───────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'doParallel'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-hieralg.R:24:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test-hybridalg.R:26:3): works with cluster ───────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'doParallel'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-hybridalg.R:26:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 46 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'doParallel', 'fGarch'

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

Packages suggested but not available for checking:
  'spdep', 'spgrass6', 'rgdal'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'tidycensus', 'tigris'
Packages required but not available: 'pedtools', 'pedprobr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arm', 'DescTools', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
get.infectiousness: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Packages required but not available: 'factoextra', 'RPostgreSQL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Packages required but not available: 'glmnet', 'Rfast', 'Cascade', 'varbvs'

Package suggested but not available for checking: ‘mixOmics’

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

Package suggested but not available for checking: ‘Rmpfr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat', 'ecespa', 'spatstat.geom', 'spatstat.core',
  'spatstat.random'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Ecdat’
Package suggested but not available for checking: ‘RSauceLabs’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/seleniumPipes.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/selfea.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/selfingTree.Rcheck/00install.out’ for details.
Package required but not available: ‘CompareCausalNetworks’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fields', 'PerformanceAnalytics', 'DescTools', 'msos'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'semPlot', 'semTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘piecewiseSEM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cate', 'ggm', 'GGMncv', 'glmnet', 'graph', 'Rgraphviz'

Packages suggested but not available for checking:
  'pcalg', 'SILGGM', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CORElearn', 'RSNNS', 'fpc', 'ks', 'mcclust', 'flexclust',
  'StatMatch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'twang', 'fastGHQuad'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SemiCompRisks.Rcheck/00install.out’ for details.
Packages required but not available: 'R.oo', 'R.utils'

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

Package which this enhances but not available for checking: ‘semPlot’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'SemNetDictionaries', 'R.matlab', 'easycsv', 'editData'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qgraph', 'car', 'effects'

Packages suggested but not available for checking: 'spreadr', 'R.matlab'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qgraph', 'sem', 'rockchalk'

Package suggested but not available for checking: ‘MplusAutomation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘semPlot’
Running examples in ‘semptools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: change_node_label
> ### Title: Change node labels
> ### Aliases: change_node_label
> 
> ### ** Examples
> 
> library(semPlot)
Error in library(semPlot) : there is no package called ‘semPlot’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘keep_or_drop_nodes.Rmd’ using rmarkdown
Quitting from lines 66-81 (keep_or_drop_nodes.Rmd) 
Error: processing vignette ‘keep_or_drop_nodes.Rmd’ failed with diagnostics:
there is no package called 'semPlot'
--- failed re-building ‘keep_or_drop_nodes.Rmd’

--- re-building ‘layout_matrix.Rmd’ using rmarkdown
Quitting from lines 48-69 (layout_matrix.Rmd) 
Error: processing vignette ‘layout_matrix.Rmd’ failed with diagnostics:
there is no package called 'semPlot'
--- failed re-building ‘layout_matrix.Rmd’

--- re-building ‘quick_start_cfa.Rmd’ using rmarkdown
Quitting from lines 65-72 (quick_start_cfa.Rmd) 
Error: processing vignette ‘quick_start_cfa.Rmd’ failed with diagnostics:
there is no package called 'semPlot'
--- failed re-building ‘quick_start_cfa.Rmd’

--- re-building ‘quick_start_sem.Rmd’ using rmarkdown
Quitting from lines 69-76 (quick_start_sem.Rmd) 
Error: processing vignette ‘quick_start_sem.Rmd’ failed with diagnostics:
there is no package called 'semPlot'
--- failed re-building ‘quick_start_sem.Rmd’

--- re-building ‘semptools.Rmd’ using rmarkdown
Quitting from lines 54-64 (semptools.Rmd) 
Error: processing vignette ‘semptools.Rmd’ failed with diagnostics:
there is no package called 'semPlot'
--- failed re-building ‘semptools.Rmd’

SUMMARY: processing the following files failed:
  ‘keep_or_drop_nodes.Rmd’ ‘layout_matrix.Rmd’ ‘quick_start_cfa.Rmd’
  ‘quick_start_sem.Rmd’ ‘semptools.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘mi’

Package suggested but not available for checking: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction-to-package-SEMrushR-.Rmd’
Packages required but not available: 'np', 'gamlss', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rockchalk’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'Amelia', 'blavaan'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/semTools.Rcheck/00install.out’ for details.
Packages required but not available:
  'rpart.plot', 'strucchange', 'future.apply'

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'stars', 'raster', 'rgdal', 'geojsonio', 'doParallel'

Packages suggested but not available for checking:
  'leaflet', 'leafpm', 'mapedit', 'httptest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
.plot_attachment: no visible global function definition for ‘dev.off’
.update_list: no visible global function definition for ‘modifyList’
mime_part.data.frame: no visible global function definition for
  ‘write.table’
mime_part.ggplot: no visible binding for global variable ‘pdf’
mime_part.matrix: no visible global function definition for
  ‘write.table’
mime_part.trellis: no visible binding for global variable ‘pdf’
Undefined global functions or variables:
  dev.off modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'mlr3', 'mlr3learners', 'mlr3filters', 'mlr3pipelines', 'mlr3viz',
  'mlr3tuning', 'bbotk', 'readr'

Packages suggested but not available for checking: 'glmnet', 'care', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'phylolm', 'caper', 'phytools', 'geiger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'relaimpo', 'ggrepel', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
gconv: no visible global function definition for ‘convolve’
sens.analysis.aberrant.rank: no visible global function definition for
  ‘pnorm’
sens.analysis.mh: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  convolve pnorm
Consider adding
  importFrom("stats", "convolve", "pnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
plot.sensitivity.2.0d: no visible global function definition for ‘gray’
sensitivitySGD: no visible global function definition for ‘tail’
sensitivitySGL: no visible global function definition for ‘tail’
Undefined global functions or variables:
  gray tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'condMVNorm', 'doParallel', 'ks', 'mc2d', 'randtoolbox', 'whitening'
Running examples in ‘sensitivity-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lmg
> ### Title: LMG R-squared decomposition for linear and logistic regression
> ###   models
> ### Aliases: lmg print.lmg plot.lmg
> ### Keywords: shapley
> 
> ### ** Examples
> 
> library(parallel)
> library(doParallel)
Error in library(doParallel) : there is no package called ‘doParallel’
Execution halted
Package required but not available: ‘maxLik’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'randtoolbox', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FactoMineR', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sensory.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘car’
Packages required but not available: 'ggmap', 'R.utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘text2vec’
Packages required but not available: 'tm', 'ngramrr', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doSNOW', 'TSdist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'glmnet'

Packages suggested but not available for checking: 'doParallel', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doFuture', 'doRNG'

Packages suggested but not available for checking:
  'plotly', 'xts', 'sentometrics'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘httptest’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mockery)
  > library(sentryR)
  
  Attaching package: 'sentryR'
  
  The following object is masked from 'package:testthat':
  
      capture_message
  
  > 
  > test_check("sentryR")
  Error in library(httptest) : there is no package called 'httptest'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/seplyr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/seqCBS.Rcheck/00install.out’ for details.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/seqDesign.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SeqDetect.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Biostrings', 'phangorn', 'calibrate', 'R2jags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'irlba', 'sva', 'matchingR', 'cate'

Packages suggested but not available for checking:
  'SummarizedExperiment', 'DESeq2', 'airway', 'edgeR'

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

Packages suggested but not available for checking:
  'FactoMineR', 'GDAtools', 'TraMineRextras', 'WeightedCluster',
  'questionr'

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

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

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

Package suggested but not available for checking: ‘doMC’

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

Packages suggested but not available for checking:
  'GenomicAlignments', 'GenomicRanges', 'IRanges', 'muscle',
  'Rsamtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘SKAT’
Found the following significant warnings:
  BGenFile.cpp:12:55: warning: member ‘BGenFile::N’ is used uninitialized [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/seqminer.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Package required but not available: ‘fitdistrplus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
plotenz : addmark: no visible global function definition for ‘par’
plotenz : addmark: no visible global function definition for ‘text’
plotenz : addmark: no visible global function definition for ‘segments’
plotenz : addband: no visible global function definition for ‘segments’
plotenz : addband: no visible global function definition for ‘text’
plotenz: no visible global function definition for ‘layout’
plotenz: no visible global function definition for ‘text’
plotenz: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  dev.new layout par segments text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "layout", "par", "segments", "text")
to your NAMESPACE file.
Rd file 'plotenz.Rd':
  \usage lines wider than 90 characters:
     plotenz(sequences, enznames, enzdata, side = TRUE, type = c("RFLP", "TRFLP"), Terminal = c("T5", "T3"))

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘total’
'LazyData' is specified without a 'data' directory
checkRd: (7) read.old.seq.Rd:41: invalid email address: Jean-sebastien.pierre\@univ-rennes1.fr
Package required but not available: ‘selectiveInference’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sequences.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'readr', 'copynumber'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bit64', 'readr'

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

Packages suggested but not available for checking:
  'DendSer', 'GA', 'dendextend'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/serieslcb.Rcheck/00install.out’ for details.
checkRd: (7) seroincidence.Rd:88: invalid email address: <p.teunis@emory.edu>
checkRd: (7) seroincidence.Rd:90: invalid email address: <daniel@nextpagesoft.net>
checkRd: (7) seroincidence.Rd:91: invalid email address: <seroincidence@ecdc.europa.eu>
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Hmisc’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/serrsBayes.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘qgraph’
Running examples in ‘SEset-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: network_to_SEset
> ### Title: SE-set from precision matrix
> ### Aliases: network_to_SEset
> 
> ### ** Examples
> 
> # first estimate the precision matrix
> data(riskcor)
> omega <- (qgraph::EBICglasso(riskcor, n = 69, returnAllResults = TRUE))$optwi
Error in loadNamespace(x) : there is no package called ‘qgraph’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Malformed Title field: should not end in a period.
capture: no visible binding for global variable ‘resultText’
restore.session: no visible binding for global variable
  ‘.save.session.packages’
restore.session: no visible binding for global variable
  ‘.save.session.search’
save.session: no visible global function definition for ‘dev.list’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.search’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.packages’
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.

Found the following calls to attach():
File ‘session/R/session.R’:
  attach(sub("file:", "", i))
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘RSession.Rda’
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'QCA', 'ggrepel', 'betareg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
setpath: no visible global function definition for ‘cov’
setpath: no visible global function definition for ‘median’
setpath: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cov median pchisq
Consider adding
  importFrom("stats", "cov", "median", "pchisq")
to your NAMESPACE file.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/setter.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: class "Graph" is inheriting an inconsistent superclass structure from class "dgCMatrix", inconsistent with "dsparseMatrix"
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SeuratObject.Rcheck/00install.out’ for details.
Packages required but not available:
  'fitdistrplus', 'future.apply', 'ggrepel', 'irlba', 'lmtest',
  'plotly', 'sctransform', 'spatstat.core', 'spatstat.geom', 'uwot'

Packages suggested but not available for checking:
  'hdf5r', 'S4Vectors', 'SummarizedExperiment', 'SingleCellExperiment',
  'MAST', 'DESeq2', 'GenomicRanges', 'GenomeInfoDb', 'IRanges',
  'rtracklayer', 'Rfast2', 'monocle', 'Biobase', 'metap', 'mixtools',
  'ggrastr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
‘library’ or ‘require’ call to ‘graphics’ which was already attached by Depends.
  Please remove these calls from your code.
severity: no visible global function definition for ‘qnorm’
severity: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
Package required but not available: ‘gmm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
L_exp: no visible global function definition for ‘pnorm’
L_hNV: no visible global function definition for ‘pnorm’
L_trunc: no visible global function definition for ‘pnorm’
L_trunc_mufest: no visible global function definition for ‘pnorm’
dgp: no visible global function definition for ‘runif’
dgp: no visible global function definition for ‘rnorm’
eff.sfa: no visible global function definition for ‘predict’
fitted.sfa: no visible global function definition for ‘predict’
predict.sfa: no visible global function definition for ‘coef’
print.sfa: no visible global function definition for ‘coef’
residuals.sfa: no visible global function definition for ‘fitted’
sfa: no visible global function definition for ‘model.frame’
sfa: no visible global function definition for ‘model.response’
sfa.fit: no visible global function definition for ‘lm’
sfa.fit: no visible global function definition for ‘resid’
sfa.fit: no visible global function definition for ‘var’
sfa.fit: no visible global function definition for ‘optim’
summary.sfa: no visible global function definition for ‘logLik’
summary.sfa: no visible global function definition for ‘pchisq’
te.eff.sfa: no visible global function definition for ‘residuals’
te.eff.sfa: no visible global function definition for ‘pnorm’
u.sfa: no visible global function definition for ‘residuals’
u.sfa: no visible global function definition for ‘dnorm’
u.sfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coef dnorm fitted lm logLik model.frame model.response optim pchisq
  pnorm predict resid residuals rnorm runif var
Consider adding
  importFrom("stats", "coef", "dnorm", "fitted", "lm", "logLik",
             "model.frame", "model.response", "optim", "pchisq", "pnorm",
             "predict", "resid", "residuals", "rnorm", "runif", "var")
to your NAMESPACE file.
Packages required but not available:
  'fBasics', 'marqLevAlg', 'maxLik', 'qrng', 'randtoolbox'

Package suggested but not available for checking: ‘mlogit’

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

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

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

Packages suggested but not available for checking: 'ggraph', 'tidyverse'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'spatstat.geom', 'spatstat.linnet', 'spatstat', 'tidyverse'
Error(s) in re-building vignettes:
  ...
--- re-building ‘sfn01_structure.Rmd’ using rmarkdown
Linking to GEOS 3.10.2, GDAL 3.4.2, PROJ 9.0.0; sf_use_s2() is TRUE

Attaching package: 'tidygraph'

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

    filter

Quitting from lines 40-45 (sfn01_structure.Rmd) 
Error: processing vignette ‘sfn01_structure.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘sfn01_structure.Rmd’

--- re-building ‘sfn02_preprocess_clean.Rmd’ using rmarkdown
Quitting from lines 38-44 (sfn02_preprocess_clean.Rmd) 
Error: processing vignette ‘sfn02_preprocess_clean.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘sfn02_preprocess_clean.Rmd’

--- re-building ‘sfn03_join_filter.Rmd’ using rmarkdown
Quitting from lines 39-44 (sfn03_join_filter.Rmd) 
Error: processing vignette ‘sfn03_join_filter.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘sfn03_join_filter.Rmd’

--- re-building ‘sfn04_routing.Rmd’ using rmarkdown
Quitting from lines 39-44 (sfn04_routing.Rmd) 
Error: processing vignette ‘sfn04_routing.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘sfn04_routing.Rmd’

--- re-building ‘sfn05_morphers.Rmd’ using rmarkdown
Quitting from lines 37-42 (sfn05_morphers.Rmd) 
Error: processing vignette ‘sfn05_morphers.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘sfn05_morphers.Rmd’

SUMMARY: processing the following files failed:
  ‘sfn01_structure.Rmd’ ‘sfn02_preprocess_clean.Rmd’
  ‘sfn03_join_filter.Rmd’ ‘sfn04_routing.Rmd’ ‘sfn05_morphers.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘plotly’
Error(s) in re-building vignettes:
  ...
--- re-building ‘v1_intro.Rmd’ using rmarkdown
--- finished re-building ‘v1_intro.Rmd’

--- re-building ‘v3_analyzing_landing.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 30-37 (v3_analyzing_landing.Rmd) 
Error: processing vignette ‘v3_analyzing_landing.Rmd’ failed with diagnostics:
there is no package called 'plotly'
--- failed re-building ‘v3_analyzing_landing.Rmd’

SUMMARY: processing the following file failed:
  ‘v3_analyzing_landing.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'mapview', 'odbc', 'raster', 'RPostgres', 'RPostgreSQL', 'RSQLite',
  'spatstat', 'spatstat.geom', 'spatstat.random', 'spatstat.linnet',
  'stars', 'tmap'
Error(s) in re-building vignettes:
  ...
--- re-building ‘sf1.Rmd’ using rmarkdown
--- finished re-building ‘sf1.Rmd’

--- re-building ‘sf2.Rmd’ using rmarkdown
--- finished re-building ‘sf2.Rmd’

--- re-building ‘sf3.Rmd’ using rmarkdown
--- finished re-building ‘sf3.Rmd’

--- re-building ‘sf4.Rmd’ using rmarkdown
--- finished re-building ‘sf4.Rmd’

--- re-building ‘sf5.Rmd’ using rmarkdown
Quitting from lines 203-205 (sf5.Rmd) 
Error: processing vignette ‘sf5.Rmd’ failed with diagnostics:
there is no package called 'tmap'
--- failed re-building ‘sf5.Rmd’

--- re-building ‘sf6.Rmd’ using rmarkdown
--- finished re-building ‘sf6.Rmd’

--- re-building ‘sf7.Rmd’ using rmarkdown
--- finished re-building ‘sf7.Rmd’

SUMMARY: processing the following file failed:
  ‘sf5.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘viridis’
Package which this enhances but not available for checking: ‘Hmisc’
Package suggested but not available for checking: ‘seriation’
Packages suggested but not available for checking:
  'spacetime', 'trajectories', 'stars'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sftime.Rcheck/00install.out’ for details.
Packages required but not available: 'wordspace', 'doParallel', 'ff'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘adehabitatLT’
Running examples in ‘sftrack-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as_sftrack
> ### Title: Convert objects into sftrack objects.
> ### Aliases: as_sftrack as_sftrack.data.frame as_sftrack.sftraj
> ###   as_sftrack.ltraj as_sftrack.sf
> 
> ### ** Examples
> 
> #'
> data("raccoon")
> raccoon$timestamp <- as.POSIXct(raccoon$timestamp, "EST")
> burstz <- list(id = raccoon$animal_id, month = as.POSIXlt(raccoon$timestamp)$mon)
> # Input is a data.frame
> my_track <- as_sftrack(raccoon,
+   group = burstz, time = "timestamp",
+   error = NA, coords = c("longitude", "latitude")
+ )
> 
> # Input is a ltraj
> library("adehabitatLT")
Error in library("adehabitatLT") : 
  there is no package called ‘adehabitatLT’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sftrack1_overview.Rmd’ using rmarkdown
--- finished re-building ‘sftrack1_overview.Rmd’

--- re-building ‘sftrack2_reading.Rmd’ using rmarkdown
Quitting from lines 112-122 (sftrack2_reading.Rmd) 
Error: processing vignette ‘sftrack2_reading.Rmd’ failed with diagnostics:
there is no package called 'adehabitatLT'
--- failed re-building ‘sftrack2_reading.Rmd’

--- re-building ‘sftrack3_workingwith.Rmd’ using rmarkdown
--- finished re-building ‘sftrack3_workingwith.Rmd’

--- re-building ‘sftrack4_groups.Rmd’ using rmarkdown
--- finished re-building ‘sftrack4_groups.Rmd’

--- re-building ‘sftrack5_spatial.Rmd’ using rmarkdown
--- finished re-building ‘sftrack5_spatial.Rmd’

SUMMARY: processing the following file failed:
  ‘sftrack2_reading.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘fda’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'glmnet', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sglasso.Rcheck/00install.out’ for details.
Packages required but not available: 'plotly', 'TeachingSampling'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sgmcmc.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sgof.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘SGP’
Package required but not available: ‘mixOmics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'doParallel', 'doRNG', 'plotly', 'quantreg', 'RSQLite', 'sn'

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

Packages suggested but not available for checking:
  'R.rsp', 'maptools', 'threejs', 'rgdal'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ShapeChange.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/shapefiles.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'rgdal', 'landscapemetrics', 'rgeos', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘geomorph’
Packages required but not available: 'wavethresh', 'vegan'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggforce', 'ggpubr'

Package suggested but not available for checking: ‘lightgbm’

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

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

Packages suggested but not available for checking:
  'caret', 'party', 'partykit'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'xts', 'timeSeries', 'quantmod', 'TTR'
Error(s) in re-building vignettes:
  ...
--- re-building ‘AsymptoticMarkowitz.Rnw’ using knitr
Quitting from lines 54-109 (AsymptoticMarkowitz.Rnw) 
Error: processing vignette ‘AsymptoticMarkowitz.Rnw’ failed with diagnostics:
there is no package called 'quantmod'
--- failed re-building ‘AsymptoticMarkowitz.Rnw’

--- re-building ‘SharpeR.Rnw’ using knitr
Quitting from lines 27-72 (SharpeR.Rnw) 
Error: processing vignette ‘SharpeR.Rnw’ failed with diagnostics:
there is no package called 'quantmod'
--- failed re-building ‘SharpeR.Rnw’

--- re-building ‘SharpeRatio.Rnw’ using knitr
Quitting from lines 34-89 (SharpeRatio.Rnw) 
Error: processing vignette ‘SharpeRatio.Rnw’ failed with diagnostics:
there is no package called 'quantmod'
--- failed re-building ‘SharpeRatio.Rnw’

SUMMARY: processing the following files failed:
  ‘AsymptoticMarkowitz.Rnw’ ‘SharpeR.Rnw’
  ‘SharpeRatio.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'glmnet', 'np'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'soilDB', 'vegan', 'Hmisc'

Packages suggested but not available for checking:
  'rgdal', 'spdep', 'rgeos', 'raster', 'dendextend', 'hydromad',
  'latticeExtra', 'daymetr', 'elevatr', 'Evapotranspiration'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'spatstat.core', 'spatstat.geom', 'spatstat.random'

Packages suggested but not available for checking:
  'future.apply', 'spatstat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dcmle', 'dclone'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'alakazam', 'doParallel', 'seqinr'

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

Package suggested but not available for checking: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rtop', 'ggpubr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘AER’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [32s/51s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ShiftShareSE)
  > 
  > test_check("ShiftShareSE")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 50 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_adh.R:28:5): Point estimates match Table 3 ──────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'AER'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_adh.R:28:4
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test_se.R:53:5): Homoscedastic and EHW standard errors on ADH data ───
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'AER'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_se.R:53:4
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 50 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'dygraphs', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) get_arg_help.Rd:12: \item in \describe must have non-empty label
checkRd: (7) get_desc_help.Rd:12: \item in \describe must have non-empty label
checkRd: (7) get_usage_help.Rd:12: \item in \describe must have non-empty label
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RSQLite’
Packages required but not available: 'brms', 'rstan'

Packages suggested but not available for checking:
  'cmdstanr', 'shinystan', 'rstanarm', 'lme4'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ShinyImage.Rcheck/00install.out’ for details.
Packages required but not available: 'mirt', 'irtoys'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'difR', 'lme4', 'mirt'

Packages suggested but not available for checking:
  'deltaPlotR', 'difNLR', 'latticeExtra', 'ltm', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'highcharter', 'plotly'
Running examples in ‘shinyjqui-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Interactions
> ### Title: Mouse interactions
> ### Aliases: Interactions jqui_draggable jqui_droppable jqui_resizable
> ###   jqui_selectable jqui_sortable
> 
> ### ** Examples
> 
> library(shiny)
> library(highcharter)
Error in library(highcharter) : there is no package called ‘highcharter’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 20-23 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'plotly'
--- failed re-building ‘introduction.Rmd’

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

--- re-building ‘save-and-restore.Rmd’ using rmarkdown
--- finished re-building ‘save-and-restore.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/shinyKGode.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘vroom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bit64', 'nanotime'

Package suggested but not available for checking: ‘RSQLite’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dygraphs', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'tune'

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

Package suggested but not available for checking: ‘chipPCR’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'styler'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'styler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dygraphs', 'showtext'
Packages suggested but not available for checking: 'leaflet', 'styler'
Packages required but not available: 'recipes', 'esquisse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'devtools', 'RSQLite'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/shiny.reglog.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'tm', 'wordcloud', 'caret', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘jsTreeR’
Packages suggested but not available for checking: 'leaflet', 'plotly'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/shinySIR.Rcheck/00install.out’ for details.
Packages required but not available: 'dygraphs', 'rstan', 'threejs', 'xts'

Packages suggested but not available for checking: 'cmdstanr', 'rstanarm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'ggpubr', 'TSA'

Package suggested but not available for checking: ‘thinkr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/shinytest2.Rcheck/00install.out’ for details.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
shrink.estim: no visible global function definition for ‘cov’
shrink.estim: no visible global function definition for ‘cor’
shrink.estim: no visible global function definition for ‘cov2cor’
targetCor: no visible global function definition for ‘cor.test’
targetCor: no visible global function definition for ‘cor’
targetCor: no visible global function definition for ‘sd’
targetCor: no visible global function definition for ‘cov’
targetD: no visible binding for global variable ‘var’
targetF: no visible global function definition for ‘cov’
targetF: no visible global function definition for ‘cor’
targetG: no visible global function definition for ‘cor’
targetG: no visible global function definition for ‘sd’
targetG: no visible global function definition for ‘cov’
targetGpos: no visible global function definition for ‘cor’
targetGpos: no visible global function definition for ‘sd’
targetGpos: no visible global function definition for ‘cov’
targetGstar: no visible global function definition for ‘cor’
targetGstar: no visible global function definition for ‘sd’
targetGstar: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cor cor.test cov cov2cor sd var
Consider adding
  importFrom("stats", "cor", "cor.test", "cov", "cov2cor", "sd", "var")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'ips', 'phangorn', 'StatMatch', 'vegan'
Running examples in ‘shipunov-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MrBayes
> ### Title: Calls MrBayes
> ### Aliases: MrBayes
> ### Keywords: interface
> 
> ### ** Examples
> 
> require(ips)
Loading required package: ips
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ips’
> data(ips.cox1)
Warning in data(ips.cox1) : data set ‘ips.cox1’ not found
> x <- ips.cox1[, 100:140]
Error: object 'ips.cox1' not found
Execution halted
Packages required but not available: 'capushe', 'GGMselect'

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

Package suggested but not available for checking: ‘tidyverse’

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

Package suggested but not available for checking: ‘mvoutlier’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/showtext.Rcheck/00install.out’ for details.
Package required but not available: ‘maptools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rms', 'mfp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package required but not available: ‘fastclime’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/shuffleCI.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘httptest’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("shutterstock")
  Loading required package: shutterstock
  Error in library(httptest) : there is no package called 'httptest'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Packages required but not available: 'hdrcde', 'spatstat'

Depends: includes the non-default packages:
  'hdrcde', 'coda', 'MASS', 'bayesm', 'mnormt', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'edgeR', 'doParallel'
Packages required but not available:
  'spatstat', 'hdrcde', 'rjags', 'spatstat.geom'

Packages suggested but not available for checking: 'tidyverse', 'viridis'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) get_sidra.Rd:102: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) info_sidra.Rd:31: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) search_sidra.Rd:28: invalid email address: <rpradosiqueira@gmail.com>
Packages required but not available: 'pcalg', 'RBGL'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘conjecture.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 195-199 (conjecture.Rmd) 
Error: processing vignette ‘conjecture.Rmd’ failed with diagnostics:
there is no package called 'readr'
--- failed re-building ‘conjecture.Rmd’

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

Error: Vignette re-building failed.
Execution halted
.cluster: no visible global function definition for ‘kmeans’
.plot.sigclust: no visible global function definition for ‘par’
.plot.sigclust: no visible global function definition for ‘density’
.plot.sigclust: no visible global function definition for ‘runif’
.plot.sigclust: no visible global function definition for ‘dnorm’
.plot.sigclust: no visible global function definition for ‘lines’
.plot.sigclust: no visible global function definition for ‘points’
.plot.sigclust: no visible global function definition for ‘title’
.plot.sigclust: no visible global function definition for ‘text’
.plot.sigclust: no visible global function definition for ‘qnorm’
.plot.sigclust: no visible global function definition for ‘abline’
.plot.sigclust: no visible global function definition for ‘quantile’
.plot.sigclust: no visible global function definition for ‘legend’
.simnull: no visible global function definition for ‘rnorm’
.vareigen: no visible global function definition for ‘mad’
.vareigen: no visible global function definition for ‘cov’
sigclust: no visible global function definition for ‘sd’
sigclust: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline cov density dnorm kmeans legend lines mad par pnorm points
  qnorm quantile rnorm runif sd text title
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "points",
             "text", "title")
  importFrom("stats", "cov", "density", "dnorm", "kmeans", "mad",
             "pnorm", "qnorm", "quantile", "rnorm", "runif", "sd")
to your NAMESPACE file.
Packages required but not available: 'msm', 'survey'

Packages suggested but not available for checking: 'car', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package vignette with placeholder title ‘Vignette Title’:
  ‘getting-started.Rmd’
Packages required but not available: 'furrr', 'ggpubr', 'NMF'

Packages suggested but not available for checking:
  'Biobase', 'Biostrings', 'BSgenome', 'BSgenome.Hsapiens.UCSC.hg19',
  'GenomicRanges', 'ggalluvial', 'ggcorrplot', 'ggrepel', 'IRanges',
  'R.utils', 'UCSCXenaTools', 'copynumber'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'GenomeInfoDb', 'GenomicRanges', 'IRanges', 'Rsamtools', 'S4Vectors',
  'Seurat', 'future.apply', 'irlba', 'ggrepel', 'lsa', 'ggforce',
  'qlcMatrix'

Packages suggested but not available for checking:
  'chromVAR', 'SummarizedExperiment', 'TFBSTools', 'motifmatchr',
  'BSgenome', 'rtracklayer', 'biovizBase', 'Biostrings'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'Seurat'

Package suggested but not available for checking: ‘hdf5r’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
signmedian.test: no visible global function definition for ‘median’
signmedian.test: no visible global function definition for ‘binom.test’
signmedian.test: no visible global function definition for ‘pbinom’
signmedian.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  binom.test median pbinom pnorm
Consider adding
  importFrom("stats", "binom.test", "median", "pbinom", "pnorm")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'ggraph', 'ROI.plugin.glpk'
Packages required but not available: 'survcomp', 'GSVA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggrepel’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘signs.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 18-23 (signs.Rmd) 
Error: processing vignette ‘signs.Rmd’ failed with diagnostics:
there is no package called 'ggrepel'
--- failed re-building ‘signs.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'phylobase', 'phyext2', 'phyloseq', 'vegan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CVXR', 'glmnet', 'scalreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'raster', 'ggforce', 'fasterize'

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SILGGM.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘trip’
Running ‘testthat.R’ [6s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(silicate)
  
  Attaching package: 'silicate'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("silicate")
  [ FAIL 2 | WARN 1 | SKIP 7 | PASS 110 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (5)
  • empty test (1)
  • no sp test for now (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-geometry-dim.R:19:3): dimensionality works ──────────────────────
  Error in `.requirePackage(package)`: unable to find required package 'trip'
  Backtrace:
      ▆
   1. ├─testthat::expect_named(TRI(.tr)$vertex, .trnames) at test-geometry-dim.R:19:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─silicate::TRI(.tr)
   5. └─methods:::.extendsForS3(`<chr>`)
   6.   └─methods::extends(Class, maybe = FALSE)
   7.     └─methods::getClassDef(class1)
   8.       └─methods:::.requirePackage(package)
  ── Error (test-trip.R:2:1): (code run outside of `test_that()`) ────────────────
  <packageNotFoundError/error/condition>
  Error in `library(trip)`: there is no package called 'trip'
  Backtrace:
      ▆
   1. └─base::library(trip) at test-trip.R:2:0
  
  [ FAIL 2 | WARN 1 | SKIP 7 | PASS 110 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'scalreg', 'glmnet', 'hdi', 'SIS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'hapsim', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘GGally’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/simboot.Rcheck/00install.out’ for details.
Packages required but not available: 'multcomp', 'mratios'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘multgee’
Running examples in ‘SimCorMultRes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rmult.acl
> ### Title: Simulating Correlated Ordinal Responses Conditional on a
> ###   Marginal Adjacent-Category Logit Model Specification
> ### Aliases: rmult.acl
> 
> ### ** Examples
> 
> ## See Example 3.4 in the Vignette.
> beta_intercepts <- c(3, 1, 2)
> beta_coefficients <- c(1, 1)
> sample_size <- 500
> cluster_size <- 3
> set.seed(321)
> x1 <- rep(rnorm(sample_size), each = cluster_size)
> x2 <- rnorm(sample_size * cluster_size)
> xdata <- data.frame(x1, x2)
> identity_matrix <- diag(4)
> equicorrelation_matrix <- toeplitz(c(1, rep(0.95, cluster_size - 1)))
> latent_correlation_matrix <- kronecker(equicorrelation_matrix,
+   identity_matrix)
> simulated_ordinal_dataset <- rmult.acl(clsize = cluster_size,
+   intercepts = beta_intercepts, betas = beta_coefficients,
+   xformula = ~ x1 + x2, xdata = xdata,
+   cor.matrix = latent_correlation_matrix)
> suppressPackageStartupMessages(library("multgee"))
Error in library("multgee") : there is no package called ‘multgee’
Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SimCorMultRes.Rmd’ using rmarkdown
Quitting from lines 72-107 (SimCorMultRes.Rmd) 
Error: processing vignette ‘SimCorMultRes.Rmd’ failed with diagnostics:
there is no package called 'multgee'
--- failed re-building ‘SimCorMultRes.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘SimMultiCorrData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package suggested but not available for checking: ‘doMPI’
Package required but not available: ‘alabama’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘FME’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/simecol.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/simEd.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SimEngine.Rcheck/00install.out’ for details.
Package required but not available: ‘cobs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plot3Drgl’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘kinship2’
Packages required but not available: 'bit64', 'future.apply'

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

Package suggested but not available for checking: ‘lme4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
Package required but not available: ‘furrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rvinecopulib', 'bde', 'ks', 'np'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘arm’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/simITS.Rcheck/00install.out’ for details.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
GNU make is a SystemRequirements.
Packages required but not available: 'plotly', 'ks', 'gganimate'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘simmer.plot’
Packages required but not available:
  'doParallel', 'Biostrings', 'BSgenome', 'GenomeInfoDb',
  'GenomicRanges', 'IRanges', 'XVector'

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R2jags', 'viridis'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Packages required but not available:
  'gRbase', 'graph', 'ggm', 'qpgraph', 'R.utils'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘simu.pheno’ ‘usedpars.txt’
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘RSQLite’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘verification’
Package required but not available: ‘SNPRelate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'leaflet', 'leafem', 'plotly', 'stars', 'viridis'

Packages suggested but not available for checking: 'pals', 'rgdal', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/simplexreg.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lme4’

Packages suggested but not available for checking:
  'tidyverse', 'readr', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'vcd', 'doParallel', 'VIM', 'party', 'fitdistrplus'

Package suggested but not available for checking: ‘haven’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'VIM', 'glmnet', 'missForest'
Packages required but not available: 'Biostrings', 'ShortRead'

Package suggested but not available for checking: ‘seqinr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘FrF2’

Package suggested but not available for checking: ‘DoE.base’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rgdal'

Packages suggested but not available for checking:
  'adehabitatLT', 'moveHMM', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'pbkrtest', 'RLRsim', 'car', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘kinship2’

Packages suggested but not available for checking: 'doParallel', 'doRNG'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'Hmisc', 'doParallel', 'fGarch'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Amelia', 'quantreg', 'semTools'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/simsem.Rcheck/00install.out’ for details.
Package required but not available: ‘future.apply’

Package suggested but not available for checking: ‘rjags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'hedgehog', 'gtsummary'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hedgehog)
  Error in library(hedgehog) : there is no package called 'hedgehog'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘clustered.Rmd’ using rmarkdown
--- finished re-building ‘clustered.Rmd’

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

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

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

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

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

--- re-building ‘simstudy.Rmd’ using rmarkdown
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
--- finished re-building ‘simstudy.Rmd’

--- re-building ‘spline.Rmd’ using rmarkdown
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
--- finished re-building ‘spline.Rmd’

--- re-building ‘survival.Rmd’ using rmarkdown
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Quitting from lines 315-316 (survival.Rmd) 
Error: processing vignette ‘survival.Rmd’ failed with diagnostics:
there is no package called 'gtsummary'
--- failed re-building ‘survival.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'raster', 'doParallel', 'plotly'

Packages suggested but not available for checking:
  'fields', 'viridis', 'lme4', 'INLA', 'rgdal', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Packages suggested but not available for checking: 'flexsurv', 'rstpm2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘simsurv_technical.Rmd’ using rmarkdown
--- finished re-building ‘simsurv_technical.Rmd’

--- re-building ‘simsurv_usage.Rmd’ using rmarkdown
Quitting from lines 15-23 (simsurv_usage.Rmd) 
Error: processing vignette ‘simsurv_usage.Rmd’ failed with diagnostics:
there is no package called 'flexsurv'
--- failed re-building ‘simsurv_usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'metafor', 'car'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'openair', 'raster'

Package suggested but not available for checking: ‘contoureR’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'SummarizedExperiment', 'SingleCellExperiment'
'LazyData' is specified without a 'data' directory
plotBGpvalues: no visible global function definition for ‘par’
plotBGpvalues: no visible global function definition for ‘title’
plotBGpvalues: no visible global function definition for ‘axis’
plotBGpvalues: no visible binding for global variable ‘abline’
plotBGpvalues: no visible global function definition for ‘box’
plotCGpvalues: no visible global function definition for ‘par’
plotCGpvalues: no visible global function definition for ‘title’
plotCGpvalues: no visible global function definition for ‘axis’
plotCGpvalues: no visible binding for global variable ‘abline’
plotCGpvalues: no visible global function definition for ‘box’
plotDAGpvalues: no visible global function definition for ‘par’
plotDAGpvalues: no visible global function definition for ‘title’
plotDAGpvalues: no visible global function definition for ‘axis’
plotDAGpvalues: no visible binding for global variable ‘abline’
plotDAGpvalues: no visible global function definition for ‘box’
plotUGpvalues: no visible global function definition for ‘par’
plotUGpvalues: no visible global function definition for ‘title’
plotUGpvalues: no visible global function definition for ‘axis’
plotUGpvalues: no visible binding for global variable ‘abline’
plotUGpvalues: no visible global function definition for ‘box’
simpvalueVec: no visible binding for global variable ‘pnorm’
sinBG: no visible global function definition for ‘cov2cor’
sinCG : sinAMP: no visible global function definition for ‘cov2cor’
sinCG : sinLWF: no visible global function definition for ‘cov2cor’
sinDAG: no visible global function definition for ‘cov2cor’
sinUG: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  abline axis box cov2cor par pnorm title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "par", "title")
  importFrom("stats", "cov2cor", "pnorm")
to your NAMESPACE file.
Packages required but not available:
  'COVIDIBGE', 'PNADcIBGE', 'PNSIBGE', 'POFIBGE'

Packages suggested but not available for checking:
  'convey', 'lavaan.survey', 'readr', 'srvyr', 'surf', 'survey',
  'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spatstat', 'spatstat.geom'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CDM', 'TAM'

Packages suggested but not available for checking:
  'lavaan.survey', 'miceadds', 'mirt', 'survey'

Package which this enhances but not available for checking: ‘immer’

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

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

Packages suggested but not available for checking: 'graph', 'Rgraphviz'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'expm', 'glmnet'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmulti', 'solaR', 'hyfo', 'hydroGOF', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sitree’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MCMCpack', 'msm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sjdbc.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'haven', 'sjPlot'
Running examples in ‘sjlabelled-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_labels
> ### Title: Add, replace or remove value labels of variables
> ### Aliases: add_labels replace_labels remove_labels
> 
> ### ** Examples
> 
> # add_labels()
> data(efc)
> get_labels(efc$e42dep)
[1] "independent"          "slightly dependent"   "moderately dependent"
[4] "severely dependent"  
> 
> x <- add_labels(efc$e42dep, labels = c(`nothing` = 5))
Error in get_na_helper(x, as.tag) : 
  Package 'haven' required for this function. Please install it.
Calls: add_labels ... add_labels_helper -> get_na -> get_na.default -> get_na_helper
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sjlabelled)
  > 
  > test_check("sjlabelled")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-remove_labels.R:6:3): remove_labels ─────────────────────────────
  Error in `get_na_helper(x, as.tag)`: Package 'haven' required for this function. Please install it.
  Backtrace:
      ▆
   1. └─sjlabelled::remove_labels(z, labels = 2) at test-remove_labels.R:6:2
   2.   └─sjlabelled:::remove_labels_helper(.dat, labels)
   3.     ├─sjlabelled::get_na(x)
   4.     └─sjlabelled:::get_na.default(x)
   5.       └─sjlabelled:::get_na_helper(x, as.tag)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking:
  'haven', 'sjPlot', 'sjstats'
Error(s) in re-building vignettes:
  ...
--- re-building ‘design_philosophy.Rmd’ using rmarkdown
Quitting from lines 38-47 (design_philosophy.Rmd) 
Error: processing vignette ‘design_philosophy.Rmd’ failed with diagnostics:
Package 'haven' required for this function. Please install it.
--- failed re-building ‘design_philosophy.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 80-88 (exploringdatasets.Rmd) 
Error: processing vignette ‘exploringdatasets.Rmd’ failed with diagnostics:
Package 'haven' required for this function. Please install it.
--- failed re-building ‘exploringdatasets.Rmd’

--- re-building ‘recodingvariables.Rmd’ using rmarkdown
Quitting from lines 202-233 (recodingvariables.Rmd) 
Error: processing vignette ‘recodingvariables.Rmd’ failed with diagnostics:
Package 'haven' required for this function. Please install it.
--- failed re-building ‘recodingvariables.Rmd’

SUMMARY: processing the following files failed:
  ‘design_philosophy.Rmd’ ‘exploringdatasets.Rmd’
  ‘recodingvariables.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘sjstats’

Packages suggested but not available for checking:
  'brms', 'car', 'haven', 'ggrepel', 'glmmTMB', 'lme4', 'nFactors',
  'rstanarm', 'survey'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Packages suggested but not available for checking:
  'brms', 'car', 'coin', 'sjPlot', 'survey', 'rstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'kinship2', 'corrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SKAT.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cvskda: no visible global function definition for ‘detectCores’
cvskda: no visible global function definition for ‘makeCluster’
cvskda: no visible global function definition for ‘clusterApplyLB’
cvskda: no visible global function definition for ‘mclapply’
cvskda: no visible global function definition for ‘stopCluster’
Undefined global functions or variables:
  clusterApplyLB detectCores makeCluster mclapply stopCluster
Packages required but not available: 'Rmpfr', 'quantreg', 'expm'

Packages suggested but not available for checking:
  'devtools', 'lmtest', 'car', 'tseries'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggrepel', 'furrr', 'haven'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'clusterGeneration', 'doParallel'

Package suggested but not available for checking: ‘sn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘haven’
Running ‘testthat.R’ [14s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(skimr)
  
  Attaching package: 'skimr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("skimr")
  [ FAIL 2 | WARN 0 | SKIP 25 | PASS 589 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (25)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-skim.R:671:3): skim handles objects containing haven_labelled vectors: double ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'haven'
  Backtrace:
      ▆
   1. ├─tibble::tibble(...) at test-skim.R:671:2
   2. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
   3. │   └─rlang::eval_tidy(xs[[j]], mask)
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base withOneRestart(expr, restarts[[1L]])
   7.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test-skim.R:716:3): skim handles objects containing haven_labelled vectors: character ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'haven'
  Backtrace:
      ▆
   1. ├─tibble::tibble(...) at test-skim.R:716:2
   2. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
   3. │   └─rlang::eval_tidy(xs[[j]], mask)
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base withOneRestart(expr, restarts[[1L]])
   7.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 25 | PASS 589 ]
  Error: Test failures
  Execution halted
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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/skm.Rcheck/00install.out’ for details.
Packages required but not available: 'modeltime', 'rsample', 'tune'

Packages suggested but not available for checking:
  'earth', 'recipes', 'timetk', 'workflowsets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'doParallel', 'doRNG', 'car', 'viridis', 'lmerTest'

Package suggested but not available for checking: ‘mbest’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'lcmm', 'globaltest', 'magic'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'fda.usc', 'cxxfunplus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'forecast', 'fGarch', 'imputeTS', 'MTS', 'TSclust',
  'tsoutliers'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
slcestimates: no visible global function definition for ‘par’
slcestimates: no visible global function definition for ‘abline’
slcestimates: no visible global function definition for ‘lines’
slcestimates: no visible global function definition for ‘axis’
slcestimates: no visible global function definition for ‘points’
slcestimates: no visible global function definition for ‘title’
Undefined global functions or variables:
  abline axis lines par points title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "points",
             "title")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sld.Rcheck/00install.out’ for details.
Package required but not available: ‘viridis’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sleev.Rcheck/00install.out’ for details.
Packages required but not available: 'Hmisc', 'doParallel', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'agricolae', 'car', 'mosaic'
Packages suggested but not available for checking:
  'CCA', 'Hmisc', 'agricolae', 'car', 'mosaic', 'multcomp'
Packages required but not available: 'fda', 'fdapace'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'alphahull', 'lle'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘leaflet’
Error(s) in re-building vignettes:
  ...
--- re-building ‘basics.Rmd’ using rmarkdown
--- finished re-building ‘basics.Rmd’

--- re-building ‘doms.Rmd’ using rmarkdown
Quitting from lines 82-91 (doms.Rmd) 
Error: processing vignette ‘doms.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
--- failed re-building ‘doms.Rmd’

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'PerformanceAnalytics', 'nonlinearTseries'

Packages suggested but not available for checking: 'xts', 'quantmod'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/slim.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'caret', 'glmnet'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [21s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(SLOPE)
  > 
  > test_check("SLOPE")
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 157 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-caret-training.R:4:3): model training with caret works ──────────
  <packageNotFoundError/error/condition>
  Error in `library(caret)`: there is no package called 'caret'
  Backtrace:
      ▆
   1. └─base::library(caret) at test-caret-training.R:4:2
  ── Error (test-lasso.R:10:3): lasso and slope fits are equivalent if all lambda are equal ──
  <packageNotFoundError/error/condition>
  Error in `library(glmnet)`: there is no package called 'glmnet'
  Backtrace:
      ▆
   1. └─base::library(glmnet) at test-lasso.R:10:2
  ── Error (test-multinomial.R:22:3): glmnet and SLOPE return same unpenalized model ──
  <packageNotFoundError/error/condition>
  Error in `library(glmnet)`: there is no package called 'glmnet'
  Backtrace:
      ▆
   1. └─base::library(glmnet) at test-multinomial.R:22:2
  ── Error (test-poisson.R:44:3): SLOPE reproduces lasso fit when all lambda are equal ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'glmnet'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-poisson.R:44:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 157 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘gam’
Running examples in ‘slp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: slp.gam
> ### Title: Generate a Basis Matrix for Discrete Prolate Spheroidal
> ###   (Slepian) Sequences
> ### Aliases: slp.gam slp
> ### Keywords: models smooth regression Slepian gam
> 
> ### ** Examples
> 
>     # Examples using pkg:gam
>     library("gam")
Error in library("gam") : there is no package called ‘gam’
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Hmisc', 'weights', 'wordcloud', 'candisc', 'doParallel'

Packages suggested but not available for checking: 'prefmod', 'calibrate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat.geom', 'spatstat.random', 'spatstat.core', 'smerc'

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

Package suggested but not available for checking: ‘sdcHierarchies’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'doSNOW'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

Package suggested but not available for checking: ‘rgdal’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'bootSVD', 'Rfast', 'vegan', 'vroom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sva', 'isva'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sqldf', 'partykit', 'gsubfn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘smco/R/smco.R’:
  .onAttach calls:
    cat(paste("This is smco package", version, "\n"))

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in ‘?.onAttach’.

smco: no visible global function definition for ‘runif’
smco: no visible global function definition for ‘rnorm’
smco: no visible global function definition for ‘qnorm’
smco: no visible global function definition for ‘pnorm’
smco: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "optim", "pnorm", "qnorm", "rnorm", "runif")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smcure.Rcheck/00install.out’ for details.
Packages required but not available: 'GSVA', 'survminer'

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

Package suggested but not available for checking: ‘SpatialEpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SMFI5.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smfishHmrf.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smfsb.Rcheck/00install.out’ for details.
Packages required but not available: 'lme4', 'Hmisc', 'weights'

Packages suggested but not available for checking:
  'mlmRev', 'R.rsp', 'Kernelheaping'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
lines.SmithWilsonYieldCurve: no visible global function definition for
  ‘lines’
points.SmithWilsonYieldCurve: no visible global function definition for
  ‘points’
Undefined global functions or variables:
  lines points
Consider adding
  importFrom("graphics", "lines", "points")
to your NAMESPACE file.
Package required but not available: ‘Biostrings’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘SMITIDstruct’
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'seqinr', 'DiscreteWeibull'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DiscreteWeibull', 'seqinr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SSN', 'RSQLite'

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

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

Package suggested but not available for checking: ‘rPython’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantreg', 'lmtest'

Package suggested but not available for checking: ‘demography’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'prodlim', 'lava'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smoothHR.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'SpatialVx', 'fields'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smoothmest.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'legion', 'doMC', 'doParallel'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smooth.Rcheck/00install.out’ for details.
Package required but not available: ‘ks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rgeos'

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

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

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

Package suggested but not available for checking: ‘fGarch’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SMPracticals.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘gam’
Malformed Description field: should contain one or more complete sentences.
dNMR: no visible global function definition for ‘pnorm’
dNMR: no visible global function definition for ‘dnorm’
pNMR: no visible global function definition for ‘pnorm’
pNMR: no visible global function definition for ‘dnorm’
rMR: no visible global function definition for ‘rnorm’
rMR: no visible global function definition for ‘rchisq’
Undefined global functions or variables:
  dnorm pnorm rchisq rnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm", "rchisq", "rnorm")
to your NAMESPACE file.
checkRd: (7) SMR.Rd:79: invalid email address: <danielff@dex.ufla.br>
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'catdata', 'glmnet', 'speedglm'

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

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

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

Package suggested but not available for checking: ‘ggforce’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sna.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘sn’
'LazyData' is specified without a 'data' directory
Running examples in ‘snem-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: snem
> ### Title: EM algorithm for multivariate skew normal distribution.
> ### Aliases: snem
> 
> ### ** Examples
> 
> library(sn)
Error in library(sn) : there is no package called ‘sn’
Execution halted
Package required but not available: ‘prodlim’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'leaflet', 'plotly'
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/snowfall.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/snowFT.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
KS.test: no visible global function definition for ‘quantile’
KS.test : Fgaus: no visible global function definition for ‘pnorm’
KS.test: no visible global function definition for ‘setNames’
cs.test: no visible global function definition for ‘pbinom’
cs.test: no visible global function definition for ‘pnorm’
cs.test: no visible global function definition for ‘setNames’
kde: no visible global function definition for ‘quantile’
kde : Fgaus: no visible global function definition for ‘pnorm’
kde: no visible global function definition for ‘par’
kre: no visible global function definition for ‘quantile’
kre: no visible global function definition for ‘lines’
ns.test: no visible global function definition for ‘complete.cases’
ns.test: no visible global function definition for ‘qnorm’
ns.test: no visible global function definition for ‘pnorm’
ns.test: no visible global function definition for ‘pchisq’
ns.test: no visible global function definition for ‘setNames’
ns.test: no visible global function definition for ‘qt’
quant.test: no visible global function definition for ‘complete.cases’
quant.test: no visible global function definition for ‘pbinom’
quant.test: no visible global function definition for ‘pnorm’
quant.test: no visible global function definition for ‘setNames’
quant.test: no visible global function definition for ‘quantile’
quant.test: no visible global function definition for ‘phyper’
runs.test: no visible global function definition for ‘median’
runs.test: no visible global function definition for ‘setNames’
runs.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  complete.cases lines median par pbinom pchisq phyper pnorm qnorm qt
  quantile setNames
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "complete.cases", "median", "pbinom", "pchisq",
             "phyper", "pnorm", "qnorm", "qt", "quantile", "setNames")
to your NAMESPACE file.
Packages required but not available:
  'haplo.stats', 'Biostrings', 'VariantAnnotation',
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'GenomicRanges', 'IRanges',
  'S4Vectors', 'org.Hs.eg.db'

Packages suggested but not available for checking:
  'biomaRt', 'SNPlocs.Hsapiens.dbSNP144.GRCh38',
  'MafDb.1Kgenomes.phase3.GRCh38', 'BSgenome.Hsapiens.NCBI.GRCh38',
  'GenomicScores', 'BSgenome'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'vcfR', 'adegenet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘doParallel’
Packages required but not available: 'RSQLite', 'biomaRt', 'R.utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'future.apply', 'ggrepel', 'ks'

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

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

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

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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’
Packages required but not available: 'DoE.base', 'FrF2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FactoMineR', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘wpp2015’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
calculate.areas: no visible global function definition for ‘runif’
calculate.gradedareas: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Packages required but not available: 'tidyverse', 'devtools'

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

Package suggested but not available for checking: ‘tigris’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sodavis.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Sofi.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/softclassval.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/softImpute.Rcheck/00install.out’ for details.
Packages required but not available:
  'arm', 'caret', 'Cubist', 'FuzzyAHP', 'Hmisc', 'quantregForest',
  'raster', 'rgdal'

Package suggested but not available for checking: ‘maptools’

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

Packages suggested but not available for checking:
  'rgdal', 'odbc', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'snowfall', 'Rmpfr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) Kcap.Rd:28-31: \item in \describe must have non-empty label
checkRd: (7) Kfilm.Rd:29-31: \item in \describe must have non-empty label
checkRd: (7) Ku.Rd:38-41: \item in \describe must have non-empty label
checkRd: (7) Ku.Rd:42-45: \item in \describe must have non-empty label
checkRd: (7) SEM.Rd:49: \item in \describe must have non-empty label
checkRd: (7) SEM.Rd:50: \item in \describe must have non-empty label
checkRd: (7) SEM.Rd:51: \item in \describe must have non-empty label
checkRd: (7) SWC.Rd:43-44: \item in \describe must have non-empty label
checkRd: (7) SWC.Rd:45-49: \item in \describe must have non-empty label
checkRd: (7) Sad.Rd:28-30: \item in \describe must have non-empty label
checkRd: (7) Sat.Rd:31-34: \item in \describe must have non-empty label
checkRd: (7) Sat_old.Rd:26-29: \item in \describe must have non-empty label
checkRd: (7) Scap.Rd:27-31: \item in \describe must have non-empty label
checkRd: (7) dataSEM.Rd:18: \item in \describe must have non-empty label
checkRd: (7) dataSEM.Rd:19: \item in \describe must have non-empty label
checkRd: (7) dataSEM.Rd:20: \item in \describe must have non-empty label
checkRd: (7) dataSHP.Rd:18: \item in \describe must have non-empty label
checkRd: (7) dataSHP.Rd:19: \item in \describe must have non-empty label
checkRd: (7) dataSHP.Rd:20: \item in \describe must have non-empty label
checkRd: (7) dataTestthat.Rd:19: \item in \describe must have non-empty label
checkRd: (7) dataTestthat.Rd:20: \item in \describe must have non-empty label
checkRd: (7) dataTestthat.Rd:21: \item in \describe must have non-empty label
checkRd: (7) dataTestthat.Rd:22: \item in \describe must have non-empty label
checkRd: (7) dataTestthat.Rd:23: \item in \describe must have non-empty label
checkRd: (7) dataTestthat.Rd:24: \item in \describe must have non-empty label
checkRd: (7) dataTestthat.Rd:25: \item in \describe must have non-empty label
checkRd: (7) dataTestthat.Rd:26: \item in \describe must have non-empty label
Package required but not available: ‘fields’

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

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

Package suggested but not available for checking: ‘FME’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘raster’
Package required but not available: ‘PAutilities’

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

Packages suggested but not available for checking:
  'raster', 'rasterVis', 'tdr', 'meteoForecast'

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

Packages suggested but not available for checking:
  'tidyverse', 'uwot', 'rsample'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘SolveRationalMatrixEquation.Rmd’
soma: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages required but not available: 'ggwordcloud', 'metR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
bm: no visible global function definition for ‘rnorm’
bm: no visible global function definition for ‘ts’
fbm: no visible global function definition for ‘fft’
fbm: no visible global function definition for ‘rnorm’
fbm: no visible global function definition for ‘ts’
gbm: no visible global function definition for ‘rnorm’
gbm: no visible global function definition for ‘ts’
Undefined global functions or variables:
  fft rnorm ts
Consider adding
  importFrom("stats", "fft", "rnorm", "ts")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘openair’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘orthopolynom’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sommer.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/somplot.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘Hmisc’
Error(s) in re-building vignettes:
  ...
--- re-building ‘SongEvo.Rmd’ using rmarkdown
Quitting from lines 158-159 (SongEvo.Rmd) 
Error: processing vignette ‘SongEvo.Rmd’ failed with diagnostics:
there is no package called 'Hmisc'
--- failed re-building ‘SongEvo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘devtools’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sonify.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘elasticnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SOPIE.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘SpATS’
Running examples in ‘SOP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rae
> ### Title: Defining random effects in SOP formula
> ### Aliases: rae
> ### Keywords: models smooth regression
> 
> ### ** Examples
> 
> library(SOP)
> require(SpATS)
Loading required package: SpATS
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘SpATS’
> ## An example of use of SOP package for the analysis of field trials experiments.
> ## Taken from the SpATS package.
> data(wheatdata)
Warning in data(wheatdata) : data set ‘wheatdata’ not found
> 
> # Create factor variable for row and columns
> wheatdata$R <- as.factor(wheatdata$row)
Error in is.factor(x) : object 'wheatdata' not found
Calls: as.factor -> is.factor
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/soptdmaeA.Rcheck/00install.out’ for details.
Package required but not available: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SOR.Rcheck/00install.out’ for details.
Packages required but not available: 'Hmisc', 'quantreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
convert_municipality_names: no visible global function definition for
  ‘read.csv’
regression_plot: no visible binding for global variable ‘loess’
regression_plot: no visible global function definition for
  ‘colorRampPalette’
regression_plot: no visible global function definition for
  ‘loess.control’
regression_plot: no visible global function definition for ‘predict’
regression_plot : <anonymous>: no visible global function definition
  for ‘quantile’
regression_plot : <anonymous>: no visible global function definition
  for ‘pnorm’
regression_plot: no visible global function definition for
  ‘flush.console’
regression_plot: no visible global function definition for ‘density’
Undefined global functions or variables:
  colorRampPalette density flush.console loess loess.control pnorm
  predict quantile read.csv
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "density", "loess", "loess.control", "pnorm",
             "predict", "quantile")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sos.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'devtools', 'ggrepel'
Package required but not available: ‘RSQLite’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘SciencesPo’

Package which this enhances but not available for checking: ‘RecordLinkage’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dtw', 'doParallel'

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

Package suggested but not available for checking: ‘vegan’

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

Packages suggested but not available for checking: 'rstan', 'DropletUtils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gRbase', 'graph'

Packages suggested but not available for checking:
  'Rgraphviz', 'r2cytoscape', 'Biobase', 'graphite', 'hgu95av2.db',
  'ALL', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'furrr', 'lmtest', 'strucchange', 'xts'

Package suggested but not available for checking: ‘quantmod’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘vegan’
Packages required but not available:
  'crsuggest', 'ggraph', 'spatstat.random', 'spatstat.geom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rfast', 'sna', 'vegan'

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

Packages suggested but not available for checking:
  'adehabitatLT', 'cshapes', 'gstat', 'mapdata', 'maptools', 'plm',
  'raster', 'rgdal', 'rgeos', 'RPostgreSQL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rayshader', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package required but not available: ‘mapproj’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'devtools', 'reproducible', 'SpaDES.core'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quickPlot', 'reproducible', 'raster'

Packages suggested but not available for checking:
  'DiagrammeR', 'future.callr', 'RandomFields', 'rgdal', 'SpaDES.tools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'quickPlot', 'reproducible', 'SpaDES.core', 'SpaDES.tools'

Package suggested but not available for checking: ‘SpaDES.addins’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CircStats', 'quickPlot', 'raster', 'rgeos'

Packages suggested but not available for checking:
  'fasterize', 'ff', 'ffbase', 'gdalUtils', 'RandomFields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'earlywarnings', 'np'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'spatstat.geom', 'spatstat.core', 'spatstat.linnet',
  'spatstat.random', 'spatstat', 'RandomFields', 'sparr'

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

Packages suggested but not available for checking:
  'lme4', 'pedigreemm', 'future.apply', 'multilevel', 'Infusion',
  'IsoriX', 'blackbox', 'ROI.plugin.glpk'

Packages which this enhances but not available for checking:
  'multcomp', 'RLRsim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'fields', 'R.rsp', 'truncdist'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Running examples in ‘spam-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: covmat
> ### Title: Covariance functions
> ### Aliases: covmat cov.exp cov.sph cor.sph cov.nug cov.wu1 cov.wu2 cov.wu3
> ###   cov.wend1 cov.wend2 cov.mat
> ### Keywords: algebra
> 
> ### ** Examples
> 
> set.seed(123)
> n <- 200
> locs <- cbind(runif(n),runif(n))
> h <- nearest.dist(locs, delta=sqrt(2), upper = NULL)
> Sigma <- cov.sph(h, c(.3, 1, .1))
> 
> iidsample <- rnorm(n)
> cholS <- chol.spam(as.spam(Sigma))
> iorder <- iord <- ordering(cholS, inv = TRUE)
> sample <- (iidsample %*% as.spam(cholS))[iorder]
> plot(locs, col = fields::tim.colors(n = 256)[cut(sample, n)], pch = 20)
Error in loadNamespace(x) : there is no package called ‘fields’
Calls: plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Errors in running code in vignettes:
when running code in ‘spam.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘spam.Rmd’ using ‘UTF-8’... failed to complete the test
hausman: no visible global function definition for ‘pchisq’
span.formula: no visible global function definition for ‘model.frame’
span.formula: no visible global function definition for ‘model.matrix’
span.formula: no visible global function definition for
  ‘model.response’
spbe: no visible global function definition for ‘cor’
spbe: no visible global function definition for ‘pt’
spfe: no visible global function definition for ‘cor’
spfe: no visible global function definition for ‘pt’
sprandom: no visible global function definition for ‘cor’
sprandom: no visible global function definition for ‘pt’
summary.span: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  cor model.frame model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "pchisq", "printCoefmat", "pt")
to your NAMESPACE file.
Packages required but not available: 'expm', 'smoother', 'fields', 'irlba'

Package suggested but not available for checking: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘arrow’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SPARQL.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
f.I2.cont: no visible global function definition for ‘combn’
f.I2.dich: no visible global function definition for ‘combn’
f.pstar.cont: no visible global function definition for ‘combn’
f.pstar.dich: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Packages required but not available:
  'doFuture', 'doRNG', 'fields', 'raster', 'sparr', 'spatstat.geom',
  'spatstat.random'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat', 'spatstat.geom', 'spatstat.core', 'spatstat.random',
  'doParallel'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'graph', 'RCy3'
Packages unavailable to check Rd xrefs: ‘RCy3’, ‘graph’
Unknown package ‘sparsebn’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SparseFactorAnalysis.Rcheck/00install.out’ for details.
Package required but not available: ‘refund’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘glmnet’
Running ‘testthat.R’ [5s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sparsegl)
  > 
  > test_check("sparsegl")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 42 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-predict.R:1:1): (code run outside of `test_that()`) ─────────────
  <packageNotFoundError/error/condition>
  Error in `library(glmnet)`: there is no package called 'glmnet'
  Backtrace:
      ▆
   1. └─base::library(glmnet) at test-predict.R:1:0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 42 ]
  Error: Test failures
  Execution halted
Malformed Description field: should contain one or more complete sentences.
Skipping vignette re-building
Packages suggested but not available for checking: 'R.rsp', 'xts'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Running examples in ‘sparseIndexTracking-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: spIndexTrack
> ### Title: Sparse Index Tracking
> ### Aliases: spIndexTrack
> 
> ### ** Examples
> 
> library(sparseIndexTracking)
> library(xts)
Error in library(xts) : there is no package called ‘xts’
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'elasticnet', 'mda'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'future.apply', 'tidyverse', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sparsenet.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'msm', 'MCMCpack', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sparsestep.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘longitudinal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'glmnet', 'picasso'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'selectiveInference', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'FactoMineR', 'plotly', 'fpc', 'ks', 'rgdal', 'maptools', 'leaflet',
  'mapview'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat', 'spatstat.geom', 'spatstat.core', 'spatstat.linnet',
  'spatstat.random'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Starting.Rmd’
Package suggested but not available for checking: ‘RandomFields’
Packages required but not available:
  'raster', 'spatstat.geom', 'spatstat.core', 'spdep', 'rgeos'

Packages suggested but not available for checking:
  'exactextractr', 'readr', 'rms', 'SpatialPack', 'maptools',
  'GeNetIt', 'gstat', 'RStoolbox', 'tabularaster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'maptools', 'spdep'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'fields'

Packages suggested but not available for checking:
  'INLA', 'geoR', 'SDraw', 'tmap', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
Packages required but not available: 'rgeos', 'splancs'

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

Packages suggested but not available for checking: 'tmap', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SpatialML.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spatialnbda.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'ICSNP', 'MNM'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SpatialPack.Rcheck/00install.out’ for details.
Package required but not available: ‘raster’

Packages suggested but not available for checking:
  'doParallel', 'cartography'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid NAMESPACE file, parsing gives:
Error in packageVersion("spdep"): there is no package called ‘spdep’

See section ‘Package namespaces’ in the ‘Writing R Extensions’ manual.
Packages required but not available:
  'spdep', 'quantreg', 'GWmodel', 'plm', 'spatialreg'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spData', 'spdep', 'expm'

Packages suggested but not available for checking: 'tmap', 'lmtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'leafem', 'leafgl', 'leaflet', 'tmap', 'viridis'

Packages suggested but not available for checking:
  'automap', 'gstat', 'vroom'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat.geom', 'spatstat.core', 'furrr', 'ggpubr', 'viridis'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat', 'fields', 'turboEM', 'spatstat.geom', 'spatstat.core',
  'spatstat.linnet', 'CircStats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'future.apply', 'segmented'

Packages suggested but not available for checking:
  'acss', 'gstat', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘doParallel’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spatPomp.Rcheck/00install.out’ for details.
Packages required but not available: 'rgeos', 'adehabitatHR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'plot3Drgl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat.geom', 'spatstat.random', 'spatstat.sparse'

Packages suggested but not available for checking:
  'maptools', 'RandomFields', 'spatstat.linnet', 'spatstat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'spatstat.geom', 'spatstat.random', 'spatstat.core',
  'spatstat.linnet'
Packages suggested but not available for checking:
  'spatstat.core', 'spatstat.random', 'spatstat.linnet', 'maptools',
  'spatstat'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spatstat.geom.Rcheck/00install.out’ for details.
Packages required but not available:
  'spatstat.geom', 'spatstat.random', 'spatstat.core',
  'spatstat.linnet', 'spatstat'

Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.core',
  'spatstat.linnet', 'spatstat.data', 'spatstat', 'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat.sparse', 'spatstat.geom', 'spatstat.random',
  'spatstat.core', 'spatstat.linnet', 'spatstat'

Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat.geom', 'spatstat.random', 'spatstat.core',
  'spatstat.sparse'

Package suggested but not available for checking: ‘spatstat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat.sparse', 'spatstat.geom', 'spatstat.random',
  'spatstat.core', 'spatstat'

Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

Packages suggested but not available for checking:
  'RandomFields', 'spatstat.linnet', 'spatstat.core', 'spatstat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat.geom', 'spatstat.random', 'spatstat.core',
  'spatstat.linnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spatstat.sparse.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘spatstat.core’
Packages required but not available:
  'spatstat.core', 'spatstat.geom', 'spatstat.random', 'spatstat',
  'raster', 'RandomFields', 'fields', 'rgeos'

Packages suggested but not available for checking: 'rgdal', 'OpenStreetMap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'maptools', 'raster', 'trip', 'viridis'
Package required but not available: ‘magic’

Package suggested but not available for checking: ‘geoR’

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

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

Package suggested but not available for checking: ‘womblR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘LS2Wstat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SPCALDA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SPCAvRP.Rcheck/00install.out’ for details.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rgdal’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spcosa.Rcheck/00install.out’ for details.
GenerateCliquesCovariance: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Package required but not available: ‘msm’

Package suggested but not available for checking: ‘womblR’

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

Packages suggested but not available for checking:
  'maptools', 'rgdal', 'spDataLarge', 'spdep', 'spatialreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rcarbon', 'gdistance', 'raster', 'gstat'

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

Packages suggested but not available for checking:
  'spatialreg', 'rgeos', 'maptools', 'rgdal', 'tmap', 'rgeoda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'maptools', 'raster'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spdplyr.Rcheck/00install.out’ for details.
Packages required but not available: 'forecast', 'separationplot'

Package suggested but not available for checking: ‘devtools’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mQTL', 'doSNOW', 'Rfast', 'missForest'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
bartlett: no visible global function definition for ‘pchisq’
local.rbfdot: no visible binding for global variable ‘sd’
local.rbfdot: no visible global function definition for ‘dist’
local.rbfdot : <anonymous>: no visible global function definition for
  ‘median’
speccalt: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  dist kmeans median pchisq sd
Consider adding
  importFrom("stats", "dist", "kmeans", "median", "pchisq", "sd")
to your NAMESPACE file.
Packages required but not available: 'gsubfn', 'splancs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'imager', 'tidyverse', 'mrbsizeR'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggraph', 'lme4'

Package suggested but not available for checking: ‘tidyverse’

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

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'calendR', 'httptest'
Packages required but not available: 'NMF', 'plotly', 'viridis', 'hNMF'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'CVXR', 'R.rsp', 'pals', 'clusterSim', 'viridis'

VignetteBuilder packages required for checking but not installed:
  'CVXR', 'R.rsp'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spectralGraphTopology.Rcheck/00install.out’ for details.
Package required but not available: ‘fields’

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

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

Package suggested but not available for checking: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ClusterR', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘raster’
Package required but not available: ‘httptest’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/speedglm.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'labelled', 'readroper'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/speff2trial.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SPEI.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘spdep’

Package suggested but not available for checking: ‘gstat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quadmesh', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘refund’
Package suggested but not available for checking: ‘spdep’
Running examples in ‘spflow-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sp_network_nodes
> ### Title: Create a 'sp_network_nodes-class()'
> ### Aliases: sp_network_nodes
> 
> ### ** Examples
> 
> sp_network_nodes("germany",
+                  spdep::nb2mat(spdep::poly2nb(germany_grid)),
+                  as.data.frame(germany_grid),
+                  "ID_STATE")
Error in loadNamespace(x) : there is no package called ‘spdep’
Calls: sp_network_nodes ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘paris_commute_flows.Rmd’ using rmarkdown
Linking to GEOS 3.10.2, GDAL 3.4.2, PROJ 9.0.0; sf_use_s2() is TRUE
Quitting from lines 21-24 (paris_commute_flows.Rmd) 
Error: processing vignette ‘paris_commute_flows.Rmd’ failed with diagnostics:
there is no package called 'spdep'
--- failed re-building ‘paris_commute_flows.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘mlr’

Package suggested but not available for checking: ‘caret’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rgdal’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spgrass6.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘seqinr’
Package required but not available: ‘spData’

Packages suggested but not available for checking:
  'spdep', 'maptools', 'rgdal'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spatialreg', 'spdep', 'spData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doFuture', 'rotasym'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'genlasso'

Package suggested but not available for checking: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘robotstxt’
Package required but not available: ‘pegas’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rworldmap', 'rworldxtra'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MCMCpack', 'R2WinBUGS'

Package suggested but not available for checking: ‘mboost’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gganimate', 'plotly', 'Rdimtools'

Package suggested but not available for checking: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SPIn.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'ComplexHeatmap', 'grImport', 'dendextend'
Package unavailable to check Rd xrefs: ‘ComplexHeatmap’
Running examples in ‘spiralize-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: phylo_to_dendrogram
> ### Title: Convert a phylo object to a dendrogram object
> ### Aliases: phylo_to_dendrogram
> 
> ### ** Examples
> 
> require(ape)
Loading required package: ape
> data(bird.families)
> d = phylo_to_dendrogram(bird.families)
> 
> require(ComplexHeatmap)
Loading required package: ComplexHeatmap
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ComplexHeatmap’
> grid.dendrogram(d, test = TRUE)
Error in grid.dendrogram(d, test = TRUE) : 
  could not find function "grid.dendrogram"
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

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

Package suggested but not available for checking: ‘spdep’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ChainLadder’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SPLICE.Rcheck/00install.out’ for details.
Packages required but not available: 'mosaic', 'treeClust'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/splitFeas.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmnet’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(SplitGLM)
  > 
  > test_check("SplitGLM")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_cv_function.R:8:1): (code run outside of `test_that()`) ─────────
  <packageNotFoundError/error/condition>
  Error in `library(glmnet)`: there is no package called 'glmnet'
  Backtrace:
      ▆
   1. └─base::library(glmnet) at test_cv_function.R:8:0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘glmnet’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(SplitReg)
  > 
  > test_check("SplitReg")
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_CV.R:1:1): (code run outside of `test_that()`) ──────────────────
  <packageNotFoundError/error/condition>
  Error in `library(glmnet)`: there is no package called 'glmnet'
  Backtrace:
      ▆
   1. └─base::library(glmnet) at test_CV.R:1:0
  ── Error (test_glmnet.R:1:1): (code run outside of `test_that()`) ──────────────
  <packageNotFoundError/error/condition>
  Error in `library(glmnet)`: there is no package called 'glmnet'
  Backtrace:
      ▆
   1. └─base::library(glmnet) at test_glmnet.R:1:0
  ── Error (test_obj_decrease.R:3:1): (code run outside of `test_that()`) ────────
  <packageNotFoundError/error/condition>
  Error in `library(glmnet)`: there is no package called 'glmnet'
  Backtrace:
      ▆
   1. └─base::library(glmnet) at test_obj_decrease.R:3:0
  ── Error (test_pred_method.R:1:1): (code run outside of `test_that()`) ─────────
  <packageNotFoundError/error/condition>
  Error in `library(glmnet)`: there is no package called 'glmnet'
  Backtrace:
      ▆
   1. └─base::library(glmnet) at test_pred_method.R:1:0
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'multicool', 'glmnet', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'emulator', 'penalized'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid NAMESPACE file, parsing gives:
Error in packageVersion("spdep"): there is no package called ‘spdep’

See section ‘Package namespaces’ in the ‘Writing R Extensions’ manual.
checkRd: (7) event.Rd:13-16: \item in \arguments must have non-empty label
checkRd: (7) groupvec.Rd:13-16: \item in \arguments must have non-empty label
checkRd: (7) numseq.Rd:13-16: \item in \arguments must have non-empty label
checkRd: (7) options.Rd:24-27: \item in \describe must have non-empty label
checkRd: (7) timedate.Rd:15-18: \item in \arguments must have non-empty label
checkRd: (7) timespan.Rd:13-17: \item in \arguments must have non-empty label
checkRd: (7) timzns.Rd:19-22: \item in \arguments must have non-empty label
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/splusTimeSeries.Rcheck/00install.out’ for details.
Packages required but not available: 'spm', 'gstat', 'fields', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rgeos'

Package suggested but not available for checking: ‘antaresViz’

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

Packages suggested but not available for checking: 'R.rsp', 'rgdal'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gstat', 'biomod2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spdep', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat.geom', 'spatstat.core', 'spatstat.linnet', 'spatstat',
  'leaflet', 'raster', 'maptools', 'rgdal', 'prodlim'

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

Packages suggested but not available for checking: 'tmap', 'smoothr'

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

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

Package suggested but not available for checking: ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'doParallel', 'spBayes'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'readr', 'imputeTS', 'modeest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘archetypes’
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fetch_NBAPlayerStatistics: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Package required but not available: ‘CausalImpact’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'smoof', 'SPOT', 'plotly'

Package suggested but not available for checking: ‘devtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'benchmarkme', 'mlr', 'plotly', 'rpart.plot', 'smoof', 'SPOT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggrepel', 'ggbeeswarm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'laGP', 'plgp', 'plotly'

Packages suggested but not available for checking:
  'babsim.hospital', 'car', 'farff', 'party', 'readr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rgeoda', 'rsample', 'spatialreg', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'magic', 'disordR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rgdal', 'rgeos', 'gstat', 'maptools'
Running examples in ‘sp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: disaggregate-methods
> ### Title: disaggregate SpatialLines, SpatialLinesDataFrame,
> ###   SpatialPolygons, or SpatialPolygonsDataFrame objects
> ### Aliases: disaggregate disaggregate-methods
> ###   disaggregate,SpatialPolygons-method
> ###   disaggregate,SpatialPolygonsDataFrame-method
> ###   disaggregate,SpatialLines-method
> ###   disaggregate,SpatialLinesDataFrame-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> Sr1 = Polygon(cbind(c(2,4,4,1,2),c(2,3,5,4,2)), hole = FALSE)
> Sr2 = Polygon(cbind(c(5,4,2,5),c(2,3,2,2)), hole = FALSE)
> Sr3 = Polygon(cbind(c(4,4,5,10,4),c(5,3,2,5,5)), hole = FALSE)
> Sr4 = Polygon(cbind(c(5,6,6,5,5),c(4,4,3,3,4)), hole = TRUE)
> 
> Srs1 = Polygons(list(Sr1, Sr2), "s1/2")
> Srs3 = Polygons(list(Sr3, Sr4), "s3/4")
> sp = SpatialPolygons(list(Srs1,Srs3), 1:2)
> length(sp) ## [1] 2
[1] 2
> length(disaggregate(sp)) ## [1] 3 
Error in explodePolygons(x, ...) : 
  package rgeos is needed to relate holes to their corresponding polygons
Calls: disaggregate -> disaggregate -> explodePolygons
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CRS_warnings.Rmd’ using rmarkdown
--- finished re-building ‘CRS_warnings.Rmd’

--- re-building ‘csdacm.Rnw’ using Sweave

Error: processing vignette ‘csdacm.Rnw’ failed with diagnostics:
 chunk 70 
Error in library(gstat) : there is no package called ‘gstat’

--- failed re-building ‘csdacm.Rnw’

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

--- re-building ‘over.Rnw’ using Sweave

Error: processing vignette ‘over.Rnw’ failed with diagnostics:
 chunk 10 
Error in over(pol, pol, returnList = TRUE) : 
  package rgeos is required for additional over methods

--- failed re-building ‘over.Rnw’

SUMMARY: processing the following files failed:
  ‘csdacm.Rnw’ ‘over.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'gganimate', 'ggraph'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spreadr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SPREDA.Rcheck/00install.out’ for details.
Package required but not available: ‘sn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fields’
Running examples in ‘spreval-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: catchcan
> ### Title: catch can data
> ### Aliases: catchcan
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(fields) # for easy grid construction
Error in library(fields) : there is no package called ‘fields’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘landscape.Rmd’ using rmarkdown
Quitting from lines 45-56 (landscape.Rmd) 
Error: processing vignette ‘landscape.Rmd’ failed with diagnostics:
there is no package called 'fields'
--- failed re-building ‘landscape.Rmd’

--- re-building ‘lateral-move.Rmd’ using rmarkdown
Quitting from lines 45-55 (lateral-move.Rmd) 
Error: processing vignette ‘lateral-move.Rmd’ failed with diagnostics:
there is no package called 'fields'
--- failed re-building ‘lateral-move.Rmd’

--- re-building ‘solid-set.Rmd’ using rmarkdown
Quitting from lines 37-48 (solid-set.Rmd) 
Error: processing vignette ‘solid-set.Rmd’ failed with diagnostics:
there is no package called 'fields'
--- failed re-building ‘solid-set.Rmd’

--- re-building ‘traveling-sys.Rmd’ using rmarkdown
--- finished re-building ‘traveling-sys.Rmd’

SUMMARY: processing the following files failed:
  ‘landscape.Rmd’ ‘lateral-move.Rmd’ ‘solid-set.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘swfscMisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Rd file 'SlrArd.Rd':
  \usage lines wider than 90 characters:
     SlrArd(T, X, bias = TRUE, method = c("VB", "VBMacKay", "PX-VB"), control = list(), check.lb=TRUE, a0 = 0, b0 = 0, mu0 = 0, xi0 = 1)

These lines will be truncated in the PDF manual.
plot.SPRT: no visible global function definition for ‘par’
plot.SPRT: no visible global function definition for ‘abline’
print.SPRT: no visible global function definition for ‘head’
Undefined global functions or variables:
  abline head par
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("utils", "head")
to your NAMESPACE file.
Package suggested but not available for checking: ‘testthis’
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sprtt)
  > test_check("sprtt")
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 153 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-seq_ttest-error_rates.R:5:3): Check error rates ─────────────────
  <packageNotFoundError/error/condition>
  Error in `library(testthis)`: there is no package called 'testthis'
  Backtrace:
      ▆
   1. └─base::library(testthis) at test-seq_ttest-error_rates.R:5:2
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 153 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'MCMCpack', 'Seurat'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'lmtest', 'spatialreg', 'spdep', 'sphet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survey', 'crossdes', 'lme4'

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

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spTimer', 'spacetime'

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

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

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

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

Packages suggested but not available for checking: 'rgeos', 'gstat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gstat', 'raster'

Packages suggested but not available for checking: 'GGally', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spuRs.Rcheck/00install.out’ for details.
Packages required but not available:
  'edgeR', 'spatstat', 'spatstat.core', 'spatstat.geom',
  'spatstat.sparse', 'spatstat.linnet', 'viridis', 'imager', 'irlba',
  'doSNOW'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
sGda : <anonymous>: no visible global function definition for ‘cov’
sortgene: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  cov model.matrix
Consider adding
  importFrom("stats", "cov", "model.matrix")
to your NAMESPACE file.
Packages required but not available: 'gsubfn', 'RSQLite'

Packages suggested but not available for checking:
  'RH2', 'RMySQL', 'RPostgreSQL'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'arm', 'glmnet', 'mboost'
Package suggested but not available for checking: ‘sqldf’

Packages which this enhances but not available for checking:
  'RPostgreSQL', 'RMySQL', 'RSQLite', 'RJDBC'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sqlutils.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SQN.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'multiridge'

Package suggested but not available for checking: ‘ecpc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'lme4', 'arm', 'brms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSQLite’
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Packages required but not available: 'doParallel', 'elasticnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gamlss', 'gamlss.dist', 'TeachingSampling', 'caret'

Package suggested but not available for checking: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘TripleR’
Packages required but not available: 'DESeq2', 'VennDiagram'

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

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

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

Packages suggested but not available for checking: 'convey', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘doParallel’
Packages required but not available: 'tsBSS', 'ICtest', 'xts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SSBtools.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sscor.Rcheck/00install.out’ for details.
Skipping vignette re-building
Packages suggested but not available for checking: 'caret', 'C50', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Running examples in ‘ssc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coBC
> ### Title: CoBC method
> ### Aliases: coBC
> 
> ### ** Examples
> 
> 
> library(ssc)
> 
> ## Load Wine data set
> data(wine)
> 
> cls <- which(colnames(wine) == "Wine")
> x <- wine[, -cls] # instances without classes
> y <- wine[, cls] # the classes
> x <- scale(x) # scale the attributes
> 
> ## Prepare data
> set.seed(20)
> # Use 50% of instances for training
> tra.idx <- sample(x = length(y), size = ceiling(length(y) * 0.5))
> xtrain <- x[tra.idx,] # training instances
> ytrain <- y[tra.idx]  # classes of training instances
> # Use 70% of train instances as unlabeled set
> tra.na.idx <- sample(x = length(tra.idx), size = ceiling(length(tra.idx) * 0.7))
> ytrain[tra.na.idx] <- NA # remove class information of unlabeled instances
> 
> # Use the other 50% of instances for inductive testing
> tst.idx <- setdiff(1:length(y), tra.idx)
> xitest <- x[tst.idx,] # testing instances
> yitest <- y[tst.idx] # classes of testing instances
> 
> ## Example: Training from a set of instances with 1-NN as base classifier.
> set.seed(1)
> m1 <- coBC(x = xtrain, y = ytrain, 
+            learner = caret::knn3, 
+            learner.pars = list(k = 1),
+            pred = "predict")
Error in loadNamespace(x) : there is no package called ‘caret’
Calls: coBC ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'TTR', 'metafor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bigstatsr', 'chickn', 'glmnet', 'doParallel', 'doRNG', 'rmio'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'earth', 'dismo', 'spThin'

Package suggested but not available for checking: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
ssd : correction_method_D: no visible global function definition for
  ‘rnorm’
ssd : generate_bootstrap: no visible global function definition for
  ‘rmultinom’
ssd : bootstrap_method: no visible global function definition for
  ‘median’
ssd : bootstrap_method: no visible global function definition for
  ‘quantile’
ssd : unbalanced_generate_bootstrap: no visible global function
  definition for ‘rmultinom’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘median’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘quantile’
ssd: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  median qchisq quantile rmultinom rnorm
Consider adding
  importFrom("stats", "median", "qchisq", "quantile", "rmultinom",
             "rnorm")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sSDR.Rcheck/00install.out’ for details.
Packages required but not available: 'doFuture', 'furrr'

Packages suggested but not available for checking:
  'fitdistrplus', 'R.rsp', 'readr', 'tidyverse'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid NAMESPACE file, parsing gives:
Error in packageVersion("spdep"): there is no package called ‘spdep’

See section ‘Package namespaces’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘survey’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘httptest’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sship)
  > 
  > test_check("sship")
  Error in library(httptest) : there is no package called 'httptest'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ssh.utils.Rcheck/00install.out’ for details.
Packages required but not available: 'Biobase', 'edgeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'caret', 'tidymodels', 'C50', 'doParallel', 'tidyverse', 'factoextra'
Running examples in ‘SSLR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EMLeastSquaresClassifierSSLR
> ### Title: General Interface for EMLeastSquaresClassifier model
> ### Aliases: EMLeastSquaresClassifierSSLR
> 
> ### ** Examples
> 
> library(tidyverse)
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘classification.Rmd’ using rmarkdown
Quitting from lines 23-33 (classification.Rmd) 
Error: processing vignette ‘classification.Rmd’ failed with diagnostics:
there is no package called 'tidymodels'
--- failed re-building ‘classification.Rmd’

--- re-building ‘clustering.Rmd’ using rmarkdown
Quitting from lines 24-29 (clustering.Rmd) 
Error: processing vignette ‘clustering.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘clustering.Rmd’

--- re-building ‘fit.Rmd’ using rmarkdown
Quitting from lines 27-37 (fit.Rmd) 
Error: processing vignette ‘fit.Rmd’ failed with diagnostics:
there is no package called 'tidymodels'
--- failed re-building ‘fit.Rmd’

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

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

--- re-building ‘regression.Rmd’ using rmarkdown
Quitting from lines 20-29 (regression.Rmd) 
Error: processing vignette ‘regression.Rmd’ failed with diagnostics:
there is no package called 'tidymodels'
--- failed re-building ‘regression.Rmd’

SUMMARY: processing the following files failed:
  ‘classification.Rmd’ ‘clustering.Rmd’ ‘fit.Rmd’ ‘regression.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'truncdist', 'sn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'CircStats', 'dtw'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'SSN'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'RSQLite', 'maptools', 'rgdal', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gganimate’
Malformed Description field: should contain one or more complete sentences.
map.world: no visible global function definition for ‘par’
map.world: no visible global function definition for ‘plot.new’
map.world: no visible global function definition for ‘plot.window’
map.world: no visible global function definition for ‘lines’
map.world: no visible global function definition for ‘title’
map.world: no visible global function definition for ‘axis’
map.world: no visible global function definition for ‘box’
plot.smooth.sspline: no visible global function definition for
  ‘predict’
plot.smooth.sspline: no visible global function definition for
  ‘filled.contour’
plot.smooth.sspline: no visible binding for global variable
  ‘terrain.colors’
plot.smooth.sspline: no visible global function definition for ‘title’
plot.smooth.sspline: no visible global function definition for ‘axis’
station: no visible binding for global variable ‘WTdiff’
station: no visible global function definition for ‘points’
Undefined global functions or variables:
  WTdiff axis box filled.contour lines par plot.new plot.window points
  predict terrain.colors title
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "box", "filled.contour", "lines", "par",
             "plot.new", "plot.window", "points", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
Package required but not available: ‘vegan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RDS', 'scam'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘survRM2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘scanstatistics’
Package required but not available: ‘caret’

Package suggested but not available for checking: ‘tgp’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
error.est : <anonymous>: no visible global function definition for
  ‘median’
holm.robust: no visible global function definition for ‘pnorm’
holm.robust: no visible global function definition for ‘median’
holm.robust: no visible global function definition for ‘mad’
huberize: no visible global function definition for ‘quantile’
ssvd.initial: no visible global function definition for ‘mad’
ssvd.iter.thresh: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median pnorm quantile
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "quantile")
to your NAMESPACE file.
Package required but not available: ‘BoomSpikeSlab’

Package suggested but not available for checking: ‘AER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'gam', 'sn'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ssym.Rcheck/00install.out’ for details.
Packages required but not available:
  'glmnet', 'bigstep', 'rsample', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggfortify', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'ggrepel'

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

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

Package suggested but not available for checking: ‘evtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/stable.Rcheck/00install.out’ for details.
Packages required but not available:
  'ggm', 'sem', 'nsga2R', 'graph', 'Rgraphviz'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'glmnet', 'mboost', 'gamboostLSS', 'TH.data', 'hdi'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'tune', 'recipes', 'rsample', 'workflowsets', 'dials', 'glmnet'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
genericPlot: no visible global function definition for ‘dev.new’
genericPlot: no visible global function definition for ‘par’
genericPlot: no visible global function definition for ‘rainbow’
genericPlot: no visible global function definition for ‘lines’
genericPlot: no visible global function definition for ‘legend’
genericPlot: no visible global function definition for ‘dev.copy2pdf’
genericPlot: no visible global function definition for ‘dev.copy2eps’
genericPlot: no visible global function definition for ‘dev.print’
genericPlot: no visible binding for global variable ‘png’
genericPlot: no visible binding for global variable ‘tiff’
plotStrains: no visible global function definition for ‘rainbow’
plotStrains: no visible global function definition for ‘dev.new’
plotStrains: no visible global function definition for ‘par’
plotStrains: no visible global function definition for ‘lines’
plotStrains: no visible global function definition for ‘legend’
plotStrains: no visible global function definition for ‘dev.copy2pdf’
plotStrains: no visible global function definition for ‘dev.copy2eps’
plotStrains: no visible global function definition for ‘dev.print’
plotStrains: no visible binding for global variable ‘png’
plotStrains: no visible binding for global variable ‘tiff’
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par")
to your NAMESPACE file.
Found the following files/directories:
  ‘Rplot001.pdf’
Packages required but not available: 'pegas', 'doParallel', 'adegenet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rgeos', 'raster', 'rgdal', 'maptools', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/stan4bart.Rcheck/00install.out’ for details.
Package required but not available: ‘lme4’

Packages suggested but not available for checking: 'afex', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/STAND.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘shinystan’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/stanette.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rstan’
Packages required but not available: 'rstan', 'tidyverse', 'ggfan'

Package suggested but not available for checking: ‘shinystan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'raster', 'geoTS', 'doParallel', 'mapview', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'eemR', 'multiway', 'GGally', 'doParallel', 'drc', 'R.matlab',
  'readr'

Packages suggested but not available for checking: 'plotly', 'xlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking:
  'AER', 'betareg', 'brglm', 'censReg', 'dynlm', 'erer', 'ergm',
  'fGarch', 'glmx', 'gmm', 'lfe', 'lme4', 'lmtest', 'mclogit',
  'mlogit', 'plm', 'quantreg', 'rms', 'relevent', 'sampleSelection',
  'spdep', 'survey'
Package suggested but not available for checking: ‘spdep’
Running examples in ‘starma-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: starma-package
> ### Title: Space Time AutoRegressive Moving Average (STARMA) modelling for
> ###   space-time series
> ### Aliases: starma-package
> ### Keywords: package starma space-time
> 
> ### ** Examples
> 
> # Load spdep library to easily create weight matrices
> library(spdep)
Error in library(spdep) : there is no package called ‘spdep’
Execution halted
Packages required but not available: 'glmnet', 'cornet'

Package which this enhances but not available for checking: ‘CVXR’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stars', 'nngeo'

Package suggested but not available for checking: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'exactextractr', 'future.apply', 'ggforce', 'gstat', 'mapdata',
  'plm', 'raster', 'rgdal', 'spacetime', 'spatstat', 'spatstat.geom',
  'starsdata', 'viridis', 'xts'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/stars.Rcheck/00install.out’ for details.
Packages required but not available: 'leaflet', 'stars'

Packages suggested but not available for checking:
  'leaflet.extras', 'mapview'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R.utils', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'multiApply', 'easyNCDF', 's2dv', 'ClimProjDiags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CDM', 'LAM', 'sirt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ks', 'doSNOW', 'vars', 'xts', 'lessR', 'quantmod'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'arrow'

Packages suggested but not available for checking:
  'flexmix', 'car', 'viridis'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘BSDA’
Package required but not available: ‘readr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/StatDataML.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘viridis’
Package suggested but not available for checking: ‘YieldCurve’
Error(s) in re-building vignettes:
  ...
--- re-building ‘boxjenkins.Rmd’ using rmarkdown
--- finished re-building ‘boxjenkins.Rmd’

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

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

--- re-building ‘seatbelt.Rmd’ using rmarkdown
Warning: Number of initial parameters is less than the required amount of parameters (3), recycling the initial parameters the required amount of times.
Warning: Number of initial parameters is less than the required amount of parameters (6), recycling the initial parameters the required amount of times.
--- finished re-building ‘seatbelt.Rmd’

--- re-building ‘selfspec.Rmd’ using rmarkdown
Quitting from lines 47-56 (selfspec.Rmd) 
Error: processing vignette ‘selfspec.Rmd’ failed with diagnostics:
there is no package called 'YieldCurve'
--- failed re-building ‘selfspec.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘sommer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'statgenSTA'

Package suggested but not available for checking: ‘asreml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'factoextra', 'ggforce', 'SpATS'

Package suggested but not available for checking: ‘asreml’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggrepel', 'lme4', 'mapproj', 'SpATS'

Package suggested but not available for checking: ‘asreml’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rockchalk’
Error(s) in re-building vignettes:
  ...
--- re-building ‘HTML_special_features.Rmd’ using rmarkdown
Quitting from lines 534-553 (HTML_special_features.Rmd) 
Error: processing vignette ‘HTML_special_features.Rmd’ failed with diagnostics:
there is no package called 'rockchalk'
--- failed re-building ‘HTML_special_features.Rmd’

--- re-building ‘Rmarkdown.Rmd’ using rmarkdown
Quitting from lines 746-749 (Rmarkdown.Rmd) 
Error: processing vignette ‘Rmarkdown.Rmd’ failed with diagnostics:
there is no package called 'rockchalk'
--- failed re-building ‘Rmarkdown.Rmd’

--- re-building ‘code_chunks.Rmd’ using rmarkdown
Quitting from lines 754-762 (code_chunks.Rmd) 
Error: processing vignette ‘code_chunks.Rmd’ failed with diagnostics:
there is no package called 'rockchalk'
--- failed re-building ‘code_chunks.Rmd’

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

SUMMARY: processing the following files failed:
  ‘HTML_special_features.Rmd’ ‘Rmarkdown.Rmd’
  ‘code_chunks.Rmd’

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

Packages suggested but not available for checking: 'Hmisc', 'mipfp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
actvspred: no visible global function definition for ‘quantile’
actvspred: no visible global function definition for ‘aggregate’
actvspred: no visible global function definition for ‘par’
actvspred: no visible global function definition for ‘lines’
auc: no visible global function definition for ‘par’
decile: no visible global function definition for ‘quantile’
dqcontinuous : numoutliers: no visible global function definition for
  ‘quantile’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘sd’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘quantile’
gini: no visible global function definition for ‘par’
gini: no visible global function definition for ‘abline’
iv: no visible global function definition for ‘quantile’
iv: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘par’
ks: no visible global function definition for ‘lines’
outliers: no visible global function definition for ‘quantile’
outliers: no visible global function definition for ‘na.omit’
pentile: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline aggregate lines na.omit par quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par")
  importFrom("stats", "aggregate", "na.omit", "quantile", "sd")
to your NAMESPACE file.
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Packages required but not available:
  'tergm', 'ergm.count', 'sna', 'tsna', 'ergm', 'networkDynamic'

Packages suggested but not available for checking:
  'ergm.rank', 'ergm.ego', 'EpiModel', 'latentnet', 'networksis',
  'relevent', 'ndtv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ergm', 'latticeExtra', 'sna'

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

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

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

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

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

Packages suggested but not available for checking:
  'leaflet', 'tmap', 'pct', 'spatstat.core', 'spatstat.geom',
  'spatstat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BayesFactor', 'WRS2'

Packages suggested but not available for checking:
  'afex', 'metaBMA', 'metafor', 'metaplus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'car'

Packages suggested but not available for checking:
  'lmtest', 'DescTools', 'Hmisc', 'PerformanceAnalytics', 'semTools',
  'semPlot', 'FactoMineR', 'FactoInvestigate', 'factoextra', 'rrcov',
  'onewaytests'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Biobase', 'GGally', 'ggfortify', 'ggrepel', 'forestplot',
  'rpart.plot', 'factoextra', 'pvca', 'glmnet', 'tidyverse'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/stcos.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'irlba', 'ProDenICA'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/steadyICA.Rcheck/00install.out’ for details.
getStp: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘axis’
plot.steeptest: no visible global function definition for ‘box’
plot.steeptest: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘abline’
plot.steeptest: no visible global function definition for ‘legend’
plot.steeptest: no visible global function definition for
  ‘as.graphicsAnnot’
steeptest: no visible global function definition for ‘lm’
summary.steeptest: no visible global function definition for ‘var’
summary.steeptest: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline as.graphicsAnnot axis box legend lm quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend")
  importFrom("stats", "lm", "quantile", "var")
to your NAMESPACE file.
Running examples in ‘steepness-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getDS
> ### Title: David's scores -DS-
> ### Aliases: getDS
> ### Keywords: misc htest
> 
> ### ** Examples
> 
> 
> ##############################################################################
> ###               Example taken from Vervaecke et al. (2007):              ###
> ##############################################################################
> 
> X <- matrix(c(0,58,50,61,32,37,29,39,25,8,0,22,22,9,27,20,10,48,
+               3,3,0,19,29,12,13,19,8,5,8,9,0,33,38,35,32,57,
+               4,7,9,1,0,28,26,16,23,4,3,0,0,6,0,7,6,12,
+               2,0,4,1,4,4,0,5,3,0,2,1,1,5,8,3,0,10,3,1,3,0,0,4,1,2,0),
+               nrow=9,byrow=TRUE)
> 
> individuals <- c("V","VS","B","FJ","PR","VB","TOR","MU","ZV")
> 
> res <- getDS(X,names=individuals,method="Dij")
Error in is.na(X) || !is.numeric(X) : 
  'length = 81' in coercion to 'logical(1)'
Calls: getDS
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SteinerNet.Rcheck/00install.out’ for details.
Packages required but not available: 'tmvtnorm', 'MCMCglmm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FD', 'vcd', 'geometry'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spm', 'steprf'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'caret'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spm', 'spm2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'future.apply', 'rasterVis'

Package suggested but not available for checking: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tseries’
Running examples in ‘StepwiseTest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: StepwiseTest-package
> ### Title: Multiple Testing Method to Control Generalized Family-Wise Error
> ###   Rate and False Discovery Proportion
> ### Aliases: StepwiseTest-package StepwiseTest FWERkControl FDPControl
> 
> ### ** Examples
> 
> # Specify the model parameters
> m_null = 3
> m_alt  = 7
> m = m_null + m_alt
> mu = c( rep(0, m_null), rep(0.5,m_alt) )
> rho = 0.25
> omega= (1-rho)*diag(1,m) + rho*matrix(1,m,m)
> v=t(chol(omega))
> 
> # generate the data
> n = 100
> y = mu%*%matrix(1,1,n)+ v %*% matrix(rnorm(m*n),m,n)
> 
> # calculate the test statistics and bootstrap statistics
> library(foreach)
> library(tseries)
Error in library(tseries) : there is no package called ‘tseries’
Execution halted
Packages required but not available: 'labelled', 'arm', 'lme4'

Package suggested but not available for checking: ‘RSQLite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'doParallel', 'fda', 'raster', 'rasterVis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'brnn'

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

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

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

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

Package suggested but not available for checking: ‘mapview’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'nnfor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat', 'spatstat.geom', 'spatstat.random', 'spatstat.core',
  'spatstat.linnet'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stm', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'maptools', 'spacetime', 'gstat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stm', 'ggraph', 'ggrepel', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'fields'

Packages suggested but not available for checking: 'demography', 'MTS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Package required but not available: ‘glmnet’

Packages suggested but not available for checking:
  'geometry', 'tm', 'wordcloud'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantmod', 'dvmisc', 'Hmisc', 'TTR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spray', 'permutations', 'disordR'

Package suggested but not available for checking: ‘emulator’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'changepoint', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Storm.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'RSQLite', 'RPostgres'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'R.rsp', 'EMMREML', 'UsingR', 'glmnet'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/STPGA.Rcheck/00install.out’ for details.
Packages required but not available: 'maptools', 'raster', 'rgeos'

Packages suggested but not available for checking:
  'leaflet', 'rgdal', 'pct', 'tmap', 'mapsapi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'splancs', 'spatstat.core', 'spatstat.geom', 'spatstat.random'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'splancs', 'rgdal', 'ks', 'raster', 'SiMRiv', 'spatstat.geom',
  'sparr', 'leaflet', 'gstat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rglpk', 'arrow'

Package suggested but not available for checking: ‘plotly’

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

Packages suggested but not available for checking: 'optmatch', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rglpk', 'snowfall'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DiagrammeR’
Package required but not available: ‘NetIndices’

Package suggested but not available for checking: ‘StrathE2E2examples’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'partykit', 'glmnet', 'ggparty', 'coin'

Packages suggested but not available for checking:
  'BART', 'survRM2', 'TH.data'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘C50’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘StatMatch’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/StratifiedSampling.Rcheck/00install.out’ for details.
Packages required but not available: 'fitdistrplus', 'mc2d'

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

Packages suggested but not available for checking:
  'astrochron', 'RFOC', 'tidyverse'

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

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

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

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

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

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

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

Packages suggested but not available for checking:
  'dismo', 'raster', 'rgeos'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'clusterGeneration', 'fpc'

Package suggested but not available for checking: ‘RSQLite’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xts', 'latticeExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/strex.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/String2AdjMatrix.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘faraway’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/stripless.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘caret’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Biostrings', 'ShortRead', 'IRanges'

Package suggested but not available for checking: ‘STRaitRazoR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spatialreg', 'rgdal'

Packages suggested but not available for checking:
  'spdep', 'rgeos', 'Ecdat', 'tidycensus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'lme4', 'lmerTest', 'lsmeans', 'mutoss', 'pbkrtest', 'phia',
  'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantreg', 'forecast'

Packages suggested but not available for checking:
  'demography', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'car', 'dynlm', 'lmtest', 'tseries'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/strucchange.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'car', 'dynlm', 'lmtest', 'tseries', 'bfast'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/strucchangeRcpp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/StructFDR.Rcheck/00install.out’ for details.
Packages required but not available: 'lme4', 'penalized'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/StructureMC.Rcheck/00install.out’ for details.
Package required but not available: ‘gWidgets2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MplusAutomation’
Packages required but not available: 'readr', 'R.utils', 'visdat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'tidyverse', 'CCA'

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

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

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

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'diagram', 'ggrepel', 'survRM2', 'VennDiagram'

Package suggested but not available for checking: ‘rgeos’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lmtest’
Running examples in ‘subgxe-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pasta
> ### Title: pasta for multi-phenotype analysis
> ### Aliases: pasta
> 
> ### ** Examples
> 
> # grab synthetic study for example
> data("studies")
> n.studies <- 5
> study.sizes <- c(nrow(studies[[1]]), nrow(studies[[2]]), nrow(studies[[3]]),
+                    nrow(studies[[4]]), nrow(studies[[5]]))
> study.pvals <- rep(0, n.studies)
> # Correlations of p-values among the studies.
> # In this case the studies were generated independently so its just I
> cor.matrix <- diag(1, n.studies)
> # load the lrtest() function to conduct the likelihood ratio test
> # Used just to generate the input p-values, not required in pasta itself.
> 
> library(lmtest)
Error in library(lmtest) : there is no package called ‘lmtest’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘subgxe.Rmd’ using rmarkdown
Quitting from lines 73-87 (subgxe.Rmd) 
Error: processing vignette ‘subgxe.Rmd’ failed with diagnostics:
there is no package called 'lmtest'
--- failed re-building ‘subgxe.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'siar', 'wordcloud'

Packages suggested but not available for checking:
  'adegraphics', 'CircStats', 'maptools', 'spdep', 'splancs'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'irtoys', 'sirt', 'ltm'

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

Packages suggested but not available for checking:
  'arm', 'caret', 'earth', 'gam', 'glmnet', 'Hmisc', 'ipred',
  'LogicReg', 'mda', 'party', 'SIS'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'readr', 'ggrepel', 'naniar'

Package suggested but not available for checking: ‘haven’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
SUE.fitted.values: no visible global function definition for
  ‘model.frame’
SUE.lm: no visible global function definition for ‘model.frame’
SUE.lm: no visible global function definition for ‘lm’
SUE.lm: no visible global function definition for ‘anova’
SUE.residuals: no visible global function definition for ‘model.frame’
parameters : para2: no visible global function definition for ‘uniroot’
parameters: no visible global function definition for ‘optimize’
parameters: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  anova lm model.frame optimize uniroot
Consider adding
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
Rd file 'SUE.lm.Rd':
  \examples lines wider than 100 characters:
     ##We analysis the well known stackloss data by using ordinary linear method and the subsampling method. 
     ##proportion of outliers in the data. The subsample size is chosen to be the default size of ns = 11.
     plot(SUE.fitted.values(a2),SUE.residuals(a2),xlab="(b) fitted values",ylab="residuals",ylim=c(-12,12))
     plot(SUE.fitted.values(a3),SUE.residuals(a3),xlab="(c) fitted values",ylab="residuals",ylim=c(-12,12))

These lines will be truncated in the PDF manual.
Package required but not available: ‘rmapshaper’

Package suggested but not available for checking: ‘spData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'plotly', 'readr', 'viridis'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sugrrants.Rcheck/00install.out’ for details.
Package required but not available: ‘GBJ’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SummaryLasso.Rcheck/00install.out’ for details.
checkRd: (7) cleartmp.Rd:29: invalid email address: dominic.comtois@gmail.com>
checkRd: (7) parse_args.Rd:52: invalid email address: dominic.comtois@gmail.com>
Packages required but not available: 'survey', 'spdep', 'viridis'

Packages suggested but not available for checking:
  'INLA', 'rdhs', 'R.rsp', 'fields'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
sunter: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
supcluster : itgamma: no visible global function definition for
  ‘rgamma’
supcluster : itgamma: no visible global function definition for
  ‘dgamma’
supcluster : itgamma: no visible global function definition for ‘runif’
supcluster : itbeta: no visible global function definition for ‘rnorm’
supcluster : itbeta: no visible global function definition for ‘runif’
supcluster : itj: no visible global function definition for ‘dmultinom’
supcluster: no visible global function definition for ‘kmeans’
tab1: no visible global function definition for ‘image’
tab1: no visible global function definition for ‘gray’
tab1: no visible global function definition for ‘var’
Undefined global functions or variables:
  dgamma dmultinom gray image kmeans rgamma rnorm runif var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "dgamma", "dmultinom", "kmeans", "rgamma", "rnorm",
             "runif", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘fields’
Error(s) in re-building vignettes:
  ...
--- re-building ‘supc.Rmd’ using rmarkdown
--- finished re-building ‘supc.Rmd’

--- re-building ‘supc_demo.Rmd’ using rmarkdown
Quitting from lines 135-137 (supc_demo.Rmd) 
Error: processing vignette ‘supc_demo.Rmd’ failed with diagnostics:
there is no package called 'fields'
--- failed re-building ‘supc_demo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'biclust', 'fabia'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'emojifont', 'fMultivar', 'car', 'sadists'
Running ‘testthat.R’ [41s/65s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("superb")
  Loading required package: superb
  ==> THIS IS A TEST OF runDebug <==
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 167 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_GRD.R:59:5): A complete test with plots and anova ───────────────
  <packageNotFoundError/error/condition>
  Error in `library(car)`: there is no package called 'car'
  Backtrace:
      ▆
   1. └─base::library(car) at test_GRD.R:59:4
  ── Error (test_GRD.R:595:5): page 18 ───────────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(fMultivar)`: there is no package called 'fMultivar'
  Backtrace:
      ▆
   1. └─base::library(fMultivar) at test_GRD.R:595:4
  ── Error (test_GRD.R:759:5): figure 3: ─────────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(fMultivar)`: there is no package called 'fMultivar'
  Backtrace:
      ▆
   1. └─base::library(fMultivar) at test_GRD.R:759:4
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 167 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘future.apply’

Package suggested but not available for checking: ‘stars’

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

Packages suggested but not available for checking:
  'arm', 'bartMachine', 'biglasso', 'caret', 'devtools', 'earth',
  'extraTrees', 'genefilter', 'glmnet', 'ipred', 'LogicReg', 'party',
  'SIS', 'speedglm', 'sva'

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

Packages suggested but not available for checking:
  'arm', 'bartMachine', 'earth', 'extraTrees', 'glmnet', 'ipred',
  'LogicReg', 'party', 'speedglm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ClusterR', 'caret', 'glmnet'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/superml.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'car', 'lme4'
Packages required but not available:
  'fBasics', 'R.matlab', 'glmnet', 'timeSeries'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'afex', 'Hmisc'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/supervisedPRIM.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘DoE.base’
Packages suggested but not available for checking:
  'crossdes', 'DoE.base', 'support.CEs'
Running examples in ‘support.BWS3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bws3.dataset
> ### Title: Creating a dataset suitable for Case 3 best-worst scaling
> ###   analysis
> ### Aliases: bws3.dataset
> ### Keywords: manip
> 
> ### ** Examples
> 
> # The following lines of code construct choice sets for Case 3 BWS
> # using rotation.design() in the package support.CEs; create a dataset
> # for the analysis using bws3.dataset(); and then conduct a maxdiff model
> # analysis on the basis of a conditional logit model specification
> # using clogit() in the package survival.
> 
> # Load packages
> library(support.CEs)
Error in library(support.CEs) : there is no package called ‘support.CEs’
Execution halted
Packages suggested but not available for checking:
  'DoE.base', 'crossdes', 'mlogit', 'gmnl', 'apollo'
Running examples in ‘support.BWS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ricebws1
> ### Title: Consumers' preferences for rice characteristics
> ### Aliases: ricebws1
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # Respondents were asked to select their most and least important
> # characteristics of rice when purchasing rice. Rice characteristics
> # were assumed to be place of origin, variety, price, taste, safety,
> # wash-free rice, and milling date. BWS questions were created from
> # a balanced incomplete block design (BIBD) with seven treatments
> # (items), four columns (four items per question), and seven rows
> # (seven questions).
> 
> # Generate the BIBD using find.BIB() in the crossdes package:
> require("crossdes")
Loading required package: crossdes
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘crossdes’
> set.seed(8041)
> bibd.ricebws1 <- find.BIB(trt = 7, b = 7, k = 4)
Error in find.BIB(trt = 7, b = 7, k = 4) : 
  could not find function "find.BIB"
Execution halted
Package required but not available: ‘DoE.base’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) glmLikSI.Rd:25: \item in \value must have non-empty label
checkRd: (7) lmLikSI.Rd:24: \item in \value must have non-empty label
Packages required but not available: 'randtoolbox', 'MHadaptive'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'glmnet', 'MAP', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rms’
Package required but not available: ‘geiger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'gstat', 'rgeos'

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

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

Package suggested but not available for checking: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'latticeExtra', 'lme4', 'msm', 'OrdinalLogisticBiplot', 'rms',
  'mixtools', 'ks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'msm', 'parfm', 'SurvCorr'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rms’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/survAUC.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/survBootOutliers.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/survC1.Rcheck/00install.out’ for details.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mstate’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘survCurve.Rmd’ using rmarkdown
Quitting from lines 26-29 (survCurve.Rmd) 
Error: processing vignette ‘survCurve.Rmd’ failed with diagnostics:
there is no package called 'mstate'
--- failed re-building ‘survCurve.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘spatstat.geom’

Packages suggested but not available for checking:
  'msm', 'rgeos', 'maptools', 'spdep', 'maxLik', 'hhh4contacts',
  'splancs', 'gamlss', 'INLA'

Package which this enhances but not available for checking: ‘xts’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'RSQLite', 'quantreg', 'AER'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/survey.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'flexsurv', 'rms', 'xlsx', 'rstan'

Packages suggested but not available for checking: 'shinystan', 'INLA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readr', 'tidyverse', 'glmnet', 'factoextra', 'useful'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survC1’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'np', 'doParallel', 'doRNG', 'TPmsm', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readr', 'rjags', 'R2jags', 'tidyverse', 'icenReg', 'ICBayes'

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

Package suggested but not available for checking: ‘tidyverse’

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

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pseudo’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/survivalMPL.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘glmnet’

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

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

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

Packages suggested but not available for checking:
  'caret', 'ggpubr', 'pec', 'randomForestSRC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggpubr', 'survMisc'

Packages suggested but not available for checking: 'flexsurv', 'cmprsk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/survMisc.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/survMS.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘survminer’
Error(s) in re-building vignettes:
  ...
--- re-building ‘survParamSim.Rmd’ using rmarkdown
Quitting from lines 53-58 (survParamSim.Rmd) 
Error: processing vignette ‘survParamSim.Rmd’ failed with diagnostics:
there is no package called 'survminer'
--- failed re-building ‘survParamSim.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SurvRegCensCov.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/survRM2.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/survsim.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘latticeExtra’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/survSNP.Rcheck/00install.out’ for details.
Packages required but not available: 'speedglm', 'SuperLearner'

Package suggested but not available for checking: ‘cmprsk’

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

Packages suggested but not available for checking: 'genlasso', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'robets', 'forecastHybrid'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'vars', 'expm', 'steadyICA', 'strucchange'

Package suggested but not available for checking: ‘tsDyn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/svDialogstcltk.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/svdvisual.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
startHttpServer : <anonymous> : Rjsonp: no visible global function
  definition for ‘localeToCharset’
Undefined global functions or variables:
  localeToCharset
Consider adding
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
Packages required but not available:
  'rvinecopulib', 'univariateML', 'fGarch'

Package suggested but not available for checking: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/svKomodo.Rcheck/00install.out’ for details.
‘gs+qpdf’ made some significant size reductions:
     compacted ‘paper.pdf’ from 561Kb to 298Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/svmpath.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/svmplus.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SVN.Rcheck/00install.out’ for details.
Package required but not available: ‘survey’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/svSweave.Rcheck/00install.out’ for details.
Package required but not available: ‘survey’

Package suggested but not available for checking: ‘doBy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'rms', 'survey'

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

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

Packages suggested but not available for checking:
  'doParallel', 'glmnet', 'recipes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/swamp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/swa.Rcheck/00install.out’ for details.
checkRd: (7) swPwr.Rd:86-88: \item in \value must have non-empty label
Packages suggested but not available for checking: 'fields', 'devtools'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘swdft-intro.Rmd’ using rmarkdown
Quitting from lines 211-212 (swdft-intro.Rmd) 
Error: processing vignette ‘swdft-intro.Rmd’ failed with diagnostics:
there is no package called 'fields'
--- failed re-building ‘swdft-intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘spatstat.random’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'timetk'

Packages suggested but not available for checking:
  'readr', 'robets', 'tidyquant', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘swephRdata’
Packages required but not available: 'readr', 'swfscDAS', 'swfscMisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'swfscMisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggrepel', 'mapdata', 'spatstat.geom'

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

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

Package suggested but not available for checking: ‘ggpubr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'arm', 'lme4', 'maptools', 'blme'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fda', 'expm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SWMPr', 'ggimage'

Package suggested but not available for checking: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'maptools', 'oce', 'openair'

Package suggested but not available for checking: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readr', 'ggmap', 'hydroTSM', 'segmented'

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

Package suggested but not available for checking: ‘cplexAPI’

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

Package suggested but not available for checking: ‘cplexAPI’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'cplexAPI', 'clpAPI'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sybil.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sylly.en.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'sylly.de', 'sylly.en', 'sylly.es'
Packages required but not available: 'clusterSim', 'RSDA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Hmisc’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/symbols.Rcheck/00install.out’ for details.
Package required but not available: ‘ff’

Package suggested but not available for checking: ‘BGData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'sn', 'fGarch'
'LazyData' is specified without a 'data' directory
Running examples in ‘symmetry-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: symmetry_test
> ### Title: Perform symmetry tests
> ### Aliases: symmetry_test symmetry_test.default symmetry_test.lm
> ###   symmetry_test.fGARCH
> 
> ### ** Examples
> 
> set.seed(1)
> 
> # IID samples
> x <- rnorm(50)
> symmetry_test(x, "MOI", bootstrap = FALSE, k = 3, mu = 0)

	Symmetry test
	Null hypothesis: Data is symmetric around 0

data:  x
MOI = 0.60574, k = 3, p-value = 0.1379

> symmetry_test(x, "MOI", bootstrap = TRUE, k = 3, mu = 0)

	Symmetry test
	Null hypothesis: Data is symmetric around 0

data:  x
MOI = 0.60574, k = 3, B = 1000, p-value = 0.15

> symmetry_test(x, "MOI", bootstrap = TRUE, k = 3)

	Symmetry test
	Null hypothesis: Data is symmetric

data:  x
MOI = 0.27738, k = 3, B = 1000, p-value = 0.043
sample estimates:
       mu 
0.1004483 

> x <- rsl(50, alpha = 1.5)
> symmetry_test(x, "MOI", bootstrap = FALSE, k = 3, mu = 0)

	Symmetry test
	Null hypothesis: Data is symmetric around 0

data:  x
MOI = 1.1368, k = 3, p-value = 0.00536

> symmetry_test(x, "MOI", bootstrap = TRUE, k = 3, mu = 0)

	Symmetry test
	Null hypothesis: Data is symmetric around 0

data:  x
MOI = 1.1368, k = 3, B = 1000, p-value = 0.001

> symmetry_test(x, "MOI", bootstrap = TRUE, k = 3)

	Symmetry test
	Null hypothesis: Data is symmetric

data:  x
MOI = -0.32892, k = 3, B = 1000, p-value = 0.029
sample estimates:
      mu 
1.294132 

> 
> # Linear models
> lin_model <- lm(dist ~ speed, cars)
> symmetry_test(lin_model, "B1")

	Symmetry test of linear model residuals
	Null hypothesis: The residuals are symmetric around 0

data:  Residuals from model lin_model
B1 = 0.85863, B = 1000, p-value = 0.025

> 
> # Garch models
> library(fGarch)
Error in library(fGarch) : there is no package called ‘fGarch’
Execution halted
Package required but not available: ‘multipol’

Package suggested but not available for checking: ‘mpoly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'harmony', 'uwot', 'irlba', 'ggrastr', 'ggrepel'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'vegan', 'FD'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘L1pack’

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

Packages suggested but not available for checking: 'maptools', 'rgeos'

Suggests orphaned package: ‘udunits2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
Error(s) in re-building vignettes:
  ...
--- re-building ‘dingemanse-data-example.Rmd’ using rmarkdown
--- finished re-building ‘dingemanse-data-example.Rmd’

--- re-building ‘quick-start.Rmd’ using rmarkdown
--- finished re-building ‘quick-start.Rmd’

--- re-building ‘synr-creategroup.Rmd’ using rmarkdown
--- finished re-building ‘synr-creategroup.Rmd’

--- re-building ‘synr-tutorial.Rmd’ using rmarkdown
--- finished re-building ‘synr-tutorial.Rmd’

--- re-building ‘validate-data.Rmd’ using rmarkdown
Quitting from lines 24-26 (validate-data.Rmd) 
Error: processing vignette ‘validate-data.Rmd’ failed with diagnostics:
there is no package called 'plotly'
--- failed re-building ‘validate-data.Rmd’

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

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

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package suggested but not available for checking: ‘ChainLadder’
Error(s) in re-building vignettes:
  ...
--- re-building ‘SynthETIC-demo.Rmd’ using rmarkdown
Quitting from lines 992-1007 (SynthETIC-demo.Rmd) 
Error: processing vignette ‘SynthETIC-demo.Rmd’ failed with diagnostics:
there is no package called 'ChainLadder'
--- failed re-building ‘SynthETIC-demo.Rmd’

SUMMARY: processing the following file failed:
  ‘SynthETIC-demo.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'party', 'mipfp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
‘library’ or ‘require’ calls in package code:
  ‘LowRankQP’ ‘rgenoud’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for ‘LowRankQP’
gaps.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘lines’
path.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘legend’
synth: no visible binding for global variable ‘sd’
synth: no visible binding for global variable ‘var’
synth: no visible global function definition for ‘LowRankQP’
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘synthpop’
'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
Packages required but not available: 'car', 'lmtest'

Packages suggested but not available for checking: 'plm', 'sem'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantreg', 'xts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rdimtools', 'ADMM', 'fda', 'maotai'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tablaxlsx.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Table1Heatmap.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘.xls’ ‘attenu.xls’ ‘chick1.xls’ ‘chick2.xls’ ‘generic1.xls’
  ‘hands.xls’ ‘table1.xls’
Packages required but not available: 'lmtest', 'tableone'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TableMonster.Rcheck/00install.out’ for details.
Packages required but not available: 'survey', 'labelled'

Packages suggested but not available for checking:
  'Matching', 'lme4', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Hmisc’
Packages suggested but not available for checking: 'haven', 'R.utils'
Running examples in ‘tablet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as_kable.tablet
> ### Title: Coerce Tablet to Kable
> ### Aliases: as_kable.tablet
> 
> ### ** Examples
> 
> library(boot)
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(magrittr)
> library(haven)
Error in library(haven) : there is no package called ‘haven’
Execution halted
Package required but not available: ‘torch’

Packages suggested but not available for checking:
  'recipes', 'dials', 'tidyverse', 'tune'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readr’
Packages required but not available: 'fasterize', 'raster', 'spatstat.geom'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tabularMLC.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘readr’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘tabulog.Rmd’ using rmarkdown
Quitting from lines 13-17 (tabulog.Rmd) 
Error: processing vignette ‘tabulog.Rmd’ failed with diagnostics:
there is no package called 'readr'
--- failed re-building ‘tabulog.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘DescTools’

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

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

Package suggested but not available for checking: ‘forecast’

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

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

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

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

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

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

Packages suggested but not available for checking: 'miceadds', 'sirt'

Package which this enhances but not available for checking: ‘LSAmitR’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tangram.pipe.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'rms', 'Hmisc', 'Matching'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tangram.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TapeR.Rcheck/00install.out’ for details.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Packages required but not available:
  'bipartite', 'MPSEM', 'phytools', 'vegan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lava', 'future.apply'

Package suggested but not available for checking: ‘grf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'arrow', 'future.batchtools', 'future.callr', 'torch'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TAR.Rcheck/00install.out’ for details.
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tashudata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tm’
Packages required but not available: 'readr', 'duckdb', 'R.utils'

Package suggested but not available for checking: ‘RSQLite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/taxa.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘GA’
Packages required but not available: 'RSQLite', 'readr'

Package suggested but not available for checking: ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'wikitaxa', 'phangorn'

Package suggested but not available for checking: ‘vegan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'taxa', 'taxize', 'vegdata'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSQLite', 'R.utils'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'GISTools', 'rgeos'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tbart.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tbd.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TBEST.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TBFmultinomial.Rcheck/00install.out’ for details.
Package required but not available: ‘xts’

Package suggested but not available for checking: ‘PerformanceAnalytics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'mlt', 'mboost', 'basefun'

Packages suggested but not available for checking:
  'TH.data', 'tram', 'partykit', 'latticeExtra', 'trtf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'TreeDist', 'TreeTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggalt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_to_tbrf.Rmd’ using rmarkdown
Quitting from lines 123-138 (intro_to_tbrf.Rmd) 
Error: processing vignette ‘intro_to_tbrf.Rmd’ failed with diagnostics:
there is no package called 'ggalt'
--- failed re-building ‘intro_to_tbrf.Rmd’

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

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

Packages suggested but not available for checking:
  'viridis', 'future.apply', 'censReg', 'truncreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'multtest'

Packages suggested but not available for checking:
  'doParallel', 'dearseq', 'GEOquery'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘sn’
Error(s) in re-building vignettes:
  ...
--- re-building ‘tclust.rnw’ using Sweave
Warning in .tkmeans.warn(O, ret) :
  Less than 50% of the iterations (44%) converged - please increase iter.max.

Error: processing vignette ‘tclust.rnw’ failed with diagnostics:
 chunk 6 (label = chunk6) 
Error in library(sn) : there is no package called 'sn'

--- failed re-building 'tclust.rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'Mcomp', 'forecast'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RMariaDB', 'sqldf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'T4cluster', 'maotai'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
cluster_cutoff_at_first_empty_bin: no visible global function
  definition for ‘hist’
mapper1D: no visible global function definition for ‘dist’
mapper1D: no visible global function definition for ‘as.dist’
mapper1D: no visible global function definition for ‘hclust’
mapper1D: no visible global function definition for ‘cutree’
mapper2D: no visible global function definition for ‘dist’
mapper2D: no visible global function definition for ‘as.dist’
mapper2D: no visible global function definition for ‘hclust’
mapper2D: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  as.dist cutree dist hclust hist
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cutree", "dist", "hclust")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDboost.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDCor.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDD.Rcheck/00install.out’ for details.
Packages required but not available: 'SPOT', 'adabag'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘xts’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tdROC.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘latticeExtra’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tdr.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'devtools', 'GA'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TeachHist.Rcheck/00install.out’ for details.
Package required but not available: ‘devtools’

Packages suggested but not available for checking:
  'diagram', 'DiagrammeR', 'leaflet', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'maptools', 'R2wd'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TeachingSampling.Rcheck/00install.out’ for details.
Package required but not available: ‘furrr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fields', 'itertools', 'raster'

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

Packages suggested but not available for checking:
  'rgdal', 'stars', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tm', 'wordcloud', 'arules', 'arulesViz'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ciftiTools', 'excursions'

Packages suggested but not available for checking: 'doParallel', 'INLA'

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

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

Package suggested but not available for checking: ‘devtools’

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for global variable ‘ID’
TER.deesc.1.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B: no visible binding for global variable ‘ID’
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A3.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A2.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : B1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B: no visible binding for global variable ‘ID’
Undefined global functions or variables:
  ID
Package required but not available: ‘rainbow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ergm', 'tergm', 'networkDynamic'

Package suggested but not available for checking: ‘EpiModel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ergm', 'networkDynamic'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘labelled’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/testdat.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'gurobi', 'Rglpk', 'mirt'
Packages required but not available: 'caret', 'Morpho', 'tmvtnorm'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DoseFinding', 'alabama'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FactoMineR', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'imputeTS', 'modeest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'readr'
Packages suggested but not available for checking: 'devtools', 'ismev'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/texmex.Rcheck/00install.out’ for details.
Package required but not available: ‘ExPosition’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lmtest’

Packages which this enhances but not available for checking:
  'AER', 'betareg', 'Bergm', 'biglm', 'brglm', 'brms', 'btergm',
  'dynlm', 'erer', 'ergm', 'feisr', 'fGarch', 'forecast', 'gamlss',
  'gamlss.inf', 'glmmTMB', 'gmm', 'latentnet', 'lfe', 'lme4', 'maxLik',
  'metaSEM', 'mfx', 'mhurdle', 'miceadds', 'mlogit', 'mnlogit',
  'oglmx', 'pglm', 'plm', 'relevent', 'rms', 'robust', 'spatialreg',
  'spdep', 'speedglm', 'truncreg', 'Zelig'
Running ‘testthat.R’ [5s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("texreg")
  Version:  1.38.6
  Date:     2022-04-06
  Author:   Philip Leifeld (University of Essex)
  
  Consider submitting praise using the praise or praise_interactive functions.
  Please cite the JSS article in your publications -- see citation("texreg").
  > 
  > test_check("texreg")
  [ FAIL 1 | WARN 0 | SKIP 33 | PASS 203 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (31)
  • biglm cannot be loaded (1)
  • lme4 cannot be loaded (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-jss.R:79:3): texreg returns output as in the JSS 2013 article ───
  <packageNotFoundError/error/condition>
  Error in `library("lmtest")`: there is no package called 'lmtest'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-jss.R:79:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::library("lmtest") at test-jss.R:81:6
  
  [ FAIL 1 | WARN 0 | SKIP 33 | PASS 203 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'text2vec', 'doParallel', 'qgraph'

Package suggested but not available for checking: ‘tm’

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

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

Package suggested but not available for checking: ‘glmnet’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘text2vec’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forecast', 'tm', 'wordcloud', 'glmnet', 'doParallel'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘text2vec’

Packages suggested but not available for checking:
  'topicmodels', 'wordcloud'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tm', 'ggwordcloud'

Packages suggested but not available for checking:
  'ggrepel', 'ggpubr', 'ggraph', 'topicmodels', 'corrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
phyper_right: no visible global function definition for ‘dhyper’
progression: no visible global function definition for ‘density’
progression: no visible global function definition for ‘points’
progression: no visible global function definition for ‘legend’
progression: no visible global function definition for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘dhyper’
specificities.distribution.plot: no visible global function definition
  for ‘Axis’
specificities.distribution.plot: no visible global function definition
  for ‘arrows’
specificities.distribution.plot: no visible global function definition
  for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘title’
specificities.probabilities.vector: no visible global function
  definition for ‘phyper’
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "points", "text",
             "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'graph', 'Rgraphviz', 'qgraph', 'ggraph', 'ggforce', 'ggrepel',
  'ggalt', 'uwot'
Packages required but not available:
  'ggrepel', 'recipes', 'rsample', 'tune', 'furrr', 'overlapping'

Packages suggested but not available for checking: 'rio', 'glmnet'

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

Packages suggested but not available for checking:
  'text2vec', 'textfeatures'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'koRpus.lang.en', 'koRpus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/textTinyR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/textTools.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ forming offset [176, 183] is out of the bounds [0, 176] of object ‘b’ with type ‘arma::vec’ {aka ‘arma::Col<double>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tfarima.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rsample’
Package suggested but not available for checking: ‘cloudml’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘recipes’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘tframePlus’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tfplot.Rcheck/00install.out’ for details.
Package required but not available: ‘timeSeries’

Packages suggested but not available for checking: 'tfplot', 'xts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ParseTrueFX: no visible global function definition for ‘read.csv’
TrueFXRef: no visible global function definition for ‘download.file’
TrueFXRef: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL download.file read.csv
Consider adding
  importFrom("utils", "browseURL", "download.file", "read.csv")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tggd.Rcheck/00install.out’ for details.
Package required but not available: ‘doFuture’

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

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

Package suggested but not available for checking: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'ggraph'
Error(s) in re-building vignettes:
  ...
--- re-building ‘dev-plan.Rmd’ using rmarkdown
--- finished re-building ‘dev-plan.Rmd’

--- re-building ‘r-and-js.Rmd’ using rmarkdown
Quitting from lines 31-67 (r-and-js.Rmd) 
Error: processing vignette ‘r-and-js.Rmd’ failed with diagnostics:
there is no package called 'ggraph'
--- failed re-building ‘r-and-js.Rmd’

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

SUMMARY: processing the following file failed:
  ‘r-and-js.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'trtf', 'tram', 'rms', 'coin', 'ATR', 'multcomp', 'vcd'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TH.data.Rcheck/00install.out’ for details.
Packages required but not available:
  'tsfeatures', 'feasts', 'R.matlab', 'plotly', 'caret'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'showtext', 'gganimate'
Packages required but not available: 'recipes', 'unbalanced'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fields’
Running examples in ‘Thermimage-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: diffFrame
> ### Title: A frame difference function for subtracting adjacent frames from
> ###   an imported thermal image sequence.
> ### Aliases: diffFrame
> 
> ### ** Examples
> 
> 
> # set w to 640 and h to 480
> w<-640
> h<-480
> f<-system.file("extdata", "SampleSEQ.seq", package = "Thermimage")
> x<-frameLocates(f, w=w, h=h)
> suppressWarnings(templookup<-raw2temp(1:65535))
> alldata<-unlist(lapply(x$f.start, getFrames, vidfile=f, w=w, h=h))
> alldata<-matrix(alldata, nrow=w*h, byrow=FALSE)
> alltemperature<-templookup[alldata]
> alltemperature<-unname(matrix(alltemperature, nrow=w*h, byrow=FALSE))
> 
> dalltemperature<-as.matrix(diffFrame(alltemperature, absolute=TRUE), nrow=w)
> 
> # Plot 
> plotTherm(dalltemperature[,1], templookup=NULL, w=w, h=h,  minrangeset=min(dalltemperature),
+           maxrangeset=max(dalltemperature), trans="mirror.matrix")
Error in loadNamespace(x) : there is no package called ‘fields’
Calls: plotTherm ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/thestats.Rcheck/00install.out’ for details.
Packages required but not available: 'tidyverse', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'hts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Thinknum: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Packages required but not available: 'devtools', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
coef_traceplot: no visible global function definition for ‘rainbow’
coef_traceplot: no visible global function definition for ‘abline’
coef_traceplot : <anonymous>: no visible global function definition for
  ‘lines’
coef_traceplot: no visible global function definition for ‘text’
ee.GEE.aux : <anonymous>: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  abline combn lines rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
Packages required but not available: 'dipsaus', 'gifti'

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

Package suggested but not available for checking: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/thregI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/threg.Rcheck/00install.out’ for details.
Packages required but not available: 'ClassDiscovery', 'PCDimension'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
summary.tsls: no visible global function definition for ‘printCoefmat’
threesls: no visible global function definition for ‘cor’
threesls: no visible global function definition for ‘pt’
tsls.formula: no visible global function definition for ‘model.matrix’
tsls.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  cor model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response",
             "printCoefmat", "pt")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'MplusAutomation', 'rstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'bit64', 'DiagrammeR'
Error(s) in re-building vignettes:
  ...
--- re-building ‘digits.Rmd’ using rmarkdown
--- finished re-building ‘digits.Rmd’

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

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

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

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

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

--- re-building ‘types.Rmd’ using rmarkdown
Quitting from lines 106-117 (types.Rmd) 
Error: processing vignette ‘types.Rmd’ failed with diagnostics:
[1m[22mProblem while computing `Value = map(Expression, rlang::eval_tidy)`.
[1mCaused by error in [1m[1m`loadNamespace()`:[22m
[33m![39m there is no package called 'bit64'
--- failed re-building ‘types.Rmd’

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

Error: Vignette re-building failed.
Execution halted
.LoadTickDataHK: no visible global function definition for ‘read.csv’
.LoadTickDataSHSZ: no visible global function definition for ‘read.csv’
DrawDown: no visible global function definition for ‘na.omit’
PerformanceReport: no visible global function definition for
  ‘aggregate’
PerformanceReport: no visible global function definition for ‘sd’
Undefined global functions or variables:
  aggregate na.omit read.csv sd
Consider adding
  importFrom("stats", "aggregate", "na.omit", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Package suggested but not available for checking: ‘combiter’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tictactoe)
  > 
  > test_check("tictactoe")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-game.R:3:1): (code run outside of `test_that()`) ────────────────
  <packageNotFoundError/error/condition>
  Error in `library(combiter)`: there is no package called 'combiter'
  Backtrace:
      ▆
   1. └─base::library(combiter) at test-game.R:3:0
  ── Error (test-xhash.R:3:1): (code run outside of `test_that()`) ───────────────
  <packageNotFoundError/error/condition>
  Error in `library(combiter)`: there is no package called 'combiter'
  Backtrace:
      ▆
   1. └─base::library(combiter) at test-xhash.R:3:0
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Malformed Title field: should not end in a period.
newTiddler: no visible global function definition for ‘new’
twImage: no visible global function definition for ‘new’
twLink: no visible global function definition for ‘new’
twList: no visible global function definition for ‘new’
twTable: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rstan', 'rjags', 'jagsUI', 'rstanarm', 'dotwhisker', 'MCMCglmm',
  'brms', 'ggrepel', 'gganimate'
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'strex', 'ClusterR', 'framecleaner'

Packages suggested but not available for checking:
  'arulesCBA', 'embed', 'recipes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggforce’
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 127-143 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
there is no package called 'ggforce'
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'tigris', 'readr'

Packages suggested but not available for checking: 'survey', 'srvyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyverse’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tidycharts.Rcheck/00install.out’ for details.
Packages required but not available: 'cmprsk', 'gtsummary'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'framecleaner', 'validata', 'presenter', 'autostats', 'tidybins'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘explore’
Error(s) in re-building vignettes:
  ...
--- re-building ‘tidydice.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 32-35 (tidydice.Rmd) 
Error: processing vignette ‘tidydice.Rmd’ failed with diagnostics:
there is no package called 'explore'
--- failed re-building ‘tidydice.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘readr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 48-49 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'readr'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggrepel’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggrepel’
Package required but not available: ‘strex’

Package suggested but not available for checking: ‘httptest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'graph', 'seriation', 'NetSwan'
Packages required but not available:
  'ComplexHeatmap', 'viridis', 'dendextend'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'wordcloud', 'viridis'
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-tidyjson.Rmd’ using rmarkdown

Attaching package: 'tidyjson'

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

    filter


Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building ‘introduction-to-tidyjson.Rmd’

--- re-building ‘visualizing-json.Rmd’ using rmarkdown

Attaching package: 'jsonlite'

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

    flatten

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

    read_json


Attaching package: 'magrittr'

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

    set_names


Attaching package: 'igraph'

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

    compose, simplify

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

    as_data_frame, groups, union

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

    as_data_frame

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

    decompose, spectrum

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

    union

Quitting from lines 64-78 (visualizing-json.Rmd) 
Error: processing vignette ‘visualizing-json.Rmd’ failed with diagnostics:
there is no package called 'wordcloud'
--- failed re-building ‘visualizing-json.Rmd’

SUMMARY: processing the following file failed:
  ‘visualizing-json.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘tm’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [10s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidylda)
  tidylda is under active development. The API and behavior may change.
  > 
  > test_check("tidylda")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 153 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-utils.R:15:1): (code run outside of `test_that()`) ──────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'tm'
  Backtrace:
      ▆
   1. ├─tidytext::cast_dtm(...) at test-utils.R:15:0
   2. └─base::loadNamespace(x)
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base withOneRestart(expr, restarts[[1L]])
   5.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 153 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘MplusAutomation’

Packages suggested but not available for checking: 'lme4', 'missForest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dials', 'recipes', 'rsample', 'tune', 'workflowsets'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'styler', 'rioja'

Package suggested but not available for checking: ‘vegan’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rsample', 'rstanarm', 'tune', 'workflowsets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'earth', 'RSQLite', 'Cubist', 'partykit'
Error(s) in re-building vignettes:
  ...
--- re-building ‘cubist.Rmd’ using rmarkdown
Quitting from lines 11-18 (cubist.Rmd) 
Error: processing vignette ‘cubist.Rmd’ failed with diagnostics:
there is no package called 'Cubist'
--- failed re-building ‘cubist.Rmd’

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

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

--- re-building ‘mars.Rmd’ using rmarkdown
Quitting from lines 11-18 (mars.Rmd) 
Error: processing vignette ‘mars.Rmd’ failed with diagnostics:
there is no package called 'earth'
--- failed re-building ‘mars.Rmd’

--- re-building ‘non-r.Rmd’ using rmarkdown
--- finished re-building ‘non-r.Rmd’

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

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

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

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

--- re-building ‘sql.Rmd’ using rmarkdown
Quitting from lines 45-49 (sql.Rmd) 
Error: processing vignette ‘sql.Rmd’ failed with diagnostics:
error in evaluating the argument ‘drv’ in selecting a method for function ‘dbConnect’: there is no package called 'RSQLite'
--- failed re-building ‘sql.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘cubist.Rmd’ ‘mars.Rmd’ ‘sql.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'PerformanceAnalytics', 'quantmod', 'Quandl', 'readr',
  'alphavantager', 'timetk', 'TTR', 'xts'

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSQLite’
Packages required but not available: 'labelled', 'furrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘redcapAPI’
Package suggested but not available for checking: ‘readr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘in-packages.Rmd’ using rmarkdown
--- finished re-building ‘in-packages.Rmd’

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

--- re-building ‘pivot.Rmd’ using rmarkdown
Quitting from lines 44-47 (pivot.Rmd) 
Error: processing vignette ‘pivot.Rmd’ failed with diagnostics:
there is no package called 'readr'
--- failed re-building ‘pivot.Rmd’

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘httptest’
Running ‘testthat.R’ [1s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyRSS)
  > 
  > test_check("tidyRSS")
  Error in library(httptest) : there is no package called 'httptest'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Package required but not available: ‘partykit’

Packages suggested but not available for checking:
  'C50', 'Cubist', 'rpart.plot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'blavaan', 'MplusAutomation'

Packages suggested but not available for checking:
  'tidyLPA', 'poLCA', 'umx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Seurat', 'plotly'

Packages suggested but not available for checking: 'GGally', 'SingleR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'bioseq', 'Biostrings', 'seqinr'
Running examples in ‘tidysq-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: export_sq
> ### Title: Export sq objects into other formats
> ### Aliases: export_sq
> 
> ### ** Examples
> 
> # DNA and amino acid sequences can be exported to most packages
> sq_ami <- sq(c("MVVGL", "LAVPP"), alphabet = "ami_bsc")
> export_sq(sq_ami, "ape::AAbin")
2 amino acid sequences in a list

All sequences of the same length: 5 

> export_sq(sq_ami, "bioseq::bioseq_aa")
Error in export_sq.sq_ami_bsc(sq_ami, "bioseq::bioseq_aa") : 
  Assertion on '"bioseq"' failed: you need to install 'bioseq' package.
Calls: export_sq ... export_sq.sq_ami_bsc -> assert_package_installed -> <Anonymous> -> mstop
Execution halted
Package required but not available: ‘readr’

Packages suggested but not available for checking:
  'BayesFactor', 'lme4', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘bit64’
Packages suggested but not available for checking:
  'mallet', 'readr', 'stm', 'textdata', 'tm', 'topicmodels',
  'wordcloud'
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘BART’

Package which this enhances but not available for checking: ‘bartMachine’

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

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

Packages suggested but not available for checking: 'rgdal', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'haven', 'readr'

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

Package suggested but not available for checking: ‘vpc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'WikidataR', 'RSQLite', 'WikidataQueryServiceR'

Package suggested but not available for checking: ‘odbc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qualV', 'klaR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'abd', 'mosaic'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'alakazam', 'shazam', 'doParallel'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rgdal', 'maptools'

Packages suggested but not available for checking:
  'leaflet', 'rgeos', 'tidycensus'

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

Package suggested but not available for checking: ‘bit64’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘leaflet’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tilegramsR.Rcheck/00install.out’ for details.
Packages required but not available: 'APfun', 'raster', 'rgeos'

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

Package suggested but not available for checking: ‘spData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rgdal', 'raster'

Package suggested but not available for checking: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tilting.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/timedeppar.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/timeline.Rcheck/00install.out’ for details.
Package required but not available: ‘mtconnectR’

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

Package suggested but not available for checking: ‘mets’

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

Package suggested but not available for checking: ‘timereg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/timesboot.Rcheck/00install.out’ for details.
Packages required but not available: 'RPostgres', 'xts'

Package suggested but not available for checking: ‘dygraphs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'tseries'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'xts', 'PerformanceAnalytics', 'fTrading'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/timeSeries.Rcheck/00install.out’ for details.
Packages required but not available:
  'recipes', 'rsample', 'plotly', 'readr', 'xts', 'forecast',
  'tsfeatures'

Packages suggested but not available for checking:
  'tidyquant', 'tidymodels', 'modeltime', 'tune', 'tidyverse',
  'robets', 'timeSeries', 'tseries'

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

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

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'gclus'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'clusterProfiler', 'org.Hs.eg.db', 'survminer'

Packages suggested but not available for checking:
  'AnnoProbe', 'GEOquery', 'Biobase', 'VennDiagram', 'FactoMineR',
  'factoextra', 'ggpubr', 'ComplexHeatmap'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bayesSurv’
Running examples in ‘TippingPoint-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TippingPoint
> ### Title: Generic function for Enhanced Tipping Point Displays
> ### Aliases: TippingPoint
> 
> ### ** Examples
> 
> TippingPoint(outcome=tippingdata$binary, treat= tippingdata$treat,
+   group.infor=TRUE, plot.type = "estimate",ind.values = TRUE,
+   impValuesT  = NA,  impValuesC = NA,
+   summary.type = "density", alpha = 0.95, S=1.5, n.grid = 100,
+   HistMeanT = c(0.38,0.4), HistMeanC =  c(0.2,0.55))
Error: Package "pkg" must be installed to use this function.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘TippingPoint.Rmd’ using rmarkdown
Quitting from lines 58-105 (TippingPoint.Rmd) 
Error: processing vignette ‘TippingPoint.Rmd’ failed with diagnostics:
Package "pkg" must be installed to use this function.
--- failed re-building ‘TippingPoint.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'rstan', 'maptools', 'rgeos', 'spdep', 'ggpubr'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘flexmix’
FLXmclust.Density: no visible global function definition for ‘dmvnorm’
FLXmclust.Estimate: no visible global function definition for ‘flexmix’
FLXmclust.Estimate: no visible global function definition for
  ‘FLXmclust’
coefmclust: no visible global function definition for ‘parameters’
flexmix.Density: no visible global function definition for
  ‘model.matrix’
flexmix.Density: no visible global function definition for
  ‘model.response’
flexmix.Density: no visible global function definition for
  ‘model.frame’
flexmix.Density: no visible global function definition for ‘dnorm’
flexmix.Density: no visible global function definition for ‘dpois’
flexmix.Density: no visible global function definition for ‘dbinom’
flexmix.Estimate: no visible global function definition for ‘flexmix’
flexmix.Estimate: no visible global function definition for ‘FLXglm’
tleplot,TLE-data.frame: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  FLXglm FLXmclust dbinom dmvnorm dnorm dpois flexmix legend
  model.frame model.matrix model.response parameters
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "dbinom", "dnorm", "dpois", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tlmec.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TLMoments.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tlm.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'tmaptools', 'stars', 'widgetframe', 'leaflet', 'leafsync', 'leafem'

Package suggested but not available for checking: ‘rmapshaper’

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

Packages suggested but not available for checking:
  'tmap', 'rmapshaper', 'OpenStreetMap', 'raster'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tm’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TMDb.Rcheck/00install.out’ for details.
Packages required but not available: 'R.utils', 'R.oo', 'geometry'

Packages suggested but not available for checking: 'SuperLearner', 'gam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'SuperLearner'

Package suggested but not available for checking: ‘gam’

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

Package suggested but not available for checking: ‘R.rsp’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'koRpus', 'tm'

Package suggested but not available for checking: ‘koRpus.lang.en’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tmpm.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'Rcampdf', 'Rgraphviz', 'tm.lexicon.GeneralInquirer'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tm.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘dexterMST’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘gmm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tnet.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘devtools’
Packages suggested but not available for checking: 'AER', 'censReg'
Error(s) in re-building vignettes:
  ...
--- re-building ‘charitable.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required namespace: AER
Failed with error:  'there is no package called 'AER''
Loading required namespace: censReg
Failed with error:  'there is no package called 'censReg''
Loading required namespace: modelsummary
Quitting from lines 129-131 (charitable.Rmd) 
Error: processing vignette ‘charitable.Rmd’ failed with diagnostics:
object ‘ml_aer’ not found
--- failed re-building ‘charitable.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'raster', 'rgdal'

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

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

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

Package suggested but not available for checking: ‘tidycensus’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'calibrate', 'HardyWeinberg'

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

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

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

Packages suggested but not available for checking:
  'uwot', 'ggrepel', 'ggalt'

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

Package suggested but not available for checking: ‘corpus.JSS.papers’

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

Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2', 'gWidgets2RGtk2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘topmodel-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: topmodel
> ### Title: implementation of the hydrological model TOPMODEL
> ### Aliases: topmodel
> ### Keywords: models
> 
> ### ** Examples
> 
> data(huagrahuma)
> attach(huagrahuma)
> 
> ## returns the simulated runoff (Qobs not given)
> Qsim <- topmodel(parameters, topidx, delay, rain, ETp)
> 
> ## returns a list of simulated runoff (Q), overland flow (qo), subsurface flow (qs) and storage (S):
> Qsim <- topmodel(parameters, topidx, delay, rain,ETp, verbose = TRUE)
> 
> ## plot observed and simulated discharge:
> plot(Qobs)
> points(Qsim$Q, col="red", type="l")
> 
> ## For a Monte carlo sampling from a uniform distribution, we construct a parameter matrix:
> 
> runs<-10
> 
> qs0   <- runif(runs, min=0, max=4e-5)
> lnTe  <- runif(runs, min=-2, max=1)
> m     <- runif(runs, min=0, max=0.2)
> Sr0   <- runif(runs, min=0, max=0.02)
> Srmax <- runif(runs, min=0, max=2)
> td    <- runif(runs, min=0, max=3)
> vch   <- 1000
> vr    <- runif(runs, min=100, max=2500)
> k0    <- runif(runs, min=0, max=0.01)
> CD    <- runif(runs, min=0, max=5)
> dt    <- 0.25
> 
> parameters<-cbind(qs0,lnTe,m,Sr0,Srmax,td,vch,vr,k0,CD,dt)
> 
> ## returns an array of 10 Nash Sutcliffe efficiencies; one for each parameter set:
> result<-topmodel(parameters, topidx, delay, rain, ETp, Qobs = Qobs)
Iteration:                1       2       3       4       5       6       7       8       9      10
Error in (Qobs == -9999) && (iterations > 1) : 
  'length = 10000' in coercion to 'logical(1)'
Calls: topmodel
Execution halted
Packages required but not available: 'gdistance', 'plotly', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'graph', 'gRbase', 'qpgraph', 'fields'

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'ggrepel', 'egg'

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

Packages suggested but not available for checking: 'monitoR', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'torch', 'pins', 'torchvision'

Package suggested but not available for checking: ‘readr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bit64’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'caret', 'glmnet'
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tornado)
  > 
  > test_check("tornado")
  Error in loadNamespace(x) : there is no package called 'caret'
  Calls: test_check ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tornadoVignette.Rmd’ using rmarkdown
Quitting from lines 159-165 (tornadoVignette.Rmd) 
Error: processing vignette ‘tornadoVignette.Rmd’ failed with diagnostics:
could not find function "ggtitle"
--- failed re-building ‘tornadoVignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘readr’

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

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

Packages suggested but not available for checking: 'toscaData', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Tosls.formula: no visible global function definition for ‘model.matrix’
Tosls.formula: no visible global function definition for
  ‘model.response’
summary: no visible global function definition for ‘coef’
summary: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
Packages required but not available: 'bibliometrix', 'CINNA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'car', 'afex'
Running ‘testthat.R’ [75s/108s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(TOSTER)
  > 
  > test_check("TOSTER")
  Note: this function is defunct. Please use power_t_TOST instead
  
  Note: this function is defunct. Please use power_t_TOST instead
  
  Note: this function is defunct. Please use power_t_TOST instead
  
  Note: this function is defunct. Please use power_t_TOST instead
  
  Note: this function is defunct. Please use power_t_TOST instead
  
  Note: this function is defunct. Please use power_t_TOST instead
  
  
  Note: this function is defunct. Please use power_t_TOST instead
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 372 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-ftests.R:91:3): Equivalence F-tests ─────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(afex, verbose = FALSE, quietly = TRUE)`: there is no package called 'afex'
  Backtrace:
      ▆
   1. ├─base::suppressMessages(...) at test-ftests.R:91:2
   2. │ └─base::withCallingHandlers(...)
   3. ├─TOSTER hush(suppressWarnings(library(afex, verbose = FALSE, quietly = TRUE)))
   4. ├─base::suppressWarnings(library(afex, verbose = FALSE, quietly = TRUE)) at test-ftests.R:10:4
   5. │ └─base::withCallingHandlers(...)
   6. └─base::library(afex, verbose = FALSE, quietly = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 372 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘TreeTools’

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

Package suggested but not available for checking: ‘tcpl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘S4Vectors’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
ConfA: no visible global function definition for ‘qf’
EstM2Sn: no visible global function definition for ‘nlm’
EstM2Sn: no visible global function definition for ‘qnorm’
TV.model: no visible global function definition for ‘dev.new’
TV.model: no visible global function definition for ‘points’
betaBino: no visible global function definition for ‘pbinom’
doseD: no visible global function definition for ‘lm’
doseD: no visible global function definition for ‘dev.new’
doseD: no visible global function definition for ‘par’
doseD: no visible global function definition for ‘axTicks’
doseD: no visible global function definition for ‘axis’
doseD: no visible global function definition for ‘lines’
doseD: no visible global function definition for ‘abline’
doseD: no visible global function definition for ‘legend’
setD: no visible global function definition for ‘dev.new’
setD: no visible global function definition for ‘par’
setD: no visible global function definition for ‘pbinom’
setD: no visible global function definition for ‘abline’
setD: no visible global function definition for ‘axis’
setD: no visible global function definition for ‘rect’
setD: no visible global function definition for ‘lines’
setD: no visible global function definition for ‘text’
setD: no visible global function definition for ‘axTicks’
setD: no visible global function definition for ‘legend’
spoD : spoD_A: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘01_spontaneous lethality.txt’ ‘02.sample size.txt’
  ‘03.dosestrategy.txt’ ‘doseD4.txt’ ‘setD.txt’ ‘spoDa.txt’ ‘spoDb.txt’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ks’

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

Package suggested but not available for checking: ‘geeM’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'haven', 'tidyverse', 'readr'
Running ‘testthat.R’ [62s/90s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Tplyr)
  > 
  > test_check("Tplyr")
  [ FAIL 3 | WARN 0 | SKIP 52 | PASS 539 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (52)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-count.R:742:3): Posix columns don't cause the build to error out. ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'haven'
  Backtrace:
      ▆
   1. ├─... %>% rename(TRTA = TRT01A) at test-count.R:742:2
   2. ├─dplyr::rename(., TRTA = TRT01A)
   3. ├─dplyr::mutate(...)
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base withOneRestart(expr, restarts[[1L]])
   7.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test-desc.R:202:3): Auto precision builds correctly ──────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'readr'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-desc.R:202:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test-sort.R:148:1): (code run outside of `test_that()`) ──────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'haven'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-sort.R:148:0
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 3 | WARN 0 | SKIP 52 | PASS 539 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Tplyr.Rmd’ using rmarkdown
Quitting from lines 20-27 (Tplyr.Rmd) 
Error: processing vignette ‘Tplyr.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘Tplyr.Rmd’

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

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

--- re-building ‘desc.Rmd’ using rmarkdown
Quitting from lines 20-26 (desc.Rmd) 
Error: processing vignette ‘desc.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘desc.Rmd’

--- re-building ‘options.Rmd’ using rmarkdown
Quitting from lines 20-28 (options.Rmd) 
Error: processing vignette ‘options.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘options.Rmd’

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

--- re-building ‘table.Rmd’ using rmarkdown
Quitting from lines 20-26 (table.Rmd) 
Error: processing vignette ‘table.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘table.Rmd’

SUMMARY: processing the following files failed:
  ‘Tplyr.Rmd’ ‘desc.Rmd’ ‘options.Rmd’ ‘table.Rmd’

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: ‘p3state.msm’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TPmsm.Rcheck/00install.out’ for details.
Package required but not available: ‘skewMLRM’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘phangorn’
Error(s) in re-building vignettes:
  ...
--- re-building ‘demo.Rmd’ using rmarkdown
Quitting from lines 106-110 (demo.Rmd) 
Error: processing vignette ‘demo.Rmd’ failed with diagnostics:
there is no package called 'phangorn'
--- failed re-building ‘demo.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adehabitatHR', 'maptools', 'Matching', 'move', 'raster', 'rgdal',
  'rgeos'

Packages suggested but not available for checking:
  'adehabitatLT', 'doParallel'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'readr', 'adehabitatLT', 'move', 'moveVis', 'ctmm', 'moveHMM',
  'mapproj'
Running examples in ‘trackdf-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: projection
> ### Title: Access/Modify the Projection of a Track Table
> ### Aliases: projection projection<- project
> 
> ### ** Examples
> 
> data(tracks)
> 
> projection(tracks)
Coordinate Reference System:
Deprecated Proj.4 representation: +proj=longlat +ellps=WGS84 
Warning in wkt(x) : CRS object has no comment
> tracks_projected <- project(tracks, "+proj=somerc")
Error in sp::spTransform(tmp, value) : 
  package rgdal is required for spTransform methods
Calls: project -> projection<- -> <Anonymous> -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘z1_install.Rmd’ using rmarkdown
--- finished re-building ‘z1_install.Rmd’

--- re-building ‘z2_build.Rmd’ using rmarkdown

Attaching package: 'lubridate'

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

    date, intersect, setdiff, union

Quitting from lines 31-35 (z2_build.Rmd) 
Error: processing vignette ‘z2_build.Rmd’ failed with diagnostics:
arguments imply differing number of rows: 0, 1
--- failed re-building ‘z2_build.Rmd’

--- re-building ‘z3_manipulate.Rmd’ using rmarkdown
Quitting from lines 136-138 (z3_manipulate.Rmd) 
Error: processing vignette ‘z3_manipulate.Rmd’ failed with diagnostics:
package rgdal is required for spTransform methods
--- failed re-building ‘z3_manipulate.Rmd’

SUMMARY: processing the following files failed:
  ‘z2_build.Rmd’ ‘z3_manipulate.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'trackeR', 'plotly', 'changepoint'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'RSQLite', 'raster', 'scam', 'fda', 'leaflet', 'ggmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘scriptests’
Found the following calls to attach():
File ‘track/R/track.attach.R’:
  attach(what = NULL, pos = pos, name = name)
See section ‘Good practice’ in ‘?attach’.
Package required but not available: ‘fields’

Package suggested but not available for checking: ‘onion’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Momocs', 'raster', 'features'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘arrow’
Package required but not available: ‘PerformanceAnalytics’

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

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ada', 'adabag', 'glmnet', 'rpart.plot'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'taxize'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'trajectories', 'xts', 'spacetime', 'RPostgreSQL', 'rgdal'

Package suggested but not available for checking: ‘rgeos’

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

Packages suggested but not available for checking:
  'rgdal', 'rgeos', 'OpenStreetMap', 'adehabitatLT', 'xts', 'forecast',
  'spatstat', 'spatstat.core', 'spatstat.geom', 'taxidata'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readr’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [17s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(trajr)
  > 
  > test_check("trajr")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 191 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_basic.R:420:3): works with readr ────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'readr'
  Backtrace:
      ▆
   1. ├─trajr::TrajsBuild(...) at test_basic.R:420:2
   2. │ └─trajr:::.readAndCheckCoords(fn, csvReadFn, ...)
   3. └─base::loadNamespace(x)
   4.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   5.     └─base withOneRestart(expr, restarts[[1L]])
   6.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 191 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'TraMineR', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'weights', 'cNORM'

Package suggested but not available for checking: ‘TraMineRextras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tram', 'mlt', 'alabama', 'lme4', 'basefun'

Packages suggested but not available for checking:
  'multcomp', 'coxme', 'ordinalCont', 'gamm4', 'gamlss.dist', 'glmmTMB'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tram', 'CVXR', 'mlrMBO', 'mlt', 'basefun', 'mlr', 'smoof'

Packages suggested but not available for checking:
  'penalized', 'TH.data', 'glmnet', 'trtf', 'coin', 'tbm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mlt', 'multcomp', 'basefun'

Packages suggested but not available for checking:
  'TH.data', 'trtf', 'quantreg', 'ATR', 'lme4', 'merDeriv', 'alabama',
  'latticeExtra', 'ordinalCont', 'coxme', 'glmmsr', 'mlt.docreg',
  'coin', 'asht', 'gamlss'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
microsoftTranslate: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggformula’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TransModel.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ks’
Running examples in ‘transport-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: transport_track
> ### Title: Create a Dynamic Visualization of a Transference Plan Between
> ###   Two pgrids
> ### Aliases: transport_track
> 
> ### ** Examples
> 
> tplan <- transport(random32a,random32b)
Power p of Euclidean distance assumed to be 1 
> series <- transport_track(random32a, random32b, tplan, scmult=3, create.file="none")
Error in transport_track(random32a, random32b, tplan, scmult = 3, create.file = "none") : 
  Package 'ks' required. Please install it.
Execution halted
Package required but not available: ‘truncSP’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DescTools’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [13s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(transx)
  > 
  > test_check("transx")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 115 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-outliers.R:8:3): winsorize ──────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'DescTools'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(out_winsorise(x), DescTools::Winsorize(x)) at test-outliers.R:8:2
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base withOneRestart(expr, restarts[[1L]])
   7.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 115 ]
  Error: Test failures
  Execution halted
rtrapezoid: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
checkRd: (7) Dados6.Rd:27: invalid email address: <alcineimistico@hotmail.com>
Packages required but not available: 'ggpubr', 'TSA'

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

Package suggested but not available for checking: ‘PerformanceAnalytics’

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

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lmtest', 'np'

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

Package suggested but not available for checking: ‘adaptiveGPCA’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'phangorn', 'TreeTools'

Packages suggested but not available for checking:
  'hypervolume', 'kdensity', 'Quartet', 'TreeDistData', 'TreeSearch',
  'Umatrix', 'uwot'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Seurat', 'plotly'
Running examples in ‘treefit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generate_n_arms_star_data
> ### Title: Generate a multi-dimensional star tree data
> ### Aliases: generate_n_arms_star_data
> 
> ### ** Examples
> 
> # Generate a 100-dimensional star tree data that contain 500 data points
> # and fit a star tree with 3 arms. The generated data are a bit noisy but
> # tree-like.
> star100.tree_like <- treefit::generate_n_arms_star_data(100, 500, 3, 0.1)
> # Reduce dimension to visualize.
> star3.tree_like = prcomp(star100.tree_like, rank.=3)$x
> plotly::plot_ly(data.frame(star3.tree_like),
+                 x=~PC1,
+                 y=~PC2,
+                 z=~PC3,
+                 type="scatter3d",
+                 mode="markers",
+                 marker=list(size=1))
Error in loadNamespace(x) : there is no package called ‘plotly’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'ggparty', 'partykit', 'seriation'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Build_JTree: no visible global function definition for ‘flush.console’
Run_JTree: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  cov2cor flush.console
Consider adding
  importFrom("stats", "cov2cor")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Packages required but not available: 'phytools', 'geiger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rogue', 'TreeDist', 'TreeTools'

Packages suggested but not available for checking: 'phangorn', 'Quartet'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'adegraphics', 'adephylo', 'distory', 'fields',
  'phangorn', 'phytools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bit64', 'R.cache'

Package suggested but not available for checking: ‘phangorn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat.geom', 'spatstat.core', 'raster', 'rasterVis', 'geometry',
  'rgdal', 'rgeos', 'lidR', 'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
Running examples in ‘trelliscopejs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cog
> ### Title: Cast Column as a Cognostic
> ### Aliases: cog
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(tidyr)
> library(purrr)
> library(ggplot2)
> library(plotly)
Error in library(plotly) : there is no package called ‘plotly’
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(trelliscopejs)
  > 
  > test_check("trelliscopejs")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-trelliscope.R:8:3): examples run without barfing ────────────────
  <packageNotFoundError/error/condition>
  Error in `library(plotly)`: there is no package called 'plotly'
  Backtrace:
      ▆
   1. ├─base::suppressPackageStartupMessages(library(plotly)) at test-trelliscope.R:8:2
   2. │ └─base::withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
   3. └─base::library(plotly)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘trelliscopejs.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 174-192 (trelliscopejs.Rmd) 
Error: processing vignette ‘trelliscopejs.Rmd’ failed with diagnostics:
there is no package called 'plotly'
--- failed re-building ‘trelliscopejs.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'trending', 'rsample'

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

Package suggested but not available for checking: ‘brms’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘strucchange’
Packages required but not available:
  'changepoint', 'forecast', 'Rssa', 'tseries', 'imputeTS'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'solaR', 'doParallel', 'randtoolbox', 'doSNOW', 'msm'

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'snpStats', 'doParallel'

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

Package suggested but not available for checking: ‘DiagrammeR’

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

Package suggested but not available for checking: ‘leaflet’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fpc’
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘trimr-vignette.Rmd’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/trimTrees.Rcheck/00install.out’ for details.
Package required but not available: ‘msm’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'lme4', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TripleR.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'spatstat.geom', 'spatstat.core', 'viridis'

Package suggested but not available for checking: ‘adehabitatLT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/triversity.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'viridis', 'haven'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'msm', 'GA', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'hdrcde', 'MCMCglmm', 'rjags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Packages required but not available: 'mlt', 'partykit', 'tram'

Packages suggested but not available for checking: 'TH.data', 'coin'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
DrawMargin: no visible global function definition for ‘qnorm’
DrawProbability: no visible global function definition for ‘pnorm’
Factor: no visible global function definition for ‘new’
Gaussian: no visible global function definition for ‘new’
LikelihoodFactor: no visible global function definition for ‘new’
Parameters: no visible global function definition for ‘new’
Player: no visible global function definition for ‘new’
PriorFactor: no visible global function definition for ‘new’
SumFactor: no visible global function definition for ‘new’
TruncateFactor: no visible global function definition for ‘new’
Variable: no visible global function definition for ‘new’
Vdraw: no visible global function definition for ‘dnorm’
Vdraw: no visible global function definition for ‘pnorm’
Vwin: no visible global function definition for ‘dnorm’
Vwin: no visible global function definition for ‘pnorm’
Wdraw: no visible global function definition for ‘dnorm’
Wdraw: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm new pnorm qnorm
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages required but not available: 'Rfast', 'doParallel', 'fpc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'randtoolbox', 'alabama'

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

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

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

Package suggested but not available for checking: ‘R.utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'readr', 'ez'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'vars', 'hdm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'forecast', 'dygraphs', 'xts', 'tseries', 'timeSeries', 'imputeTS'
Running examples in ‘tsbox-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ts_c
> ### Title: Collect Time Series
> ### Aliases: ts_c
> 
> ### ** Examples
> 
> head(ts_c(ts_df(EuStockMarkets), AirPassengers))
   id                time   value
1 DAX 1991-07-01 03:18:27 1628.75
2 DAX 1991-07-02 13:01:32 1613.63
3 DAX 1991-07-03 22:44:38 1606.51
4 DAX 1991-07-05 08:27:43 1621.04
5 DAX 1991-07-06 18:10:48 1618.16
6 DAX 1991-07-08 03:53:53 1610.61
> 
> # labeling
> x <- ts_c(
+   `International Airline Passengers` = ts_xts(AirPassengers),
+   `Deaths from Lung Diseases` = ldeaths
+ )
Loading required namespace: xts
Failed with error:  ‘there is no package called ‘xts’’
Error in ts_xts_dts(ts_dts(x)) : requireNamespace("xts") is not TRUE
Calls: ts_c -> ts_xts -> ts_xts_dts -> stopifnot
Execution halted
Packages required but not available: 'ICtest', 'forecast', 'xts'

Packages suggested but not available for checking: 'MTS', 'dr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dtw', 'longitudinalData', 'forecast'

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

Packages suggested but not available for checking:
  'tframePlus', 'TSsql', 'TSMySQL', 'TSSQLite', 'TSmisc'

Packages which this enhances but not available for checking:
  'TSPostgreSQL', 'TSodbc', 'TSfame'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'xts', 'rvinecopulib', 'FitAR', 'arfima'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘surveillance’
Qhat: no visible global function definition for ‘pnorm’
plrt: no visible global function definition for ‘uniroot’
plrt: no visible global function definition for ‘optimize’
simulatedata: no visible global function definition for ‘rnorm’
tsc.test: no visible global function definition for ‘shapiro.test’
tsc.test: no visible global function definition for ‘p.adjust’
tsc.test: no visible global function definition for ‘glm’
tsc.test : f: no visible global function definition for ‘pnorm’
tsc.test: no visible global function definition for ‘uniroot’
tsc.test: no visible global function definition for ‘optimize’
variance: no visible global function definition for ‘density’
variance: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  density ecdf glm optimize p.adjust pnorm rnorm shapiro.test uniroot
Consider adding
  importFrom("stats", "density", "ecdf", "glm", "optimize", "p.adjust",
             "pnorm", "rnorm", "shapiro.test", "uniroot")
to your NAMESPACE file.
Package required but not available: ‘tseries’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'tframePlus', 'tfplot', 'TSsql', 'TSPostgreSQL', 'TSMySQL',
  'TSSQLite', 'TSodbc', 'TSsdmx', 'TSmisc', 'TScompare', 'xts',
  'tseries', 'RPostgreSQL', 'RSQLite', 'RMySQL', 'RJSDMX'
Packages suggested but not available for checking:
  'tseries', 'tfplot', 'tframePlus'
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Packages required but not available:
  'dtw', 'longitudinalData', 'TSclust', 'xts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'party', 'survRM2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tseries', 'vars', 'forecast'

Packages suggested but not available for checking: 'tidyverse', 'rugarch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'xts', 'glmnet', 'earth', 'Cubist', 'monmlp', 'doParallel',
  'softImpute'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xts', 'quantmod'

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

Packages suggested but not available for checking: 'tseries', 'tfplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'tseries', 'furrr'

Packages suggested but not available for checking: 'Mcomp', 'GGally'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'edgeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘nanotime’
Packages required but not available: 'dendextend', 'plotly'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TSMCP.Rcheck/00install.out’ for details.
Func.SAX: no visible global function definition for ‘sd’
Func.SAX: no visible global function definition for ‘qnorm’
Func.matrix: no visible global function definition for ‘qnorm’
Func.motif: no visible global function definition for ‘sd’
Func.motif: no visible global function definition for ‘na.omit’
Func.motif: no visible global function definition for ‘combn’
Func.motif.multivariate: no visible global function definition for
  ‘txtProgressBar’
Func.motif.multivariate: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  combn na.omit qnorm sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "qnorm", "sd")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages required but not available: 'tframePlus', 'tseries', 'quantmod'

Packages suggested but not available for checking:
  'tfplot', 'xts', 'timeSeries'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gam’
Malformed Description field: should contain one or more complete sentences.
dLag : dlag.f: no visible global function definition for
  ‘complete.cases’
distmat: no visible global function definition for ‘dist’
fitCity: no visible global function definition for ‘glm.control’
fitCity: no visible global function definition for ‘terms’
ldmvnorm: no visible global function definition for ‘mahalanobis’
lspline: no visible global function definition for ‘quantile’
plot.tsdecomp: no visible global function definition for ‘par’
setupFormula: no visible global function definition for ‘as.formula’
spatialgibbs: no visible global function definition for ‘rnorm’
spatialgibbs: no visible global function definition for ‘rgamma’
spatialgibbs: no visible global function definition for ‘runif’
tsdecomp: no visible global function definition for ‘fft’
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
Package required but not available: ‘doSNOW’

Package suggested but not available for checking: ‘raster’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'TSsql', 'RMySQL'

Packages suggested but not available for checking:
  'tseries', 'tfplot', 'tframePlus', 'timeSeries'

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

Packages suggested but not available for checking:
  'networkDynamicData', 'sna', 'relevent', 'ergm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tframePlus', 'TSsql'

Packages suggested but not available for checking: 'tseries', 'tfplot'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fpc', 'vegan', 'splancs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tframePlus', 'TSsql', 'RPostgreSQL'

Packages suggested but not available for checking: 'tseries', 'tfplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'maptools', 'doParallel'
Error(s) in re-building vignettes:
  ...
--- re-building ‘TSP.Rnw’ using Sweave
Loading required package: sp
Loading required package: maps
Loading required package: maptools
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'maptools'

Error: processing vignette ‘TSP.Rnw’ failed with diagnostics:
 chunk 12 (label = map2) 
Error in plot_path(path) : could not find function "plot_path"

--- failed re-building 'TSP.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'forecast', 'EMD', 'vars', 'RSNNS', 'elmNNRcpp'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'glmnet', 'quantreg', 'textTinyR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tframePlus', 'RJSDMX'

Package suggested but not available for checking: ‘tfplot’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xts', 'dsa'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tframePlus', 'TSsql', 'RSQLite'

Packages suggested but not available for checking: 'tseries', 'tfplot'

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

Packages suggested but not available for checking:
  'tseries', 'tfplot', 'RMySQL', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bfast', 'strucchange'

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forecast', 'forecastHybrid', 'future.apply', 'plotly', 'viridis',
  'xts'

Packages suggested but not available for checking:
  'devtools', 'quantmod', 'UKgrid'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘TSTr.Rmd’ using rmarkdown
Quitting from lines 167-170 (TSTr.Rmd) 
Error: processing vignette ‘TSTr.Rmd’ failed with diagnostics:
'length = 1876' in coercion to 'logical(1)'
--- failed re-building ‘TSTr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘XMIwords.txt’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TSTutorial.Rcheck/00install.out’ for details.
Packages required but not available: 'forecast', 'MAPA'

Package suggested but not available for checking: ‘thief’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AER’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TSVC.Rcheck/00install.out’ for details.
Packages required but not available: 'plotly', 'forecast'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat', 'spatstat.geom', 'spatstat.core', 'spatstat.random',
  'spatstat.linnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantreg', 'VennDiagram'

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

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

Package which this enhances but not available for checking: ‘quantmod’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ttwa.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'raster', 'readr', 'rgdal', 'gstat'

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

Packages suggested but not available for checking: 'pbkrtest', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ddalpha', 'Rglpk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'multcomp', 'pbkrtest', 'lme4'

Package suggested but not available for checking: ‘SimComp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tumblR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tumgr.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'snowfall', 'desire', 'klaR'
Packages required but not available: 'mlrMBO', 'mlr', 'smoof'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dials', 'recipes', 'rsample'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'quantreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyverse', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tvem.Rcheck/00install.out’ for details.
Packages required but not available: 'garchx', 'hier.part'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'systemfit', 'vars', 'plm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'twang', 'latticeExtra', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survey', 'latticeExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/twangRDC.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'readr', 'topicmodels', 'stm', 'leaflet', 'ldatuning', 'tm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bit64’

Packages suggested but not available for checking: 'RSQLite', 'RMySQL'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readr’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TwoArmSurvSim.Rcheck/00install.out’ for details.
TwoCop: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'multcomp', 'glmmTMB', 'doParallel'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'hal9001', 'haldensify'

Packages suggested but not available for checking:
  'future.apply', 'origami'

Package which this enhances but not available for checking: ‘sl3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'raster', 'rgdal', 'rgeos', 'link2GI'

Packages suggested but not available for checking: 'mapview', 'maptools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Crm: no visible global function definition for ‘integrate’
Crm : <anonymous>: no visible global function definition for
  ‘integrate’
Crm: no visible global function definition for ‘optimize’
ail1: no visible global function definition for ‘uniroot’
ail2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ail2: no visible global function definition for ‘uniroot’
aip : fu : <anonymous>: no visible global function definition for
  ‘integrate’
aip: no visible global function definition for ‘uniroot’
ait1: no visible global function definition for ‘uniroot’
ait2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ait2: no visible global function definition for ‘uniroot’
sim3p3: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘palette’
simCrm: no visible global function definition for ‘gray’
simCrm: no visible global function definition for ‘abline’
simCrm: no visible global function definition for ‘lines’
ssim3p3: no visible global function definition for ‘txtProgressBar’
ssim3p3: no visible global function definition for ‘setTxtProgressBar’
ssimCrm: no visible global function definition for ‘txtProgressBar’
ssimCrm: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  abline gray integrate lines optimize palette rbinom setTxtProgressBar
  txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package required but not available: ‘doParallel’

Packages suggested but not available for checking:
  'GA', 'GGally', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gstat', 'automap'

Package suggested but not available for checking: ‘DMwR2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'unmarked', 'lme4', 'rstan'

Packages suggested but not available for checking: 'devtools', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
rmd2pdf: no visible global function definition for ‘tail’
rnw2pdf: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Packages required but not available: 'geometry', 'ptinpoly'

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

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

Packages suggested but not available for checking:
  'furrr', 'ggrepel', 'ggstatsplot', 'plotly', 'survminer'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘topicmodels’
Packages required but not available: 'esemifar', 'rugarch', 'smoots'

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

Packages suggested but not available for checking:
  'bootES', 'car', 'GGally', 'MBESS', 'rio', 'viridis'

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

Packages suggested but not available for checking: 'xts', 'dygraphs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gamlss', 'gamlss.dist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'clValid', 'FactoMineR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'questionr', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'doParallel'

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

Packages suggested but not available for checking: 'devtools', 'TSstudio'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘leaflet’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Ultimixt.Rcheck/00install.out’ for details.
Packages required but not available: 'fields', 'geometry'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'readr', 'Rsamtools', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘mc2d’

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

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

Packages suggested but not available for checking: 'devtools', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mlr', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/uncertainty.Rcheck/00install.out’ for details.
Package required but not available: ‘NlcOptim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'R.utils'

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

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

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rstan’
Package suggested but not available for checking: ‘geometry’
Error(s) in re-building vignettes:
  ...
--- re-building ‘convexhull.Rmd’ using rmarkdown
Quitting from lines 41-44 (convexhull.Rmd) 
Error: processing vignette ‘convexhull.Rmd’ failed with diagnostics:
there is no package called 'geometry'
--- failed re-building ‘convexhull.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘orthopolynom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyverse', 'ggpubr', 'alakazam', 'gprofiler2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
cumcount: no visible global function definition for ‘setNames’
uniqtag: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Packages required but not available: 'DoseFinding', 'SEL'

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

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

Packages suggested but not available for checking: 'tidyverse', 'devtools'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lme4’

Packages suggested but not available for checking: 'AHMbook', 'raster'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘ltm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doFuture', 'doRNG'

Packages suggested but not available for checking:
  'VariantAnnotation', 'GenomicRanges', 'S4Vectors', 'IRanges'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSQLite', 'dimRed', 'loe'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'sampleSelection', 'maxLik', 'mfx', 'mlogit', 'mvProbit'
Error(s) in re-building vignettes:
  ...
--- re-building ‘ExtendedAppendix.Rnw’ using knitr
--- finished re-building ‘ExtendedAppendix.Rnw’

--- re-building ‘Manuscript.Rnw’ using knitr
Quitting from lines 159-160 (Manuscript.Rnw) 
Error: processing vignette ‘Manuscript.Rnw’ failed with diagnostics:
there is no package called 'sampleSelection'
--- failed re-building ‘Manuscript.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Tutorial.Rmd’ using rmarkdown
Quitting from lines 117-118 (Tutorial.Rmd) 
Error: processing vignette ‘Tutorial.Rmd’ failed with diagnostics:
lexical error: invalid char in json text.
                                       <!DOCTYPE html> <!--[if lt IE 7
                     (right here) ------^

--- failed re-building ‘Tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘rgdal’

Packages suggested but not available for checking:
  'raster', 'fasterize', 'rgeos', 'leaflet', 'leafem', 'widgetframe'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'USAboundariesData', 'leaflet'
Error(s) in re-building vignettes:
  ...
--- re-building ‘usaboundaries-sample-analysis.Rmd’ using rmarkdown
The USAboundariesData package needs to be installed.
 Please try installing the package using the following command: 
     install.packages("USAboundariesData", repos = "https://ropensci.r-universe.dev", type = "source")

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Linking to GEOS 3.10.2, GDAL 3.4.2, PROJ 9.0.0; sf_use_s2() is TRUE
Quitting from lines 23-30 (usaboundaries-sample-analysis.Rmd) 
Error: processing vignette ‘usaboundaries-sample-analysis.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
--- failed re-building ‘usaboundaries-sample-analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘usaboundaries-sample-analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'USA.state.boundaries.data', 'rgdal', 'raster', 'ggspatial'
Package required but not available: ‘rgdal’

Package suggested but not available for checking: ‘diseasemapping’

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

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

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

Package suggested but not available for checking: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘tidyverse’

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

Package suggested but not available for checking: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/useful.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘readr’
'LazyData' is specified without a 'data' directory
Running examples in ‘usefun-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_roc_stats
> ### Title: Generate ROC statistics
> ### Aliases: get_roc_stats
> 
> ### ** Examples
> 
> # load libraries
> library(readr)
Error in library(readr) : there is no package called ‘readr’
Execution halted
Packages required but not available: 'recipes', 'tune'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘styler’
Package required but not available: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'plotly'
Running examples in ‘USgrid-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Cal_elec
> ### Title: Demand for California Independent System Operator (CISO)
> ### Aliases: Cal_elec
> ### Keywords: datasets time-series
> 
> ### ** Examples
> 
> 
> data(Cal_elec)
> 
> library(plotly)
Error in library(plotly) : there is no package called ‘plotly’
Execution halted
Package suggested but not available for checking: ‘GGally’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ushr.Rcheck/00install.out’ for details.
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘vcd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tmvtnorm', 'MCMCpack'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggrepel', 'maptools', 'rgdal'
Running examples in ‘usmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: usmap_transform
> ### Title: Convert coordinate date frame to usmap projection
> ### Aliases: usmap_transform usmap_transform.data.frame
> 
> ### ** Examples
> 
> data <- data.frame(
+   lon = c(-74.01, -95.36, -118.24, -87.65, -134.42, -157.86),
+   lat = c(40.71, 29.76, 34.05, 41.85, 58.30, 21.31),
+   pop = c(8398748, 2325502, 3990456, 2705994, 32113, 347397)
+ )
> 
> # Transform data
> transformed_data <- usmap_transform(data)
Error in usmap_transform(data) : 
  `maptools` must be installed to use `usmap_transform`.
         Use: install.packages("maptools") and try again.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘advanced-mapping.Rmd’ using rmarkdown
Quitting from lines 83-95 (advanced-mapping.Rmd) 
Error: processing vignette ‘advanced-mapping.Rmd’ failed with diagnostics:
`maptools` must be installed to use `usmap_transform`.
         Use: install.packages("maptools") and try again.
--- failed re-building ‘advanced-mapping.Rmd’

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

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

SUMMARY: processing the following file failed:
  ‘advanced-mapping.Rmd’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘xts’
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggdag’
Package required but not available: ‘spatstat.geom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘C50’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/utiml.Rcheck/00install.out’ for details.
Packages required but not available:
  'doParallel', 'readr', 'biomaRt', 'vcfR', 'Biostrings',
  'AnnotationHub', 'ensembldb', 'AnnotationFilter', 'GenomicFeatures',
  'GenomicRanges', 'IRanges', 'rtracklayer'

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

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

Package suggested but not available for checking: ‘bigstatsr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
Package suggested but not available for checking: ‘tm’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘gamm4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'GenomicAlignments', 'GenomicRanges', 'IRanges', 'Rsamtools',
  'ggpubr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'leaflet', 'ggspatial', 'geojsonio'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
Package required but not available: ‘framecleaner’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSQLite’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/validatedb.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/validateRS.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/validatetools.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'readr', 'rtracklayer'

Packages suggested but not available for checking:
  'devtools', 'GenomicRanges', 'IRanges', 'RMariaDB', 'S4Vectors'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘capushe’
Packages required but not available: 'leaflet', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'EFA.MRFA', 'PCovR', 'fungible', 'semPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Seurat', 'sctransform'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VAM.Rcheck/00install.out’ for details.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyverse', 'car', 'rstatix'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘readr’
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘intro-to-varbundle.Rmd’
Package required but not available: ‘latticeExtra’

Package suggested but not available for checking: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'doRNG'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Mammen: no visible global function definition for ‘runif’
PR2: no visible global function definition for ‘ar.burg’
PR2: no visible global function definition for ‘pt’
PR2: no visible global function definition for ‘pf’
PR3: no visible global function definition for ‘ar.burg’
PR3: no visible global function definition for ‘pt’
PR3: no visible global function definition for ‘pf’
VAR.FOR: no visible global function definition for ‘qnorm’
VAR.ForeB: no visible global function definition for ‘runif’
VAR.LRtest: no visible global function definition for ‘pchisq’
VAR.LRtest: no visible global function definition for ‘pf’
VAR.PI: no visible global function definition for ‘quantile’
VAR.Waldtest: no visible global function definition for ‘pf’
VAR.irf: no visible global function definition for ‘par’
VAR.irf: no visible global function definition for ‘abline’
VAR1.sim: no visible global function definition for ‘rnorm’
resamp: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline ar.burg par pchisq pf pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
Package required but not available: ‘XML2R’

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

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

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

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

Package suggested but not available for checking: ‘geoR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'VennDiagram', 'doParallel'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'gstat', 'hydroGOF'

Packages suggested but not available for checking: 'rgdal', 'RFmerge'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'vars', 'strucchange'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'strucchange', 'lmtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
black_scholes: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Packages required but not available:
  'alabama', 'merDeriv', 'lme4', 'saemix', 'msm', 'doParallel'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'mlr', 'mlrMBO', 'RandomFields', 'smoof'

Packages suggested but not available for checking: 'gstat', 'spData'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
burdenPlot: no visible global function definition for ‘density’
burdenPlot: no visible global function definition for ‘axis’
burdenPlot: no visible global function definition for ‘points’
burdenPlot: no visible global function definition for ‘lines’
burdenPlot: no visible global function definition for ‘abline’
burdenPlot: no visible global function definition for ‘text’
burdenPlot: no visible global function definition for ‘sd’
burdenPlot: no visible global function definition for ‘segments’
vbdm: no visible global function definition for ‘var’
vbdm: no visible global function definition for ‘pchisq’
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for ‘var’
vbdmR: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
Packages required but not available: 'ergm', 'sna'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
compute_KL : rtnorm: no visible global function definition for ‘runif’
compute_KL : rtnorm: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘qnorm’
compute_KL: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘pnorm’
compute_KL: no visible global function definition for ‘var’
compute_KL: no visible global function definition for ‘rbinom’
compute_KL: no visible global function definition for ‘rnorm’
compute_KL: no visible global function definition for ‘sd’
vbsr: no visible global function definition for ‘qchisq’
vbsr: no visible global function definition for ‘var’
vbsr: no visible global function definition for ‘pchisq’
vbsr: no visible global function definition for ‘sd’
vbsr: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘VBTree_vignette.Rmd’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VC2copula.Rcheck/00install.out’ for details.
Package required but not available: ‘lme4’

Packages suggested but not available for checking: 'VFP', 'STB'

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

Packages suggested but not available for checking:
  'effects', 'lmtest', 'car', 'AER', 'coin', 'Hmisc'

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

Package suggested but not available for checking: ‘coin’

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

Packages suggested but not available for checking: 'adegenet', 'poppr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'partykit', 'strucchange'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bit64’
Package suggested but not available for checking: ‘geomorph’
Error(s) in re-building vignettes:
  ...
--- re-building ‘vcvComp-worked-example.Rmd’ using rmarkdown
Quitting from lines 46-54 (vcvComp-worked-example.Rmd) 
Error: processing vignette ‘vcvComp-worked-example.Rmd’ failed with diagnostics:
there is no package called 'geomorph'
--- failed re-building ‘vcvComp-worked-example.Rmd’

SUMMARY: processing the following file failed:
  ‘vcvComp-worked-example.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘drc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggtern’
Compare2FDS: no visible global function definition for ‘runif’
Compare2FDS: no visible global function definition for ‘lm’
Compare2FDS: no visible global function definition for ‘model.matrix’
Compare2FDS: no visible global function definition for ‘abline’
Compare2FDS: no visible global function definition for ‘lines’
Compare2FDS: no visible global function definition for ‘text’
Compare2Vdg: no visible global function definition for ‘par’
Compare2Vdg: no visible global function definition for ‘lines’
Compare2Vdg: no visible global function definition for ‘legend’
FDSPlot: no visible global function definition for ‘runif’
FDSPlot: no visible global function definition for ‘lm’
FDSPlot: no visible global function definition for ‘model.matrix’
FDSPlot: no visible global function definition for ‘abline’
Vdgraph: no visible global function definition for ‘par’
Vdgraph: no visible global function definition for ‘lines’
Vdgraph: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend lines lm model.matrix par runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
Package required but not available: ‘quantreg’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vec2dtransf.Rcheck/00install.out’ for details.
Packages required but not available: 'qgraph', 'VennDiagram'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VecStatGraphs2D.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VecStatGraphs3D.Rcheck/00install.out’ for details.
Packages required but not available: 'biwavelet', 'fields'

Package suggested but not available for checking: ‘devtools’

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

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

Package suggested but not available for checking: ‘smacof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSQLite', 'readr'

Packages suggested but not available for checking:
  'vegan', 'labdsv', 'indicspecies'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'taxlist', 'vegdata'

Package suggested but not available for checking: ‘vegan’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VennDiagram.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/venneuler.Rcheck/00install.out’ for details.
Package required but not available: ‘VennDiagram’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'QCA', 'ggpolypath'
Packages required but not available: 'pedtools', 'ribd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fields', 'CircStats', 'dtw'

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

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

Packages suggested but not available for checking:
  'caret', 'mlr3', 'mlr3learners', 'recipes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'maptools', 'xts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'lmerTest', 'multcomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VEwaning.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VEwaningVariant.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vfcp.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘VCA’

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

Package which this enhances but not available for checking: ‘VGAMdata’
Packages required but not available: 'Biostrings', 'coRdon', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pamr’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VHDClassification.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘seqinr’
Running examples in ‘vhica-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CUB
> ### Title: Computes the Codon Usage Bias of DNA sequences
> ### Aliases: CUB
> 
> ### ** Examples
> 
> 	seq.file <- system.file("extdata/Genes", "Amd.fas", package="vhica")
> 	CUB(seq.file)
Error in CUB(seq.file) : Reading FASTA files require package seqinr
Execution halted
Package suggested but not available for checking: ‘doParallel’
Package required but not available: ‘rjags’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘leaflet’
Package required but not available: ‘gsubfn’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'JBrowseR', 'ggpubr', 'plotly', 'vroom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
vif: no visible global function definition for ‘sd’
vif: no visible global function definition for ‘lm’
vif: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  lm pnorm sd
Consider adding
  importFrom("stats", "lm", "pnorm", "sd")
to your NAMESPACE file.
Rd file 'vif.Rd':
  \usage lines wider than 90 characters:
             vif(y, x, w0 = 0.05, dw = 0.05, subsize = 200, trace = TRUE, mode = c("dense", "sparse"))
  \examples lines wider than 100 characters:
             vif.sel <- vif(housingexp$y, housingexp$x, w0 = 0.0005, dw = 0.005, subsize = 300, trace = FALSE);

These lines will be truncated in the PDF manual.
Package required but not available: ‘readr’

Packages suggested but not available for checking: 'leaflet', 'plotly'

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

Packages suggested but not available for checking: 'gam', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'vcd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘kdecopula’
Running examples in ‘VineCopula-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BiCopKDE
> ### Title: Kernel estimate of a Bivariate Copula Density
> ### Aliases: BiCopKDE
> 
> ### ** Examples
> 
> # simulate data from Joe copula
> cop <- BiCop(3, tau = 0.3)
> u <- BiCopSim(1000, cop)
> contour(cop)  # true contours
> 
> # kernel contours with standard normal margins
> BiCopKDE(u[, 1], u[, 2])
Error in BiCopKDE(u[, 1], u[, 2]) : 
  The 'kdecopula' package must be installed.
Execution halted
Packages required but not available: 'rvinecopulib', 'kde1d'

Packages suggested but not available for checking:
  'AppliedPredictiveModeling', 'quantreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vines.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vioplot.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'vioplot', 'ggbeeswarm'
Error(s) in re-building vignettes:
  ...
--- re-building ‘methodComparison.Rnw’ using Sweave

Error: processing vignette ‘methodComparison.Rnw’ failed with diagnostics:
 chunk 2 (label = simData) 
Error in library(vioplot) : there is no package called ‘vioplot’

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

--- re-building ‘usageExamples.Rnw’ using Sweave

Error: processing vignette ‘usageExamples.Rnw’ failed with diagnostics:
 chunk 18 (label = showGg) 
Error in library(ggbeeswarm) : there is no package called ‘ggbeeswarm’

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

SUMMARY: processing the following files failed:
  ‘methodComparison.Rnw’ ‘usageExamples.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'C50', 'caret', 'Cubist', 'doParallel', 'earth', 'glmnet', 'mlr',
  'mlr3', 'party', 'partykit', 'pdp', 'RSNNS', 'varImp'
'LazyData' is specified without a 'data' directory
Running examples in ‘vip-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vi
> ### Title: Variable importance
> ### Aliases: vi vi.default vi.model_fit vi.WrappedModel vi.Learner
> 
> ### ** Examples
> 
> #
> # A projection pursuit regression example
> #
> 
> # Load the sample data
> data(mtcars)
> 
> # Fit a projection pursuit regression model
> mtcars.ppr <- ppr(mpg ~ ., data = mtcars, nterms = 1)
> 
> # Compute variable importance scores
> vi(mtcars.ppr, method = "firm", ice = TRUE)
Error: Package "pdp" needed for this function to work. Please install it.
Execution halted
Packages required but not available:
  'rmgarch', 'mgarchBEKK', 'expm', 'BigVAR', 'ks', 'matlib'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'raster', 'rasterVis', 'mapproj', 'rgdal'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/viridis.Rcheck/00install.out’ for details.
Package required but not available: ‘viridis’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rworldmap'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyverse’
Running examples in ‘visachartR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alluvial_diagram
> ### Title: alluvial_diagram
> ### Aliases: alluvial_diagram
> 
> ### ** Examples
> 
> library(tidyverse)
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
Package required but not available: ‘ggrepel’

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

Packages suggested but not available for checking: 'devtools', 'flux'

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

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

Package suggested but not available for checking: ‘plotly’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'sqldf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggraph’
Package required but not available: ‘parcats’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'ggrepel'

Package suggested but not available for checking: ‘highcharter’

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

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

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

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FactoMineR', 'ggrepel'

Package suggested but not available for checking: ‘egg’

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

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readr', 'dendextend', 'ComplexHeatmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'condvis2', 'GGally', 'DendSer', 'ggalt', 'flashlight'

Packages suggested but not available for checking:
  'sna', 'mlr', 'tidymodels', 'mlr3', 'mlr3learners', 'zenplots'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Decile.Plot: no visible global function definition for ‘barplot’
Decile.Plot: no visible global function definition for ‘axis’
Sliding.Window: no visible global function definition for ‘lines’
Sliding.Window: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis barplot legend lines
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines")
to your NAMESPACE file.
Packages required but not available: 'dtw', 'tseries', 'RTransferEntropy'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readr', 'ggpubr', 'imager', 'doFuture'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plotly', 'ggpubr', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/volesti.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘diverse’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Datasets-for-Seminars.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 20-35 (Datasets-for-Seminars.Rmd) 
Error: processing vignette ‘Datasets-for-Seminars.Rmd’ failed with diagnostics:
there is no package called 'diverse'
--- failed re-building ‘Datasets-for-Seminars.Rmd’

--- re-building ‘Introduction-to-volleystat.Rmd’ using rmarkdown
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 9 rows containing non-finite values (stat_bin).
`summarise()` has grouped output by 'league_gender'. You can override using the
`.groups` argument.
`summarise()` has grouped output by 'league_gender'. You can override using the
`.groups` argument.
--- finished re-building ‘Introduction-to-volleystat.Rmd’

SUMMARY: processing the following file failed:
  ‘Datasets-for-Seminars.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dismo', 'fields', 'latticeExtra', 'raster', 'rangeBuilder', 'rgeos'

Package suggested but not available for checking: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'tm', 'vosonSML', 'wordcloud'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vottrans.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lmerTest', 'gamm4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rfast', 'geometry', 'raster'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'oce', 'metR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vrcp.Rcheck/00install.out’ for details.
‘library’ or ‘require’ call to ‘misc3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package required but not available: ‘bit64’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
plot.vscc: no visible global function definition for ‘rainbow’
plot.vscc: no visible global function definition for ‘pairs’
Undefined global functions or variables:
  pairs rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "pairs")
to your NAMESPACE file.
Packages required but not available: 'Hmisc', 'lfe'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survminer', 'flexsurv', 'ggpubr'

Package suggested but not available for checking: ‘plotly’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'invertiforms', 'LRMF3'

Package suggested but not available for checking: ‘GGally’

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

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

Package suggested but not available for checking: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'rquery', 'rqdatatable', 'lme4', 'RSQLite', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vtreat.Rcheck/00install.out’ for details.
Package required but not available: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vtype.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Calculate_WACC_in_R.Rmd’ using rmarkdown
Quitting from lines 30-36 (Calculate_WACC_in_R.Rmd) 
Error: processing vignette ‘Calculate_WACC_in_R.Rmd’ failed with diagnostics:
server certificate verification failed. CAfile: none CRLfile: none
--- failed re-building ‘Calculate_WACC_in_R.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘viridis’
Package required but not available: ‘tmvtnorm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘text2vec’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/waffle.Rcheck/00install.out’ for details.
summary.whc: no visible global function definition for ‘printCoefmat’
wahc.fit: no visible global function definition for ‘pt’
wahc.fit: no visible global function definition for ‘cor’
whc: no visible global function definition for ‘model.frame’
whc: no visible global function definition for ‘model.matrix’
whc: no visible global function definition for ‘model.response’
Undefined global functions or variables:
  cor model.frame model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "printCoefmat", "pt")
to your NAMESPACE file.
Packages required but not available: 'rstan', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'leaflet', 'dismo', 'ecospat', 'ENMeval', 'leaflet.extras', 'raster',
  'rgeos', 'rgdal', 'spocc', 'spThin'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'prodlim', 'riskRegression'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘WRS2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'NatureSounds', 'dtw', 'monitoR'

Packages suggested but not available for checking:
  'soundgen', 'wavethresh', 'leaflet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'fields', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘linout.csv’ ‘linout.pdf’ ‘out.csv’ ‘out.pdf’ ‘tabel_out.csv’
Packages suggested but not available for checking:
  'readr', 'SPEI', 'fitdistrplus'
Running examples in ‘WASP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: at.vt
> ### Title: Variance Transformation Operation - AT(a trous)
> ### Aliases: at.vt
> 
> ### ** Examples
> 
> data(rain.mon)
> data(obs.mon)
> 
> ## response SPI - calibration
> # SPI.cal <- SPI.calc(window(rain.mon, start=c(1949,1), end=c(1979,12)),sc=12)
> SPI.cal <- SPEI::spi(window(rain.mon, start = c(1949, 1), end = c(1979, 12)), scale = 12)$fitted
Error in loadNamespace(x) : there is no package called ‘SPEI’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘WASP.Rmd’ using rmarkdown
Quitting from lines 46-107 (WASP.Rmd) 
Error: processing vignette ‘WASP.Rmd’ failed with diagnostics:
there is no package called 'readr'
--- failed re-building ‘WASP.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'latticeExtra', 'dataRetrieval'

Package suggested but not available for checking: ‘mapdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/waterfall.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'raster', 'rgdal', 'caret'

Packages suggested but not available for checking:
  'tmap', 'tmaptools', 'OpenStreetMap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'maptools', 'rgeos', 'splancs'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FinTS', 'forecast', 'rugarch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'tsutils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'tsutils'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/WaverR.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ggvoronoi’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/WaveSampling.Rcheck/00install.out’ for details.
Packages required but not available: 'caret', 'readr', 'spectacles'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘latticeExtra’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.Rmd’ using rmarkdown
Quitting from lines 36-51 (examples.Rmd) 
Error: processing vignette ‘examples.Rmd’ failed with diagnostics:
there is no package called 'latticeExtra'
--- failed re-building ‘examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘cellWise’
Error(s) in re-building vignettes:
  ...
--- re-building ‘wbacon.Rmd’ using rmarkdown
Quitting from lines 173-175 (wbacon.Rmd) 
Error: processing vignette ‘wbacon.Rmd’ failed with diagnostics:
there is no package called 'cellWise'
--- failed re-building ‘wbacon.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘readr’

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

Package suggested but not available for checking: ‘tidyverse’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘doBy’
onesamplemeantest: no visible global function definition for ‘pnorm’
twosamplemeantest: no visible global function definition for ‘pnorm’
wcq: no visible global function definition for ‘var’
wcq: no visible global function definition for ‘pnorm’
wcq.fdrc: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  p.adjust pnorm var
Consider adding
  importFrom("stats", "p.adjust", "pnorm", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Hmisc’
Running ‘testthat.R’ [13s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(wdm)
  > 
  > test_check("wdm")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 73 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_computations_unweighted.R:24:5): method hoeffding is correct ────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'Hmisc'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(wdm(x, method = "hoeffd"), Hmisc::hoeffd(x)$D) at test_computations_unweighted.R:24:4
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base withOneRestart(expr, restarts[[1L]])
   7.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test_computations_unweighted.R:79:5): method hoeffding is correct ────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'Hmisc'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test_computations_unweighted.R:79:4
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base withOneRestart(expr, restarts[[1L]])
   7.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 73 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘arcpullr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggmap', 'prepr'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wdpar.Rcheck/00install.out’ for details.
Package required but not available: ‘vars’

Package suggested but not available for checking: ‘timeSeries’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xts', 'RHRV', 'varian', 'R.utils'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/WebAnalytics.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'rcdk', 'robotstxt'
Packages suggested but not available for checking: 'dbWebForms', 'pgTools'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/webdeveloper.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'doRNG', 'readr', 'doParallel'

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

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lme4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rrtable', 'ggforce', 'vcd'

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

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

Package suggested but not available for checking: ‘devtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘weco-vignette.Rmd’
Package required but not available: ‘rgeos’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantreg', 'doParallel'

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

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

Packages suggested but not available for checking: 'ggrepel', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sqldf', 'R.oo', 'kSamples'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'segmented', 'SPREDA'

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

Package suggested but not available for checking: ‘vegan’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Weighted.Box.test: no visible global function definition for ‘acf’
Weighted.Box.test: no visible binding for global variable ‘na.pass’
Weighted.Box.test: no visible global function definition for ‘pgamma’
Weighted.Box.test: no visible global function definition for ‘pchisq’
Weighted.LM.test: no visible global function definition for ‘acf’
Weighted.LM.test: no visible binding for global variable ‘na.pass’
Weighted.LM.test: no visible global function definition for ‘pgamma’
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'glmnet', 'GsymPoint', 'geometry'
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("WeightedROC")
  Loading required package: WeightedROC
  label
  -1 
   4 
  label
  1 
  4 
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-auc.R:3:1): (code run outside of `test_that()`) ─────────────────
  <packageNotFoundError/error/condition>
  Error in `library(GsymPoint)`: there is no package called 'GsymPoint'
  Backtrace:
      ▆
   1. └─base::library(GsymPoint) at test-auc.R:3:0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/weightedScores.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'twang', 'CBPS', 'SuperLearner', 'mlogit', 'mclogit', 'MNP', 'survey'
Running examples in ‘WeightIt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: method_cbps
> ### Title: Covariate Balancing Propensity Score Weighting
> ### Aliases: method_cbps
> 
> ### ** Examples
> 
> library("cobalt")
 cobalt (Version 4.3.2, Build Date: 2022-01-19)
> data("lalonde", package = "cobalt")
> 
> #Balancing covariates between treatment groups (binary)
> (W1 <- weightit(treat ~ age + educ + married +
+                   nodegree + re74, data = lalonde,
+                 method = "cbps", estimand = "ATT"))
Error: Package 'CBPS' is needed for this function to work. Please install it.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘WeightIt.Rmd’ using rmarkdown
Quitting from lines 86-90 (WeightIt.Rmd) 
Error: processing vignette ‘WeightIt.Rmd’ failed with diagnostics:
there is no package called 'survey'
--- failed re-building ‘WeightIt.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'quantreg', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/weightr.Rcheck/00install.out’ for details.
Packages required but not available: 'Hmisc', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘leaflet’
Running examples in ‘wellknown-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multilinestring
> ### Title: Make WKT multilinestring objects
> ### Aliases: multilinestring
> 
> ### ** Examples
> 
> ## empty multilinestring
> multilinestring("empty")
[1] "MULTILINESTRING EMPTY"
> # multilinestring("stuff")
> 
> # character string
> x <- "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> multilinestring(x)
[1] "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> 
> # data.frame
> df <- data.frame(long = c(30, 45, 10), lat = c(20, 40, 40))
> df2 <- data.frame(long = c(15, 40, 10), lat = c(5, 10, 20))
> multilinestring(df, df2, fmt=0)
[1] "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> lint(multilinestring(df, df2, fmt=0))
[1] TRUE
> wktview(multilinestring(df, df2), zoom=3)
Error: Please install leaflet
Execution halted
Package required but not available: ‘xts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'Rmpfr', 'NPflow'

Package suggested but not available for checking: ‘EdSurvey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spray', 'disordR', 'freealg'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wfg.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wgaim.Rcheck/00install.out’ for details.
Packages required but not available:
  'Hmisc', 'doParallel', 'GO.db', 'AnnotationDbi'

Packages suggested but not available for checking:
  'org.Hs.eg.db', 'org.Mm.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'PoisNor', 'CRTgeeDR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'datapasta', 'readr', 'anomalize', 'ggforce'
Running examples in ‘whippr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: perform_max
> ### Title: Perform VO2max calculation
> ### Aliases: perform_max
> 
> ### ** Examples
> 
> 
> ## get file path from example data
> path_example <- system.file("ramp_cosmed.xlsx", package = "whippr")
> 
> ## read data from ramp test
> df <- read_data(path = path_example, metabolic_cart = "cosmed")
> 
> ## normalize incremental test data
> ramp_normalized <- df %>%
+  incremental_normalize(
+    .data = .,
+    incremental_type = "ramp",
+    has_baseline = TRUE,
+    baseline_length = 240,
+    work_rate_magic = TRUE,
+    baseline_intensity = 20,
+    ramp_increase = 25
+  )
> 
> ## detect outliers
> data_ramp_outliers <- detect_outliers(
+  .data = ramp_normalized,
+  test_type = "incremental",
+  vo2_column = "VO2",
+  cleaning_level = 0.95,
+  method_incremental = "linear",
+  verbose = TRUE
+ )
✔ Detecting outliers
• 2 outlier(s) found in baseline
• 15 outlier(s) found in ramp
> 
> ## analyze VO2max
> perform_max(
+  .data = data_ramp_outliers,
+  vo2_column = "VO2",
+  vo2_relative_column = "VO2/Kg",
+  heart_rate_column = "HR",
+  rer_column = "R",
+  average_method = "bin",
+  average_length = 30,
+  plot = TRUE,
+  verbose = FALSE
+ )
Error in loadNamespace(x) : there is no package called ‘ggforce’
Calls: perform_max ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [91s/108s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(whippr)
  > 
  > test_check("whippr")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 12 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-incremental.R:67:3): plot_incremental ramp works ────────────────
  Error: You need to install the ggforce package to use this function.
  Backtrace:
      ▆
   1. ├─testthat::expect_s3_class(...) at test-incremental.R:67:2
   2. │ └─testthat::quasi_label(enquo(object), arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─whippr::plot_incremental(ramp_normalized)
   5. └─whippr:::plot_incremental.ramp(ramp_normalized)
  ── Error (test-incremental.R:93:3): plot_incremental step works ────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'ggforce'
  Backtrace:
      ▆
   1. ├─testthat::expect_s3_class(...) at test-incremental.R:93:2
   2. │ └─testthat::quasi_label(enquo(object), arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─whippr::plot_incremental(ramp_normalized)
   5. ├─whippr:::plot_incremental.step(ramp_normalized)
   6. └─base::loadNamespace(x)
   7.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8.     └─base withOneRestart(expr, restarts[[1L]])
   9.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 12 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking: 'raster', 'rgdal'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/whitening.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'vcfR', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggraph', 'lordif', 'nFactors', 'readr', 'srvyr', 'survey', 'TAM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bit64’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplR', 'imager', 'plotly', 'raster', 'rgdal', 'readr'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘snowfall’

Package suggested but not available for checking: ‘SSsimple’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/widgetframe.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'ggraph', 'irlba'
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘wikibooks/R/Bundesliga.Mannschaft.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.Tabelle.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.XML.R’:
  data(Bundesliga)
See section ‘Good practice’ in ‘?data’.
Found the following files/directories:
  ‘Bundesliga.xml’ ‘myfile.xml’
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'WikidataQueryServiceR', 'Hmisc', 'readr'

Package suggested but not available for checking: ‘tidyverse’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'WikidataQueryServiceR', 'WikidataR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
wilcox.selection.split: no visible global function definition for
  ‘pnorm’
wilcox.test2: no visible global function definition for ‘wilcox.test’
Undefined global functions or variables:
  pnorm wilcox.test
Consider adding
  importFrom("stats", "pnorm", "wilcox.test")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'adehabitatLT', 'rgeos'

Packages suggested but not available for checking: 'adehabitatHR', 'GGally'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSQLite', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'viridis', 'ComplexHeatmap', 'ggrepel', 'DESeq2',
  'FactoMineR', 'factoextra', 'heatmaply'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSQLite’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/windAC.Rcheck/00install.out’ for details.
Packages required but not available: 'drc', 'imputeTestbench'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geiger', 'phangorn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rnrfa’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wingui.Rcheck/00install.out’ for details.
Packages required but not available: 'pssm', 'JM'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggpubr', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'secr', 'rjags'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wiqid.Rcheck/00install.out’ for details.
Packages required but not available:
  'Rgraphviz', 'RBGL', 'graph', 'HydeNet', 'arules', 'DescTools',
  'linkcomm'

Package suggested but not available for checking: ‘rcompanion’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSQLite’
Running examples in ‘withr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: with_db_connection
> ### Title: DBMS Connections which disconnect themselves.
> ### Aliases: with_db_connection local_db_connection
> 
> ### ** Examples
> 
> db <- tempfile()
> with_db_connection(
+   list(con = DBI::dbConnect(RSQLite::SQLite(), db)), {
+     DBI::dbWriteTable(con, "mtcars", mtcars)
+ })
Error in (function (cond)  : 
  error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called ‘RSQLite’
Calls: with_db_connection ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package suggested but not available for checking: ‘readr’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘genlasso’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
dbayes: no visible global function definition for ‘mahalanobis’
dbayes: no visible global function definition for ‘var’
wmd: no visible global function definition for ‘cor’
wmd: no visible global function definition for ‘var’
Undefined global functions or variables:
  cor mahalanobis var
Consider adding
  importFrom("stats", "cor", "mahalanobis", "var")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wmlf.Rcheck/00install.out’ for details.
Package required but not available: ‘smoothmest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wnl.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wnominate.Rcheck/00install.out’ for details.
Package required but not available: ‘msm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'quantmod', 'xts'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introductory-Econometrics-Examples.Rmd’ using rmarkdown

Please cite as: 

 Hlavac, Marek (2022). stargazer: Well-Formatted Regression and Summary Statistics Tables.
 R package version 5.2.3. https://CRAN.R-project.org/package=stargazer 

Quitting from lines 729-750 (Introductory-Econometrics-Examples.Rmd) 
Error: processing vignette ‘Introductory-Econometrics-Examples.Rmd’ failed with diagnostics:
there is no package called 'xts'
--- failed re-building ‘Introductory-Econometrics-Examples.Rmd’

SUMMARY: processing the following file failed:
  ‘Introductory-Econometrics-Examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/word.alignment.Rcheck/00install.out’ for details.
Packages required but not available: 'quantregGrowth', 'RMySQL'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘text2vec’

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

Packages suggested but not available for checking:
  'readr', 'recipes', 'tidymodels', 'tune'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'rsample', 'tune'

Packages suggested but not available for checking: 'dials', 'recipes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dials', 'recipes'
Running examples in ‘workflows-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_recipe
> ### Title: Add a recipe to a workflow
> ### Aliases: add_recipe remove_recipe update_recipe
> 
> ### ** Examples
> 
> library(recipes)
Error in library(recipes) : there is no package called ‘recipes’
Execution halted
Packages required but not available:
  'openair', 'doParallel', 'leaflet', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/worms.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (7) wowa.Rd:14: \item in \value must have non-empty label
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggrepel', 'ggraph', 'ggwordcloud'

Packages suggested but not available for checking: 'lmtest', 'portes'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wpp2015.Rcheck/00install.out’ for details.
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘wpp2015’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyverse', 'coin'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wrassp.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'factoextra', 'FactoMineR'
Error(s) in re-building vignettes:
  ...
--- re-building ‘wrGraphVignette1.Rmd’ using rmarkdown
Quitting from lines 27-33 (wrGraphVignette1.Rmd) 
Error: processing vignette ‘wrGraphVignette1.Rmd’ failed with diagnostics:
there is no package called 'FactoMineR'
--- failed re-building ‘wrGraphVignette1.Rmd’

SUMMARY: processing the following file failed:
  ‘wrGraphVignette1.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'fdapace', 'fdadensity', 'Rfast', 'CVXR', 'expm', 'modeest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘bit64’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [27s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(writexl)
  > 
  > test_check("writexl")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-types.R:13:3): Types roundtrip properly ─────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'bit64'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-types.R:13:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking:
  'coin', 'flexclust', 'vsn'
Package unavailable to check Rd xrefs: ‘vsn’
Packages suggested but not available for checking: 'ROTS', 'R.utils'
Package required but not available: ‘mc2d’

Packages suggested but not available for checking:
  'car', 'mediation', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BatchExperiments', 'metap'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'caret', 'fields', 'forecast', 'quantreg'

Packages suggested but not available for checking:
  'doParallel', 'EGRET', 'plotly'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'expm', 'imager'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package vignette with placeholder title ‘Vignette Title’:
  ‘wTOvignette.Rmd’
Packages required but not available:
  'fields', 'rgdal', 'rgeos', 'Hmisc', 'rworldmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cdata', 'rqdatatable', 'rquery'

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sde', 'ftsa', 'rainbow'

Package suggested but not available for checking: ‘fOptions’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/x12.Rcheck/00install.out’ for details.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘showtext’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RP2_data_1.txt’ ‘RP2_data_4.txt’ ‘RP2_qtl_1.txt’ ‘RP2_qtl_4.txt’
  ‘hp1_effect_qtl.txt’ ‘hp1_freq_mrk.txt’ ‘hp1_freq_qtl.txt’
  ‘hp1_genome.txt’ ‘hp1_last_hp_data.txt’ ‘hp1_lm_mrk.txt’
  ‘hp1_lm_qtl.txt’ ‘hp1_lm_qtl_mrk.txt’ ‘hp1_mrk.txt’ ‘hp1_qtl.txt’
  ‘hp2_effect_qtl.txt’ ‘hp2_freq_mrk.txt’ ‘hp2_freq_qtl.txt’
  ‘hp2_genome.txt’ ‘hp2_last_hp_data.txt’ ‘hp2_lm_mrk.txt’
  ‘hp2_lm_qtl.txt’ ‘hp2_lm_qtl_mrk.txt’ ‘hp2_mrk.txt’ ‘hp2_qtl.txt’
  ‘my_RP_data_1.txt’ ‘my_RP_data_4.txt’ ‘my_RP_mrk_1.txt’
  ‘my_RP_mrk_4.txt’
Package suggested but not available for checking: ‘rugarch’
Running examples in ‘xdcclarge-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cdcc_estimation
> ### Title: This function estimates the parameters(alpha,beta) and
> ###   time-varying correlation matrices(Rt) of cDCC-GARCH model.
> ### Aliases: cdcc_estimation
> 
> ### ** Examples
> 
>   library(rugarch)
Error in library(rugarch) : there is no package called ‘rugarch’
Execution halted
Package required but not available: ‘ergm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xgb.txt’
Packages suggested but not available for checking: 'DiagrammeR', 'vcd'
GNU make is a SystemRequirements.
Running examples in ‘xgboost-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xgb.plot.multi.trees
> ### Title: Project all trees on one tree and plot it
> ### Aliases: xgb.plot.multi.trees
> 
> ### ** Examples
> 
> 
> data(agaricus.train, package='xgboost')
> 
> bst <- xgboost(data = agaricus.train$data, label = agaricus.train$label, max_depth = 15,
+                eta = 1, nthread = 2, nrounds = 30, objective = "binary:logistic",
+                min_child_weight = 50, verbose = 0)
> 
> p <- xgb.plot.multi.trees(model = bst, features_keep = 3)
Column 2 ['No'] of item 2 is missing in item 1. Use fill=TRUE to fill with NA (NULL for list columns), or use.names=FALSE to ignore column names. use.names='check' (default from v1.12.2) emits this message and proceeds as if use.names=FALSE for  backwards compatibility. See news item 5 in v1.12.2 for options to control this message.
Error in loadNamespace(x) : there is no package called ‘DiagrammeR’
Calls: xgb.plot.multi.trees ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘discoverYourData.Rmd’ using rmarkdown
Loading required package: xgboost
Loading required package: Matrix
Loading required package: data.table
Loading required package: vcd
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'vcd'
Installing package into '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages'
(as 'lib' is unspecified)
Warning in install.packages("vcd") :
  ‘lib = "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages"’ is not writable
Quitting from lines 28-32 (discoverYourData.Rmd) 
Error: processing vignette ‘discoverYourData.Rmd’ failed with diagnostics:
unable to install packages
--- failed re-building ‘discoverYourData.Rmd’

--- re-building ‘xgboostPresentation.Rmd’ using rmarkdown
Warning in xgb.load(rawVec) :
  The support for loading raw booster with `xgb.load` will be  discontinued in upcoming release. Use `xgb.load.raw` or  `xgb.unserialize` instead. 
--- finished re-building ‘xgboostPresentation.Rmd’

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

--- re-building ‘xgboost.Rnw’ using knitr
Loading required package: knitr
--- finished re-building ‘xgboost.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'DescTools', 'Hmisc', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
XHWE: no visible global function definition for ‘read.table’
result: no visible global function definition for ‘pchisq’
result: no visible global function definition for ‘rbinom’
result: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘results.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'capushe', 'glmnet', 'mda'

Package suggested but not available for checking: ‘shock’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/xlsx2dfs.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/xlsxjars.Rcheck/00install.out’ for details.
Package required but not available: ‘xlsxjars’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
R5.value.default: no visible binding for global variable ‘data.table’
R5.value.default: no visible global function definition for
  ‘as.data.table’
R5.value.parse: no visible binding for global variable ‘data.table’
R5.value.parse: no visible global function definition for
  ‘is.data.table’
R5.value.parse: no visible global function definition for
  ‘as.data.table’
stampme: no visible global function definition for ‘flush.console’
stampmsg: no visible global function definition for ‘flush.console’
write.data.table: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/XML2R.Rcheck/00install.out’ for details.
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘xlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘fmcsR’
Package suggested but not available for checking: ‘devtools’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/xoi.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'blorr', 'haven', 'highcharter', 'olsrr', 'plotly', 'readr'
Packages required but not available:
  'FactoMineR', 'tm', 'ggforce', 'ggrepel', 'flexclust'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'gam', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xpose', 'nlmixr', 'vpc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggforce', 'readr', 'vpc'

Package suggested but not available for checking: ‘plotly’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplR', 'imager'

Package suggested but not available for checking: ‘detrendeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘doParallel’
Running ‘testthat.R’ [14s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(xrnet)
  > test_check("xrnet")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 172 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-CV-errors.R:1:1): (code run outside of `test_that()`) ───────────
  <packageNotFoundError/error/condition>
  Error in `library(doParallel)`: there is no package called 'doParallel'
  Backtrace:
      ▆
   1. └─base::library(doParallel) at test-CV-errors.R:1:0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 172 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'raster', 'rgdal'

Package suggested but not available for checking: ‘plotly’

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

Packages suggested but not available for checking: 'factorMerger', 'caret'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plm’
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
Found the following files/directories:
  ‘OPT.csv’ ‘testTecan_defaultLiquid.csv’ ‘testTecan_setLiquid.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'timeSeries', 'tseries', 'fts'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/xts.Rcheck/00install.out’ for details.
Packages required but not available: 'glmnet', 'selectiveInference'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SACCR', 'Trading'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'vegan', 'ccaPP', 'gam'
Malformed Title field: should not end in a period.
big.read.table: no visible global function definition for ‘read.table’
big.read.table: no visible global function definition for ‘object.size’
sparkline: no visible global function definition for ‘is.ts’
sparkline: no visible global function definition for ‘time’
sparkline: no visible global function definition for ‘boxplot’
Undefined global functions or variables:
  boxplot is.ts object.size read.table time
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "is.ts", "time")
  importFrom("utils", "object.size", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘CO2.csv’
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'depth', 'OjaNP'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggrepel', 'splusTimeSeries', 'viridis'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
kmeansN: no visible global function definition for ‘kmeans’
kmeansN: no visible global function definition for ‘aggregate’
kmeansN2: no visible global function definition for ‘aggregate’
kmeansN2: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/yonder.Rcheck/00install.out’ for details.
Package required but not available: ‘rpart.plot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/yowie.Rcheck/00install.out’ for details.
Package required but not available: ‘rstan’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'yuima', 'quantmod', 'sde', 'plotly', 'ghyp'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'RNRCS', 'metScanR', 'neonUtilities'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘fitdistrplus’
Error(s) in re-building vignettes:
  ...
--- re-building ‘zalpha.Rmd’ using rmarkdown
Quitting from lines 226-227 (zalpha.Rmd) 
Error: processing vignette ‘zalpha.Rmd’ failed with diagnostics:
Package "fitdistrplus" needed for Beta parameters to be calculated. Please install it.
--- failed re-building ‘zalpha.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘NADA’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'behavr', 'lomb'

Packages suggested but not available for checking: 'ggetho', 'damr'

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

Packages suggested but not available for checking:
  'Rgraphviz', 'qrmdata', 'qrmtools', 'rugarch', 'scagnostics'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'scam', 'car', 'vegan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'scater', 'mixtools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gamlss', 'gamlss.dist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘TSA’
Packages required but not available: 'raster', 'tidycensus', 'RSQLite'

Package suggested but not available for checking: ‘readr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘ZipRadius.Rmd’
Package suggested but not available for checking: ‘ggrepel’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ZIprop.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rjags’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rgdal'

Packages suggested but not available for checking: 'rasterVis', 'zdat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'tmap', 'tmaptools', 'pct', 'leaflet'
Error(s) in re-building vignettes:
  ...
--- re-building ‘demo_dutch_cities.Rmd’ using rmarkdown
--- finished re-building ‘demo_dutch_cities.Rmd’

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

--- re-building ‘paper.Rmd’ using rmarkdown
Quitting from lines 56-66 (paper.Rmd) 
Error: processing vignette ‘paper.Rmd’ failed with diagnostics:
there is no package called 'tmap'
--- failed re-building ‘paper.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/zooaRch.Rcheck/00install.out’ for details.
Packages required but not available: 'mlearning', 'mda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Packages required but not available:
  'raster', 'dismo', 'rgdal', 'rworldmap'

Packages suggested but not available for checking: 'maxlike', 'SDMTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AER', 'fts', 'strucchange', 'timeSeries', 'tseries', 'xts'
Running ‘as.Date.R’ [1s/1s]
  Comparing ‘as.Date.Rout’ to ‘as.Date.Rout.save’ ... OK
  Running ‘bugfixes.R’ [0s/0s]
  Comparing ‘bugfixes.Rout’ to ‘bugfixes.Rout.save’ ... OK
  Running ‘na.fill.R’ [0s/0s]
  Comparing ‘na.fill.Rout’ to ‘na.fill.Rout.save’ ... OK
  Running ‘na.locf.R’ [0s/0s]
  Comparing ‘na.locf.Rout’ to ‘na.locf.Rout.save’ ... OK
  Running ‘vignette-zoo-quickref.R’ [0s/0s]
  Running ‘vignette-zoo.R’ [0s/0s]
Running the tests in ‘tests/vignette-zoo-quickref.R’ failed.
Complete output:
  > ###################################################
  > ### chunk number 1: preliminaries
  > ###################################################
  > library("zoo")
  
  Attaching package: 'zoo'
  
  The following objects are masked from 'package:base':
  
      as.Date, as.Date.numeric
  
  > library("tseries")
  Error in library("tseries") : there is no package called 'tseries'
  Execution halted
Running the tests in ‘tests/vignette-zoo.R’ failed.
Complete output:
  > ###################################################
  > ### chunk number 1: preliminaries
  > ###################################################
  > library("zoo")
  
  Attaching package: 'zoo'
  
  The following objects are masked from 'package:base':
  
      as.Date, as.Date.numeric
  
  > library("tseries")
  Error in library("tseries") : there is no package called 'tseries'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘zoo-design.Rnw’ using Sweave

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

--- finished re-building ‘zoo-design.Rnw’

--- re-building ‘zoo-faq.Rnw’ using Sweave

Error: processing vignette ‘zoo-faq.Rnw’ failed with diagnostics:
 chunk 29 (label = Rmetrics) 
Error in library("timeSeries") : there is no package called ‘timeSeries’

--- failed re-building ‘zoo-faq.Rnw’

--- re-building ‘zoo-quickref.Rnw’ using Sweave

Error: processing vignette ‘zoo-quickref.Rnw’ failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library("tseries") : there is no package called ‘tseries’

--- failed re-building ‘zoo-quickref.Rnw’

--- re-building ‘zoo-read.Rnw’ using Sweave
--- finished re-building ‘zoo-read.Rnw’

--- re-building ‘zoo.Rnw’ using Sweave

Error: processing vignette ‘zoo.Rnw’ failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library("tseries") : there is no package called ‘tseries’

--- failed re-building ‘zoo.Rnw’

SUMMARY: processing the following files failed:
  ‘zoo-faq.Rnw’ ‘zoo-quickref.Rnw’ ‘zoo.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'forecast', 'dygraphs'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/zyp.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘httptest’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(zzlite)
  > 
  > test_check("zzlite")
  Error in library(httptest) : there is no package called 'httptest'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinydashboard’
  All declared Imports should be used.
checkRd: (7) Cruciani.Rd:9: \item in \describe must have non-empty label
checkRd: (7) Fasgai.Rd:9: \item in \describe must have non-empty label
checkRd: (7) Kidera.Rd:9: \item in \describe must have non-empty label
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Found the following files/directories:
  ‘CVrej.ps’ ‘linhc.pdf’
checkRd: (7) err.abcrf.Rd:18: \item in \value must have non-empty label
checkRd: (7) err.regAbcrf.Rd:19: \item in \value must have non-empty label
'LazyData' is specified without a 'data' directory
installed size is 72.2Mb
  sub-directories of 1Mb or more:
    libs  71.2Mb
multiplot: no visible global function definition for ‘rainbow’
multiplot: no visible global function definition for ‘text’
multiplot: no visible global function definition for ‘lines’
multiplot: no visible global function definition for ‘par’
plot.abf2: no visible global function definition for ‘abline’
plot.abf2: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline lines par rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "text")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Undeclared package ‘CCA’ in Rd xrefs
Found the following files/directories:
  ‘acceldata2.RData’
File ‘acc/libs/acc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ACDm/libs/ACDm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
print.funlinWLS: no visible global function definition for ‘pchisq’
print.linML: no visible global function definition for ‘pchisq’
print.loglinML: no visible global function definition for ‘pchisq’
print.satMarML: no visible global function definition for ‘pchisq’
print.satMcarWLS: no visible global function definition for ‘pchisq’
summary.funlinWLS: no visible global function definition for ‘pchisq’
summary.linML: no visible global function definition for ‘pchisq’
summary.loglinML: no visible global function definition for ‘pchisq’
summary.satMarML: no visible global function definition for ‘pchisq’
summary.satMcarWLS: no visible global function definition for ‘pchisq’
summary.waldTest: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
File ‘acepack/libs/acepack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘hunspell’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
File ‘acrt/libs/acrt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
‘configure’: /bin/bash is not portable
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R  13.9Mb
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 305 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘HI’, ‘MHadaptive’ in Rd xrefs
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
critical.values: no visible global function definition for ‘rnorm’
critical.values: no visible global function definition for ‘quantile’
mandel.test: no visible global function definition for ‘qf’
mtukey.test : p.test: no visible global function definition for ‘qf’
mtukey.test: no visible binding for global variable ‘quantile’
mtukey.test: no visible global function definition for ‘rnorm’
tukey.test: no visible global function definition for ‘qf’
Undefined global functions or variables:
  qf quantile rnorm
Consider adding
  importFrom("stats", "qf", "quantile", "rnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       3.0Mb
    pictures   2.1Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘filehash’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘parallel’ ‘rsvg’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘admiral.test’ ‘hms’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
File ‘ADMMnet/libs/ADMMnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (7) k12fun.Rd:66: \item in \value must have non-empty label
checkRd: (7) kdfun.Rd:43: \item in \value must have non-empty label
checkRd: (7) kfun.Rd:48: \item in \value must have non-empty label
checkRd: (7) kmfun.Rd:42: \item in \value must have non-empty label
checkRd: (7) kp.fun.Rd:31: \item in \value must have non-empty label
checkRd: (7) kpqfun.Rd:31: \item in \value must have non-empty label
checkRd: (7) krfun.Rd:47: \item in \value must have non-empty label
checkRd: (7) ksfun.Rd:45: \item in \value must have non-empty label
'LazyData' is specified without a 'data' directory
Running examples in ‘advclust-Ex.R’ failed
The error most likely occurred in:

> ### Name: biploting
> ### Title: Biploting Fuzzy Cluster Result
> ### Aliases: biploting
> 
> ### ** Examples
> 
> fuzzy.CM(iris[,1:4],K=3,m=2,max.iteration=100,threshold=1e-5,RandomNumber=1234)->cl1

Membership initialiazed randomly
Error in member(object) < 0 || member(object) > 1 : 
  'length = 450' in coercion to 'logical(1)'
Calls: fuzzy.CM ... validObject -> anyStrings -> isTRUE -> validityMethod
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘advclust.Rmd’ using rmarkdown
Quitting from lines 28-32 (advclust.Rmd) 
Error: processing vignette 'advclust.Rmd' failed with diagnostics:
'length = 450' in coercion to 'logical(1)'
--- failed re-building ‘advclust.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    tutorials   5.6Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘Hmisc’ ‘WRS2’ ‘boot’ ‘car’ ‘dplyr’ ‘effects’
  ‘effsize’ ‘forcats’ ‘ggplot2’ ‘lm.beta’ ‘nlme’ ‘readr’ ‘robust’
  ‘sandwich’ ‘sjstats’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘table_AeRobiology’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
checkRd: (7) fDfPfunctions.Rd:23: \item in \arguments must have non-empty label
Namespaces in Imports field not imported from:
  ‘regclass’ ‘writexl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Undeclared packages ‘epiR’, ‘cccrm’ in Rd xrefs
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘myplot.pdf’ ‘myplot.png’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
File ‘ahaz/libs/ahaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘randomNames’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘multcomp’, ‘gmodels’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘ans_19-2.jpg’ ‘display2d_19-2.jpg’ ‘dist(3)_19-2.jpg’
  ‘dist(4)_19-2.jpg’ ‘dist(mirror)_19-2.jpg’ ‘dist(mirror2)_19-2.jpg’
Namespaces in Imports field not imported from:
  ‘Rsolnp’ ‘SuperLearner’ ‘future.apply’ ‘ggplot2’ ‘progressr’ ‘stats’
  ‘utils’
  All declared Imports should be used.
Note: found 53 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Imports includes 34 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 90 marked UTF-8 strings
Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
Undeclared package ‘SnowballC’ in Rd xrefs
dke.fun.default: no visible global function definition for ‘hist’
kef: no visible global function definition for ‘dbinom’
kef: no visible global function definition for ‘dgamma’
kef: no visible global function definition for ‘dlnorm’
plot.dke.fun: no visible global function definition for ‘hist’
plot.dke.fun: no visible global function definition for ‘lines’
plot.hcvc.fun1d: no visible global function definition for
  ‘plot.default’
plot.hcvd.fun1d: no visible global function definition for
  ‘plot.default’
plot.kern.fun1d: no visible global function definition for
  ‘plot.default’
plot.kpmfe.fun1d: no visible global function definition for
  ‘plot.default’
plot.reg.fun1d: no visible global function definition for
  ‘plot.default’
simp_int: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dbinom dgamma dlnorm hist lines plot.default
Consider adding
  importFrom("graphics", "hist", "lines", "plot.default")
  importFrom("stats", "approx", "dbinom", "dgamma", "dlnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
akmeans: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans
Consider adding
  importFrom("stats", "kmeans")
to your NAMESPACE file.
Found the following significant warnings:
  fun_sublr.cpp:18:22: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/ALassoSurvIC.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘AlgDesign/libs/AlgDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without 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.
batch.possSpells.fnc: no visible binding for global variable ‘words’
possSpells.fnc: no visible binding for global variable ‘len.phons’
possSpells.fnc: no visible binding for global variable ‘phon1’
possSpells.fnc: no visible binding for global variable ‘len.total’
possSpells.fnc: no visible binding for global variable ‘poss.spells’
Undefined global functions or variables:
  len.phons len.total phon1 poss.spells words
Found the following files/directories:
  ‘more.words.rda’ ‘more.words.txt’ ‘more.words_log.txt’
  ‘other.words.rda’ ‘other.words.txt’ ‘other.words_log.txt’
  ‘some.words.rda’ ‘some.words.txt’ ‘some.words_log.txt’
  ‘yet.more.words.rda’ ‘yet.more.words.txt’ ‘yet.more.words_log.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘alphabetr/libs/alphabetr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
'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
Note: found 171 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metaboliteIDmapping’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
EXP.step: no visible global function definition for ‘rgamma’
EXP.step: no visible global function definition for ‘rnorm’
MAX.step: no visible global function definition for ‘uniroot’
Norm.GMedian: no visible binding for global variable ‘median’
RNASeq.Data.Gene: no visible binding for global variable ‘quantile’
decom.initial: no visible global function definition for ‘kmeans’
decom.initial: no visible global function definition for ‘quantile’
decom.initial: no visible global function definition for ‘var’
dispersion.nb.QL: no visible binding for global variable ‘quantile’
est.mu.nb.mle: no visible global function definition for ‘runif’
est.v.nb.QL: no visible global function definition for ‘runif’
pdf2grid: no visible global function definition for ‘dnorm’
pdf2grid: no visible global function definition for ‘dgamma’
prior.grid: no visible global function definition for ‘sd’
prior.grid: no visible global function definition for ‘dnorm’
test.AMAP: no visible global function definition for ‘rgamma’
test.AMAP: no visible global function definition for ‘rnorm’
test.AMAP: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  dgamma dnorm kmeans median quantile rgamma rnorm runif sd uniroot var
Consider adding
  importFrom("stats", "dgamma", "dnorm", "kmeans", "median", "quantile",
             "rgamma", "rnorm", "runif", "sd", "uniroot", "var")
to your NAMESPACE file.
Rd file 'MGN.EM.Rd':
  \usage lines wider than 90 characters:
     MGN.EM(data, nK, p0 = NULL, d0 = 0, nK0 = 0, iter.max = 10, print.steps = FALSE, MGN0 = NULL, model = NULL, nMC = 10000)

Rd file 'test.AMAP.Rd':
  \usage lines wider than 90 characters:
     test.AMAP(data, MGN, del.lim = NULL, FC = NULL, print.steps = FALSE, Integration = "MC",nMC=NULL)
  \examples lines wider than 100 characters:
     data("SimuHapMap")  # a matrix 'counts' storing simulated data with 10000 genes, two treatments, of which each has 5 replicates

These lines will be truncated in the PDF manual.
Undeclared package ‘sf’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘promises’ ‘websocket’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Zelig’
Found the following significant warnings:
  em.cpp:89:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  em.cpp:89:53: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/Amelia.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
amltest: no visible global function definition for ‘var’
amltest: no visible global function definition for ‘optim’
amltest: no visible global function definition for ‘lm’
cleanclust: no visible global function definition for ‘cor’
cleanclust: no visible global function definition for ‘hclust’
cleanclust: no visible global function definition for ‘as.dist’
cleanclust: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  as.dist cor cutree hclust lm optim var
Consider adding
  importFrom("stats", "as.dist", "cor", "cutree", "hclust", "lm",
             "optim", "var")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘dplyr’ ‘gridExtra’
  All declared Imports should be used.
AMOEBA : Classi: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘vegan’ in Rd xrefs
Package which this enhances but not available for checking: ‘SparkR’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Analyz.loadSteps,Analyz: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
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’
Malformed Description field: should contain one or more complete sentences.
andrews: no visible global function definition for ‘plot.new’
andrews: no visible global function definition for ‘plot.window’
andrews: no visible global function definition for ‘title’
andrews: no visible global function definition for ‘axis’
andrews: no visible global function definition for ‘box’
andrews: no visible global function definition for ‘lines’
andrews: no visible global function definition for ‘rainbow’
andrews: no visible global function definition for ‘hsv’
selectand: no visible global function definition for ‘lines’
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window rainbow title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "title")
to your NAMESPACE file.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Malformed Title field: should not end in a period.
Namespaces in Imports field not imported from:
  ‘lazyeval’ ‘tibble’
  All declared Imports should be used.
Undeclared package ‘RColorBrewer’ in Rd xrefs
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tmg’
'LazyData' is specified without a 'data' directory
installed size is 37.1Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    35.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   2.1Mb
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    test_v8    2.0Mb
    testdata   2.4Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mcclust’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘geepack’, ‘dispmod’ in Rd xrefs
Packages in Depends field not imported from:
  ‘boot’ ‘lme4’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.6Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  get_subplot_boundary_pixels.cpp:37:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  polygonize_class.cpp:52:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  polygonize_class.cpp:78:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  polygonize_class.cpp:99:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  polygonize_class.cpp:102:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/APAtree.Rcheck/00install.out’ for details.
checkRd: (7) APResult-class.Rd:92-94: \item in \describe must have non-empty label
checkRd: (7) APResult-class.Rd:95-99: \item in \describe must have non-empty label
checkRd: (7) AggExResult-class.Rd:81-84: \item in \describe must have non-empty label
checkRd: (7) AggExResult-class.Rd:85-89: \item in \describe must have non-empty label
checkRd: (7) ExClust-class.Rd:69-71: \item in \describe must have non-empty label
checkRd: (7) ExClust-class.Rd:72-76: \item in \describe must have non-empty label
Namespaces in Imports field not imported from:
  ‘AER’ ‘ChainLadder’ ‘ISLR’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ViterbiC.cpp:217:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ViterbiC.cpp:528:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ViterbiC.cpp:814:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ViterbiC.cpp:1104:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ViterbiC.cpp:1242:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:45:40: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:59:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:60:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:61:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:62:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:63:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:64:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:65:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:66:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  utils.cpp:67:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/aphid.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ../inst/include/tree_meat.hpp:375:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/aphylo.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
File ‘APIS/libs/APIS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘yulab.utils’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 30.4Mb
  sub-directories of 1Mb or more:
    libs  30.0Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of 'nline' to
  'nlines'
runAPSIM: no visible global function definition for ‘write.table’
runAPSIM: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
Found the following files/directories:
  ‘APBinary_PPV.csv’ ‘APBinary_TPF.csv’
  ‘APBinary_ap_summary(method=perturbation,B=1500).csv’
  ‘APBinary_auc_summary(method=perturbation,B=1500).csv’
  ‘APSurv_PPV.csv’ ‘APSurv_TPF.csv’
  ‘APSurv_ap_summary(method=bootstrap,B=500).csv’
  ‘APSurv_auc_summary(method=bootstrap,B=500).csv’
  ‘CompareAP_Binary_dap_summary(method=none).csv’
  ‘CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggthemes’ ‘shinythemes’ ‘tibble’
  All declared Imports should be used.
Note: found 76 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘bannerCommenter’ ‘config’ ‘feather’ ‘here’ ‘knitr’ ‘log4r’ ‘ps’
  ‘rmarkdown’ ‘skimr’ ‘snakecase’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘rmarkdown’ in Rd xrefs
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘methods’ ‘rgdal’
  All declared Imports should be used.
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ardec: no visible global function definition for ‘filter’
ardec.lm: no visible global function definition for ‘ar’
ardec.lm: no visible global function definition for ‘lm’
Undefined global functions or variables:
  ar filter lm
Consider adding
  importFrom("stats", "ar", "filter", "lm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  aricode.cpp:22:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  aricode.cpp:41:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/aricode.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Crashpad’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Undeclared packages ‘survey’, ‘Matching’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.1Mb
    testScripts   1.3Mb
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘gmm’ ‘graphics’ ‘sandwich’ ‘stats4’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 54.1Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    libs  49.2Mb
Package which this enhances but not available for checking: ‘ARTP’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
Undeclared package ‘proxy’ in Rd xrefs
Note: found 328 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ash/libs/ash.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MSToutput.txt’
ASP.Score: no visible global function definition for ‘pnorm’
Graphs.Bayesian: no visible global function definition for ‘dev.new’
colorhex: no visible global function definition for ‘gray’
colorhex: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  dev.new gray pnorm rgb
Consider adding
  importFrom("grDevices", "dev.new", "gray", "rgb")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
File ‘ASPBay/libs/ASPBay.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
Undeclared packages ‘assertive.properties’, ‘assertive.types’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘rstudioapi’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘sets’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘pryr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘arules’ ‘arulesViz’ ‘dplyr’ ‘methods’ ‘plotly’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CALPHA: no visible global function definition for ‘dbinom’
CALPHA: no visible global function definition for ‘pchisq’
CAST: no visible global function definition for ‘fisher.test’
CAST: no visible global function definition for ‘chisq.test’
CMC: no visible global function definition for ‘pf’
MULTI: no visible global function definition for ‘complete.cases’
RVT1: no visible global function definition for ‘pchisq’
RVT2: no visible global function definition for ‘pchisq’
RWAS: no visible global function definition for ‘pnorm’
SKAT: no visible global function definition for ‘dbeta’
SKAT: no visible global function definition for ‘pchisq’
TTEST: no visible global function definition for ‘complete.cases’
TTEST: no visible global function definition for ‘pf’
WST: no visible global function definition for ‘mvfft’
WST: no visible global function definition for ‘pnorm’
my_cmc_method: no visible global function definition for
  ‘complete.cases’
my_getUV: no visible global function definition for ‘complete.cases’
my_orwss_method: no visible global function definition for ‘sd’
my_rarecov_method: no visible global function definition for
  ‘chisq.test’
my_rbt_method: no visible global function definition for ‘ppois’
my_score_method: no visible global function definition for ‘pchisq’
my_ssu_method: no visible global function definition for ‘pchisq’
my_ssuw_method: no visible global function definition for ‘pchisq’
my_sum_method: no visible global function definition for ‘pchisq’
my_uminp_method: no visible global function definition for ‘pchisq’
my_uminp_method: no visible global function definition for ‘pmvnorm’
Undefined global functions or variables:
  chisq.test complete.cases dbeta dbinom fisher.test mvfft pchisq pf
  pmvnorm pnorm ppois sd
Consider adding
  importFrom("stats", "chisq.test", "complete.cases", "dbeta", "dbinom",
             "fisher.test", "mvfft", "pchisq", "pf", "pnorm", "ppois",
             "sd")
to your NAMESPACE file.
File ‘AssotesteR/libs/AssotesteR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘asteRiskData’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   2.6Mb
GNU make is a SystemRequirements.
beamDiskOverlap: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
fm_unred: no visible global function definition for ‘spline’
galage: no visible global function definition for ‘integrate’
lumdist: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate spline
Consider adding
  importFrom("stats", "integrate", "spline")
to your NAMESPACE file.
checkRd: (7) ten.Rd:23: \item in \value must have non-empty label
'LazyData' is specified without a 'data' directory
VPC.graph : findQuantile: no visible global function definition for
  ‘quantile’
VPC.graph : findQuantileCI : <anonymous>: no visible global function
  definition for ‘quantile’
asVPC.binW: no visible global function definition for ‘median’
asVPC.binW : <anonymous>: no visible global function definition for
  ‘quantile’
asVPC.binW: no visible global function definition for ‘quantile’
asVPC.distanceW: no visible global function definition for ‘median’
asVPC.distanceW : <anonymous>: no visible global function definition
  for ‘quantile’
asVPC.distanceW: no visible global function definition for ‘quantile’
makeCOVbin: no visible global function definition for ‘quantile’
makeCOVbin: no visible global function definition for ‘median’
read_Simdata: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  median quantile read.table
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "read.table")
to your NAMESPACE file.
get.est.ATT: no visible global function definition for ‘tail’
get.est.MT: no visible global function definition for ‘tail’
get.est.simple: no visible global function definition for ‘tail’
newton.r: no visible global function definition for ‘tail’
plot.ATE: no visible global function definition for ‘par’
plot.ATE: no visible global function definition for ‘axis’
plot.ATE: no visible global function definition for ‘abline’
plot.ATE: no visible global function definition for ‘lines’
plot.ATE: no visible global function definition for ‘legend’
plot.ATE: no visible global function definition for ‘points’
print.summary.ATE: no visible global function definition for
  ‘printCoefmat’
summary.ATE: no visible global function definition for ‘qnorm’
summary.ATE: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline axis legend lines par pnorm points printCoefmat qnorm tail
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "points")
  importFrom("stats", "pnorm", "printCoefmat", "qnorm")
  importFrom("utils", "tail")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘lubridate’ ‘openair’ ‘plotly’
  All declared Imports should be used.
atmcmc : rmvtnorm: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘runif’
atmcmc: no visible global function definition for ‘par’
atmcmc: no visible global function definition for ‘lm’
atmcmc: no visible global function definition for ‘lines’
atmcmc: no visible global function definition for ‘var’
atmcmc: no visible global function definition for ‘cov’
atmcmc: no visible global function definition for ‘quantile’
atmcmc: no visible global function definition for ‘sd’
plotmcmc: no visible global function definition for ‘pdf’
plotmcmc: no visible global function definition for ‘par’
plotmcmc: no visible global function definition for ‘dev.new’
plotmcmc: no visible global function definition for ‘png’
plotmcmc: no visible global function definition for ‘hist’
plotmcmc: no visible global function definition for ‘dev.off’
plotmcmc: no visible global function definition for ‘lines’
Undefined global functions or variables:
  cov dev.new dev.off hist lines lm par pdf png quantile rnorm runif sd
  var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "png")
  importFrom("graphics", "hist", "lines", "par")
  importFrom("stats", "cov", "lm", "quantile", "rnorm", "runif", "sd",
             "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
PlotAtm.lin : scale_image: no visible global function definition for
  ‘heat.colors’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘par’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘sd’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘approx’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘image’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘axis’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘mtext’
PlotAtm.lin: no visible global function definition for ‘arrows’
PlotAtm.lin: no visible global function definition for ‘text’
PlotAtm.lin: no visible global function definition for ‘polygon’
sky.colors: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  approx arrows axis heat.colors image mtext par polygon rgb sd text
Consider adding
  importFrom("grDevices", "heat.colors", "rgb")
  importFrom("graphics", "arrows", "axis", "image", "mtext", "par",
             "polygon", "text")
  importFrom("stats", "approx", "sd")
to your NAMESPACE file.
Rd file 'MakeArrivals.lin.Rd':
  \examples lines wider than 100 characters:
     MakeArrivals.lin(xs = c(100, 150), ys = c(100, 150), zs = c(100, 150), xr = 0, yr = 0, zr = 0, dt = 0.01, nt = 100, timing = c(0, 0), A ... [TRUNCATED]

Rd file 'MakeAtmList.lin.Rd':
  \usage lines wider than 90 characters:
     MakeAtmList.lin(z0 = 0, c0 = 343, gc = 0, wx0 = 0, gwx = 0, wy0 = 0, gwy = 0, rho0 = 1.2929 * exp(-z0/6800), grho = -0.0001901323 * exp ... [TRUNCATED]

These lines will be truncated in the PDF manual.
File ‘AtmRay/libs/AtmRay.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Scaled_loops.cpp:203:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Unscaled_loops.cpp:147:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Unscaled_nuts_loops.cpp:206:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/ATNr.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Undeclared package ‘snpar’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dlnm’ ‘ggplot2’ ‘lubridate’ ‘mvmeta’ ‘pbs’ ‘tsModel’
  All declared Imports should be used.
AUCRFcv: no visible global function definition for ‘predict’
plot.AUCRF: no visible global function definition for ‘par’
plot.AUCRF: no visible global function definition for ‘dotchart’
plot.AUCRF: no visible global function definition for ‘title’
plot.AUCRF: no visible global function definition for ‘text’
Undefined global functions or variables:
  dotchart par predict text title
Consider adding
  importFrom("graphics", "dotchart", "par", "text", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘RJSONIO’ ‘hexbin’ ‘plotrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
audioHist: no visible global function definition for ‘hist’
audioHist: no visible global function definition for ‘rescale’
audioHist: no visible global function definition for ‘toJSON’
audioScatter: no visible binding for global variable ‘formula’
audioScatter: no visible global function definition for ‘hexbinplot’
audioScatter: no visible global function definition for ‘cor’
audioScatter: no visible global function definition for ‘toJSON’
audioSplom: no visible global function definition for ‘hexplom’
audioSplom: no visible binding for global variable ‘BTY’
audioSplom: no visible binding for global variable ‘panel.hexboxplot’
audioSplom: no visible global function definition for ‘combn’
audioSplom : <anonymous>: no visible global function definition for
  ‘cor’
audioSplom : <anonymous>: no visible global function definition for
  ‘toJSON’
audiolyzRcheck: no visible global function definition for
  ‘download.file’
audiolyzRcheck: no visible global function definition for ‘unzip’
matricize: no visible global function definition for ‘hexbin’
panel.audiolyzR: no visible global function definition for
  ‘panel.hexbinplot’
Undefined global functions or variables:
  BTY combn cor download.file formula hexbin hexbinplot hexplom hist
  panel.hexbinplot panel.hexboxplot rescale toJSON unzip
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "formula")
  importFrom("utils", "combn", "download.file", "unzip")
to your NAMESPACE file.
Undeclared package ‘gtable’ in Rd xrefs
Note: found 1 marked UTF-8 string
Note: found 899 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 552 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘broom’ ‘tibble’ ‘usethis’
  All declared Imports should be used.
Undeclared package ‘tensorflow’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.rsp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
gLog.ep: no visible global function definition for ‘quantile’
gedestp: no visible global function definition for ‘na.omit’
gedestp: no visible global function definition for ‘optim’
gets.mean: no visible global function definition for ‘start’
gets.mean: no visible global function definition for ‘end’
gets.mean: no visible global function definition for ‘window’
gets.mean: no visible global function definition for ‘pt’
gets.mean: no visible global function definition for ‘Box.test’
gets.mean: no visible global function definition for ‘pchisq’
gets.vol: no visible global function definition for ‘start’
gets.vol: no visible global function definition for ‘end’
gets.vol: no visible global function definition for ‘window’
gets.vol: no visible global function definition for ‘pt’
gets.vol: no visible global function definition for ‘Box.test’
gets.vol: no visible global function definition for ‘pchisq’
jb.test: no visible global function definition for ‘pchisq’
skewness.test: no visible global function definition for ‘pchisq’
sm: no visible global function definition for ‘start’
sm: no visible global function definition for ‘end’
sm: no visible global function definition for ‘window’
sm: no visible global function definition for ‘pt’
sm: no visible global function definition for ‘pchisq’
sm: no visible global function definition for ‘Box.test’
Undefined global functions or variables:
  Box.test end na.omit optim pchisq pt quantile start window
Consider adding
  importFrom("stats", "Box.test", "end", "na.omit", "optim", "pchisq",
             "pt", "quantile", "start", "window")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Imports includes 44 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘BBmisc’ ‘Ckmeans.1d.dp’ ‘Matrix’ ‘broom.mixed’ ‘ggstance’ ‘glmnet’
  ‘hardhat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinycssloaders’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘readxl’ ‘reshape2’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘rclipboard’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MixAll’ ‘dplyr’ ‘lqmm’ ‘matrixcalc’ ‘rmutil’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
Undeclared package ‘AzureAuth’ in Rd xrefs
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jose’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httr’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
CRexp_set: no visible global function definition for ‘runif’
b6e6rl: no visible global function definition for ‘runif’
derand_RL: no visible global function definition for ‘runif’
derandexp_RL: no visible global function definition for ‘runif’
nahvyb_expt: no visible global function definition for ‘runif’
roulete: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
.generateTransform: no visible global function definition for ‘sd’
.generateUnitHyperCube: no visible global function definition for
  ‘runif’
.makeBoundedSingleStep: no visible global function definition for
  ‘runif’
.makeBoundedStep: no visible global function definition for ‘runif’
.makeStep: no visible global function definition for ‘runif’
.staircaseSampling: no visible global function definition for ‘runif’
GaussianPrior: no visible global function definition for ‘qnorm’
LogNormalPrior: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
File ‘BaBooN/libs/BaBooN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 64209 marked UTF-8 strings
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.3Mb
    libs   2.3Mb
Namespace in Imports field not imported from: ‘glpkAPI’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘InvariantCausalPrediction’, ‘CompareCausalNetworks’ in Rd xrefs
BACprior.CV: no visible global function definition for ‘na.fail’
BACprior.CV: no visible global function definition for ‘abline’
BACprior.boot: no visible global function definition for ‘na.fail’
BACprior.boot: no visible global function definition for ‘abline’
BACprior.lm: no visible global function definition for ‘na.fail’
BACprior.lm: no visible global function definition for ‘coef’
BACprior.lm: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  abline coef na.fail vcov
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "coef", "na.fail", "vcov")
to your NAMESPACE file.
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘tkrplot’
  All declared Imports should be used.
installed size is 65.4Mb
  sub-directories of 1Mb or more:
    libs  63.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Undeclared package ‘plyr’ in Rd xrefs
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Found the following files/directories:
  ‘exemplary_input1.txt’ ‘exemplary_input2.txt’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats4’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fs’ ‘testthat’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.3Mb
    doc    1.9Mb
Undeclared package ‘BayesXsrc’ in Rd xrefs
best_binomial_bandit : f: no visible global function definition for
  ‘dbeta’
best_binomial_bandit : f: no visible global function definition for
  ‘pbeta’
best_binomial_bandit: no visible global function definition for
  ‘integrate’
best_poisson_bandit : f: no visible global function definition for
  ‘dgamma’
best_poisson_bandit : f: no visible global function definition for
  ‘pgamma’
best_poisson_bandit: no visible global function definition for
  ‘integrate’
deseasonalized_trend: no visible global function definition for
  ‘predict’
distribution_estimate: no visible global function definition for
  ‘quantile’
distribution_estimate: no visible global function definition for
  ‘qbeta’
significance_analysis: no visible global function definition for
  ‘prop.test’
sim_post: no visible global function definition for ‘rbeta’
summarize_metrics: no visible global function definition for ‘median’
summarize_metrics: no visible global function definition for
  ‘prop.test’
Undefined global functions or variables:
  dbeta dgamma integrate median pbeta pgamma predict prop.test qbeta
  quantile rbeta
Consider adding
  importFrom("stats", "dbeta", "dgamma", "integrate", "median", "pbeta",
             "pgamma", "predict", "prop.test", "qbeta", "quantile",
             "rbeta")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Note: found 148 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'library' or 'require' calls to packages already attached by Depends:
  ‘grid’ ‘lattice’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘grid’ ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
barcode: no visible global function definition for ‘unit’
barcode: no visible global function definition for ‘grid.newpage’
barcode: no visible global function definition for ‘grid.text’
barcode: no visible global function definition for ‘gpar’
barcode: no visible global function definition for ‘pushViewport’
barcode: no visible global function definition for ‘viewport’
barcode: no visible global function definition for ‘convertHeight’
barcode: no visible global function definition for ‘convertWidth’
barcode: no visible global function definition for ‘grid.rect’
barcode: no visible global function definition for ‘popViewport’
barcode.panel: no visible global function definition for ‘unit’
barcode.panel: no visible global function definition for ‘hist’
barcode.panel: no visible global function definition for ‘pushViewport’
barcode.panel: no visible global function definition for ‘viewport’
barcode.panel: no visible global function definition for ‘grid.xaxis’
barcode.panel: no visible global function definition for ‘gpar’
barcode.panel: no visible global function definition for ‘grid.text’
barcode.panel: no visible global function definition for ‘popViewport’
barcode.panel: no visible global function definition for
  ‘grid.segments’
barcode.panel: no visible global function definition for ‘grid.points’
Undefined global functions or variables:
  convertHeight convertWidth gpar grid.newpage grid.points grid.rect
  grid.segments grid.text grid.xaxis hist popViewport pushViewport unit
  viewport
Consider adding
  importFrom("graphics", "hist")
to your NAMESPACE file.
Undeclared package ‘YaleToolkit’ in Rd xrefs
Note: found 13825 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
File ‘Barnard/libs/Barnard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
Namespace in Imports field not imported from: ‘mvnfast’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   3.1Mb
Undeclared package ‘Rraven’ in Rd xrefs
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.3Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
File ‘base64enc/libs/base64enc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘pitchRx’ ‘progressr’
  All declared Imports should be used.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dbplyr’ ‘dotenv’ ‘googleAuthR’ ‘writexl’ ‘xml2’
  All declared Imports should be used.
Undeclared packages ‘jsonlite’, ‘arrow’ in Rd xrefs
Namespace in Imports field not imported from: ‘splines’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘BASIX/libs/BASIX.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘circlize’ ‘hexbin’ ‘scales’ ‘sna’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘Rmpi’ in Rd xrefs
Namespace in Imports field not imported from: ‘vtable’
  All declared Imports should be used.
Note: found 19 marked UTF-8 strings
File ‘batman/libs/batman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 52.9Mb
  sub-directories of 1Mb or more:
    libs  50.9Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘utils’
  All declared Imports should be used.
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
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
File ‘BayesComm/libs/BayesComm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
FECRT: no visible global function definition for ‘pdf’
FECRT: no visible global function definition for ‘hist’
FECRT: no visible global function definition for ‘abline’
FECRT: no visible global function definition for ‘dev.off’
FECRT.analysis: no visible global function definition for ‘pdf’
FECRT.analysis: no visible global function definition for ‘hist’
FECRT.analysis: no visible global function definition for ‘abline’
FECRT.analysis: no visible global function definition for ‘dev.off’
fecrt: no visible global function definition for ‘pdf’
fecrt: no visible global function definition for ‘hist’
fecrt: no visible global function definition for ‘abline’
fecrt: no visible global function definition for ‘dev.off’
fecrt.analysis: no visible global function definition for ‘pdf’
fecrt.analysis: no visible global function definition for ‘hist’
fecrt.analysis: no visible global function definition for ‘abline’
fecrt.analysis: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  abline dev.off hist pdf
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "hist")
to your NAMESPACE file.
File ‘bayescount/libs/bayescount.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 73.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  72.0Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  jzs_Gauss_approx_aov.cpp:51:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/BayesFactor.Rcheck/00install.out’ for details.
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  12.9Mb
installed size is 55.5Mb
  sub-directories of 1Mb or more:
    libs  54.1Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘StanHeaders’ ‘astsa’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 74.0Mb
  sub-directories of 1Mb or more:
    libs  73.0Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppParallel’ ‘mlbench’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Undeclared package ‘fGarch’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘BayesGPfit/libs/BayesGPfit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
BMAnimalTrack: no visible global function definition for ‘nlm’
BMAnimalTrack: no visible global function definition for ‘qnorm’
dataSim: no visible global function definition for ‘rnorm’
rBBridge: no visible global function definition for ‘rnorm’
rBMotion: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  nlm qnorm rnorm
Consider adding
  importFrom("stats", "nlm", "qnorm", "rnorm")
to your NAMESPACE file.
File ‘bayesianETAS/libs/bayesianETAS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘shinytest’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   3.1Mb
Undeclared packages ‘rworldmap’, ‘snowFT’ in Rd xrefs
Packages required but not available: 'ghyp', 'fAsianOptions'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘bayesloglin/libs/bayesloglin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘FastGP’
  All declared Imports should be used.
Found the following significant warnings:
  clusterMix_rcpp_loop.cpp:39:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/bayesm.Rcheck/00install.out’ for details.
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  18.8Mb
Malformed Description field: should contain one or more complete sentences.
noninform_prior : a : f1: no visible global function definition for
  ‘pbeta’
noninform_prior : a : f1: no visible global function definition for
  ‘dbeta’
noninform_prior : a: no visible global function definition for
  ‘integrate’
noninform_prior: no visible global function definition for ‘rbeta’
noninform_prior: no visible global function definition for ‘optim’
postNullFun : b : f1: no visible global function definition for ‘pbeta’
postNullFun : b : f1: no visible global function definition for ‘dbeta’
postNullFun : b: no visible global function definition for ‘integrate’
prior_prob : a : f1: no visible global function definition for ‘pbeta’
prior_prob : a : f1: no visible global function definition for ‘dbeta’
prior_prob : a: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  dbeta integrate optim pbeta rbeta
Consider adding
  importFrom("stats", "dbeta", "integrate", "optim", "pbeta", "rbeta")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘fda’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   3.8Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Namespaces in Imports field not imported from:
  ‘HDInterval’ ‘MCMCpack’ ‘R2WinBUGS’ ‘R2jags’ ‘carData’ ‘rjags’
  All declared Imports should be used.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Namespace in Imports field not imported from: ‘RcppNumerical’
  All declared Imports should be used.
MHratioPopPref: no visible global function definition for ‘runif’
MratioPopMult: no visible global function definition for ‘dunif’
MratioPopMult: no visible global function definition for ‘runif’
bayesPref: no visible global function definition for ‘runif’
calcP: no visible global function definition for ‘dunif’
calcP: no visible global function definition for ‘dmultinom’
calcdic: no visible global function definition for ‘median’
calcdic: no visible binding for global variable ‘median’
calcdic: no visible global function definition for ‘dmultinom’
calcdicExtern: no visible global function definition for ‘median’
calcdicExtern: no visible global function definition for ‘dmultinom’
calcdicExtern: no visible binding for global variable ‘median’
credibleIntervals: no visible global function definition for ‘quantile’
prefPlot: no visible global function definition for ‘postscript’
prefPlot: no visible global function definition for ‘lines’
prefPlot: no visible global function definition for ‘density’
prefPlot: no visible global function definition for ‘median’
prefPlot: no visible global function definition for ‘legend’
prefPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  density dev.off dmultinom dunif legend lines median postscript
  quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "density", "dmultinom", "dunif", "median",
             "quantile", "runif")
to your NAMESPACE file.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
File ‘bayesQR/libs/bayesQR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  BayesReversePLLH.cpp:439:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BayesReversePLLH.cpp:1129:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BayesReversePLLH.cpp:1172:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BayesReversePLLH.cpp:3029:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/BayesReversePLLH.Rcheck/00install.out’ for details.
Note: found 1924 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘matrixcalc’ ‘stats’
  All declared Imports should be used.
installed size is 60.8Mb
  sub-directories of 1Mb or more:
    libs  60.4Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘MASS’ ‘combinat’ ‘gplots’ ‘mnormt’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs  10.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Undeclared package ‘mvtnorm’ in Rd xrefs
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    ex-data   4.7Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘rjags’
  All declared Imports should be used.
File ‘BayesTree/libs/BayesTree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  priorprob.c:45:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  priorprob.c:93:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  priorprob.c:141:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/BayesVarSel.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 68.4Mb
  sub-directories of 1Mb or more:
    libs  68.3Mb
GNU make is a SystemRequirements.
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
GNU make is a SystemRequirements.
'library' or 'require' call to ‘coda’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Rd file 'BPSpostSample.Rd':
  \usage lines wider than 90 characters:
     BPSpostSample(hyp, times, obs = NULL, mclen = 10, burnin = 0, thin = 1, df = 10, etastar = NULL)
  \examples lines wider than 100 characters:
     post<-BPSpostSample(hypars, times = earthquakes$ti, obs = earthquakes$ob, etastar = postmode$etastar)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘diagnostics.pdf’ ‘post.rda’
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘rgl’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘fields’ ‘poibin’ ‘rjags’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BMR.plot: no visible global function definition for ‘heat.colors’
BMR.plot: no visible global function definition for ‘image.plot’
BMR.plot: no visible global function definition for ‘title’
BMR.plot: no visible global function definition for ‘mtext’
BMR.plot: no visible global function definition for ‘par’
baysic.data: no visible global function definition for ‘layout’
baysic.data: no visible global function definition for ‘barplot’
baysic.data: no visible global function definition for ‘rainbow’
baysic.fit: no visible global function definition for ‘jags.model’
baysic.fit: no visible global function definition for ‘update’
baysic.fit: no visible global function definition for ‘coda.samples’
baysic.test: no visible global function definition for ‘ppois’
baysic.test : <anonymous>: no visible global function definition for
  ‘ppoibin’
baysic.test: no visible global function definition for ‘pbinom’
fuzzy.FDR.approx: no visible global function definition for ‘p.adjust’
fuzzy.FDR.approx: no visible global function definition for ‘runif’
Undefined global functions or variables:
  barplot coda.samples heat.colors image.plot jags.model layout mtext
  p.adjust par pbinom ppoibin ppois rainbow runif title update
Consider adding
  importFrom("grDevices", "heat.colors", "rainbow")
  importFrom("graphics", "barplot", "layout", "mtext", "par", "title")
  importFrom("stats", "p.adjust", "pbinom", "ppois", "runif", "update")
to your NAMESPACE file.
Rd file 'baysic.fit.Rd':
  \usage lines wider than 90 characters:
     baysic.fit(dat.out, snv.cat, covar = NULL, excl.list = NULL, burn.in = 10000,n.samp = 25000, fn.jags = "baysic.jags", prior = NULL)
  \examples lines wider than 100 characters:
     snv.cat.ex[[2]]<-unique(c(grep("TC.",colnames(ccds.19)[-c(1:2)]),grep(".CG",colnames(ccds.19)[-c(1:2)])))

Rd file 'baysic.test.Rd':
  \usage lines wider than 90 characters:
     baysic.test(dat.out, fit.out, fdr.level = 0.15, fuzzy.cnt = 10000, r = NULL,subtype = NULL, PB.approx = FALSE)
  \examples lines wider than 100 characters:
     snv.cat.ex[[2]]<-unique(c(grep("TC.",colnames(ccds.19)[-c(1:2)]),grep(".CG",colnames(ccds.19)[-c(1:2)])))

These lines will be truncated in the PDF manual.
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
BAYSTAR: no visible global function definition for ‘median’
BAYSTAR: no visible global function definition for ‘ar’
BAYSTAR: no visible global function definition for ‘quantile’
BAYSTAR: no visible global function definition for ‘dev.new’
BAYSTAR: no visible global function definition for ‘ts.plot’
BAYSTAR: no visible global function definition for ‘title’
BAYSTAR: no visible global function definition for ‘par’
BAYSTAR: no visible global function definition for ‘plot.ts’
BAYSTAR: no visible global function definition for ‘lines’
BAYSTAR: no visible global function definition for ‘acf’
TAR.lagd: no visible global function definition for ‘runif’
TAR.sigma: no visible global function definition for ‘rgamma’
TAR.simu: no visible global function definition for ‘rnorm’
TAR.summary: no visible global function definition for ‘quantile’
TAR.summary: no visible global function definition for ‘sd’
TAR.thres: no visible global function definition for ‘rnorm’
TAR.thres: no visible global function definition for ‘runif’
Undefined global functions or variables:
  acf ar dev.new lines median par plot.ts quantile rgamma rnorm runif
  sd title ts.plot
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "lines", "par", "title")
  importFrom("stats", "acf", "ar", "median", "plot.ts", "quantile",
             "rgamma", "rnorm", "runif", "sd", "ts.plot")
to your NAMESPACE file.
Undeclared package ‘formula.tools’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package in Depends field not imported from: ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
LaplaceMetropolis_admkr: no visible binding for global variable
  ‘median’
LaplaceMetropolis_admkr: no visible global function definition for
  ‘mad’
LaplaceMetropolis_gaussian: no visible binding for global variable
  ‘median’
LaplaceMetropolis_gaussian: no visible global function definition for
  ‘mad’
cost_admkr: no visible global function definition for ‘sd’
cov_chol: no visible global function definition for ‘qchisq’
cov_chol_admkr: no visible global function definition for ‘qchisq’
gibbs_admkr_erro: no visible global function definition for ‘rnorm’
gibbs_admkr_erro: no visible global function definition for ‘runif’
gibbs_admkr_nw: no visible global function definition for ‘qnorm’
gibbs_admkr_nw: no visible global function definition for ‘rnorm’
gibbs_admkr_nw: no visible global function definition for ‘runif’
loglikelihood_admkr: no visible global function definition for ‘sd’
margin_like_admkr: no visible global function definition for ‘sd’
np_gibbs: no visible global function definition for ‘qnorm’
np_gibbs: no visible global function definition for ‘rnorm’
np_gibbs: no visible global function definition for ‘runif’
np_gibbs: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  mad median qchisq qnorm rgamma rnorm runif sd
Consider adding
  importFrom("stats", "mad", "median", "qchisq", "qnorm", "rgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
bbmm.contour: no visible global function definition for ‘na.omit’
bbmm.contour: no visible global function definition for ‘optimize’
bbmm.contour: no visible global function definition for ‘contour’
bbmm.contour: no visible global function definition for ‘points’
bbmm.contour: no visible global function definition for ‘lines’
brownian.bridge: no visible global function definition for ‘sd’
brownian.motion.variance: no visible global function definition for
  ‘optimize’
Undefined global functions or variables:
  contour lines na.omit optimize points sd
Consider adding
  importFrom("graphics", "contour", "lines", "points")
  importFrom("stats", "na.omit", "optimize", "sd")
to your NAMESPACE file.
bbo: no visible global function definition for ‘runif’
bbo: no visible global function definition for ‘tail’
Undefined global functions or variables:
  runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
Undeclared package ‘mlr3’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘locfit’ ‘secr’
  All declared Imports should be used.
Undeclared package ‘betareg’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘latticeExtra’ ‘rgdal’
  All declared Imports should be used.
checkRd: (7) bootBW.Rd:27: \item in \describe must have non-empty label
checkRd: (7) bootBW.Rd:28: \item in \describe must have non-empty label
checkRd: (7) bootBW.Rd:29: \item in \describe must have non-empty label
File ‘BCBCSF/libs/BCBCSF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following 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’
pairs.bce : panel.cor: no visible global function definition for ‘text’
pairs.bce : panel.cor: no visible global function definition for ‘cor’
pairs.bce : panel.hist: no visible global function definition for ‘par’
pairs.bce : panel.hist: no visible global function definition for
  ‘hist’
pairs.bce : panel.hist: no visible global function definition for
  ‘rect’
pairs.bce: no visible global function definition for ‘pairs’
panel.cor: no visible global function definition for ‘par’
panel.cor: no visible global function definition for ‘cor’
panel.cor: no visible global function definition for ‘strwidth’
panel.cor: no visible global function definition for ‘text’
rdirichlet2: no visible global function definition for ‘rgamma’
summary.bce: no visible global function definition for ‘cov’
summary.bce: no visible binding for global variable ‘sd’
summary.bce: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  cor cov hist pairs par quantile rect rgamma sd strwidth text
Consider adding
  importFrom("graphics", "hist", "pairs", "par", "rect", "strwidth",
             "text")
  importFrom("stats", "cor", "cov", "quantile", "rgamma", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘coda’ ‘knitr’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘bcpa/libs/bcpa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
bcpmeta.model: no visible global function definition for ‘rbinom’
bcpmeta.model: no visible global function definition for ‘runif’
bcpmeta.parameters: no visible global function definition for ‘runif’
cp.plot: no visible global function definition for ‘postscript’
cp.plot: no visible global function definition for ‘lines’
cp.plot: no visible global function definition for ‘axis’
cp.plot: no visible global function definition for ‘box’
cp.plot: no visible global function definition for ‘points’
cp.plot: no visible global function definition for ‘dev.off’
lMarLik.EB.normAR: no visible global function definition for ‘optimize’
lMarLik.normAR: no visible global function definition for ‘integrate’
marginal.plot: no visible global function definition for ‘postscript’
marginal.plot: no visible global function definition for ‘axis’
marginal.plot: no visible global function definition for ‘box’
marginal.plot: no visible global function definition for ‘points’
marginal.plot: no visible global function definition for ‘dev.off’
simgen: no visible global function definition for ‘rnorm’
up.eta.MH.normAR: no visible global function definition for ‘runif’
up.eta.RS.normAR: no visible global function definition for ‘runif’
up.parameters.EB.normAR: no visible global function definition for
  ‘rnorm’
up.parameters.normAR: no visible global function definition for ‘rnorm’
up.parameters.normAR: no visible global function definition for ‘runif’
up.parameters.normAR: no visible global function definition for
  ‘rgamma’
Undefined global functions or variables:
  axis box dev.off integrate lines optimize points postscript rbinom
  rgamma rnorm runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "axis", "box", "lines", "points")
  importFrom("stats", "integrate", "optimize", "rbinom", "rgamma",
             "rnorm", "runif")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’
  All declared Imports should be used.
Package suggested but not available for checking: ‘webshot2’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
Namespace in Imports field not imported from: ‘splatter’
  All declared Imports should be used.
Note: found 72 marked UTF-8 strings
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.1Mb
'LazyData' is specified without a 'data' directory
mise: no visible global function definition for ‘integrate’
density,BrVitale : density.vitale : <anonymous>: no visible global
  function definition for ‘dbeta’
density,Chen99Kernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,HirukawaJLNKernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,MicroBetaChen99Kernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,Vitale : <anonymous>: no visible global function definition for
  ‘dbeta’
distribution,BernsteinPolynomials : <anonymous>: no visible global
  function definition for ‘integrate’
distribution,KernelDensity : <anonymous>: no visible global function
  definition for ‘integrate’
print,BoundedDensity: no visible global function definition for ‘str’
print,KernelDensity: no visible global function definition for ‘str’
rsample,BoundedDensity: no visible global function definition for
  ‘runif’
setNormalizationConst,MacroBetaChen99Kernel: no visible global function
  definition for ‘integrate’
setNormalizationConst,MacroBetaHirukawaTSKernel: no visible global
  function definition for ‘integrate’
setNormalizationConstant,MacroBetaHirukawaJLNKernel: no visible global
  function definition for ‘integrate’
setNormalizationConstants,MicroBetaChen99Kernel :
  density.kernelFunction: no visible global function definition for
  ‘dbeta’
setNormalizationConstants,MicroBetaChen99Kernel : <anonymous>: no
  visible global function definition for ‘integrate’
show,BoundedDensity: no visible global function definition for ‘str’
show,KernelDensity: no visible global function definition for ‘str’
Undefined global functions or variables:
  dbeta integrate runif str
Consider adding
  importFrom("stats", "dbeta", "integrate", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘dump.txt’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘bferrbars.eps’ ‘dataplot.eps’ ‘ppdat.eps’ ‘ppmod.eps’
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘beadarray’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
beadtypeFilter: no visible global function definition for ‘na.omit’
beadtypeFilter: no visible global function definition for ‘exprs’
beadtypeFilter: no visible global function definition for ‘se.exprs’
beadtypeFilter: no visible global function definition for ‘beadNum’
beadtypeFilter: no visible global function definition for ‘fData’
emCDF: no visible global function definition for ‘brewer.pal’
emCDF: no visible global function definition for ‘ecdf’
emCDF: no visible global function definition for ‘legend’
emCDF: no visible global function definition for ‘lines’
emCDF: no visible global function definition for ‘text’
emCDF: no visible global function definition for ‘reshape’
iccFun : <anonymous>: no visible global function definition for
  ‘quantile’
varianceplot: no visible global function definition for ‘reshape’
varianceplot: no visible global function definition for ‘points’
varianceplot: no visible global function definition for ‘legend’
Undefined global functions or variables:
  beadNum brewer.pal ecdf exprs fData legend lines na.omit points
  quantile reshape se.exprs text
Consider adding
  importFrom("graphics", "legend", "lines", "points", "text")
  importFrom("stats", "ecdf", "na.omit", "quantile", "reshape")
to your NAMESPACE file.
Rd file 'iccFun.Rd':
  \examples lines wider than 100 characters:
     aaa<-na.omit(data.frame(I(rownames(exprs(exampleSummaryDataNorm))),exprs(exampleSummaryDataNorm)))[1:40,]

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘flowCore’
installed size is 72.1Mb
  sub-directories of 1Mb or more:
    libs  70.5Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘beast_plot_toy.pdf’
Undeclared package ‘RCurl’ in Rd xrefs
Found the following files/directories:
  ‘alist.txt’ ‘rpkg’
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespaces in Imports field not imported from:
  ‘expm’ ‘forecast’ ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  get_boltzmann_aggregation.cpp:16:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/belg.Rcheck/00install.out’ for details.
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    libs  30.9Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
checkRd: (7) cost.opt.Rd:37-38: \item in \arguments must have non-empty label
checkRd: (7) dea.merge.Rd:17-18: \item in \arguments must have non-empty label
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘BenfordTests/libs/BenfordTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘zoo’ in Rd xrefs
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  24.5Mb
Namespace in Imports field not imported from: ‘BiDAG’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
installed size is 59.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs  56.4Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘ggplot2’ ‘readxl’ ‘rlist’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘coda’ ‘splines’
  All declared Imports should be used.
checkRd: (7) beta4reg.Rd:138: invalid email address: <zhouh@niu.edu>
checkRd: (7) beta4reg.Rd:138: invalid email address: <huang@stat.sc.edu>
checkRd: (7) cox.snell.beta4reg.Rd:48: invalid email address: <zhouh@niu.edu>
checkRd: (7) cox.snell.beta4reg.Rd:48: invalid email address: <huang@stat.sc.edu>
checkRd: (7) predictl.beta4reg.Rd:31: invalid email address: <zhouh@niu.edu>
checkRd: (7) predictl.beta4reg.Rd:31: invalid email address: <huang@stat.sc.edu>
Note: found 20 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Checking should be performed on sources prepared by ‘R CMD build’.
'LazyData' is specified without a 'data' directory
File ‘betategarch/libs/betategarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Note: found 10089 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    help   1.1Mb
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
block.gibbs: no visible global function definition for ‘rmultinom’
rdirichlet: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  rgamma rmultinom
Consider adding
  importFrom("stats", "rgamma", "rmultinom")
to your NAMESPACE file.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   4.8Mb
Note: found 582 marked UTF-8 strings
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
global: no visible global function definition for ‘par’
global: no visible global function definition for ‘runif’
global: no visible global function definition for ‘cov’
mymcmc: no visible global function definition for ‘par’
mymcmc: no visible global function definition for ‘rnorm’
mymcmc: no visible global function definition for ‘runif’
mymcmc: no visible global function definition for ‘cov’
mymcmc: no visible global function definition for ‘lines’
plkhci: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  cov lines par qchisq rnorm runif
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "cov", "qchisq", "rnorm", "runif")
to your NAMESPACE file.
Undeclared package ‘conf.design’ in Rd xrefs
installed size is 150.7Mb
  sub-directories of 1Mb or more:
    include  150.6Mb
Found the following significant warnings:
  BHSBVAR.cpp:236:71: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:236:23: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:246:72: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:246:23: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:256:97: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:256:122: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:256:23: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:256:47: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:284:68: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:284:20: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:289:69: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:289:20: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:294:94: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:294:119: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:294:20: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  BHSBVAR.cpp:294:44: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/BHSBVAR.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘betareg’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bias: no visible global function definition for ‘predict’
bias: no visible global function definition for ‘pnorm’
bias: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  model.matrix pnorm predict
Consider adding
  importFrom("stats", "model.matrix", "pnorm", "predict")
to your NAMESPACE file.
File ‘BiasedUrn/libs/BiasedUrn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 99 marked UTF-8 strings
Note: found 1904 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘DAAG’ ‘datasets’ ‘expm’ ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nycflights13’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RBGL’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.2Mb
Package suggested but not available for checking: ‘ffbase’
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 940 marked Latin-1 strings
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’.
File ‘biglm/libs/biglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.9Mb
    libs      1.6Mb
GNU make is a SystemRequirements.
Found the following significant warnings:
  deepcopy.cpp:103:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/bigmemory.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
possible bashism in configure line 14 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 24 (echo -n):
  echo -n "  checking for OS..."
checkRd: (7) attach.big.matrix.Rd:74: invalid email address: <bigmemoryauthors@gmail.com>
checkRd: (7) big.matrix-class.Rd:104: invalid email address: <bigmemoryauthors@gmail.com>
checkRd: (7) big.matrix.Rd:279: invalid email address: <bigmemoryauthors@gmail.com>
checkRd: (7) morder.Rd:84: invalid email address: <bigmemoryauthors@gmail.com>
checkRd: (7) mwhich.Rd:99: invalid email address: <bigmemoryauthors@gmail.com>
checkRd: (7) write.big.matrix.Rd:179: invalid email address: <bigmemoryauthors@gmail.com>
Checking should be performed on sources prepared by ‘R CMD build’.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Undeclared package ‘bigrquery’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘bigReg/libs/bigReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘outputs’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      7.2Mb
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  14.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.5Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 660 marked UTF-8 strings
Undeclared package ‘BoolNet’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘CountsEPPM’, ‘betareg’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared packages ‘tint’, ‘pinp’, ‘linl’ in Rd xrefs
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
Undeclared package ‘genalg’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
bin_ps: no visible global function definition for ‘runif’
bin_ps: no visible global function definition for ‘dbinom’
draw_i: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbinom runif
Consider adding
  importFrom("stats", "dbinom", "runif")
to your NAMESPACE file.
IndivdRUMIndMH: no visible global function definition for
  ‘flush.console’
dRUMAuxMix: no visible global function definition for ‘flush.console’
dRUMHAM: no visible global function definition for ‘flush.console’
dRUMIndMH: no visible global function definition for ‘flush.console’
print.binomlogit: no visible global function definition for ‘is’
summary.binomlogit: no visible global function definition for ‘is’
Undefined global functions or variables:
  flush.console is
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Undeclared packages ‘mcmc’, ‘bayesm’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘lattice’ ‘polynom’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘binom/libs/binom.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
bins.quantiles: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 67.8Mb
  sub-directories of 1Mb or more:
    libs  67.3Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘msa’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘pvclust’ in Rd xrefs
Namespace in Imports field not imported from: ‘pkgload’
  All declared Imports should be used.
checkRd: (7) Pchron.Rd:16: \item in \describe must have non-empty label
checkRd: (7) Pchron.Rd:18-26: \item in \describe must have non-empty label
checkRd: (7) Prec.Rd:11-12: \item in \describe must have non-empty label
checkRd: (7) Temp.Rd:11-12: \item in \describe must have non-empty label
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Found the following files/directories:
  ‘Plots.pdf’
Found the following files/directories:
  ‘pointshape.dbf’ ‘pointshape.shp’ ‘pointshape.shx’
Undeclared package ‘seqinr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘desc’ ‘lme4’ ‘mitml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘spatstat’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘asreml’
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
Package suggested but not available for checking: ‘MGRASTer’
'library' or 'require' call to ‘MGRASTer’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for ‘packageVersion’
biom.matrix: no visible global function definition for ‘packageVersion’
Undefined global functions or variables:
  packageVersion
Consider adding
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
checkRd: (7) bionetdata-package.Rd:29: invalid email address: {valentini,re}@di.unimi.it
'LazyData' is specified without a 'data' directory
File ‘bioPN/libs/bioPN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    doc       1.2Mb
    extdata   1.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Note: found 46 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  24.8Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘magrittr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘BoolNet’ 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
Undeclared package ‘RColorBrewer’ in Rd xrefs
biwt.cor: no visible global function definition for ‘covMcd’
biwt.cor: no visible binding for global variable ‘mad’
biwt.est: no visible global function definition for ‘covMcd’
biwt.est: no visible global function definition for ‘mahalanobis’
chi.int: no visible global function definition for ‘pchisq’
chi.int.p: no visible global function definition for ‘dchisq’
chi.int2: no visible global function definition for ‘pchisq’
chi.int2.p: no visible global function definition for ‘dchisq’
rejpt.bw: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  covMcd dchisq mad mahalanobis pchisq
Consider adding
  importFrom("stats", "dchisq", "mad", "mahalanobis", "pchisq")
to your NAMESPACE file.
Package suggested but not available for checking: ‘RQuantLib’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 54.4Mb
  sub-directories of 1Mb or more:
    libs      51.7Mb
    testdata   1.5Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (7) build_design.Rd:19: \item in \value must have non-empty label
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.5Mb
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    libs  31.5Mb
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    extdata   7.8Mb
Undeclared packages ‘biomod2’, ‘gstat’ in Rd xrefs
Found the following significant warnings:
  Forest.cpp:350:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/blockForest.Rcheck/00install.out’ for details.
Undeclared package ‘np’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
blockMessage : <anonymous>: no visible global function definition for
  ‘head’
blockMessage: no visible global function definition for ‘head’
blockMessage: no visible global function definition for ‘tail’
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Found the following significant warnings:
  cppFunctions.cpp:171:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/BLPestimatoR.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 127.5Mb
  sub-directories of 1Mb or more:
    libs  126.7Mb
GNU make is a SystemRequirements.
installed size is 73.4Mb
  sub-directories of 1Mb or more:
    libs  72.8Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
File ‘Bmix/libs/Bmix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  ‘coda’ ‘functional’ ‘plyr’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘coda’ ‘functional’ ‘plyr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HDistNoSize: no visible global function definition for ‘density’
HDistSize: no visible global function definition for ‘density’
bmkconverge: no visible global function definition for ‘Compose’
bmksensitive: no visible global function definition for ‘Compose’
bmksummary: no visible global function definition for ‘Compose’
bmksummary: no visible global function definition for ‘Curry’
bmksummary: no visible binding for global variable ‘quantile’
bmksummary : std.error: no visible global function definition for ‘var’
bmksummary: no visible global function definition for ‘mcmc’
bmksummary: no visible global function definition for ‘mcmc.list’
bmksummary: no visible global function definition for ‘median’
bmksummary: no visible global function definition for ‘effectiveSize’
bmksummary: no visible global function definition for ‘gelman.diag’
Undefined global functions or variables:
  Compose Curry density effectiveSize gelman.diag mcmc mcmc.list median
  quantile var
Consider adding
  importFrom("stats", "density", "median", "quantile", "var")
to your NAMESPACE file.
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    libs  33.2Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
bmmix : LL.y: no visible global function definition for ‘dmultinom’
bmmix : LL.x : <anonymous>: no visible global function definition for
  ‘dmultinom’
bmmix : LPrior.alpha: no visible global function definition for ‘dexp’
bmmix : alpha.move: no visible global function definition for ‘rnorm’
bmmix : alpha.move: no visible global function definition for ‘runif’
bmmix : phi.move: no visible global function definition for ‘rnorm’
bmmix : phi.move: no visible global function definition for ‘runif’
bmmix: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  dexp dmultinom read.table rnorm runif
Consider adding
  importFrom("stats", "dexp", "dmultinom", "rnorm", "runif")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘mcmc.txt’
Found the following significant warnings:
  node_pos_all.cpp:670:55: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  node_pos_contribution.cpp:348:55: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  node_pos_motifweights.cpp:352:55: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  node_pos_nodeweights.cpp:329:55: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  node_pos_stouffer.cpp:421:55: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  sd.cpp:283:55: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/bmotif.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘BMRV/libs/BMRV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
installed size is 66.4Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  60.9Mb
Namespace in Imports field not imported from: ‘MCMCpack’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following significant warnings:
  basic-misc.cpp:29:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/bnclassify.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Malformed Description field: should contain one or more complete sentences.
make_topology: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
bnlr: no visible global function definition for ‘dnorm’
bnlr: no visible global function definition for ‘runif’
chainsum : <anonymous>: no visible global function definition for
  ‘quantile’
infocrit: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm quantile runif
Consider adding
  importFrom("stats", "dnorm", "quantile", "runif")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘fastDummies’
  All declared Imports should be used.
Found the following significant warnings:
  get_latents.cpp:216:17: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/BNPMIXcluster.Rcheck/00install.out’ for details.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
Found the following files/directories:
  ‘attractors.tex’ ‘cellcycle.sbml’ ‘cellcycle.txt’ ‘pajek_export.net’
  ‘sequence.txt’ ‘testNet.bn’
Namespace in Imports field not imported from: ‘pryr’
  All declared Imports should be used.
Found the following significant warnings:
  stats/Design.cpp:536:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/Boom.Rcheck/00install.out’ for details.
installed size is 231.7Mb
  sub-directories of 1Mb or more:
    include    9.0Mb
    lib      222.3Mb
GNU make is a SystemRequirements.
installed size is 60.9Mb
  sub-directories of 1Mb or more:
    libs  60.4Mb
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fBasics’ ‘ggfortify’ ‘matrixcalc’ ‘usethis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘HSAUR3’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘psych’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
File ‘bootruin/libs/bootruin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
specdens: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Rd file 'specdens.Rd':
  \examples lines wider than 100 characters:
                                                                                         #the first 20 values of the 
                                                                                         #time series Nile and WWWusage

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
boottol: no visible global function definition for ‘setNames’
boottol : shift: no visible global function definition for ‘tail’
boottol : shift: no visible global function definition for ‘head’
boottol: no visible global function definition for ‘na.omit’
vastol: no visible global function definition for ‘setNames’
vastol: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  head na.omit setNames tail
Consider adding
  importFrom("stats", "na.omit", "setNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd file 'beq.lin.Rd':
  \examples lines wider than 100 characters:
     plot(x,h_sol0,type="l",lty=1,main=paste("Water Surface Elevetion after",t,"days",sep=" "),xlab="x[m]",ylab="h[m]")

Rd file 'beq.song.Rd':
  \examples lines wider than 100 characters:
     plot(x,h_sol1,type="l",lty=1,main="Water Surface Elevetion (Song at's solution) ",xlab="x[m]",ylab="h[m]")

These lines will be truncated in the PDF manual.
Undeclared packages ‘data.table’, ‘readxl’, ‘openxlsx’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    libs  29.0Mb
Note: found 1448 marked UTF-8 strings
GNU make is a SystemRequirements.
Found the following significant warnings:
  calculatePostLambdaPsy.cpp:77:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  calculatePostLambdaPsy.cpp:228:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  calculatePostLambdaPsy.cpp:381:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  calculatePostLambdaPsy.cpp:542:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  calculatePostLambdaPsy.cpp:718:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  calculatePostLambdaPsy.cpp:858:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  calculatePostLambdaPsy.cpp:996:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  calculatePostLambdaPsy.cpp:1104:14: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/bpgmm.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
checkRd: (7) BP.Rd:85: invalid email address: manoel.ferreira at professor.ufcg.edu.br
checkRd: (7) diag.BP.Rd:59: invalid email address: manoel.ferreira at professor.ufcg.edu.br
checkRd: (7) envelope.Rd:61: invalid email address: manoel.ferreira at professor.ufcg.edu.br
Note: found 2487 marked UTF-8 strings
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘Branching/libs/Branching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
apply.breaks: no visible binding for global variable ‘median’
break.clust: no visible global function definition for ‘median’
breakage.plot: no visible binding for global variable ‘median’
breakage.plot: no visible global function definition for ‘abline’
breakage.plot: no visible global function definition for ‘lm’
find.bottom: no visible global function definition for ‘filter’
fit.breakage: no visible global function definition for ‘optim’
fit.breakage: no visible global function definition for ‘points’
fit.sensitivity.plot: no visible global function definition for
  ‘contour’
fit.sensitivity.plot: no visible global function definition for
  ‘points’
fit.sensitivity.plot: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline contour filter lm median optim points text
Consider adding
  importFrom("graphics", "abline", "contour", "points", "text")
  importFrom("stats", "filter", "lm", "median", "optim")
to your NAMESPACE file.
Found the following significant warnings:
  exhaust_bic.cpp:269:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  exhaust_bic.cpp:290:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/breakfast.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘breathteststan’
Undeclared package ‘generics’ in Rd xrefs
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R     4.2Mb
    doc   3.6Mb
Undeclared package ‘tibble’ in Rd xrefs
Package suggested but not available for checking: ‘glmmADMB’
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    bin    2.0Mb
    doc    1.1Mb
    libs   1.9Mb
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
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Undeclared package ‘data.table’ in Rd xrefs
installed size is 96.3Mb
  sub-directories of 1Mb or more:
    doc    7.7Mb
    libs  87.9Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
checkRd: (7) plot.bsem.Rd:25: \item in \describe must have non-empty label
checkRd: (7) plot.bsem.Rd:26: \item in \describe must have non-empty label
checkRd: (7) plot.bsem.Rd:27: \item in \describe must have non-empty label
checkRd: (7) plot.bsem.Rd:28: \item in \describe must have non-empty label
checkRd: (7) plot.bsem.Rd:29: \item in \describe must have non-empty label
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
BSGS.Sample: no visible global function definition for ‘rgamma’
BSGS.Simple: no visible global function definition for ‘rgamma’
CompWiseGibbs: no visible global function definition for ‘runif’
CompWiseGibbs: no visible global function definition for ‘rnorm’
CompWiseGibbsSMP: no visible global function definition for ‘rbinom’
CompWiseGibbsSMP: no visible global function definition for ‘runif’
CompWiseGibbsSMP: no visible global function definition for ‘rnorm’
CompWiseGibbsSimple: no visible global function definition for ‘runif’
CompWiseGibbsSimple: no visible global function definition for ‘rnorm’
CompWiseGibbsSimple: no visible global function definition for ‘rgamma’
GroupMH: no visible global function definition for ‘runif’
GroupZ.MH: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rbinom rgamma rnorm runif
Consider adding
  importFrom("stats", "rbinom", "rgamma", "rnorm", "runif")
to your NAMESPACE file.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    fonts   3.1Mb
    lib     5.4Mb
Found the following significant warnings:
  simulate_toad.cpp:155:17: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  simulate_toad.cpp:182:17: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/BSL.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘grDevices’ ‘graphics’
  All declared Imports should be used.
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.2Mb
    libs  22.2Mb
Namespaces in Imports field not imported from:
  ‘mvtnorm’ ‘ssmn’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 75.5Mb
  sub-directories of 1Mb or more:
    libs  74.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘mitools’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
Undeclared package ‘ldatuning’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘magrittr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘Hmisc’, ‘gtools’ in Rd xrefs
'LazyData' is specified without a 'data' directory
plot.bursts: no visible global function definition for ‘axis’
plot.bursts: no visible global function definition for ‘arrows’
Undefined global functions or variables:
  arrows axis
Consider adding
  importFrom("graphics", "arrows", "axis")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
File ‘bvarsv/libs/bvarsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Rd file 'bvenn.Rd':
  \examples lines wider than 100 characters:
                     bvenn(list(Set1 = sample(letters, 16), Set2 = sample(letters, 3+ 3*j), Set3 = sample(letters, 7)), add = TRUE, fontsize ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
Undeclared packages ‘quadprog’, ‘nnls’ in Rd xrefs
File ‘bvls/libs/bvls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  emm20220213.cpp:32:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/bWGR.Rcheck/00install.out’ for details.
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.6Mb
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  opt.cpp:110:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  opt.cpp:110:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/bzinb.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
makemim: no visible global function definition for ‘cor’
sigtestMTC: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  cor p.adjust
Consider adding
  importFrom("stats", "cor", "p.adjust")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘qgraph’ ‘reshape2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  calculus.cpp:6:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/calculus.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
File ‘CAMAN/libs/CAMAN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    pictures   4.0Mb
Undeclared package ‘plotrix’ in Rd xrefs
Note: found 287 marked UTF-8 strings
Note: found 512 marked UTF-8 strings
Note: found 23 marked UTF-8 strings
Found the following files/directories:
  ‘tmp.txt’
Undeclared packages ‘yacca’, ‘CCA’ in Rd xrefs
Found the following files/directories:
  ‘MDA231_tree.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 59 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘htmltools’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
bootstrapCapwire: no visible global function definition for ‘quantile’
drawCapRatesBeta : <anonymous>: no visible global function definition
  for ‘rbeta’
drawCapRatesExp : <anonymous>: no visible global function definition
  for ‘rexp’
drawCapRatesGamma : <anonymous>: no visible global function definition
  for ‘rgamma’
drawCapRatesGeom : <anonymous>: no visible global function definition
  for ‘rgeom’
drawCapRatesUnif : <anonymous>: no visible global function definition
  for ‘runif’
partitionCountData : find.3.way.partitions: no visible global function
  definition for ‘dmultinom’
Undefined global functions or variables:
  dmultinom quantile rbeta rexp rgamma rgeom runif
Consider adding
  importFrom("stats", "dmultinom", "quantile", "rbeta", "rexp", "rgamma",
             "rgeom", "runif")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
checkRd: (7) combine.data.shapefile.Rd:40-42: \item in \value must have non-empty label
checkRd: (7) highlight.borders.Rd:36-40: \item in \value must have non-empty label
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespace in Imports field not imported from: ‘details’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘methods’ ‘readr’ ‘recipes’ ‘sf’ ‘stringr’ ‘utils’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Sub.pair: no visible global function definition for ‘qnorm’
as.record: no visible global function definition for ‘capture.output’
estN: no visible global function definition for ‘sd’
estN: no visible global function definition for ‘qnorm’
estN.bootstrap: no visible global function definition for ‘runif’
Undefined global functions or variables:
  capture.output qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
barplotEQR: no visible global function definition for ‘barplot’
barplotEQR: no visible global function definition for ‘abline’
barplotEQR: no visible global function definition for ‘par’
barplotEQR: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline barplot par text
Consider adding
  importFrom("graphics", "abline", "barplot", "par", "text")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  ‘MASS’ ‘RSQLite’ ‘grid’ ‘sm’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Undeclared packages ‘DBI’, ‘gplots’, ‘limma’ in Rd xrefs
Found the following files/directories:
  ‘foo.tab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘animation’ ‘devtools’ ‘gapminder’ ‘knitr’ ‘rlist’ ‘rmarkdown’
  ‘roxygen2’ ‘sde’ ‘shiny’ ‘tidyverse’ ‘usethis’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Namespaces in Imports field not imported from:
  ‘janitor’ ‘tibble’
  All declared Imports should be used.
Note: found 75 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GAMBoost’
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
MDR.high.forward1: no visible global function definition for ‘combn’
MDR.sing.mod1: no visible global function definition for ‘combn’
MDR.sing.mod1: no visible global function definition for
  ‘complete.cases’
MDR.sing.mod1: no visible global function definition for ‘lm’
MDR.sing.mod1: no visible global function definition for ‘aov’
MDR.sing.mod1: no visible global function definition for ‘anova’
MDR.stage.forward1: no visible global function definition for ‘combn’
MDR.stage.forward1: no visible global function definition for
  ‘complete.cases’
MDR.stage.forward1: no visible global function definition for ‘lm’
MDR.stage.forward1: no visible global function definition for ‘resid’
MDR.stage.forward1: no visible global function definition for ‘pf’
MDR_forward1: no visible global function definition for
  ‘complete.cases’
MDR_forward1: no visible global function definition for ‘lm’
MDR_forward1: no visible global function definition for ‘aov’
low.anova: no visible global function definition for ‘complete.cases’
low.anova: no visible global function definition for ‘lm’
sing.mod1: no visible global function definition for ‘combn’
sing.mod1: no visible global function definition for ‘complete.cases’
sing.mod1: no visible global function definition for ‘lm’
sing.mod1: no visible global function definition for ‘pf’
Undefined global functions or variables:
  anova aov combn complete.cases lm pf resid
Consider adding
  importFrom("stats", "anova", "aov", "complete.cases", "lm", "pf",
             "resid")
  importFrom("utils", "combn")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘broom’ ‘epitools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘catIrt/libs/catIrt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 37.5Mb
  sub-directories of 1Mb or more:
    doc  37.2Mb
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tidyverse’
  All declared Imports should be used.
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
Undeclared packages ‘pixmap’, ‘XML’, ‘exactRankTests’, ‘coin’, ‘ROCR’, ‘Epi’, ‘verification’, ‘Hmisc’, ‘gtools’, ‘magic’, ‘zoo’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
mi.inference: no visible binding for global variable ‘var’
mi.inference: no visible global function definition for ‘qt’
mi.inference: no visible global function definition for ‘pt’
Undefined global functions or variables:
  pt qt var
Consider adding
  importFrom("stats", "pt", "qt", "var")
to your NAMESPACE file.
File ‘cat/libs/cat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
ctab: no visible global function definition for ‘xtabs’
mob.eqmain: no visible global function definition for ‘model.matrix’
mob.qi: no visible global function definition for ‘C’
mob.qi: no visible binding for global variable ‘contr.treatment’
mob.rc1: no visible global function definition for ‘C’
mob.rc1: no visible binding for global variable ‘contr.treatment’
mob.rc1: no visible global function definition for ‘model.matrix’
mob.symint: no visible global function definition for ‘model.matrix’
print.ctab: no visible global function definition for ‘ftable’
Undefined global functions or variables:
  C contr.treatment ftable model.matrix xtabs
Consider adding
  importFrom("stats", "C", "contr.treatment", "ftable", "model.matrix",
             "xtabs")
to your NAMESPACE file.
Rd file 'ctab.Rd':
  \usage lines wider than 90 characters:
     ctab(...,dec.places=NULL,digits=NULL,type=NULL,style=NULL,row.vars=NULL,col.vars=NULL,percentages=NULL,addmargins=NULL)

Rd file 'sqtab.Rd':
  \examples lines wider than 100 characters:
     OccFather<-gl(5,5,labels=c("Upper nonmanual","Lower nonmanual","Upper manual","Lower manual","Farm"))
     glm.q0<-glm(Freq~OccFather+OccSon+mob.qi(OccFather,OccSon,constrained=TRUE),family=poisson(),data=FHtab)
     glm.hrc1<-glm(Freq~OccFather+OccSon+mob.rc1(OccFather,OccSon,equal=TRUE),family=poisson(),data=FHtab)
     m2 <- mlogit(occupation ~ mob.qi(focc,alt)+mob.unif(focc,alt) | education+race,data=pc, reflevel = "farm")

These lines will be truncated in the PDF manual.
Undeclared package ‘gmodels’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘epitools’ ‘forcats’ ‘purrr’
  All declared Imports should be used.
Found the following significant warnings:
  Cat.cpp:230:39: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Estimator.cpp:548:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Estimator.cpp:609:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Estimator.cpp:863:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Estimator.cpp:879:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Estimator.cpp:903:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Estimator.cpp:918:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Estimator.cpp:987:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  Estimator.cpp:1135:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  QuestionSet.cpp:163:25: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  QuestionSet.cpp:167:29: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  WLEEstimator.cpp:261:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  WLEEstimator.cpp:277:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/catSurv.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
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
Note: found 32 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘CBPS’ ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  kernel_calc.cpp:242:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  kernel_calc.cpp:246:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  kernel_calc.cpp:429:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  kernel_calc.cpp:433:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  kernel_calc.cpp:537:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/causalOT.Rcheck/00install.out’ for details.
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs  22.5Mb
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    libs  22.4Mb
GNU make is a SystemRequirements.
Note: found 1 marked UTF-8 string
Undeclared package ‘sitmo’ in Rd xrefs
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.1Mb
    libs      2.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘prettydoc’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘cbird/libs/cbird.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 137.5Mb
  sub-directories of 1Mb or more:
    libs  137.0Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
VD: no visible binding for global variable ‘var’
stratcc : <anonymous>: no visible global function definition for
  ‘hclust’
stratcc : <anonymous>: no visible global function definition for
  ‘cutree’
Undefined global functions or variables:
  cutree hclust var
Consider adding
  importFrom("stats", "cutree", "hclust", "var")
to your NAMESPACE file.
Rd file 'stratcc.Rd':
  \usage lines wider than 90 characters:
     stratcc(x, groups, alloc = "Pro", fraction = 0.1, clustering = FALSE, cluster_method = "ward")

These lines will be truncated in the PDF manual.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Namespace in Imports field not imported from: ‘statmod’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘GeneNet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hotcold.csv’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Namespace in Imports field not imported from: ‘formula.tools’
  All declared Imports should be used.
'library' or 'require' call to ‘bitops’ which was already attached by Depends.
  Please remove these calls from your code.
Found the following files/directories:
  ‘Base.txt’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
File ‘CDLasso/libs/CDLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.7Mb
Undeclared package ‘car’ in Rd xrefs
Namespace in Imports field not imported from: ‘urltools’
  All declared Imports should be used.
Found the following files/directories:
  ‘out.png’ ‘out1.txt’ ‘out2.txt’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
File ‘cec2013/libs/cec2013.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 907 marked UTF-8 strings
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
'LazyData' is specified without a 'data' directory
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.1Mb
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
cenNID: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
File ‘censNID/libs/censNID.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Malformed Description field: should contain one or more complete sentences.
MomNIT: no visible global function definition for ‘dnorm’
MomNIT: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pt’
em.cens: no visible global function definition for ‘lm’
em.cens: no visible global function definition for ‘coefficients’
em.cens : ft: no visible global function definition for ‘dt’
em.cens : ft: no visible global function definition for ‘pt’
em.cens: no visible global function definition for ‘optimize’
em.cens: no visible global function definition for ‘dnorm’
em.cens: no visible global function definition for ‘pnorm’
em.cens: no visible global function definition for ‘sd’
Undefined global functions or variables:
  coefficients dnorm dt lm optimize pnorm pt sd
Consider adding
  importFrom("stats", "coefficients", "dnorm", "dt", "lm", "optimize",
             "pnorm", "pt", "sd")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 104 marked UTF-8 strings
checkRd: (7) cep.get.Rd:37: invalid email address: <zeda.li@temple.edu>
checkRd: (7) cep.lda.Rd:85: invalid email address: <zeda.li@temple.edu>
checkRd: (7) cep.lda.Rd:85: invalid email address: <rkrafty@pitt.edu>
checkRd: (7) cep.mtm.Rd:41: invalid email address: <rkrafty@pitt.edu>
checkRd: (7) r.cond.ar2.Rd:39: invalid email address: <rkrafty@pitt.edu>
checkRd: (7) recon.Rd:40: invalid email address: <rkrafty@pitt.edu>
'LazyData' is specified without a 'data' directory
Undeclared package ‘vegan’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘alr3’
select_lambda: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘base’ ‘stats’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘batchtools’ ‘data.table’ ‘dplyr’ ‘ggplot2’ ‘htmltools’
  ‘jsonlite’ ‘magrittr’ ‘methods’ ‘plotly’ ‘reshape’ ‘rlang’ ‘shiny’
  ‘shinyWidgets’ ‘shinyjqui’ ‘shinyjs’ ‘shinymaterial’ ‘sortable’ ‘ssh’
  ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
cf_estimate_quantiles: no visible global function definition for
  ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Undeclared packages ‘causaleffect’, ‘dosearch’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is 38.5Mb
  sub-directories of 1Mb or more:
    include  38.3Mb
Malformed Title field: should not end in a period.
File ‘cgAUC/libs/cgAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Undeclared packages ‘dplyr’, ‘matrixStats’, ‘filesstrings’, ‘pracma’, ‘sf’, ‘rgeos’ in Rd xrefs
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Found the following significant warnings:
  soft_impute.cpp:49:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/changepoints.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘bench’ ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ChannelAttribution.cpp:694:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ChannelAttribution.cpp:696:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/ChannelAttribution.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘AER’ ‘graphics’ ‘lmtest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Hartree2Joule: no visible binding for global variable
  ‘universalConstants’
Hertz2Joule: no visible binding for global variable
  ‘universalConstants’
Joule2Hartree: no visible binding for global variable
  ‘universalConstants’
Joule2Hertz: no visible binding for global variable
  ‘universalConstants’
Joule2Kelvin: no visible binding for global variable
  ‘universalConstants’
Joule2centimeterMinusOne: no visible binding for global variable
  ‘universalConstants’
Joule2electronVolt: no visible binding for global variable
  ‘universalConstants’
Joule2kiloCaloriePerMole: no visible binding for global variable
  ‘universalConstants’
Joule2kiloJoulePerMole: no visible binding for global variable
  ‘universalConstants’
KMC: no visible global function definition for ‘runif’
Kelvin2Joule: no visible binding for global variable
  ‘universalConstants’
LandauZener: no visible binding for global variable
  ‘universalConstants’
LandauZenerProbability: no visible binding for global variable
  ‘universalConstants’
Marcus: no visible binding for global variable ‘universalConstants’
MarcusLevichJortner: no visible binding for global variable
  ‘universalConstants’
centimeterMinusOne2Joule: no visible binding for global variable
  ‘universalConstants’
electronVolt2Joule: no visible binding for global variable
  ‘universalConstants’
kiloCaloriePerMole2Joule: no visible binding for global variable
  ‘universalConstants’
kiloJoulePerMole2Joule: no visible binding for global variable
  ‘universalConstants’
Undefined global functions or variables:
  runif universalConstants
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘ChargeTransport/libs/ChargeTransport.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘RCurl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘bitops’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createDataset: no visible global function definition for ‘read.csv’
createInventory: no visible global function definition for ‘read.csv’
downloadMaster: no visible global function definition for
  ‘getURLContent’
downloadMaster: no visible global function definition for ‘read.csv’
downloadMaster: no visible global function definition for ‘write.csv’
getMissingScrape: no visible global function definition for ‘read.csv’
readLocalMaster: no visible global function definition for ‘read.csv’
readMonthlyCsv: no visible global function definition for ‘read.csv’
scrapeToCsv: no visible global function definition for ‘download.file’
writeData: no visible global function definition for ‘write.csv’
writeGhcn: no visible global function definition for ‘write.table’
writeInventory: no visible global function definition for ‘write.table’
writeMonthlyStations: no visible global function definition for
  ‘read.csv’
writeMonthlyStations: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  download.file getURLContent read.csv write.csv write.table
Consider adding
  importFrom("utils", "download.file", "read.csv", "write.csv",
             "write.table")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘rappdirs’ ‘stringr’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/chebpol.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Rd file 'chebR.Rd':
  \examples lines wider than 100 characters:
     return(list(coefs=rlist$xx[1:n],resids=rlist$bb[1:m],rank=rlist$rank,iter=rlist$iter,ocode=rlist$ocode))

These lines will be truncated in the PDF manual.
File ‘cheb/libs/cheb.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘darts’
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  treeshap.cpp:148:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/cheem.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinycssloaders’ ‘shinythemes’
  All declared Imports should be used.
Found the following files/directories:
  ‘stepres00.txt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘countreg’
Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown'
  All declared Imports should be used.
Found the following significant warnings:
  RandIndex.cpp:28:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  RandIndex.cpp:30:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  RandIndex.cpp:33:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/chickn.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Note: found 32 marked UTF-8 strings
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Note: found 8119 marked UTF-8 strings
File ‘ChIPtest/libs/ChIPtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘cmdstanr’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Qh.times.dhyper: no visible global function definition for ‘var’
Qh.times.dhyper: no visible global function definition for ‘pnorm’
Qh.times.dhyper: no visible global function definition for ‘dhyper’
TDiM: no visible global function definition for ‘sd’
choplump.default: no visible global function definition for
  ‘flush.console’
choplump.formula: no visible global function definition for ‘terms’
cm.compact: no visible global function definition for ‘dhyper’
Undefined global functions or variables:
  dhyper flush.console pnorm sd terms var
Consider adding
  importFrom("stats", "dhyper", "pnorm", "sd", "terms", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘forcats’
  All declared Imports should be used.
Note: found 4004 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
parse_counts: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘prettydoc’ ‘rmdformats’ ‘skimr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magick’ ‘tidyr’
  All declared Imports should be used.
File ‘CHsharp/libs/CHsharp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  newplt.cc:186:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  newplt.cc:188:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/CIFsmry.Rcheck/00install.out’ for details.
File ‘CIFsmry/libs/CIFsmry.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘papayar’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   4.3Mb
Unknown package ‘papayar’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘networkD3’
  All declared Imports should be used.
cit.assignBcmst: no visible binding for global variable ‘citbcmst’
cit.assignBcmst : <anonymous>: no visible global function definition
  for ‘median’
cit.assignBcmst: no visible global function definition for ‘prcomp’
cit.assignBcmst: no visible global function definition for ‘par’
cit.assignBcmst: no visible global function definition for ‘lines’
cit.assignBcmst: no visible global function definition for ‘legend’
cit.centroids : <anonymous>: no visible global function definition for
  ‘median’
cit.centroids : <anonymous>: no visible global function definition for
  ‘var’
cit.dist: no visible global function definition for ‘dist’
cit.dist: no visible global function definition for ‘as.dist’
cit.dist: no visible global function definition for ‘cor’
cit.distToCentroids: no visible global function definition for
  ‘quantile’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘median’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘mad’
Undefined global functions or variables:
  as.dist citbcmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
cit.assignCcmst: no visible binding for global variable ‘citccmst’
cit.assignCcmst : <anonymous>: no visible global function definition
  for ‘median’
cit.assignCcmst : median.na: no visible global function definition for
  ‘median’
cit.assignCcmst: no visible global function definition for ‘prcomp’
cit.assignCcmst: no visible global function definition for ‘par’
cit.assignCcmst: no visible global function definition for ‘lines’
cit.assignCcmst: no visible global function definition for ‘legend’
cit.centroids : <anonymous>: no visible global function definition for
  ‘median’
cit.centroids : <anonymous>: no visible global function definition for
  ‘var’
cit.dist: no visible global function definition for ‘dist’
cit.dist: no visible global function definition for ‘as.dist’
cit.dist: no visible global function definition for ‘cor’
cit.distToCentroids: no visible global function definition for
  ‘quantile’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘median’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘mad’
Undefined global functions or variables:
  as.dist citccmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
CityPlot: no visible global function definition for ‘read.table’
CityPlot: no visible global function definition for ‘tail’
CityPlot: no visible global function definition for ‘pdf’
CityPlot: no visible global function definition for ‘split.screen’
CityPlot: no visible global function definition for ‘screen’
CityPlot: no visible global function definition for ‘par’
CityPlot: no visible global function definition for ‘rect’
CityPlot: no visible global function definition for ‘text’
CityPlot: no visible global function definition for ‘lines’
CityPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off lines par pdf read.table rect screen split.screen tail text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "rect", "screen",
             "split.screen", "text")
  importFrom("utils", "read.table", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinyBS’
  All declared Imports should be used.
Note: found 29 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
    help   1.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rggobi’
'library' or 'require' call to ‘rggobi’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
generate_data : <anonymous>: no visible global function definition for
  ‘runif’
knnf: no visible global function definition for ‘terms’
rescaler.default: no visible global function definition for ‘sd’
rescaler.default: no visible global function definition for ‘median’
rescaler.default: no visible global function definition for ‘mad’
simvar.numeric: no visible global function definition for ‘runif’
Undefined global functions or variables:
  mad median runif sd terms
Consider adding
  importFrom("stats", "mad", "median", "runif", "sd", "terms")
to your NAMESPACE file.
Undeclared package ‘reshape’ in Rd xrefs
Note: found 9 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  18.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ClickClust/libs/ClickClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘scio’
clime: no visible global function definition for ‘cov’
cv.clime: no visible global function definition for ‘cov’
cv.clime: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cov sd
Consider adding
  importFrom("stats", "cov", "sd")
to your NAMESPACE file.
Undeclared package ‘s2dv’ in Rd xrefs
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
gxe.cc: no visible global function definition for ‘qnorm’
gxe.coh: no visible global function definition for ‘qnorm’
utility.cc: no visible global function definition for ‘qnorm’
utility.coh: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    libs  29.9Mb
File ‘clogitboost/libs/clogitboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘clogitL1/libs/clogitL1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘mlbench’, ‘fpc’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
possible bashism in cleanup line 15 (brace expansion):
  rm -f src/*.{o,so,mod}
  possible bashism in cleanup line 17 (brace expansion):
  rm -f config.{log,status}
  possible bashism in cleanup line 22 (brace expansion):
  rm -f vignettes/*.{tex,aux,bbl,blg,log,toc,idx,ind,ilg,out,synctex.gz}
Found the following files/directories:
  ‘clusterhap_reports’
File ‘clustering.sc.dp/libs/clustering.sc.dp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘methods’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘mvoutlier’, ‘fpc’, ‘ellipse’, ‘sfsmisc’ in Rd xrefs
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
File ‘ClusterStability/libs/ClusterStability.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘sp’ ‘spdep’
  All declared Imports should be used.
File ‘ClustMMDD/libs/ClustMMDD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Note: found 5626 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘datasets’ ‘dplyr’ ‘klaR’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
braycurtis: no visible global function definition for ‘as.dist’
czekanowski: no visible global function definition for ‘as.dist’
findComplementaryIndices: no visible global function definition for
  ‘na.omit’
genSimilarityProfile: no visible global function definition for ‘dist’
simprof: no visible global function definition for ‘dist’
simprof: no visible global function definition for ‘hclust’
simprof.plot : <local> : colorizer: no visible global function
  definition for ‘is.leaf’
simprof.plot: no visible global function definition for ‘rainbow’
simprof.plot: no visible global function definition for ‘dendrapply’
simprof.plot: no visible global function definition for ‘as.dendrogram’
Undefined global functions or variables:
  as.dendrogram as.dist dendrapply dist hclust is.leaf na.omit rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "as.dendrogram", "as.dist", "dendrapply", "dist",
             "hclust", "is.leaf", "na.omit")
to your NAMESPACE file.
checkRd: (7) CLV3W_kmeans.Rd:29-37: \item in \value must have non-empty label
'LazyData' is specified without a 'data' directory
File ‘clv/libs/clv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
alpha.cronbach: no visible global function definition for ‘cov’
alpha.curve: no visible global function definition for ‘text’
Undefined global functions or variables:
  cov text
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "cov")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘cmprsk/libs/cmprsk.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘FNN’ ‘R.utils’ ‘SearchTrees’ ‘colorspace’ ‘colourpicker’
  ‘data.table’ ‘fields’ ‘mapproj’ ‘maps’ ‘maptools’ ‘ncdf4’ ‘raster’
  ‘rworldxtra’ ‘shinyFiles’ ‘shinyWidgets’ ‘shinyjs’ ‘shinythemes’ ‘sp’
  ‘tcltk’ ‘xml2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘plotKML’

Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘maptools’ ‘rgdal’ ‘rworldxtra’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘htmltools’ ‘htmlwidgets’ ‘readxl’ ‘testthat’ ‘widgetframe’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘wavethresh’ in Rd xrefs
copynumberBootstrap: no visible global function definition for
  ‘txtProgressBar’
copynumberBootstrap: no visible global function definition for
  ‘quantile’
copynumberBootstrap: no visible global function definition for
  ‘setTxtProgressBar’
gethits: no visible global function definition for ‘read.table’
normalizeGC: no visible global function definition for ‘median’
plotCNOGpro: no visible global function definition for ‘par’
plotCNOGpro: no visible global function definition for ‘rainbow’
plotCNOGpro: no visible global function definition for ‘density’
plotCNOGpro: no visible global function definition for ‘polygon’
plotCNOGpro: no visible global function definition for ‘lines’
plotCNOGpro: no visible global function definition for ‘legend’
plotCNOGpro: no visible global function definition for ‘boxplot’
sampleChromosome: no visible global function definition for ‘median’
sampleChromosome: no visible binding for global variable ‘var’
setupEmissionMatrix: no visible global function definition for ‘dgeom’
store: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  boxplot density dgeom legend lines median par polygon quantile
  rainbow read.table setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "boxplot", "legend", "lines", "par", "polygon")
  importFrom("stats", "density", "dgeom", "median", "quantile", "var")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file.
CNclusterNcenter: no visible global function definition for ‘median’
CNclusterNcenter: no visible binding for global variable ‘var’
breakIntoGaps: no visible global function definition for ‘runif’
centerprob: no visible global function definition for ‘pnorm’
getz: no visible global function definition for ‘predict’
smad: no visible global function definition for ‘mad’
smedian: no visible global function definition for ‘median’
smedian.sample: no visible global function definition for ‘median’
smedmad: no visible global function definition for ‘median’
smedmad: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median pnorm predict runif var
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "predict", "runif",
             "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
Namespace in Imports field not imported from: 'Hmisc'
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  ‘lars’ ‘randomForest’ ‘ridge’ ‘snowfall’ ‘tree’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
COBRA : COBRA.lars: no visible global function definition for ‘lars’
COBRA : COBRA.lars: no visible global function definition for
  ‘predict.lars’
COBRA : COBRA.tree: no visible global function definition for ‘tree’
COBRA : COBRA.tree: no visible global function definition for
  ‘as.formula’
COBRA : COBRA.tree: no visible global function definition for ‘predict’
COBRA : COBRA.ridge: no visible global function definition for
  ‘linearRidge’
COBRA : COBRA.ridge: no visible global function definition for
  ‘as.formula’
COBRA : COBRA.ridge: no visible global function definition for
  ‘predict’
COBRA : COBRA.randomForest: no visible global function definition for
  ‘randomForest’
COBRA : COBRA.randomForest: no visible global function definition for
  ‘predict’
COBRA: no visible global function definition for ‘sfInit’
COBRA: no visible global function definition for ‘sfLibrary’
COBRA: no visible global function definition for ‘sfExportAll’
COBRA: no visible global function definition for ‘sfSapply’
COBRA: no visible global function definition for ‘sfStop’
COBRA: no visible global function definition for ‘write.table’
COBRA: no visible global function definition for ‘pdf’
COBRA: no visible global function definition for ‘points’
COBRA: no visible global function definition for ‘legend’
COBRA: no visible global function definition for ‘abline’
COBRA: no visible global function definition for ‘lines’
COBRA: no visible global function definition for ‘dev.off’
COBRA: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  abline as.formula dev.new dev.off lars legend linearRidge lines pdf
  points predict predict.lars randomForest sfExportAll sfInit sfLibrary
  sfSapply sfStop tree write.table
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "abline", "legend", "lines", "points")
  importFrom("stats", "as.formula", "predict")
  importFrom("utils", "write.table")
to your NAMESPACE file.
File ‘COBRA/libs/COBRA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 14729 marked UTF-8 strings
Package which this enhances but not available for checking: ‘rkward’
Undeclared package ‘pls’ in Rd xrefs
Package which this enhances but not available for checking: ‘rkward’
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
Note: found 19 marked UTF-8 strings
Package in Depends field not imported from: ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘codadiags/libs/codadiags.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘userfriendlyscience’
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘rlang’ ‘tidyselect’ ‘vctrs’
  All declared Imports should be used.
Note: found 65 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 30244 marked UTF-8 strings
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘methods’ ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘codingMatrices.Rnw’ using knitr
Error: processing vignette 'codingMatrices.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'codingMatrices.tex' failed.
LaTeX errors:
! LaTeX Error: Option clash for package xcolor.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
--- failed re-building ‘codingMatrices.Rnw’

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

Error: Vignette re-building failed.
Execution halted
File ‘coenoflex/libs/coenoflex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
Rd file 'fast.flexsim.Rd':
  \usage lines wider than 90 characters:
     fast.flexsim(scale = 2, island,dispersalscale = 51, allee = 1, T = 1000, initp,parcombination, spnum = 2, sourcetype = "constant", type ... [TRUNCATED]

Rd file 'flexsim.Rd':
  \usage lines wider than 90 characters:
     flexsim(scale = 2, dispersalscale = 51, allee = 1, T = 1000, prange, initp,spnum = 2, island=10, sourcetype = "constant", type, path =  ... [TRUNCATED]

Rd file 'make.heatmap.Rd':
  \usage lines wider than 90 characters:
     make.heatmap(mat, type = "gray", xname = "x", yname = "y", xlab = NULL, ylab = NULL, title = NULL)

Rd file 'sim.coarse.Rd':
  \usage lines wider than 90 characters:
     sim.coarse(island=10,scale = 2, dispersalscale = 51, allee = 1, T = 1000, prange, type, initp, path = NULL)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BMDE: no visible global function definition for ‘quantile’
BMDU: no visible global function definition for ‘runif’
BMDU: no visible global function definition for ‘quantile’
FS: no visible global function definition for ‘qnorm’
GM: no visible global function definition for ‘qchisq’
QH: no visible global function definition for ‘qchisq’
SG : sgp: no visible global function definition for ‘ppois’
SG : sgp: no visible global function definition for ‘dpois’
WALD: no visible global function definition for ‘qchisq’
WALDCC: no visible global function definition for ‘qchisq’
WS: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  dpois ppois qchisq qnorm quantile runif
Consider adding
  importFrom("stats", "dpois", "ppois", "qchisq", "qnorm", "quantile",
             "runif")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 4186 marked UTF-8 strings
File ‘collUtils/libs/collUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (7) check_dataset.Rd:59: \item in \describe must have non-empty label
checkRd: (7) check_dataset.Rd:65: \item in \describe must have non-empty label
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
cICA: no visible global function definition for ‘mvfft’
cICA: no visible global function definition for ‘ar.yw’
cICA: no visible global function definition for ‘rnorm’
scICA: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  ar.yw mvfft rnorm
Consider adding
  importFrom("stats", "ar.yw", "mvfft", "rnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plotVenn2d : twoWayOverlap: no visible global function definition for
  ‘grid.polygon’
plotVenn2d : twoWayOverlap: no visible global function definition for
  ‘gpar’
plotVenn2d: no visible global function definition for ‘grid.text’
plotVenn2d: no visible global function definition for ‘gpar’
plotVenn2d: no visible global function definition for ‘grid.polygon’
plotVenn3d : twoWayOverlap: no visible global function definition for
  ‘grid.polygon’
plotVenn3d : twoWayOverlap: no visible global function definition for
  ‘gpar’
plotVenn3d: no visible global function definition for ‘grid.text’
plotVenn3d: no visible global function definition for ‘gpar’
plotVenn3d: no visible global function definition for ‘grid.polygon’
plotVenn4d : getCommonEllipse: no visible global function definition
  for ‘aggregate’
plotVenn4d : region.polygon: no visible global function definition for
  ‘head’
plotVenn4d : region.polygon: no visible global function definition for
  ‘grid.polygon’
plotVenn4d : region.polygon: no visible global function definition for
  ‘gpar’
plotVenn4d: no visible global function definition for ‘grid.text’
plotVenn4d: no visible global function definition for ‘gpar’
plotVenn4d: no visible global function definition for ‘pushViewport’
plotVenn4d: no visible global function definition for ‘viewport’
plotVenn4d: no visible global function definition for ‘grid.polygon’
plotVenn4d: no visible global function definition for ‘upViewport’
resizeCircles: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  aggregate gpar grid.polygon grid.text head pushViewport uniroot
  upViewport viewport
Consider adding
  importFrom("stats", "aggregate", "uniroot")
  importFrom("utils", "head")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 742 marked UTF-8 strings
generateMonochromaticColors: no visible global function definition for
  ‘col2rgb’
generateMonochromaticColors: no visible global function definition for
  ‘rgb’
generateMonochromaticColors: no visible global function definition for
  ‘tail’
hsv2rgb: no visible global function definition for ‘rgb’
rotational_dispersion: no visible global function definition for
  ‘col2rgb’
rotational_dispersion: no visible global function definition for
  ‘rgb2hsv’
tetradicColors: no visible global function definition for ‘head’
triadicColors: no visible global function definition for ‘head’
Undefined global functions or variables:
  col2rgb head rgb rgb2hsv tail
Consider adding
  importFrom("grDevices", "col2rgb", "rgb", "rgb2hsv")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
primary.colors: no visible global function definition for ‘rgb’
rgb.tables: no visible global function definition for ‘rgb’
ygobb: no visible global function definition for ‘approx’
ygobb: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  approx rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "approx")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.1Mb
Undeclared package ‘plyr’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘chi’ ‘dplyr’ ‘spatstat.utils’ ‘utils’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
competitive.test: no visible global function definition for ‘runif’
selfcontained.test : fun2: no visible global function definition for
  ‘qchisq’
selfcontained.test: no visible global function definition for ‘cov’
selfcontained.test: no visible global function definition for ‘qchisq’
selfcontained.test: no visible global function definition for ‘cor’
selfcontained.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor cov pchisq qchisq runif
Consider adding
  importFrom("stats", "cor", "cov", "pchisq", "qchisq", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘R_packages-comf.ltx’ using tex
Error: processing vignette 'R_packages-comf.ltx' failed with diagnostics:
Running 'texi2dvi' on 'R_packages-comf.ltx' failed.
LaTeX errors:
! Package siunitx Error: Package 'units' incompatible.

For immediate help type H <return>.
 ...                                              
                                                  
--- failed re-building ‘R_packages-comf.ltx’

SUMMARY: processing the following file failed:
  ‘R_packages-comf.ltx’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
CommT.anova: no visible global function definition for ‘aov’
CommT.legendpos: no visible global function definition for ‘quantile’
CommT.plotcolors: no visible global function definition for ‘hcl’
Undefined global functions or variables:
  aov hcl quantile
Consider adding
  importFrom("grDevices", "hcl")
  importFrom("stats", "aov", "quantile")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘GGally’ ‘RColorBrewer’ ‘abind’ ‘diagram’ ‘ggplot2’ ‘grid’ ‘gtable’
  ‘igraph’ ‘magrittr’ ‘plyr’ ‘purrr’ ‘reshape2’ ‘scales’ ‘useful’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
addxaxis: no visible global function definition for ‘par’
addxaxis: no visible global function definition for ‘axis’
addxaxis: no visible global function definition for ‘mtext’
eplot: no visible global function definition for ‘par’
eplot: no visible global function definition for ‘axis’
eplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis mtext par
Consider adding
  importFrom("graphics", "axis", "mtext", "par")
to your NAMESPACE file.
Package suggested but not available for checking: ‘CAM’
File ‘compareC/libs/compareC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘XML’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
compareODM: no visible global function definition for ‘xmlRoot’
compareODM: no visible global function definition for ‘xmlTreeParse’
compareODM: no visible global function definition for ‘xmlChildren’
compareODM: no visible global function definition for ‘xmlAttrs’
compareODM: no visible global function definition for ‘xmlValue’
Undefined global functions or variables:
  xmlAttrs xmlChildren xmlRoot xmlTreeParse xmlValue
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  24.6Mb
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dcomplnorm: no visible global function definition for ‘grad’
dcomplnorm : f1: no visible global function definition for ‘dlnorm’
dcomplnorm : F1: no visible global function definition for ‘plnorm’
dcomplnorm : f1L: no visible global function definition for ‘dlnorm’
dcomplnorm : F1L: no visible global function definition for ‘plnorm’
pcomplnorm: no visible global function definition for ‘grad’
pcomplnorm : f1: no visible global function definition for ‘dlnorm’
pcomplnorm : F1: no visible global function definition for ‘plnorm’
pcomplnorm : F1L: no visible global function definition for ‘plnorm’
qcomplnorm: no visible global function definition for ‘grad’
qcomplnorm : f1: no visible global function definition for ‘dlnorm’
qcomplnorm : F1q: no visible global function definition for ‘qlnorm’
qcomplnorm : F1: no visible global function definition for ‘plnorm’
rcomplnorm: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dlnorm grad plnorm qlnorm runif
Consider adding
  importFrom("stats", "dlnorm", "plnorm", "qlnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  sprinkler.c:6:14037: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/CompModels.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘hypergeo’ which was already attached by Depends.
  Please remove these calls from your code.
momentCompound: no visible global function definition for ‘integrate’
pgfIhypergeometric: no visible global function definition for ‘uniroot’
pgfIhyperpoisson: no visible global function definition for ‘uniroot’
pgfIkattitypeh1: no visible global function definition for ‘uniroot’
pgfIkattitypeh2: no visible global function definition for ‘uniroot’
pgfIneymantypeb: no visible global function definition for ‘uniroot’
pgfIneymantypec: no visible global function definition for ‘uniroot’
pgfIpoissonlindley: no visible global function definition for ‘uniroot’
pgfIthomas: no visible global function definition for ‘uniroot’
pgfIwaring: no visible global function definition for ‘uniroot’
pgfIyule: no visible global function definition for ‘uniroot’
rCompound: no visible global function definition for ‘runif’
Undefined global functions or variables:
  integrate runif uniroot
Consider adding
  importFrom("stats", "integrate", "runif", "uniroot")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
kef: no visible global function definition for ‘dgamma’
kef: no visible global function definition for ‘dlnorm’
simp_int: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dgamma dlnorm
Consider adding
  importFrom("stats", "approx", "dgamma", "dlnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
File ‘ConConPiWiFun/libs/ConConPiWiFun.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 92 marked UTF-8 strings
Undeclared package ‘rlang’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
K1.norm: no visible global function definition for ‘dnorm’
K1.norm: no visible global function definition for ‘pnorm’
K1.t3: no visible global function definition for ‘pt’
K2.norm: no visible global function definition for ‘dnorm’
K2.norm: no visible global function definition for ‘pnorm’
K2.t3: no visible global function definition for ‘pt’
Undefined global functions or variables:
  dnorm pnorm pt
Consider adding
  importFrom("stats", "dnorm", "pnorm", "pt")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kernlab’ ‘purrr’ ‘survminer’ ‘tidyverse’
  All declared Imports should be used.
File ‘condmixt/libs/condmixt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
ml_solver: no visible global function definition for ‘approx’
select_kmax: no visible global function definition for ‘median’
Undefined global functions or variables:
  approx median
Consider adding
  importFrom("stats", "approx", "median")
to your NAMESPACE file.
Undeclared package ‘mvtnorm’ 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
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
conicPlot: no visible global function definition for ‘palette’
conicPlotAsymptotes: no visible global function definition for
  ‘palette’
conicPlotAsymptotes: no visible global function definition for ‘abline’
conicPlotAxes: no visible global function definition for ‘palette’
conicPlotAxes: no visible global function definition for ‘abline’
plotDegenerateConic: no visible global function definition for ‘points’
plotDegenerateConic: no visible global function definition for ‘abline’
plotEllipsis: no visible global function definition for ‘lines’
plotEllipsis: no visible global function definition for ‘points’
plotHyperbola: no visible global function definition for ‘lines’
plotHyperbola: no visible global function definition for ‘points’
plotParabola: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline lines palette points
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "lines", "points")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'library' or 'require' call to ‘parallel’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Rmpi’ ‘snow’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ConjointChecks: no visible global function definition for ‘makeCluster’
ConjointChecks: no visible global function definition for
  ‘clusterSetRNGStream’
ConjointChecks: no visible global function definition for
  ‘clusterApply’
ConjointChecks: no visible global function definition for ‘stopCluster’
omni.check: no visible global function definition for ‘runif’
omni.check: no visible global function definition for ‘quantile’
plot.checks: no visible global function definition for ‘mtext’
plot.checks: no visible global function definition for ‘text’
Undefined global functions or variables:
  clusterApply clusterSetRNGStream makeCluster mtext quantile runif
  stopCluster text
Consider adding
  importFrom("graphics", "mtext", "text")
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Namespaces in Imports field not imported from:
  ‘base’ ‘lwgeom’ ‘s2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘dplyr’ ‘foreign’ ‘lavaan’ ‘openxlsx’ ‘purrr’ ‘semTools’
  ‘shinyWidgets’ ‘stringr’ ‘summarytools’ ‘waiter’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘xts’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘sna’
  All declared Imports should be used.
Note: found 244 marked UTF-8 strings
File ‘ConsReg/libs/ConsReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘constrainedKriging/libs/constrainedKriging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 50.5Mb
  sub-directories of 1Mb or more:
    libs  49.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
File ‘contoureR/libs/contoureR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magicaxis’
  All declared Imports should be used.
maCooperative: no visible global function definition for ‘points’
maCooperative: no visible global function definition for ‘legend’
maPessimistic: no visible global function definition for ‘combn’
maRules: no visible global function definition for ‘capture.output’
mstCooperative: no visible global function definition for ‘points’
mstCooperative: no visible global function definition for ‘legend’
mstOptimistic: no visible global function definition for ‘combn’
mstPessimistic: no visible global function definition for ‘combn’
mstRules: no visible global function definition for ‘capture.output’
plotCoreSet: no visible global function definition for ‘points’
plotCoreSet: no visible global function definition for ‘polygon’
plotImputationSet: no visible global function definition for ‘par’
plotImputationSet: no visible global function definition for ‘box’
plotImputationSet: no visible global function definition for ‘polygon’
plotImputationSet: no visible global function definition for ‘text’
shapleyValue: no visible global function definition for ‘combn’
Undefined global functions or variables:
  box capture.output combn legend par points polygon text
Consider adding
  importFrom("graphics", "box", "legend", "par", "points", "polygon",
             "text")
  importFrom("utils", "capture.output", "combn")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cec2005benchmark’
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (7) p_combine.Rd:20: \item in \value must have non-empty label
checkRd: (7) p_combine.Rd:23: \item in \value must have non-empty label
Namespace in Imports field not imported from: ‘mcc’
  All declared Imports should be used.
File ‘cord/libs/cord.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
advanceRNG: no visible global function definition for ‘runif’
randomEventMoves: no visible global function definition for ‘runif’
randomRescaledEventMoves: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
coreTDT_geneset: no visible global function definition for
  ‘write.table’
pvalue_calculator: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  dbinom write.table
Consider adding
  importFrom("stats", "dbinom")
  importFrom("utils", "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
compute.llh: no visible global function definition for ‘dnorm’
compute.u.hat.simple: no visible global function definition for ‘dnorm’
fit.CLM.1u.simple.start: no visible global function definition for
  ‘kmeans’
fit.CLMM.simple.start: no visible global function definition for
  ‘kmeans’
fit.CLMM.simple.start.NA: no visible global function definition for
  ‘kmeans’
Undefined global functions or variables:
  dnorm kmeans
Consider adding
  importFrom("stats", "dnorm", "kmeans")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘rmutil’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    help   3.8Mb
Note: found 6 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘re2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
Note: found 1187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 578 marked UTF-8 strings
Found the following significant warnings:
  coref.cpp:34:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  coref.cpp:34:32: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  coref.cpp:35:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  coref.cpp:36:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  hit_ids_sequence.cpp:20:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/corpustools.Rcheck/00install.out’ for details.
Note: found 438 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘profr’ ‘xtable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked Latin-1 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
corr.Qmatrix: no visible global function definition for ‘cor’
corr.Qmatrix: no visible global function definition for ‘cor.test’
summarise.Fst: no visible global function definition for ‘cor’
summarise.Fst: no visible global function definition for ‘sd’
summarise.lnPD: no visible global function definition for ‘sd’
Undefined global functions or variables:
  cor cor.test sd
Consider adding
  importFrom("stats", "cor", "cor.test", "sd")
to your NAMESPACE file.
Rd file 'corr.Qmatrix.Rd':
  \usage lines wider than 90 characters:
     corr.Qmatrix(filepath = "./", instruct = FALSE, rowncol = TRUE, avmax = TRUE, pvalue = FALSE, raw = TRUE, r = 0.99, p = 0.05)

Rd file 'rowncolMatrix-method.Rd':
  \examples lines wider than 100 characters:
     test <- rowncolMatrix(K = 3, filtermatrix = table(matrix(c("Y","Y","Y",NA,"Y","Y",NA,NA,"Y"),ncol = 3, byrow = TRUE)))

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
dist: no visible global function definition for ‘quantile’
edgecount: no visible global function definition for ‘reshape’
edgecutoff: no visible global function definition for ‘boxplot’
edgecutoff: no visible global function definition for ‘sd’
edgecutoff: no visible global function definition for ‘median’
edgecutoff: no visible global function definition for ‘IQR’
Undefined global functions or variables:
  IQR boxplot median quantile reshape sd
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "IQR", "median", "quantile", "reshape", "sd")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
GA_search : subset_score: no visible global function definition for
  ‘combn’
choose_lambda : subset_score: no visible global function definition for
  ‘combn’
cond.fyx: no visible global function definition for ‘var’
cond.fyx: no visible global function definition for ‘cor’
diff_gen_PPI: no visible global function definition for ‘cov’
diff_gen_PPI: no visible global function definition for ‘sd’
f.test: no visible binding for global variable ‘var’
get_quantiles : node_edge: no visible global function definition for
  ‘combn’
score_scaling: no visible global function definition for ‘hist’
score_scaling: no visible global function definition for ‘sd’
Undefined global functions or variables:
  combn cor cov hist sd var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "cov", "sd", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
cosinor.lm: no visible binding for global variable ‘na.omit’
cosinor.lm: no visible global function definition for ‘terms’
cosinor.lm: no visible global function definition for ‘as.formula’
cosinor.lm: no visible global function definition for ‘lm’
cosinor_analyzer: no visible binding for global variable ‘vitamind’
cosinor_analyzer : <anonymous>: no visible global function definition
  for ‘as.formula’
ggplot.cosinor.lm: no visible global function definition for ‘predict’
predict.cosinor.lm: no visible global function definition for ‘fitted’
predict.cosinor.lm: no visible global function definition for ‘predict’
simulate_cosinor: no visible global function definition for ‘runif’
simulate_cosinor: no visible global function definition for ‘rbinom’
simulate_cosinor: no visible global function definition for ‘rnorm’
summary.cosinor.lm: no visible global function definition for ‘vcov’
summary.cosinor.lm: no visible global function definition for ‘qnorm’
summary.cosinor.lm: no visible global function definition for ‘pnorm’
test_cosinor: no visible global function definition for ‘pchisq’
test_cosinor: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula fitted lm na.omit pchisq pnorm predict qnorm rbinom rnorm
  runif terms vcov vitamind
Consider adding
  importFrom("stats", "as.formula", "fitted", "lm", "na.omit", "pchisq",
             "pnorm", "predict", "qnorm", "rbinom", "rnorm", "runif",
             "terms", "vcov")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
D.M: no visible global function definition for ‘integrate’
lookbackTime: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
Rd file 'mass.CO.Rd':
  \usage lines wider than 90 characters:
     mass.CO(intInt, z, alpha = 0.8, f.rest = 115.27, omega.m = 0.27, omega.lambda = 0.73, H.0 = 71)

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘Rglpk’ ‘glmnet’ ‘parallel’ ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
Note: found 59 marked UTF-8 strings
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   4.1Mb
Note: found 128401 marked UTF-8 strings
Undeclared package ‘betareg’ in Rd xrefs
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘COUSCOus/libs/COUSCOus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
File ‘covBM/libs/covBM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘dplyr’ ‘markdown’ ‘shinyjs’ ‘shinymeta’ ‘table1’
  ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘covfefe_inauguration.txt’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
Note: found 2385 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mapview’ ‘plotly’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
Note: found 199 marked UTF-8 strings
'library' or 'require' calls to packages already attached by Depends:
  ‘Matrix’ ‘mlogit’ ‘poLCA’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Matrix’ ‘mlogit’ ‘poLCA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
covLCA: no visible global function definition for ‘model.response’
covLCA: no visible global function definition for ‘model.frame’
covLCA: no visible global function definition for ‘model.matrix’
covLCA: no visible global function definition for ‘rnorm’
covLCA: no visible global function definition for ‘flush.console’
covLCA: no visible global function definition for ‘ginv’
covLCA.initialAlphaGamma: no visible global function definition for
  ‘as.formula’
covLCA.initialAlphaGamma: no visible global function definition for
  ‘mlogit.data’
covLCA.initialAlphaGamma: no visible global function definition for
  ‘mlogit’
covLCA.initialBeta: no visible global function definition for
  ‘as.formula’
covLCA.initialBeta: no visible global function definition for ‘poLCA’
covLCA.initialBeta: no visible global function definition for
  ‘mlogit.data’
covLCA.initialBeta: no visible global function definition for ‘mlogit’
covLCA.paramVariance: no visible global function definition for ‘ginv’
covLCA.varianceFirst: no visible global function definition for ‘bdiag’
Undefined global functions or variables:
  as.formula bdiag flush.console ginv mlogit mlogit.data model.frame
  model.matrix model.response poLCA rnorm
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response", "rnorm")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
covreg.mcmc: no visible global function definition for ‘model.frame’
covreg.mcmc: no visible global function definition for ‘model.matrix’
covreg.mcmc: no visible global function definition for ‘model.response’
covreg.mcmc: no visible global function definition for ‘lm’
covreg.mcmc: no visible global function definition for ‘rnorm’
covreg.mcmc: no visible global function definition for ‘cov’
rmn: no visible global function definition for ‘rnorm’
rwish: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  cov lm model.frame model.matrix model.response rnorm
Consider adding
  importFrom("stats", "cov", "lm", "model.frame", "model.matrix",
             "model.response", "rnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘gsl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
coxaalen: no visible global function definition for ‘terms’
coxaalen: no visible global function definition for ‘model.matrix’
coxaalen: no visible binding for global variable ‘frame’
coxaalen: no visible global function definition for ‘update.formula’
coxaalen: no visible global function definition for ‘capture.output’
coxdual: no visible global function definition for ‘terms’
coxdual: no visible global function definition for ‘model.matrix’
coxdual: no visible binding for global variable ‘frame’
coxdual: no visible global function definition for ‘update.formula’
coxdual: no visible global function definition for ‘as.formula’
coxdual: no visible global function definition for ‘capture.output’
frame.assign: no visible global function definition for ‘model.matrix’
linapprox: no visible global function definition for ‘approx’
print.coxinterval: no visible global function definition for ‘pchisq’
print.summary.coxinterval : f: no visible global function definition
  for ‘printCoefmat’
step2stepfun : f: no visible global function definition for ‘stepfun’
summary.coxinterval : f: no visible global function definition for
  ‘pchisq’
summary.coxinterval : f: no visible global function definition for
  ‘qnorm’
Undefined global functions or variables:
  approx as.formula capture.output frame model.matrix pchisq
  printCoefmat qnorm stepfun terms update.formula
Consider adding
  importFrom("graphics", "frame")
  importFrom("stats", "approx", "as.formula", "model.matrix", "pchisq",
             "printCoefmat", "qnorm", "stepfun", "terms",
             "update.formula")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
GNU make is a SystemRequirements.
File ‘coxinterval/libs/coxinterval.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (7) coxphlb.Rd:33: \item in \value must have non-empty label
checkRd: (7) coxphlb.ftest.Rd:28: \item in \value must have non-empty label
checkRd: (7) coxphlb.phtest.Rd:26: \item in \value must have non-empty label
checkRd: (7) station.test.Rd:22: \item in \value must have non-empty label
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘CoxPlus/libs/CoxPlus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
File ‘cpm/libs/cpm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (7) capitais.Rd:29: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) condicoes_tempo.Rd:23: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) estacoes_metar.Rd:25: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) estendidaLatLon.Rd:35: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) iuv.Rd:30: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) listaCidades.Rd:28: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) metar.Rd:32: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) ondas.Rd:44: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) prev4dias.Rd:33: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) prev7dias.Rd:30: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) prevEstendida.Rd:32: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) prevLatLon.Rd:35: invalid email address: <rpradosiqueira@gmail.com>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
QR.cd: no visible global function definition for ‘quantile’
QR.lasso.cd: no visible global function definition for ‘quantile’
cqr.cd: no visible global function definition for ‘quantile’
cqr.lasso.cd: no visible global function definition for ‘quantile’
cqr.lasso.mm: no visible global function definition for ‘quantile’
cqr.mm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
File ‘cqrReg/libs/cqrReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
distance.comoving: no visible global function definition for
  ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.4Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
'LazyData' is specified without a 'data' directory
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
Package suggested but not available for checking: ‘argosfilter’
Namespaces in Imports field not imported from:
  ‘gdistance’ ‘raster’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘credule/libs/credule.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘gbm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
‘cleanup’: /bin/bash is not portable
'library' or 'require' call to ‘RCurl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘chron’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
collateDaily: no visible global function definition for ‘read.table’
collateDaily: no visible global function definition for ‘write.table’
collateHourly: no visible global function definition for ‘read.table’
collateHourly: no visible global function definition for ‘write.table’
downloadCRN: no visible global function definition for ‘download.file’
getUrlsCRN: no visible global function definition for ‘getURL’
writeDataset: no visible global function definition for ‘read.table’
writeDataset: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  download.file getURL read.table write.table
Consider adding
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
Rd file 'downloadCRN.Rd':
  \usage lines wider than 90 characters:
     downloadCRN(url = CRN.DAILY.URL, directory = DAILY_DIR, years = seq(from = 2000, to = 2011, by = 1))

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘pacman’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
crossmatchtest: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Rd file 'crossmatch-package.Rd':
  \examples lines wider than 100 characters:
                  c(0.03,0.11,0.16,-0.1,-0.05,0.16,0.12,0.4,0.04,0.71,0.01,0.21,-0.18,-0.08             ,-0.35,0.26,-0.6,-1.0))

Rd file 'crossmatchtest.Rd':
  \examples lines wider than 100 characters:
                  c(0.03,0.11,0.16,-0.1,-0.05,0.16,0.12,0.4,0.04,0.71,0.01,0.21,-0.18,-0.08             ,-0.35,0.26,-0.6,-1.0))

These lines will be truncated in the PDF manual.
BootC : BSs: no visible global function definition for ‘lm’
BootC : BSs: no visible global function definition for ‘vcov’
BootC: no visible global function definition for ‘boot’
BootC: no visible global function definition for ‘boot.ci’
DeltaC: no visible global function definition for ‘lm’
DeltaC: no visible global function definition for ‘vcov’
FiellerC: no visible global function definition for ‘lm’
FiellerC: no visible global function definition for ‘vcov’
nonLinearC: no visible global function definition for ‘nls’
Undefined global functions or variables:
  boot boot.ci lm nls vcov
Consider adding
  importFrom("stats", "lm", "nls", "vcov")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
crrp: no visible global function definition for ‘approx’
gcrrp: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx
Consider adding
  importFrom("stats", "approx")
to your NAMESPACE file.
File ‘crrp/libs/crrp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
crrc: no visible binding for global variable ‘na.omit’
crrs: no visible binding for global variable ‘na.omit’
mycrr: no visible binding for global variable ‘na.omit’
mycrr.test: no visible binding for global variable ‘na.omit’
print.crrs: no visible global function definition for ‘pnorm’
psh.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  na.omit pchisq pnorm
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pnorm")
to your NAMESPACE file.
File ‘crrSC/libs/crrSC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
crrstep : crr.makecov1: no visible global function definition for
  ‘model.matrix’
crrstep : crr.dropterm: no visible global function definition for
  ‘terms’
crrstep : crr.dropterm: no visible global function definition for
  ‘as.formula’
crrstep : crr.addterm: no visible global function definition for
  ‘terms’
crrstep : crr.addterm: no visible global function definition for
  ‘as.formula’
crrstep: no visible global function definition for ‘as.formula’
crrstep: no visible global function definition for ‘terms’
crrstep: no visible global function definition for ‘model.frame’
crrstep: no visible binding for global variable ‘na.pass’
crrstep: no visible global function definition for ‘update’
crrstep: no visible global function definition for ‘drop.terms’
Undefined global functions or variables:
  as.formula drop.terms model.frame model.matrix na.pass terms update
Consider adding
  importFrom("stats", "as.formula", "drop.terms", "model.frame",
             "model.matrix", "na.pass", "terms", "update")
to your NAMESPACE file.
Note: found 500 marked UTF-8 strings
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘geosphere’ ‘mapdata’ ‘maps’ ‘marmap’ ‘shinydashboard’
  ‘shinyjs’ ‘stringr’ ‘swfscDAS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘copula’ in Rd xrefs
Namespace in Imports field not imported from: ‘qte’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘future’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.7Mb
Note: found 3063 marked UTF-8 strings
pielou: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
cstar: no visible global function definition for ‘vcov’
cstar : utility: no visible global function definition for ‘dt’
cstar : maximand: no visible global function definition for ‘integrate’
cstar: no visible global function definition for ‘uniroot’
cstari : utility: no visible global function definition for ‘dt’
cstari : maximand: no visible global function definition for
  ‘integrate’
cstari: no visible global function definition for ‘uniroot’
cstarme : utility: no visible global function definition for ‘density’
cstarme : maximand: no visible global function definition for
  ‘integrate’
cstarme : maximand: no visible global function definition for ‘sd’
cstarme: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  density dt integrate sd uniroot vcov
Consider adding
  importFrom("stats", "density", "dt", "integrate", "sd", "uniroot",
             "vcov")
to your NAMESPACE file.
Undeclared package ‘cgam’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 1350 marked UTF-8 strings
installed size is 113.6Mb
  sub-directories of 1Mb or more:
    R       1.2Mb
    data    1.7Mb
    libs  109.5Mb
Namespace in Imports field not imported from: ‘pkgbuild’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘par-7269706c6579’
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Hello.csv’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Undeclared package ‘caret’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (7) cureph-object.Rd:25: \item in \arguments must have non-empty label
checkRd: (7) survpred-cureph.Rd:49: \item in \value must have non-empty label
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.
cci.nostrat: no visible global function definition for ‘quantile’
cci.nostrat: no visible global function definition for ‘axis’
cci.nostrat: no visible global function definition for ‘lines’
cci.nostrat: no visible global function definition for ‘legend’
cci.strat: no visible global function definition for ‘axis’
cci.strat: no visible global function definition for ‘lines’
cci.strat: no visible global function definition for ‘legend’
clfs.nostrat: no visible global function definition for ‘quantile’
clfs.nostrat: no visible global function definition for ‘axis’
clfs.nostrat: no visible global function definition for ‘lines’
clfs.nostrat: no visible global function definition for ‘legend’
clfs.strat: no visible global function definition for ‘axis’
clfs.strat: no visible global function definition for ‘lines’
clfs.strat: no visible global function definition for ‘legend’
pvals.2cat: no visible global function definition for ‘pchisq’
pvals.cat: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  axis legend lines pchisq quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Note: found 459 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
Found the following significant warnings:
  inpolygon.c:109:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/curvHDR.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Cut: no visible global function definition for ‘cor’
MissSimulation: no visible global function definition for ‘rbinom’
cutoff: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor rbinom
Consider adding
  importFrom("stats", "cor", "rbinom")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
delta.glm: no visible global function definition for ‘glm’
delta.glm: no visible global function definition for ‘residuals’
delta.glm: no visible global function definition for ‘fitted’
delta.glm: no visible global function definition for ‘predict.glm’
two.stage.model.outputs: no visible global function definition for ‘sd’
Undefined global functions or variables:
  fitted glm predict.glm residuals sd
Consider adding
  importFrom("stats", "fitted", "glm", "predict.glm", "residuals", "sd")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
checkRd: (7) predict_dim.Rd:22: \item in \describe must have non-empty label
Malformed Description field: should contain one or more complete sentences.
calfun: no visible global function definition for ‘optim’
calfun: no visible global function definition for ‘cov’
calfun: no visible global function definition for ‘var’
Undefined global functions or variables:
  cov optim var
Consider adding
  importFrom("stats", "cov", "optim", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
func.constructRegressionFormula: no visible global function definition
  for ‘as.formula’
func.crossValidationAnalysis: no visible global function definition for
  ‘glm’
func.crossValidationAnalysis: no visible global function definition for
  ‘predict’
func.crossValidationAnalysis: no visible global function definition for
  ‘write.table’
func.externalValidationAnalysis: no visible global function definition
  for ‘predict’
func.externalValidationAnalysis: no visible global function definition
  for ‘write.table’
func.linearRegressionAnalysis: no visible global function definition
  for ‘glm’
func.linearRegressionAnalysis: no visible global function definition
  for ‘predict’
func.linearRegressionAnalysis: no visible global function definition
  for ‘write.table’
func.sortDataColumns: no visible global function definition for
  ‘write.table’
mainfunc.q2: no visible global function definition for ‘write.table’
mainfunc.q2: no visible global function definition for ‘new’
mainfunc.stats: no visible global function definition for ‘write.table’
mainfunc.stats: no visible global function definition for ‘new’
Undefined global functions or variables:
  as.formula glm new predict write.table
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "as.formula", "glm", "predict")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cvimpute.by.wavelet: no visible global function definition for ‘sd’
cvimpute.by.wavelet: no visible global function definition for ‘mad’
cvimpute.image.by.wavelet: no visible global function definition for
  ‘sd’
cvimpute.image.by.wavelet: no visible global function definition for
  ‘mad’
cvwavelet.image.after.impute: no visible global function definition for
  ‘sd’
cvwavelet.image.after.impute: no visible global function definition for
  ‘mad’
Undefined global functions or variables:
  mad sd
Consider adding
  importFrom("stats", "mad", "sd")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
random.CV: no visible global function definition for ‘var’
regular.CV: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    doc    1.2Mb
    help   1.0Mb
    libs   3.7Mb
.mixgauss_init: no visible global function definition for ‘cov’
.mixgauss_init: no visible global function definition for ‘var’
Undefined global functions or variables:
  cov var
Consider adding
  importFrom("stats", "cov", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
cxxfun.from.dll: no visible global function definition for ‘new’
cxxfun.from.dso.bin: no visible global function definition for ‘new’
cxxfunctionplus: no visible global function definition for ‘getPlugin’
cxxfunctionplus: no visible global function definition for
  ‘cxxfunction’
cxxfunctionplus: no visible global function definition for ‘new’
show,cxxdso: no visible global function definition for ‘object.size’
Undefined global functions or variables:
  cxxfunction getPlugin new object.size
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "object.size")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘cycleRtools/libs/cycleRtools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    demos         4.4Mb
    extdata       1.4Mb
    htmlwidgets   1.5Mb
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Package in Depends field not imported from: ‘fda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.for.sequence.endpoint.breaks: no visible global function
  definition for ‘na.omit’
get.breaks.vector: no visible global function definition for ‘na.omit’
get.cycle.breaks: no visible global function definition for ‘na.omit’
get.cycle.counts: no visible global function definition for ‘na.omit’
get.cycle.matrix: no visible global function definition for ‘na.omit’
get.cycle.minimums: no visible global function definition for ‘na.omit’
get.peaks: no visible global function definition for ‘embed’
get.trans: no visible global function definition for
  ‘create.bspline.basis’
get.trans: no visible global function definition for ‘smooth.basis’
get.trans: no visible global function definition for ‘deriv.fd’
get.trans: no visible global function definition for ‘eval.fd’
get.transition.locations: no visible global function definition for
  ‘na.omit’
get.transition.locations.FDiff: no visible global function definition
  for ‘na.omit’
get.window: no visible global function definition for ‘sd’
Undefined global functions or variables:
  create.bspline.basis deriv.fd embed eval.fd na.omit sd smooth.basis
Consider adding
  importFrom("stats", "embed", "na.omit", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
cytoDiv: no visible global function definition for ‘colorRampPalette’
cytoDiv: no visible global function definition for ‘persp’
Undefined global functions or variables:
  colorRampPalette persp
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "persp")
to your NAMESPACE file.
Rd file 'cytoDiv.Rd':
  \usage lines wider than 90 characters:
     cytoDiv(df, x.var="fsc_small", y.var="chl_small", Ncat = 16, Nbit = 16, do.plot=FALSE, ...)
  \examples lines wider than 100 characters:
     rainbow.cols <- colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow","#FF7F00", "red", "#7F0000"))
     plot(cleaned.df[,2], cleaned.df[,3], col= densCols(cleaned.df[,2], cleaned.df[,3], colramp = rainbow.cols))

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Found the following files/directories:
  ‘GRCh38_browser’ ‘GRCh38_map’
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
checkRd: (7) capstring.Rd:16: \item in \value must have non-empty label
checkRd: (7) excessRisk.Rd:40: \item in \value must have non-empty label
checkRd: (7) excessRisk.Rd:41: \item in \value must have non-empty label
checkRd: (7) excessRisk.Rd:42: \item in \value must have non-empty label
checkRd: (7) excessRisk.Rd:43: \item in \value must have non-empty label
checkRd: (7) excessRisk.Rd:44: \item in \value must have non-empty label
checkRd: (7) excessRisk.Rd:45: \item in \value must have non-empty label
checkRd: (7) excessRisk.Rd:46-51: \item in \value must have non-empty label
Namespaces in Imports field not imported from:
  ‘plyr’ ‘simpleboot’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 109157 marked UTF-8 strings
Note: found 4 marked Latin-1 strings
  Note: found 21 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 212 marked Latin-1 strings
  Note: found 12719 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘fs’ ‘googleCloudStorageR’
  All declared Imports should be used.
File ‘DALY/libs/DALY.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.5Mb
dashboard_open: no visible global function definition for ‘write.csv’
dashboard_open: no visible global function definition for
  ‘capture.output’
dctable: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  capture.output write.csv
Consider adding
  importFrom("utils", "capture.output", "write.csv")
to your NAMESPACE file.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    deps  10.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    deps  10.3Mb
    lib    3.8Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    deps   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.8Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘miniUI’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Undeclared package ‘gdata’ in Rd xrefs
Found the following significant warnings:
  DTRegion3D.cpp:58:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  DTRegion3D.cpp:102:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/DataGraph.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘my new data set.rds’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 8 marked Latin-1 strings
installed size is 40.8Mb
  sub-directories of 1Mb or more:
    libs  39.9Mb
‘cleanup’: ‘env bash’ is not portable as bash need not be installed
Namespaces in Imports field not imported from:
  ‘R6’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
Undeclared package ‘tidyselect’ in Rd xrefs
Undeclared package ‘FCPS’ in Rd xrefs
Undeclared package ‘correlation’ in Rd xrefs
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 54314 marked UTF-8 strings
Note: found 1 marked Latin-1 string
  Note: found 360 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
dbEmpLikeGOF: no visible global function definition for ‘runif’
dbEmpLikeGOF: no visible global function definition for ‘var’
dbEmpLikeGOF: no visible global function definition for ‘rnorm’
emplikeGOFinternal: no visible global function definition for ‘var’
getCutoff: no visible binding for global variable ‘unifCut’
getCutoff: no visible binding for global variable ‘normCut’
getCutoff: no visible global function definition for ‘lm’
getCutoff: no visible binding for global variable ‘distEqCut’
getPval: no visible binding for global variable ‘unifCut’
getPval: no visible binding for global variable ‘normCut’
getPval: no visible global function definition for ‘lm’
getPval: no visible binding for global variable ‘distEqCut’
helperPval: no visible global function definition for ‘lm’
returnCutoff: no visible global function definition for ‘quantile’
testfun2: no visible global function definition for ‘runif’
testfun2: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  distEqCut lm normCut quantile rnorm runif unifCut var
Consider adding
  importFrom("stats", "lm", "quantile", "rnorm", "runif", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
computePval: no visible global function definition for ‘lm’
computeQhat: no visible global function definition for ‘pnorm’
dbELnorm: no visible global function definition for ‘rnorm’
getCutoffTableThree: no visible global function definition for ‘lm’
getCutoffTableTwo: no visible global function definition for ‘lm’
getCutoffValue: no visible global function definition for ‘lm’
helperGetTstat: no visible global function definition for ‘rnorm’
returnCutoffValue: no visible global function definition for ‘rnorm’
returnCutoffValue: no visible global function definition for ‘quantile’
varianceEstimator: no visible global function definition for ‘density’
varianceEstimator: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  density ecdf lm pnorm quantile rnorm
Consider adding
  importFrom("stats", "density", "ecdf", "lm", "pnorm", "quantile",
             "rnorm")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tidyverse’ ‘vctrs’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
'library' or 'require' call to ‘fdrtool’ which was already attached by Depends.
  Please remove these calls from your code.
avelinkdis: no visible global function definition for ‘sd’
avelinkdis: no visible global function definition for ‘dist’
centdis: no visible global function definition for ‘sd’
centdis: no visible global function definition for ‘dist’
distable: no visible global function definition for ‘write.table’
functionall: no visible global function definition for ‘read.table’
randdis: no visible global function definition for ‘write.table’
valuep: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  dist read.table sd write.csv write.table
Consider adding
  importFrom("stats", "dist", "sd")
  importFrom("utils", "read.table", "write.csv", "write.table")
to your NAMESPACE file.
Rd file 'distable.Rd':
  \examples lines wider than 100 characters:
     ##before using "b1.txt" data, we need to find "b1.txt" in the data file and  put it in the work space of R

Rd file 'functionall.Rd':
  \examples lines wider than 100 characters:
     ##before running this funtion, we need to find out "b1.txt" data file, and put it into the R workspace.
     functionall(system.file("data","b1.txt",package="DBGSA"),10,avelinkdis,"euclidean","distance",afExp,2000,10,"rand.txt","pvalue.txt")

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dblog’
File ‘dblcens/libs/dblcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.8Mb
Namespace in Imports field not imported from: ‘html5’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘lubridate’ ‘tseries’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 122 marked UTF-8 strings
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘bslib’ ‘knitr’ ‘matrixStats’ ‘rmarkdown’ ‘shinythemes’ ‘tidyverse’
  All declared Imports should be used.
Found the following files/directories:
  ‘LFC.d.jpeg’ ‘LFC.s.jpeg’ ‘TF_bridged_DCL.pdf’
  ‘TF_bridged_DCL_int.pdf’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  DCLEAR.cpp:54:5: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  DCLEAR.cpp:58:5: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  DCLEAR.cpp:71:5: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  DCLEAR.cpp:75:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/DCLEAR.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘lattice’ ‘latticeExtra’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Note: found 2 marked Latin-1 strings
File ‘DCluster/libs/DCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘CDM’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    libs  38.2Mb
Note: found 38 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   3.8Mb
Undeclared package ‘fda.usc’ in Rd xrefs
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
File ‘DDHFm/libs/DDHFm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
ifft: no visible global function definition for ‘fft’
lines.deamer: no visible global function definition for ‘lines’
rlaplace: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fft lines runif
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "fft", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
compare.relimp: no visible global function definition for ‘qchisq’
compare.relimp: no visible global function definition for ‘pchisq’
plot_transition: no visible global function definition for ‘dnorm’
plot_transition: no visible global function definition for ‘par’
plot_transition: no visible global function definition for ‘lines’
plot_transition: no visible global function definition for ‘plogis’
plot_transition: no visible global function definition for ‘axis’
plot_transition: no visible global function definition for ‘mtext’
relative.importance: no visible global function definition for ‘glm’
relative.importance: no visible global function definition for ‘sd’
relative.importance : tr.pr: no visible global function definition for
  ‘pnorm’
relative.importance: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  axis dnorm glm lines mtext par pchisq plogis pnorm qchisq sd vcov
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par")
  importFrom("stats", "dnorm", "glm", "pchisq", "plogis", "pnorm",
             "qchisq", "sd", "vcov")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (7) random.Rd:77-80: \item in \describe must have non-empty label
checkRd: (7) random.Rd:81-85: \item in \describe must have non-empty label
checkRd: (7) random.Rd:90-92: \item in \describe must have non-empty label
checkRd: (7) random.Rd:97-99: \item in \describe must have non-empty label
checkRd: (7) random.Rd:125-127: \item in \describe must have non-empty label
checkRd: (7) random.Rd:132-134: \item in \describe must have non-empty label
checkRd: (7) random.Rd:159-161: \item in \describe must have non-empty label
checkRd: (7) random.Rd:166-168: \item in \describe must have non-empty label
Undeclared package ‘future’ in Rd xrefs
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
Note: found 1 marked Latin-1 string
  Note: found 46826 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘Deducer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Depends: includes the non-default packages:
  'Deducer', 'psych', 'GPArotation', 'mvnormtest', 'irr', 'klaR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' call to ‘klaR’ which was already attached by Depends.
  Please remove these calls from your code.
.makeICCDialog: no visible global function definition for ‘J’
.makeICCDialog: no visible global function definition for ‘new’
.makeICCDialog: no visible global function definition for ‘.jnull’
.makeNewFactorAnalysisDialog: no visible global function definition for
  ‘new’
.makeNewFactorAnalysisDialog: no visible global function definition for
  ‘J’
.makeNewFactorAnalysisDialog: no visible global function definition for
  ‘toJava’
.makeNewLDADialog: no visible global function definition for ‘new’
.makeNewLDADialog: no visible global function definition for ‘J’
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for ‘new’
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for ‘toJava’
.makeNewLDADialog: no visible global function definition for ‘toJava’
.makeNewReliabilityDialog: no visible global function definition for
  ‘new’
.makeNewReliabilityDialog: no visible global function definition for
  ‘toJava’
.onLoad: no visible global function definition for ‘.jnull’
.onLoad: no visible global function definition for ‘jgr.getMenuNames’
.onLoad: no visible global function definition for ‘jgr.insertMenu’
.onLoad: no visible global function definition for ‘jgr.addMenu’
.onLoad: no visible global function definition for ‘jgr.addMenuItem’
Undefined global functions or variables:
  .jnull J jgr.addMenu jgr.addMenuItem jgr.getMenuNames jgr.insertMenu
  new toJava
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘Deducer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
.makeQuickWordcloud: no visible global function definition for ‘J’
.makeQuickWordcloud: no visible global function definition for ‘new’
.makeQuickWordcloud: no visible global function definition for ‘.jnull’
.makeTextPlot: no visible global function definition for ‘J’
.makeTextPlot: no visible global function definition for ‘new’
.makeTextPlot: no visible global function definition for ‘.jnull’
.onLoad: no visible global function definition for ‘.jpackage’
.onLoad: no visible global function definition for ‘.jnew’
.onLoad: no visible global function definition for ‘J’
make.color.scale: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  .jnew .jnull .jpackage J new rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
binary.state: no visible global function definition for ‘runif’
dbn.dnn.train: no visible global function definition for ‘runif’
dropout.mask: no visible global function definition for ‘runif’
nn.train: no visible global function definition for ‘runif’
rbm.train: no visible global function definition for ‘runif’
sae.dnn.train: no visible global function definition for ‘runif’
show.digit: no visible global function definition for ‘gray’
show.digit: no visible global function definition for ‘image’
Undefined global functions or variables:
  gray image runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Metrics’ ‘purrr’ ‘utils’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
DEEPR : perm_function: no visible global function definition for ‘head’
DEEPR : perm_function: no visible global function definition for ‘tail’
simCophy: no visible global function definition for ‘rpois’
simCophy: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  head rmultinom rpois tail
Consider adding
  importFrom("stats", "rmultinom", "rpois")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘deformula/libs/deformula.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘e1071’, ‘nloptr’ in Rd xrefs
Namespace in Imports field not imported from: ‘assertthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 67.6Mb
  sub-directories of 1Mb or more:
    libs  64.8Mb
‘configure’: /bin/bash is not portable
Namespace in Imports field not imported from: ‘lattice’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'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
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Undeclared packages ‘WGCNA’, ‘moduleColor’, ‘distory’, ‘phangorn’, ‘zoo’ in Rd xrefs
checkRd: (7) dendro.varcov.Rd:41: \item in \value must have non-empty label
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  22.6Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘rstantools’
  All declared Imports should be used.
Undeclared package ‘DEoptim’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
Package suggested but not available for checking: ‘Rdonlp2’
Package suggested but not available for checking: ‘Rdonlp2’
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
File ‘depth/libs/depth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 5764 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘htmlwidgets’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.5Mb
    libs   2.3Mb
checkRd: (7) Gini.Rd:63: \item in \value must have non-empty label
checkRd: (7) HuberM.Rd:35: \item in \value must have non-empty label
checkRd: (7) Skew.Rd:90: \item in \value must have non-empty label
Undeclared packages ‘ineq’, ‘randtests’, ‘Hmisc’, ‘plotrix’, ‘caret’, ‘pcaPP’, ‘polycor’, ‘lmtest’, ‘car’, ‘gmp’, ‘vcdExtra’, ‘chron’, ‘coin’, ‘caTools’, ‘forecast’, ‘sfsmisc’, ‘vcd’, ‘areaplot’, ‘corrgram’, ‘UsingR’, ‘memisc’, ‘gtools’, ‘BSDA’, ‘prettyR’ in Rd xrefs
ds: no visible global function definition for ‘is.ts’
ds: no visible global function definition for ‘frequency’
getds: no visible global function definition for ‘resid’
getds: no visible global function definition for ‘lm.fit’
getds: no visible global function definition for ‘sd’
getds: no visible global function definition for ‘var’
getds: no visible global function definition for ‘fitted’
Undefined global functions or variables:
  fitted frequency is.ts lm.fit resid sd var
Consider adding
  importFrom("stats", "fitted", "frequency", "is.ts", "lm.fit", "resid",
             "sd", "var")
to your NAMESPACE file.
Rd file 'ds.Rd':
  \usage lines wider than 90 characters:
     ds(z, Fm = 6, Fs = 6, type = c("daily", "monthly"), searchQ=TRUE, lag.max=20, ic=c("BIC","AIC"), standardizeQ=TRUE)

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
arrayUpdate : pairUpdate: no visible global function definition for
  ‘runif’
conditionUpdate: no visible global function definition for ‘runif’
designGG: no visible global function definition for ‘runif’
experimentDesignTable: no visible global function definition for
  ‘write.csv’
plotAllScores: no visible global function definition for ‘png’
plotAllScores: no visible global function definition for ‘par’
plotAllScores: no visible global function definition for ‘text’
plotAllScores: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off par png runif text write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par", "text")
  importFrom("stats", "runif")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘myDesignGGSAplot.png’ ‘myDesignGG_arrayDesign.csv’
  ‘myDesignGG_conditionDesign.csv’
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
Note: found 47 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
File ‘desire/libs/desire.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
fs.agreement.part: no visible global function definition for ‘as.dist’
fs.agreement.part: no visible global function definition for ‘cor’
fs.leave.k.out.combn: no visible global function definition for ‘sd’
fs.leave.k.out.sample: no visible global function definition for ‘sd’
fs.rd: no visible global function definition for ‘pchisq’
fs.selection: no visible global function definition for ‘p.adjust’
plot.FIT: no visible global function definition for ‘qchisq’
plot.FIT: no visible global function definition for ‘ppoints’
plot.FIT: no visible global function definition for ‘points’
plot.FIT: no visible global function definition for ‘abline’
plotJn: no visible global function definition for ‘points’
robust.distance.signed: no visible global function definition for
  ‘mahalanobis’
snowball: no visible global function definition for ‘is’
snowball: no visible global function definition for ‘median’
weight.sd: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  abline as.dist cor is mahalanobis median p.adjust pchisq points
  ppoints qchisq sd
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "cor", "mahalanobis", "median",
             "p.adjust", "pchisq", "ppoints", "qchisq", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
GNU make is a SystemRequirements.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘reshape2’ ‘stats’ ‘tidyr’ ‘tidyselect’
  All declared Imports should be used.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for ‘rbinom’
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for ‘rnorm’
simulate_dataframe : generate_initial: no visible global function
  definition for ‘rbinom’
simulate_dataframe: no visible binding for global variable ‘randu’
simulate_dataframe: no visible global function definition for ‘rbinom’
simulate_dataframe: no visible global function definition for ‘rnorm’
simulate_dataframe: no visible global function definition for ‘rpois’
simulate_dataframe : add_NAs: no visible global function definition for
  ‘rbinom’
Undefined global functions or variables:
  randu rbinom rnorm rpois
Consider adding
  importFrom("datasets", "randu")
  importFrom("stats", "rbinom", "rnorm", "rpois")
to your NAMESPACE file.
checkRd: (7) mtaBin_next.Rd:62: \item in \value must have non-empty label
Namespaces in Imports field not imported from:
  ‘MASS’ ‘plyr’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
installed size is 37.5Mb
  sub-directories of 1Mb or more:
    libs  36.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘integrate’
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘dchisq’
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘nlm’
cvm.test : cvm.stat.disc: no visible global function definition for
  ‘knots’
cvm.test : cvm.pval.disc.sim: no visible global function definition for
  ‘knots’
cvm.test : cvm.pval.disc.sim: no visible global function definition for
  ‘runif’
cvm.test: no visible global function definition for ‘is.stepfun’
cvm.test: no visible global function definition for ‘knots’
ks.test : exact.pval : ts.pval: no visible global function definition
  for ‘ecdf’
ks.test : sim.pval: no visible global function definition for ‘runif’
ks.test : sim.pval : getks: no visible global function definition for
  ‘ecdf’
ks.test: no visible global function definition for ‘is.stepfun’
ks.test: no visible global function definition for ‘knots’
ks.test: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  dchisq ecdf integrate is.stepfun knots nlm runif
Consider adding
  importFrom("stats", "dchisq", "ecdf", "integrate", "is.stepfun",
             "knots", "nlm", "runif")
to your NAMESPACE file.
File ‘dgof/libs/dgof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Note: found 8014 marked UTF-8 strings
dichromat: no visible global function definition for ‘col2rgb’
dichromat: no visible global function definition for ‘predict’
dichromat: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  col2rgb predict rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("stats", "predict")
to your NAMESPACE file.
le.pesquisa: no visible global function definition for ‘txtProgressBar’
le.pesquisa: no visible global function definition for ‘type.convert’
le.pesquisa: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar type.convert
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "type.convert")
to your NAMESPACE file.
Note: found 2297 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘purrr’
  All declared Imports should be used.
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘purrr’ ‘rsample’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
L2eV: no visible binding for global variable ‘constants’
L2w: no visible binding for global variable ‘constants’
dielectric: no visible global function definition for ‘new’
dielectric2plot: no visible global function definition for ‘reshape’
eV2L: no visible binding for global variable ‘constants’
t2eV: no visible binding for global variable ‘constants’
Undefined global functions or variables:
  constants new reshape
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "reshape")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘module_list.txt’ ‘res.txt’
Packages in Depends field not imported from:
  ‘PropCIs’ ‘gee’ ‘rootSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
diffpci: no visible global function definition for ‘diffpropci.Wald.mp’
diffpci: no visible global function definition for ‘diffpropci.mp’
diffpci: no visible global function definition for ‘scoreci.mp’
exact.cond : exactci: no visible global function definition for ‘qf’
exact.midp : binom.midp : f.low: no visible global function definition
  for ‘dbinom’
exact.midp : binom.midp : f.low: no visible global function definition
  for ‘pbinom’
exact.midp : binom.midp : f.up: no visible global function definition
  for ‘dbinom’
exact.midp : binom.midp : f.up: no visible global function definition
  for ‘pbinom’
exact.midp : binom.midp : one.ci: no visible global function definition
  for ‘uniroot’
np.nv: no visible global function definition for ‘qnorm’
np.t: no visible global function definition for ‘qt’
uncond: no visible global function definition for ‘qnorm’
wald.cc: no visible global function definition for ‘qnorm’
wilson: no visible global function definition for ‘qnorm’
wilson: no visible global function definition for ‘uniroot.all’
wilson.cc: no visible global function definition for ‘qnorm’
wilson.cc: no visible global function definition for ‘uniroot.all’
wilson.phi: no visible global function definition for ‘qnorm’
wilson.phi: no visible global function definition for ‘uniroot.all’
Undefined global functions or variables:
  dbinom diffpropci.Wald.mp diffpropci.mp pbinom qf qnorm qt scoreci.mp
  uniroot uniroot.all
Consider adding
  importFrom("stats", "dbinom", "pbinom", "qf", "qnorm", "qt", "uniroot")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
File ‘diffIRT/libs/diffIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gplots’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘RColorBrewer’ in Rd xrefs
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
checkRd: (7) GQD.aic.Rd:30: \item in \value must have non-empty label
checkRd: (7) GQD.dic.Rd:30: \item in \value must have non-empty label
File ‘DiffusionRgqd/libs/DiffusionRgqd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DiffusionRimp/libs/DiffusionRimp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
checkRd: (7) JGQD.dic.Rd:30: \item in \value must have non-empty label
File ‘DiffusionRjgqd/libs/DiffusionRjgqd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘igraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘dils/libs/dils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DIME/libs/DIME.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘CVST’ in Rd xrefs
checkRd: (7) luadSubset.Rd:10: \item in \describe must have non-empty label
checkRd: (7) luadSubset.Rd:11: \item in \describe must have non-empty label
checkRd: (7) luscSubset.Rd:10: \item in \describe must have non-empty label
checkRd: (7) luscSubset.Rd:11: \item in \describe must have non-empty label
checkRd: (7) pD.Rd:10: \item in \describe must have non-empty label
checkRd: (7) pD.Rd:11: \item in \describe must have non-empty label
checkRd: (7) pD.Rd:12: \item in \describe must have non-empty label
checkRd: (7) pD.Rd:13: \item in \describe must have non-empty label
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘DIRECT/libs/DIRECT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘minqa’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘splancs’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
'LazyData' is specified without a 'data' directory
p.discrete.adjust : <anonymous>: no visible global function definition
  for ‘stepfun’
Undefined global functions or variables:
  stepfun
Consider adding
  importFrom("stats", "stepfun")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
value: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Undeclared package ‘Hmisc’ in Rd xrefs
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘diversitree’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  percRank.cpp:21:16: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/dismo.Rcheck/00install.out’ for details.
Note: found 106 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Rd file 'dualFlashlight.fn.Rd':
  \usage lines wider than 90 characters:
     dualFlashlight.fn(result.df, wellName = "WELL_USAGE", x.name = "mean", y.name = "ssmd", sampleName = "Sample", sampleColor = "black", c ... [TRUNCATED]

Rd file 'imageDesign.fn.Rd':
  \usage lines wider than 90 characters:
     imageDesign.fn(dataOnePlate.df, wellName = NA, rowName, colName, wells = NULL, colors = NULL, title = " ")

Rd file 'imageIntensity.fn.Rd':
  \usage lines wider than 90 characters:
     imageIntensity.fn(data.df, intensityName = NA, plateName = "BARCODE", wellName = "WELL_USAGE", rowName, colName, sampleName = "Sample", ... [TRUNCATED]

Rd file 'plateWellSeries.fn.Rd':
  \usage lines wider than 90 characters:
     plateWellSeries.fn(data.df, intensityName = NA, plateName = "BARCODE", wellName = "WELL_USAGE", rowName, colName, show.wellTypes = NULL ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Undeclared package ‘geomorph’ in Rd xrefs
densest: no visible global function definition for ‘weighted.mean’
diss: no visible global function definition for ‘cov’
neighbors: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov weighted.mean
Consider adding
  importFrom("stats", "cov", "weighted.mean")
to your NAMESPACE file.
File ‘dissUtils/libs/dissUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘optimx’, ‘readxl’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘proxy’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help   1.2Mb
    libs   1.7Mb
Undeclared package ‘robustbase’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘RobAStBase’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared packages ‘distrMod’, ‘RobAStBase’ in Rd xrefs
Undeclared package ‘distrTEst’ in Rd xrefs
Found the following files/directories:
  ‘csim’ ‘xyz’ ‘xyz.sav’ ‘xyz.sav.comment’
Undeclared package ‘distr’ in Rd xrefs
Found the following files/directories:
  ‘csim.mean’ ‘csim.mean.comment’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Engine.cpp:73:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:79:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:84:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:94:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:102:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:109:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:116:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:124:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:132:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:140:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:148:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:156:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  Engine.cpp:164:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/divDyn.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘ggmulti’ ‘loon’ ‘loon.data’ ‘loon.ggplot’ ‘loon.shiny’ ‘loon.tourr’
  ‘stats’ ‘zenplots’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Package suggested but not available for checking: ‘BOLTSSIRR’
Found the following significant warnings:
  Forest.cpp:357:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/diversityForest.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Packages suggested but not available for checking: 'sendplot', 'HWxtest'
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plotly’ ‘pryr’ ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘dkDNA/libs/dkDNA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include  16.3Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
'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
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
DNMF: no visible global function definition for ‘runif’
NMFpval: no visible global function definition for ‘p.adjust’
ndNMF: no visible global function definition for ‘runif’
rnk: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  p.adjust runif write.table
Consider adding
  importFrom("stats", "p.adjust", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.8Mb
Note: found 9796 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ppert: no visible global function definition for ‘pbeta’
prepare8pkg: no visible global function definition for ‘glob2rx’
qpert: no visible global function definition for ‘qbeta’
rpert: no visible global function definition for ‘rbeta’
Undefined global functions or variables:
  glob2rx pbeta qbeta rbeta
Consider adding
  importFrom("stats", "pbeta", "qbeta", "rbeta")
  importFrom("utils", "glob2rx")
to your NAMESPACE file.
File ‘documair/libs/documair.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc    5.2Mb
    libs   8.3Mb
GNU make is a SystemRequirements.
checkRd: (7) add.response.Rd:72: \item in \value must have non-empty label
checkRd: (7) add.response.Rd:73: \item in \value must have non-empty label
checkRd: (7) add.response.Rd:74-75: \item in \value must have non-empty label
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
checkRd: (7) dominanceanalysis-package.Rd:98: invalid email address: clbustos_at_gmail_com
checkRd: (7) rename.vars.Rd:37: invalid email address: macq\@llnl.gov.
Namespaces in Imports field not imported from:
  ‘rjson’ ‘uuid’
  All declared Imports should be used.
checkRd: (7) domir-package.Rd:30: invalid email address: jluchman@gmail_com
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    data      2.0Mb
    extdata   2.3Mb
Note: found 100 marked UTF-8 strings
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Suggests orphaned package: ‘bibtex’
Package suggested but not available for checking: ‘DiPs’
Namespaces in Imports field not imported from:
  ‘DT’ ‘DoseFinding’ ‘ggplot2’ ‘lattice’ ‘latticeExtra’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
dostats: no visible binding for global variable ‘na.fail’
first: no visible global function definition for ‘head’
last: no visible global function definition for ‘tail’
pval.default: no visible global function definition for ‘.hasSlot’
pval.lm: no visible global function definition for ‘anova’
Undefined global functions or variables:
  .hasSlot anova head na.fail tail
Consider adding
  importFrom("methods", ".hasSlot")
  importFrom("stats", "anova", "na.fail")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘OpenMPController’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
Undeclared 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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.1Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘parallel’ ‘rgdal’ ‘sp’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘ggplot2’ ‘nloptr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Undeclared package ‘RcppEigen’ in Rd xrefs
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘sitmo’ in Rd xrefs
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Note: found 100 marked UTF-8 strings
'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’
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘purrr’ ‘rlang’
  All declared Imports should be used.
Undeclared package ‘SimMultiCorrData’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘arm’ ‘car’ ‘dotwhisker’ ‘gapminder’ ‘ggeffects’ ‘ggthemes’ ‘gt’
  ‘interplot’ ‘kableExtra’ ‘knitr’ ‘likert’ ‘modelsummary’ ‘moments’
  ‘nnet’ ‘ordinal’ ‘performance’ ‘scales’ ‘summarytools’ ‘tibble’
  ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.2Mb
File ‘drmdel/libs/drmdel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
compute_xsq: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  chisq.test
Consider adding
  importFrom("stats", "chisq.test")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘data.table’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Namespaces in Imports field not imported from:
  ‘rJava’ ‘tools’
  All declared Imports should be used.
DSBayes: no visible global function definition for ‘qnorm’
DSBayes: no visible global function definition for ‘coef’
DSBayes: no visible global function definition for ‘vcov’
DSBayes : MLE: no visible global function definition for ‘qnorm’
DSBayes: no visible global function definition for ‘integrate’
DSBayes : qfunc.numer : <anonymous>: no visible global function
  definition for ‘dnorm’
DSBayes : ds.numer: no visible global function definition for
  ‘integrate’
DSBayes : lower: no visible global function definition for ‘qlogis’
DSBayes : lower: no visible global function definition for ‘integrate’
DSBayes : upper: no visible global function definition for ‘qlogis’
DSBayes : upper: no visible global function definition for ‘integrate’
DSBayes: no visible global function definition for ‘optimize’
DSBayes: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  coef dnorm integrate optimize qlogis qnorm uniroot vcov
Consider adding
  importFrom("stats", "coef", "dnorm", "integrate", "optimize", "qlogis",
             "qnorm", "uniroot", "vcov")
to your NAMESPACE file.
Found the following significant warnings:
  dscore.cpp:135:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/dscore.Rcheck/00install.out’ for details.
Undeclared package ‘EvalEst’ in Rd xrefs
File ‘dse/libs/dse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 149 marked UTF-8 strings
Note: found 4891 marked UTF-8 strings
Package suggested but not available for checking: ‘dsBaseClient’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘dstat’, ‘sensitivity2x2xk’ in Rd xrefs
DCEA: no visible global function definition for ‘p.adjust’
DS: no visible global function definition for ‘p.adjust’
DS: no visible global function definition for ‘pdf’
DS: no visible global function definition for ‘dev.off’
LFC: no visible global function definition for ‘glm’
LFC: no visible global function definition for ‘predict’
PartialCor: no visible global function definition for ‘na.omit’
comDCGLplot: no visible global function definition for ‘pdf’
comDCGLplot: no visible global function definition for ‘dev.off’
percentLinkfilter: no visible global function definition for ‘cor’
qLinkfilter: no visible global function definition for ‘cor’
qLinkfilter: no visible global function definition for ‘pt’
qLinkfilter: no visible global function definition for ‘p.adjust’
rLinkfilter: no visible global function definition for ‘cor’
varianceBasedfilter: no visible binding for global variable ‘var’
varianceBasedfilter: no visible global function definition for ‘median’
varianceBasedfilter: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor dev.off glm median na.omit p.adjust pchisq pdf predict pt var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "cor", "glm", "median", "na.omit", "p.adjust",
             "pchisq", "predict", "pt", "var")
to your NAMESPACE file.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.3Mb
Note: found 1 marked Latin-1 string
'LazyData' is specified without a 'data' directory
Note: found 281 marked UTF-8 strings
DLR: no visible global function definition for ‘formula’
DLR: no visible global function definition for ‘terms’
DLR: no visible global function definition for ‘model.matrix’
DLR: no visible global function definition for ‘as.formula’
DLR: no visible binding for global variable ‘binomial’
DLR: no visible global function definition for ‘coef’
DLR: no visible global function definition for ‘pnorm’
DLR: no visible global function definition for ‘qnorm’
acc.1test: no visible global function definition for ‘qnorm’
pv.gs: no visible global function definition for ‘pchisq’
pv.rpv: no visible global function definition for ‘qnorm’
pv.rpv: no visible global function definition for ‘pnorm’
pv.wgs: no visible global function definition for ‘pchisq’
sesp.diff.ci: no visible global function definition for ‘qnorm’
sesp.mcnemar: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  as.formula binomial coef formula model.matrix pchisq pnorm qnorm
  terms
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "formula",
             "model.matrix", "pchisq", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
DTK.plot: no visible global function definition for ‘axis’
DTK.plot: no visible global function definition for ‘title’
DTK.plot: no visible global function definition for ‘lines’
DTK.plot: no visible global function definition for ‘points’
DTK.test: no visible binding for global variable ‘sd’
DTK.test: no visible global function definition for ‘qtukey’
TK.test: no visible global function definition for ‘TukeyHSD’
TK.test: no visible global function definition for ‘aov’
Undefined global functions or variables:
  TukeyHSD aov axis lines points qtukey sd title
Consider adding
  importFrom("graphics", "axis", "lines", "points", "title")
  importFrom("stats", "TukeyHSD", "aov", "qtukey", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   4.2Mb
GNU make is a SystemRequirements.
File ‘dualtrees/libs/dualtrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 159.5Mb
  sub-directories of 1Mb or more:
    libs  158.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2854 marked UTF-8 strings
cvSDDT: no visible global function definition for ‘qt’
cvSDDT : Cj_SD.fun: no visible global function definition for ‘combn’
cvSDDT: no visible global function definition for ‘uniroot’
cvSUDT: no visible global function definition for ‘rnorm’
cvSUDT: no visible global function definition for ‘rchisq’
cvSUDT : psi.fun: no visible global function definition for ‘pnorm’
cvSUDT: no visible global function definition for ‘qt’
cvSUDT: no visible global function definition for ‘uniroot’
cvSUDT: no visible global function definition for ‘combn’
nvDT : samplesize: no visible global function definition for ‘rnorm’
nvDT : samplesize: no visible global function definition for ‘rchisq’
nvDT : samplesize: no visible global function definition for ‘pnorm’
nvDT : ssBonf: no visible global function definition for ‘qnorm’
nvDT : ssBonf: no visible global function definition for ‘qt’
nvDT : ssBonf: no visible global function definition for ‘rnorm’
nvDT : ssBonf: no visible global function definition for ‘rchisq’
nvDT : ssBonf: no visible global function definition for ‘pnorm’
nvDT: no visible global function definition for ‘uniroot’
powDT: no visible global function definition for ‘rnorm’
powDT: no visible global function definition for ‘rchisq’
powDT: no visible global function definition for ‘pnorm’
qvSDDT: no visible global function definition for ‘pt’
qvSUDT: no visible global function definition for ‘rnorm’
qvSUDT: no visible global function definition for ‘rchisq’
qvSUDT : psi.fun: no visible global function definition for ‘pnorm’
qvSUDT: no visible global function definition for ‘pt’
qvSUDT : Pj.fun: no visible global function definition for ‘qt’
qvSUDT : Pj.fun: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn pnorm pt qnorm qt rchisq rnorm uniroot
Consider adding
  importFrom("stats", "pnorm", "pt", "qnorm", "qt", "rchisq", "rnorm",
             "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
Clough: no visible global function definition for ‘dgamma’
computePosterior,Counts: no visible global function definition for
  ‘dnbinom’
getPosteriorParam,Counts: no visible global function definition for
  ‘qgamma’
getPosteriorParam,Counts: no visible global function definition for
  ‘dgamma’
getPosteriorParam,Counts: no visible global function definition for
  ‘pgamma’
plotPosterior,Counts: no visible global function definition for ‘axis’
plotPosterior,Counts: no visible global function definition for
  ‘abline’
plotPosterior,Counts: no visible global function definition for ‘lines’
plotPosterior,Counts: no visible global function definition for ‘rect’
plotPosterior,Counts: no visible global function definition for ‘curve’
plotPosterior,Counts: no visible global function definition for
  ‘dgamma’
plotPosterior,Counts: no visible global function definition for
  ‘legend’
show,Counts: no visible global function definition for ‘head’
show,Counts: no visible global function definition for ‘tail’
Undefined global functions or variables:
  abline axis curve dgamma dnbinom head legend lines pgamma qgamma rect
  tail
Consider adding
  importFrom("graphics", "abline", "axis", "curve", "legend", "lines",
             "rect")
  importFrom("stats", "dgamma", "dnbinom", "pgamma", "qgamma")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GenEst’ ‘expint’ ‘numDeriv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘quadprog’ in Rd xrefs
Undeclared package ‘stringdist’ in Rd xrefs
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs  19.3Mb
Namespaces in Imports field not imported from:
  ‘NatureSounds’ ‘av’ ‘magrittr’ ‘stats’
  All declared Imports should be used.
Undeclared package ‘warbleR’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
GetIntMod: no visible global function definition for ‘arima’
GetLikeDI: no visible global function definition for ‘arima’
GetLikeDI: no visible global function definition for ‘logLik’
GetPV: no visible global function definition for ‘optimize’
GetPV: no visible global function definition for ‘pchisq’
fitdi: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  arima logLik optimize pchisq
Consider adding
  importFrom("stats", "arima", "logLik", "optimize", "pchisq")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘dynpred/libs/dynpred.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 9 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs        8.3Mb
    shiny_app   1.1Mb
'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.
Undeclared package ‘leaps’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘EasyABC/libs/EasyABC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Running ‘testthat.R’ [172s/312s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(easyalluvial)
  > 
  > test_check("easyalluvial")
  [ FAIL 1 | WARN 0 | SKIP 16 | PASS 47 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (15)
  • xgboost test skipped for performance (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_plot_imp.R:37:3): add_importance_plot ─────────────────────────
  `p <- alluvial_model_response_caret(train, df, degree = 4, pred_train = pred_train)` did not produce any warnings.
  
  [ FAIL 1 | WARN 0 | SKIP 16 | PASS 47 ]
  Error: Test failures
  Execution halted
'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’
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rprojroot’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RSQLite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘estimatr’
  All declared Imports should be used.
eb: no visible global function definition for ‘optimize’
ebalance: no visible global function definition for ‘var’
Undefined global functions or variables:
  optimize var
Consider adding
  importFrom("stats", "optimize", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
File ‘EBEN/libs/EBEN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘methods’ ‘rappdirs’ ‘rgdal’ ‘tools’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gtools’ ‘separationplot’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
ebSNP: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘plm’, ‘systemfit’, ‘carData’, ‘wooldridge’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'ghyp', 'fOptions'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [6m/16m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(testthat)
  > library(ecd)
  > test_check("ecd")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 356 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-option-ecop.R:2:1): (code run outside of `test_that()`) ─────────
  <packageNotFoundError/error/condition>
  Error in `library(fOptions)`: there is no package called 'fOptions'
  Backtrace:
      ▆
   1. ├─base::suppressMessages(library(fOptions)) at test-option-ecop.R:2:0
   2. │ └─base::withCallingHandlers(...)
   3. └─base::library(fOptions)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 356 ]
  Error: Test failures
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
checkRd: (7) K012.Rd:48: \item in \value must have non-empty label
checkRd: (7) K012.Rd:50-51: \item in \value must have non-empty label
checkRd: (7) K1K2.rd:43: \item in \value must have non-empty label
checkRd: (7) K1K2.rd:44: \item in \value must have non-empty label
checkRd: (7) K1K2.rd:45: \item in \value must have non-empty label
Undeclared packages ‘EnvStats’, ‘drc’, ‘zoo’, ‘prodlim’, ‘plyr’, ‘TRAMPR’, ‘raster’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1409 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lmtest’ ‘sandwich’ ‘urca’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
Running examples in ‘EcoHydRology-Ex.R’ failed
The error most likely occurred in:

> ### Name: Lumped_VSA_model
> ### Title: Lumped Variable Source Area (VSA) Watershed Model
> ### Aliases: Lumped_VSA_model
> 
> ### ** Examples
> 
> data(OwascoInlet)
> # First get rain and snow-melt input: 
> rsm <- SnowMelt(Date=OwascoInlet$date, precip_mm=OwascoInlet$P_mm, Tmax_C=OwascoInlet$Tmax_C, 
+ Tmin_C=OwascoInlet$Tmin_C, lat_deg=42.66)
Error in Tx == -999 || Tn == -999 : 
  'length = 888' in coercion to 'logical(1)'
Calls: SnowMelt -> EstCloudiness
Execution halted
dilution: no visible global function definition for ‘grey’
dilution: no visible global function definition for ‘lines’
dilution: no visible global function definition for ‘rect’
dilution: no visible global function definition for ‘segments’
dilution: no visible global function definition for ‘text’
dilution: no visible global function definition for ‘arrows’
pricefit: no visible global function definition for ‘runif’
Undefined global functions or variables:
  arrows grey lines rect runif segments text
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "arrows", "lines", "rect", "segments", "text")
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘ecolMod/libs/ecolMod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
checkRd: (7) ecospat.nichePOSNB.Rd:28: invalid email address: lucie.malard@unil.ch, olivier.broennimann@unil.ch
checkRd: (7) ecospat.testNichePOSNB.Rd:15: invalid email address: lucie.malard@unil.ch, olivier.broennimann@unil.ch
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Undeclared package ‘DBI’ in Rd xrefs
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dae’ ‘dplyr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘spc’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'ecoCusum.Rd':
  \examples lines wider than 100 characters:
     ## global optimization to h, H and n, when lambda = 0.01, "Nelder-Mead" optimization algorithm doesn't work

Rd file 'ecoEwma.Rd':
  \examples lines wider than 100 characters:
     #yy = ecoEwma(h = seq(.7,1,by=.01), w = seq(0.8,1,by=.01),k = seq(2.9,3.3, by = 0.01), n = 4:5, P0 = 110, P1 = 10, Cf = 50, contour.plo ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Undeclared package ‘magrittr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tmplp.dat’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  forceBundle.cpp:14:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  forceBundle.cpp:269:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/edgebundle.Rcheck/00install.out’ for details.
Note: found 22 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
UCexactTest: no visible global function definition for ‘is’
UCexactTest: no visible global function definition for ‘new’
pvalue: no visible global function definition for ‘dnbinom’
pvalue: no visible global function definition for ‘pnbinom’
sup.mu: no visible global function definition for ‘predict’
Undefined global functions or variables:
  dnbinom is new pnbinom predict
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "dnbinom", "pnbinom", "predict")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘tibble’
  All declared Imports should be used.
Undeclared package ‘ndl’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘T2EQ’ in Rd xrefs
geteegdata: no visible global function definition for ‘untar’
geteegdata: no visible global function definition for ‘read.table’
geteegdata: no visible global function definition for ‘write.csv’
geteegdata: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  read.table untar write.csv write.table
Consider adding
  importFrom("utils", "read.table", "untar", "write.csv", "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘PCovR’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
checkRd: (7) effectFusion.Rd:160-161: \item in \describe must have non-empty label
checkRd: (7) effectFusion.Rd:193: \item in \describe must have non-empty label
checkRd: (7) effectFusion.Rd:200: \item in \describe must have non-empty label
checkRd: (7) effectFusion.Rd:67-68: \item in \describe must have non-empty label
checkRd: (7) effectFusion.Rd:81-82: \item in \describe must have non-empty label
checkRd: (7) effectFusion.Rd:83-84: \item in \describe must have non-empty label
checkRd: (7) effectFusion.Rd:92-93: \item in \describe must have non-empty label
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘poLCA’
Malformed Title field: should not end in a period.
Undeclared package ‘PsumtSim’ in Rd xrefs
Undeclared package ‘carData’ in Rd xrefs
Undeclared packages ‘carData’, ‘faraway’ in Rd xrefs
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
'LazyData' is specified without a 'data' directory
Note: found 24 marked UTF-8 strings
Found the following files/directories:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Package suggested but not available for checking: ‘eggCountsExtra’
installed size is 73.1Mb
  sub-directories of 1Mb or more:
    libs  72.4Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘lme4’
  All declared Imports should be used.
checkRd: (7) egor-package-doc.Rd:28: invalid email address: m.bojanowski at icm.edu.pl
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc       6.1Mb
    extdata   5.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
eiginv: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
boot_pr_comp: no visible global function definition for ‘cov’
boot_pr_comp: no visible global function definition for ‘quantile’
boot_pr_comp: no visible global function definition for ‘segments’
boot_pr_comp: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cov quantile segments
Consider adding
  importFrom("graphics", "abline", "segments")
  importFrom("stats", "cov", "quantile")
to your NAMESPACE file.
installed size is 120.8Mb
  sub-directories of 1Mb or more:
    libs  120.6Mb
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘class’ ‘quantreg’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cluster.segment: no visible global function definition for ‘kmeans’
cluster.segment: no visible global function definition for ‘knn’
comp.anc.dist: no visible global function definition for ‘wilcox.test’
eila: no visible global function definition for ‘hasArg’
get.prob.score: no visible global function definition for ‘glm’
get.prob.score: no visible global function definition for ‘binomial’
get.prob.score: no visible binding for global variable ‘logit’
get.prob.score: no visible global function definition for ‘predict’
quantreg.est: no visible global function definition for ‘rnorm’
quantreg.est: no visible global function definition for ‘rq.fit.fnb’
Undefined global functions or variables:
  binomial glm hasArg kmeans knn logit predict rnorm rq.fit.fnb
  wilcox.test
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "binomial", "glm", "kmeans", "predict", "rnorm",
             "wilcox.test")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is 40.0Mb
  sub-directories of 1Mb or more:
    libs  39.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Undeclared package ‘eRm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘elec’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BaB: no visible binding for global variable ‘calc.pairwise.e_p’
BaB: no visible global function definition for ‘weight.function’
BaB: no visible global function definition for ‘compute.stark.t’
LKPBound: no visible binding for global variable ‘calc.pairwise.e_p’
LKPBound: no visible global function definition for ‘weight.function’
LKPBound: no visible global function definition for ‘compute.stark.t’
eqValBound: no visible binding for global variable ‘calc.pairwise.e_p’
eqValBound: no visible global function definition for ‘weight.function’
eqValBound: no visible global function definition for ‘compute.stark.t’
getEbsMargin: no visible global function definition for ‘is.elec.data’
getEbsMargin: no visible global function definition for
  ‘maximumMarginBound’
makeStratObj: no visible global function definition for ‘is.elec.data’
makeStratObj: no visible global function definition for
  ‘maximumMarginBound’
strat.elec.data: no visible global function definition for ‘elec.data’
takeOutZeroMMB: no visible global function definition for
  ‘maximumMarginBound’
withReplaceBound: no visible binding for global variable
  ‘calc.pairwise.e_p’
withReplaceBound: no visible global function definition for
  ‘weight.function’
withReplaceBound: no visible global function definition for
  ‘compute.stark.t’
Undefined global functions or variables:
  calc.pairwise.e_p compute.stark.t elec.data is.elec.data
  maximumMarginBound weight.function
File ‘elec.strat/libs/elec.strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘EloRating’ in Rd xrefs
File ‘elsa/libs/elsa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Likelihood: no visible global function definition for
  ‘makePSOCKcluster’
Likelihood: no visible global function definition for ‘clusterExport’
Likelihood: no visible global function definition for ‘makeForkCluster’
Likelihood.first.run: no visible global function definition for
  ‘clusterApply’
Likelihood.next.runs: no visible global function definition for
  ‘clusterApply’
es.stopCluster: no visible global function definition for ‘stopCluster’
plot.es.pedigree: no visible global function definition for ‘hasArg’
Undefined global functions or variables:
  clusterApply clusterExport hasArg makeForkCluster makePSOCKcluster
  stopCluster
Consider adding
  importFrom("methods", "hasArg")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
Undeclared package ‘textrecipes’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rtsne’ ‘uwot’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 155 marked UTF-8 strings
Package which this enhances but not available for checking: ‘PPtree’
'LazyData' is specified without a 'data' directory
Undeclared package ‘mvtnorm’ in Rd xrefs
Note: found 50 marked Latin-1 strings
File ‘emdist/libs/emdist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  12.0Mb
Package suggested but not available for checking: ‘eixport’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘reshape’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MFFetch: no visible global function definition for ‘melt’
Undefined global functions or variables:
  melt
Rd file 'emme2.Rd':
  \usage lines wider than 90 characters:
          write.mf(data, numname, bank, file0, mcent, mmat, mat.dir, newname=NULL, newdesc=NULL)
  \examples lines wider than 100 characters:
          x <- matrix(rnorm(mf2), nrow(mf2), ncol(mf2)) #Random generate length(mf) numbers to write dummy data to bank
          write.mf(x, 2, "emme2/emme2ban", file0, file1$global["mcent"], file1$global["mmat"], mat.dir, newname="test", newdesc="test matrix ... [TRUNCATED]
          link.data <- read.link.data("emme2/emme2ban", 1, file0, file1$global["mscen"], file1$global["mlink"], file1$global["mnode"])
          nodes <- read.nodes("emme2/emme2ban", 1, file0, file1$global["mscen"], file1$global["mlink"], file1$global["mnode"])

These lines will be truncated in the PDF manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.7Mb
File ‘emoa/libs/emoa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.5Mb
Note: found 9451 marked UTF-8 strings
Undeclared packages ‘Kendall’, ‘geoR’ in Rd xrefs
'LazyData' is specified without a 'data' directory
empiricalFDR: no visible global function definition for ‘axis’
empiricalFDR: no visible global function definition for ‘loess’
empiricalFDR: no visible global function definition for ‘predict’
empiricalFDR: no visible global function definition for ‘lines’
empiricalFDR: no visible global function definition for ‘abline’
fdrBiCurve: no visible global function definition for ‘axis’
fdrBiCurve: no visible global function definition for ‘lines’
fdrBiCurve: no visible global function definition for ‘abline’
fdrBiCurve: no visible global function definition for ‘legend’
simulateCounts: no visible global function definition for
  ‘txtProgressBar’
simulateCounts: no visible global function definition for
  ‘setTxtProgressBar’
simulateCounts: no visible global function definition for ‘rnorm’
simulateCounts: no visible global function definition for ‘hist’
simulateCounts: no visible global function definition for ‘colData’
Undefined global functions or variables:
  abline axis colData hist legend lines loess predict rnorm
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines")
  importFrom("stats", "loess", "predict", "rnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Note: found 23639 marked Latin-1 strings
Namespace in Imports field not imported from: ‘BBmisc’
  All declared Imports should be used.
Found the following significant warnings:
  conj_EMVS.cpp:68:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  conj_EMVS.cpp:77:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  conj_EMVS.cpp:135:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ind_EMVS.cpp:67:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ind_EMVS.cpp:77:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ind_EMVS.cpp:124:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/EMVS.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Found the following files/directories:
  ‘file.path(temp_dir, gp2.csv)’
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘sp’ ‘testthat’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
checkRd: (7) p300cbp.1000bp.Rd:18: \item in \describe must have non-empty label
checkRd: (7) p300cbp.1000bp.Rd:19: \item in \describe must have non-empty label
checkRd: (7) p300cbp.1000bp.Rd:24-25: \item in \describe must have non-empty label
checkRd: (7) p300cbp.1000bp.Rd:26-27: \item in \describe must have non-empty label
checkRd: (7) p300cbp.200bp.Rd:18: \item in \describe must have non-empty label
checkRd: (7) p300cbp.200bp.Rd:19: \item in \describe must have non-empty label
checkRd: (7) p300cbp.200bp.Rd:23-24: \item in \describe must have non-empty label
checkRd: (7) p300cbp.200bp.Rd:25-26: \item in \describe must have non-empty label
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘DECIPHER’ ‘ggplot2’ ‘reshape2’ ‘usethis’
  All declared Imports should be used.
File ‘EntropyEstimation/libs/EntropyEstimation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
diffcv: no visible global function definition for ‘sd’
diffcvall: no visible global function definition for ‘sd’
diffcvall: no visible global function definition for ‘fligner.test’
diffcvall: no visible global function definition for ‘p.adjust’
diffcvpFK: no visible global function definition for ‘fligner.test’
diffcvpFK: no visible global function definition for ‘p.adjust’
diffexp: no visible global function definition for ‘var’
diffexp: no visible global function definition for ‘t.test’
diffexp: no visible global function definition for ‘p.adjust’
diffexp2: no visible global function definition for ‘var’
diffexp2: no visible global function definition for ‘t.test’
diffexp2: no visible global function definition for ‘p.adjust’
diffnsepperm: no visible global function definition for ‘p.adjust’
diffseall: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  fligner.test p.adjust sd t.test var
Consider adding
  importFrom("stats", "fligner.test", "p.adjust", "sd", "t.test", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
File ‘enviPick/libs/enviPick.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘EnviroStat/libs/EnviroStat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘Environmental variables.csv’ ‘Inf.txt’ ‘List of species.csv’ ‘Mean
  overlap among taxa.csv’ ‘Overlap among taxa.csv’ ‘Pointsize.dat’
  ‘Polar coordinates.csv’
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.4Mb
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘plotrix’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Hmisc’ ‘survival’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘plotrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘a.alpha.ade’ ‘a.coladd.ade’ ‘a.getcol.ade’ ‘a.glc’
Rd file 'scatter.ade.Rd':
  \examples lines wider than 100 characters:
     scatter.ade(x, y, g, z, vnames=c("blue","red"), alpha=0.25, xlim=c(-5, 5), zticks=c(1, 2, 3, 4, 5), wall=3)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
Namespaces in Imports field not imported from:
  ‘RSpectra’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘readr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 1 marked Latin-1 string
  Note: found 721 marked UTF-8 strings
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tinytest’
  All declared Imports should be used.
installed size is 47.4Mb
  sub-directories of 1Mb or more:
    libs  46.2Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.
Package suggested but not available for checking: ‘epidict’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘EpiSoon’
installed size is 99.1Mb
  sub-directories of 1Mb or more:
    libs  97.3Mb
'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’
plot.episplineDensity: no visible global function definition for
  ‘points’
postproc: no visible global function definition for ‘points’
preprocess.data: no visible global function definition for ‘sd’
Undefined global functions or variables:
  points sd
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taskscheduleR’

Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    java   1.3Mb
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘knitr’ ‘plyr’ ‘tidyverse’ ‘tokenizers’ ‘xml2’
  All declared Imports should be used.
FCIplot: no visible global function definition for ‘na.omit’
FCIplot: no visible global function definition for ‘tail’
FCIplot: no visible global function definition for ‘grid’
FCIplot: no visible global function definition for ‘polygon’
FCIplot: no visible global function definition for ‘rgb’
linpred: no visible global function definition for ‘lm’
mplott: no visible global function definition for ‘par’
mplott: no visible global function definition for ‘na.omit’
mplott: no visible global function definition for ‘lines’
mplott: no visible global function definition for ‘legend’
mplott: no visible global function definition for ‘grid’
plott: no visible global function definition for ‘lines’
plott: no visible global function definition for ‘par’
plott: no visible global function definition for ‘grid’
tsideplot: no visible global function definition for ‘par’
tsideplot: no visible global function definition for ‘axis’
tsideplot: no visible global function definition for ‘grid’
Undefined global functions or variables:
  axis grid legend lines lm na.omit par polygon rgb tail
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "polygon")
  importFrom("stats", "lm", "na.omit")
  importFrom("utils", "tail")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘tidyselect’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 15 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
eqs2lavaan: no visible global function definition for ‘ignore.case’
eqs2lavaan: no visible global function definition for ‘str_join’
eqs2lavaan: no visible binding for global variable ‘r’
eqsCorr: no visible global function definition for ‘cov2cor’
plotCov: no visible global function definition for ‘cov2cor’
plotCov: no visible global function definition for ‘par’
plotCov: no visible global function definition for ‘image’
plotCov: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis cov2cor ignore.case image par r str_join
Consider adding
  importFrom("graphics", "axis", "image", "par")
  importFrom("stats", "cov2cor")
to your NAMESPACE file.
Undeclared package ‘OpenMx’ in Rd xrefs
Found the following significant warnings:
  EqMult.cpp:542:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/equateMultiple.Rcheck/00install.out’ for details.
checkRd: (7) presmoothing.Rd:108-109: \item in \value must have non-empty label
checkRd: (7) presmoothing.Rd:109-110: \item in \value must have non-empty label
checkRd: (7) presmoothing.Rd:110-112: \item in \value must have non-empty label
checkRd: (7) presmoothing.Rd:112-113: \item in \value must have non-empty label
checkRd: (7) presmoothing.Rd:113-115: \item in \value must have non-empty label
The following files contain a license that requires
distribution of original sources:
  ‘upgreek.sty’
Please ensure that you have complied with it.
'LazyData' is specified without a 'data' directory
File ‘equivalence/libs/equivalence.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘cubature’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘erboost/libs/erboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘methods’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
Undeclared package ‘margins’ in Rd xrefs
Found the following significant warnings:
  directed.cpp:65:30: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:66:30: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:67:30: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:96:28: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:97:28: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:121:28: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:256:28: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:257:28: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:258:28: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:269:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:291:24: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:292:24: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:307:24: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:367:24: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:368:24: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  directed.cpp:369:24: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  undirected.cpp:141:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/ergmclust.Rcheck/00install.out’ for details.
Found the following significant warnings:
  induced_submat.cpp:25:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  induced_submat.cpp:27:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/ergmito.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.9Mb
    libs   2.2Mb
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ESA: no visible binding for global variable ‘var’
plot.esabcv: no visible global function definition for ‘points’
plot.esabcv: no visible global function definition for ‘axis’
plot.esabcv: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis points title var
Consider adding
  importFrom("graphics", "axis", "points", "title")
  importFrom("stats", "var")
to your NAMESPACE file.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc  13.1Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘metafor’ in Rd xrefs
'LazyData' is specified without a 'data' directory
ESEA.Main: no visible global function definition for ‘rnorm’
ESEA.Main: no visible global function definition for ‘sd’
ESEA.Main: no visible global function definition for ‘p.adjust’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘lines’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘colors’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘points’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘legend’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘text’
PlotPathwayGraph: no visible global function definition for ‘par’
PlotRunEnrichment: no visible global function definition for ‘lines’
PlotRunEnrichment: no visible global function definition for ‘colors’
PlotRunEnrichment: no visible global function definition for ‘text’
SavePathway2File: no visible global function definition for ‘is’
calEdgeCorScore: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  colors is legend lines na.omit p.adjust par points rnorm sd text
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "legend", "lines", "par", "points", "text")
  importFrom("methods", "is")
  importFrom("stats", "na.omit", "p.adjust", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Namespaces in Imports field not imported from:
  ‘EMMAgeo’ ‘limSolve’ ‘shinyFiles’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
cv.ES: no visible binding for global variable ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    help   1.5Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘EstHer/libs/EstHer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘matrixStats’
  All declared Imports should be used.
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
'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:
  ‘estoutstorage’
descsto: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.Transition: no visible global function definition for ‘rnorm’
.Transition.DC: no visible global function definition for ‘runif’
Simu.Cond.HR: no visible global function definition for ‘rpois’
Simu.Cond.HR: no visible global function definition for ‘runif’
Simu.Cond.HR: no visible global function definition for ‘hist’
Simu.Cond.HR: no visible global function definition for ‘var’
Simu.HR: no visible global function definition for ‘rpois’
Simu.HR: no visible global function definition for ‘runif’
Simu.HR: no visible global function definition for ‘hist’
Simu.HR: no visible global function definition for ‘var’
Undefined global functions or variables:
  hist rnorm rpois runif var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "rnorm", "rpois", "runif", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 595 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘openxlsx’ ‘stringr’
  All declared Imports should be used.
Undeclared package ‘R6’ in Rd xrefs
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Undeclared packages ‘ks’, ‘evd’, ‘ismev’, ‘mixtools’, ‘evir’, ‘smoothtail’ in Rd xrefs
Found the following files/directories:
  ‘sample .nwk’
Undeclared package ‘PHENIX’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
EW : PhiP : Phi: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
BinomialCIone: no visible global function definition for ‘na.omit’
PairedCIone: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Undeclared package ‘exact2x2’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
build.mcx.obj: no visible global function definition for ‘glm’
build.mcx.obj: no visible binding for global variable ‘poisson’
build.mcx.obj: no visible global function definition for ‘fitted’
cab: no visible global function definition for ‘rbinom’
cab: no visible global function definition for ‘runif’
mcexact: no visible global function definition for ‘update’
rounded.tprob: no visible global function definition for ‘pt’
simtable.cab: no visible global function definition for ‘rbinom’
simtable.cab: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fitted glm poisson pt rbinom runif update
Consider adding
  importFrom("stats", "fitted", "glm", "poisson", "pt", "rbinom",
             "runif", "update")
to your NAMESPACE file.
File ‘exactLoglinTest/libs/exactLoglinTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘ExactData’
Undeclared package ‘tth’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 342 marked UTF-8 strings
File ‘exif/libs/exif.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘readr’ ‘tibble’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
Undeclared packages ‘tseriesChaos’, ‘rSFA’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Undeclared package ‘quantreg’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘RColorBrewer’ ‘Rcpp’ ‘e1071’ ‘foreach’ ‘gam’ ‘ggplot2’
  ‘glmnet’ ‘nnet’ ‘polspline’ ‘repmis’ ‘splines’ ‘xgboost’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
index.citations: no visible global function definition for
  ‘txtProgressBar’
read.exsic: no visible global function definition for ‘read.csv’
update.pb: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  read.csv setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "read.csv", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘rmeta’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
extfunnel: no visible global function definition for ‘qnorm’
extfunnel: no visible global function definition for ‘meta.summaries’
extfunnel: no visible global function definition for ‘flush.console’
extfunnel: no visible global function definition for ‘qt’
extfunnel: no visible global function definition for ‘dev.new’
extfunnel: no visible global function definition for ‘par’
extfunnel: no visible global function definition for ‘polygon’
extfunnel: no visible global function definition for ‘segments’
extfunnel: no visible global function definition for ‘abline’
extfunnel: no visible global function definition for ‘axis’
extfunnel: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box dev.new flush.console meta.summaries par polygon
  qnorm qt segments
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "box", "par", "polygon",
             "segments")
  importFrom("stats", "qnorm", "qt")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
bars: no visible global function definition for ‘segments’
cv.binomial: no visible binding for global variable ‘var’
cv.binomial: no visible global function definition for ‘abline’
cv.normal: no visible binding for global variable ‘var’
cv.normal: no visible global function definition for ‘abline’
cv.poisson: no visible binding for global variable ‘var’
cv.poisson: no visible global function definition for ‘abline’
plot.extlasso: no visible global function definition for ‘matplot’
plot.extlasso: no visible global function definition for ‘axis’
Undefined global functions or variables:
  abline axis matplot segments var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "segments")
  importFrom("stats", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
'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
toJavaMatrix2D: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘temp.Rdata’
bootstrapCMLE: no visible global function definition for ‘qweibull’
bootstrapCMLE: no visible binding for global variable ‘sd’
bootstrapCMLE: no visible global function definition for ‘quantile’
bootstrapCenWbMix: no visible binding for global variable ‘sd’
bootstrapCenWbMix: no visible global function definition for ‘quantile’
cenWeibullMLE: no visible global function definition for ‘sd’
expmx.p2.censor: no visible global function definition for ‘dweibull’
expmx.p2.censor: no visible global function definition for ‘pweibull’
genWbMixIni: no visible global function definition for ‘runif’
log.llh.p2.censor: no visible global function definition for ‘dweibull’
log.llh.p2.censor: no visible global function definition for ‘pweibull’
quanWbMix : t.fun: no visible global function definition for ‘pweibull’
quanWbMix: no visible global function definition for ‘uniroot’
quanWbMix.int : t.fun: no visible global function definition for
  ‘pweibull’
quanWbMix.int: no visible global function definition for ‘uniroot’
simWbMix: no visible global function definition for ‘rbinom’
simWbMix: no visible global function definition for ‘rweibull’
Undefined global functions or variables:
  dweibull pweibull quantile qweibull rbinom runif rweibull sd uniroot
Consider adding
  importFrom("stats", "dweibull", "pweibull", "quantile", "qweibull",
             "rbinom", "runif", "rweibull", "sd", "uniroot")
to your NAMESPACE file.
File ‘extWeibQuant/libs/extWeibQuant.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘exuberdata’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Rd file 'distance2point.Rd':
  \usage lines wider than 90 characters:
     distance2point(x, y, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)
  \examples lines wider than 100 characters:
     function( x, y, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight ) {

Rd file 'subtendedAngle.Rd':
  \usage lines wider than 90 characters:
     subtendedAngle(x1, y1, x2, y2, viewerDistance = 58.74, viewerHeight = 4.55, resolutionX = 1280, resolutionY = 1024, screenWidth = 33.97 ... [TRUNCATED]
  \examples lines wider than 100 characters:
     function( x1, y1, x2, y2, viewerDistance=58.74, viewerHeight=4.55, resolutionX=1280, resolutionY=1024, screenWidth=33.97, screenHeight= ... [TRUNCATED]
         d1 <- distance2point(x1, y1, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)
         d2 <- distance2point(x2, y2, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
File ‘ezglm/libs/ezglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
createFormula: no visible global function definition for ‘tail’
createFormula: no visible global function definition for ‘head’
createFormula: no visible global function definition for ‘as.formula’
ezsim: no visible global function definition for ‘runif’
plot.ezsim: no visible global function definition for ‘quantile’
plot.ezsim: no visible global function definition for ‘head’
plot.ezsim: no visible global function definition for ‘tail’
plot.ezsim: no visible binding for global variable ‘dnorm’
plot.ezsim: no visible binding for global variable ‘pdf’
plot.ezsim: no visible global function definition for ‘dev.off’
plot.ezsim : <anonymous>: no visible global function definition for
  ‘dev.new’
plot.summary.ezsim: no visible global function definition for ‘head’
plot.summary.ezsim: no visible global function definition for ‘tail’
plot.summary.ezsim: no visible binding for global variable ‘pdf’
plot.summary.ezsim: no visible global function definition for ‘dev.off’
plot.summary.ezsim : <anonymous>: no visible global function definition
  for ‘dev.new’
Undefined global functions or variables:
  as.formula dev.new dev.off dnorm head pdf quantile runif tail
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("stats", "as.formula", "dnorm", "quantile", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘lmtest’ in Rd xrefs
Undeclared package ‘future’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
gibbs2: no visible global function definition for ‘rnorm’
gibbs_sampling: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘test_30iter.RData’ ‘test_50iter.RData’ ‘test_v2_50iter.RData’
Malformed Description field: should contain one or more complete sentences.
fma: no visible global function definition for ‘factanal’
fma: no visible global function definition for ‘runif’
fma: no visible global function definition for ‘kmeans’
fma: no visible global function definition for ‘var’
fma.em.alg: no visible global function definition for ‘var’
misc : q: no visible global function definition for ‘name’
Undefined global functions or variables:
  factanal kmeans name runif var
Consider adding
  importFrom("stats", "factanal", "kmeans", "runif", "var")
to your NAMESPACE file.
Rd file 'fma.Rd':
  \usage lines wider than 90 characters:
     fma(y, k, r, x.z = NULL, x.w = NULL, it = 15, eps = 1e-04, seed = 4, scaling = FALSE, init = NULL)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘Bogota.tex’ ‘DogBreeds1.tex’
Namespaces in Imports field not imported from:
  ‘forcats’ ‘formula.tools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Undeclared package ‘SciViews’ in Rd xrefs
Note: found 5 marked Latin-1 strings
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.5Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘caTools’ ‘httr’ ‘jsonlite’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘base’ ‘data.table’
  All declared Imports should be used.
faisalconjoint: no visible global function definition for ‘barplot’
faisalconjoint: no visible global function definition for ‘text’
faisalconjoint: no visible global function definition for ‘jpeg’
faisalconjoint: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  barplot dev.off jpeg text
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "barplot", "text")
to your NAMESPACE file.
Found the following files/directories:
  ‘FCMgraph.jpg’
File ‘falcon/libs/falcon.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fame/R/windows/zzz.R’:
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section ‘Good practice’ in '?.onAttach'.
File ‘fame/libs/fame.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    help   1.0Mb
File ‘Familias/libs/Familias.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
coef.FAMILY: no visible global function definition for ‘glm’
coef.FAMILY: no visible global function definition for ‘lm’
fm2v: no visible global function definition for ‘na.omit’
l_inf_prox: no visible global function definition for ‘tail’
predict.FAMILY: no visible global function definition for ‘coef’
predict.FAMILY: no visible global function definition for ‘lm’
predict.FAMILY: no visible global function definition for ‘predict’
predict.FAMILY: no visible global function definition for ‘glm’
predict.FAMILY: no visible global function definition for ‘predict.glm’
v2fm: no visible global function definition for ‘tail’
Undefined global functions or variables:
  coef glm lm na.omit predict predict.glm tail
Consider adding
  importFrom("stats", "coef", "glm", "lm", "na.omit", "predict",
             "predict.glm")
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘impute’ ‘mnormt’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘fanc/libs/fanc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 179 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘RWeka’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘far/libs/far.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘fastAdaboost/libs/fastAdaboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘FastBandChol/libs/FastBandChol.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastclime/libs/fastclime.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘default5.eps’
File ‘fastcmh/libs/fastcmh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘fastdigest/libs/fastdigest.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  pixelfn.cpp:15:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  pixelfn.cpp:34:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  pixelfn.cpp:41:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/fasterize.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
installed size is 41.6Mb
  sub-directories of 1Mb or more:
    libs  41.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
File ‘FastGP/libs/FastGP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  FastHCS.cpp:88:5: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  FastHCS.cpp:127:5: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/FastHCS.Rcheck/00install.out’ for details.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  13.7Mb
File ‘FastHCS/libs/FastHCS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
basis_hica: no visible global function definition for ‘princomp’
energy_hica: no visible global function definition for ‘dev.new’
energy_hica: no visible global function definition for ‘points’
energy_hica: no visible global function definition for ‘legend’
Undefined global functions or variables:
  dev.new legend points princomp
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "points")
  importFrom("stats", "princomp")
to your NAMESPACE file.
installed size is 42.3Mb
  sub-directories of 1Mb or more:
    libs  42.0Mb
Package suggested but not available for checking: ‘coxKM’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’
File ‘fastmatch/libs/fastmatch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘ICSNP’, ‘ICS’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  code.cpp:64:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/fastqq.Rcheck/00install.out’ for details.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
.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
File ‘FastRWeb/libs/null.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   2.7Mb
Found the following significant warnings:
  clean.cc:18:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  clean.cc:29:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  clean.cc:70:25: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  clean.cc:74:25: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/fastTextR.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.2Mb
Namespaces in Imports field not imported from:
  ‘collapse’ ‘data.table’ ‘fst’ ‘kit’ ‘magrittr’ ‘matrixStats’
  All declared Imports should be used.
File ‘fBasics/libs/fBasics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.4Mb
File ‘FBFsearch/libs/FBFsearch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
FBN.histogramMaxima: no visible global function definition for ‘hist’
FBN.kmeans: no visible global function definition for ‘median’
FBN.kmeans: no visible global function definition for ‘kmeans’
FBNormalization: no visible global function definition for ‘read.table’
FBNormalization: no visible global function definition for ‘median’
FBNormalization: no visible global function definition for ‘hist’
FBNormalization: no visible global function definition for ‘par’
FBNormalization: no visible global function definition for ‘dev.print’
FBNormalization: no visible binding for global variable ‘bmp’
FBNormalization: no visible global function definition for ‘sd’
FBNormalization: no visible global function definition for
  ‘write.table’
medianFilter: no visible global function definition for ‘median’
Undefined global functions or variables:
  bmp dev.print hist kmeans median par read.table sd write.table
Consider adding
  importFrom("grDevices", "bmp", "dev.print")
  importFrom("graphics", "hist", "par")
  importFrom("stats", "kmeans", "median", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Rd file 'FBNormalization.Rd':
  \usage lines wider than 90 characters:
             normDataFileName = NULL, debugFlag = FALSE, plotFlag = FALSE, plotAndSaveFlag = FALSE)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  ‘RCurl’ ‘RJSONIO’ ‘XML’ ‘glmnet’ ‘httr’ ‘speedglm’ ‘tcltk’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘MASS’ ‘combinat’ ‘glmnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fcd.cluster: no visible global function definition for ‘kmeans’
fcd.start: no visible global function definition for ‘ginv’
fcd.start: no visible global function definition for ‘glmnet’
gen.dcbm: no visible global function definition for ‘rbinom’
gen.sbm: no visible global function definition for ‘rbinom’
mis.cluster: no visible global function definition for ‘permn’
spectral.clustering: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  ginv glmnet kmeans permn rbinom
Consider adding
  importFrom("stats", "kmeans", "rbinom")
to your NAMESPACE file.
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following significant warnings:
  func.cpp:124:17: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/fclust.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    3.5Mb
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.Rprofile’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Note: found 75 marked UTF-8 strings
installed size is 40.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  38.6Mb
installed size is 62.7Mb
  sub-directories of 1Mb or more:
    libs  62.4Mb
Namespaces in Imports field not imported from:
  ‘FastGP’ ‘MASS’ ‘fdapace’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.4Mb
Note: found 76 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘usethis’ ‘utils’
  All declared Imports should be used.
Note: found 1 marked Latin-1 string
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 3 marked Latin-1 strings
  Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘data.table’ ‘ggplot2’ ‘randomcoloR’ ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘FD/libs/FD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘vert.txt’
FDRreg: no visible global function definition for ‘dnorm’
colnormalize: no visible global function definition for ‘sd’
efron: no visible global function definition for ‘median’
efron: no visible global function definition for ‘hist’
efron: no visible global function definition for ‘glm’
efron: no visible binding for global variable ‘poisson’
efron: no visible global function definition for ‘qchisq’
efron: no visible global function definition for ‘predict’
efron: no visible global function definition for ‘quantile’
efron: no visible global function definition for ‘lm’
efron: no visible global function definition for ‘coef’
make.bspline.matrix: no visible global function definition for
  ‘quantile’
plotFDR: no visible global function definition for ‘hist’
plotFDR: no visible global function definition for ‘par’
plotFDR: no visible global function definition for ‘axis’
plotFDR: no visible global function definition for ‘lines’
plotFDR: no visible global function definition for ‘legend’
plotFDR: no visible global function definition for ‘rug’
plotFDR: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis coef dnorm glm hist legend lines lm median par poisson predict
  qchisq quantile rug sd title
Consider adding
  importFrom("graphics", "axis", "hist", "legend", "lines", "par", "rug",
             "title")
  importFrom("stats", "coef", "dnorm", "glm", "lm", "median", "poisson",
             "predict", "qchisq", "quantile", "sd")
to your NAMESPACE file.
File ‘FDRreg/libs/FDRreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘treesAll.txt’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./vector_converter.h:249:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ./vector_converter.h:259:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/FeatureHashing.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘lattice’ ‘randomForest’ ‘tibble’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 20 marked UTF-8 strings
File ‘fechner/libs/fechner.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Note: found 43825 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘prettycode’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘FFD/libs/FFD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘gridExtra’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
FFieldPtRepDemo: no visible global function definition for ‘ggplot’
FFieldPtRepDemo: no visible binding for global variable ‘mtcars’
FFieldPtRepDemo: no visible global function definition for ‘aes’
FFieldPtRepDemo: no visible binding for global variable ‘mpg’
FFieldPtRepDemo: no visible global function definition for ‘geom_point’
FFieldPtRepDemo: no visible global function definition for ‘geom_text’
FFieldPtRepDemo: no visible global function definition for ‘ggtitle’
FFieldPtRepDemo: no visible global function definition for
  ‘geom_segment’
FFieldPtRepDemo: no visible global function definition for
  ‘grid.arrange’
Undefined global functions or variables:
  aes geom_point geom_segment geom_text ggplot ggtitle grid.arrange mpg
  mtcars
Consider adding
  importFrom("datasets", "mtcars")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
checkRd: (7) ff.rd:262: invalid email address: christian\_glaeser@gmx.de
Namespace in Imports field not imported from: ‘nflreadr’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
ftest: no visible global function definition for ‘wilcox.test’
ftest: no visible global function definition for ‘t.test’
Undefined global functions or variables:
  t.test wilcox.test
Consider adding
  importFrom("stats", "t.test", "wilcox.test")
to your NAMESPACE file.
File ‘fGarch/libs/fGarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
fgeasy: no visible global function definition for ‘dist’
fgeasy : cor.est: no visible global function definition for ‘cor.test’
fgeasy: no visible binding for global variable ‘var’
fgperm : runrand: no visible global function definition for ‘runif’
fgperm : runrand: no visible global function definition for ‘ave’
fgploc : runrand: no visible global function definition for ‘runif’
fgploc : runrand: no visible global function definition for ‘ave’
fyshuffle: no visible global function definition for ‘runif’
plot.fg: no visible global function definition for ‘par’
plot.fg: no visible global function definition for ‘segments’
plot.fg: no visible binding for global variable ‘quantile’
plot.fg: no visible global function definition for ‘abline’
plot.fg: no visible global function definition for ‘axis’
summary.fg: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  abline ave axis cor.test dist par quantile runif segments var
Consider adding
  importFrom("graphics", "abline", "axis", "par", "segments")
  importFrom("stats", "ave", "cor.test", "dist", "quantile", "runif",
             "var")
to your NAMESPACE file.
File ‘FGSG/libs/FGSG.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Undeclared packages ‘MLEcens’, ‘Icens’ in Rd xrefs
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
Package suggested but not available for checking: ‘MicrobeDS’
installed size is 36.9Mb
  sub-directories of 1Mb or more:
    libs  35.2Mb
Namespace in Imports field not imported from: ‘phyloseq’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘attempt’ ‘glue’
  All declared Imports should be used.
fieldsim: no visible global function definition for ‘rnorm’
midpoint: no visible global function definition for ‘rnorm’
setAtlas_under: no visible global function definition for ‘runif’
setCovf_under : Ibeta: no visible global function definition for
  ‘pbeta’
visualize: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette pbeta rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "pbeta", "rnorm", "runif")
to your NAMESPACE file.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.5Mb
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘filehash’ ‘DBI’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘RSQLite’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createSQLite: no visible global function definition for ‘dbDriver’
createSQLite: no visible global function definition for ‘dbConnect’
createSQLite: no visible global function definition for
  ‘dbUnloadDriver’
createSQLite: no visible global function definition for ‘dbGetQuery’
initializeSQLite: no visible global function definition for ‘dbDriver’
initializeSQLite: no visible global function definition for ‘dbConnect’
initializeSQLite: no visible global function definition for ‘new’
dbDelete,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
dbDisconnect,filehashSQLite: no visible global function definition for
  ‘dbUnloadDriver’
dbFetch,filehashSQLite-character: no visible global function definition
  for ‘dbGetQuery’
dbInsert,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
dbList,filehashSQLite: no visible global function definition for
  ‘dbGetQuery’
dbMultiFetch,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
Undefined global functions or variables:
  dbConnect dbDriver dbGetQuery dbUnloadDriver new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘myTestDB’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rclipboard’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘FinePop’ 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’
Namespace in Imports field not imported from: ‘vctrs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
lsmacof: no visible global function definition for ‘cmdscale’
plotInc: no visible global function definition for ‘rainbow’
prepareCalib: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cmdscale lm rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "cmdscale", "lm")
to your NAMESPACE file.
File ‘FisHiCal/libs/FisHiCal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 7 marked UTF-8 strings
File ‘fishMod/libs/fishMod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
fishmove : coefs: no visible global function definition for ‘coef’
fishmove : coefs: no visible global function definition for ‘pf’
fishmove: no visible global function definition for ‘lm’
fishmove: no visible global function definition for ‘predict.lm’
fishmove.estimate: no visible global function definition for ‘quantile’
fishmove.estimate : ddoublenorm: no visible global function definition
  for ‘dnorm’
fishmove.query: no visible global function definition for ‘hasArg’
fishmove.query : f: no visible global function definition for ‘pnorm’
fishmove.query: no visible global function definition for ‘uniroot’
pdk: no visible global function definition for ‘hasArg’
pdk : eq: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  coef dnorm hasArg lm pf pnorm predict.lm quantile uniroot
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "coef", "dnorm", "lm", "pf", "pnorm", "predict.lm",
             "quantile", "uniroot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    lib    8.7Mb
    libs  15.2Mb
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘leaps’ ‘ltsa’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘bestglm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'GetLeapsAR.Rd':
  \usage lines wider than 90 characters:
     GetLeapsAR(z, lag.max = 15, Criterion = "UBIC", Best = 3, Candidates=5, t="default", ExactQ=FALSE)

Rd file 'PlotARSdf.Rd':
  \usage lines wider than 90 characters:
     PlotARSdf(phi = NULL, theta = NULL, units = "radial", logSdf = FALSE, InnovationVariance = 1, main = NULL, sub = NULL, lwd=3, col="blue ... [TRUNCATED]

Rd file 'SelectModel.Rd':
  \usage lines wider than 90 characters:
     SelectModel(z, lag.max = 15, ARModel = c("AR", "ARz", "ARp"), Criterion = "default", Best = 3, Candidates = 5, t="default")

Rd file 'UnitRootTest.Rd':
  \usage lines wider than 90 characters:
     UnitRootTest(z, method = c("MLE", "ExactMLE", "LS", "All"), statistic = c("Z", "T"), NumBoot = 1000, PValueMethod = c("DH", "ET"))

These lines will be truncated in the PDF manual.
Undeclared package ‘zoo’ in Rd xrefs
File ‘FitAR/libs/FitAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘FitAR-Ex.R’ failed
The error most likely occurred in:

> ### Name: AcfPlot
> ### Title: Basic ACF Plotting
> ### Aliases: AcfPlot
> ### Keywords: ts
> 
> ### ** Examples
> 
> #
> #Simple example, plot acf for AR(1)
>  phi<-0.8
>  maxLag<-20
>  g<-phi^(1:maxLag)
>  AcfPlot(g)
>  AcfPlot(g, LagZeroQ=FALSE)
> #
> # Plot the sample inverse partial autocorrelations. 
> # On the basis of this plot, Cleveland (1972) suggested an ARp(1,2,7)
> # for this data
> "InverseAcf" <-
+ function(z, p=15){
+ g<-TacvfMA(GetFitARpLS(z-mean(z),1:p)$phiHat, lag.max=p)
+ g/g[1]
+ }
> #
> data(SeriesA)
> AcfPlot(InverseAcf(SeriesA),LagZeroQ=FALSE)
Error in length(pvec) == 0 || pvec == 0 : 
  'length = 15' in coercion to 'logical(1)'
Calls: AcfPlot -> plot -> InverseAcf -> TacvfMA -> GetFitARpLS
Execution halted
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
Undeclared package ‘conicfit’ in Rd xrefs
Package required but not available: ‘ghyp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Undeclared packages ‘BinaryEPPM’, ‘extraDistr’, ‘triangle’ in Rd xrefs
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'GLDEX', 'reliaR'
Package suggested but not available for checking: ‘RSvgDevice’
'library' or 'require' calls in package code:
  ‘devEMF’ ‘doMC’ ‘foreach’ ‘grDevices’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘modelfile.dat’ ‘plots’ ‘scorefile.dat’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fivethirtyeightdata’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
Note: found 584 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.6Mb
    libs   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘curl’ ‘mathjaxr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘evaluate’ ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   2.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
File ‘flashClust/libs/flashClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘xtable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Note: found 82 marked UTF-8 strings
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘mixture’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 109.7Mb
  sub-directories of 1Mb or more:
    libs  109.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘pbapply’
  All declared Imports should be used.
File ‘flock/libs/flock.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
RIind: no visible global function definition for ‘aggregate’
RIind: no visible binding for global variable ‘sd’
RIpop: no visible global function definition for ‘aggregate’
RIpop: no visible binding for global variable ‘sd’
SI: no visible global function definition for ‘sd’
SI2: no visible global function definition for ‘sd’
SI3: no visible global function definition for ‘aggregate’
SI3: no visible global function definition for ‘pairs’
SI3: no visible global function definition for ‘cor’
SI4: no visible global function definition for ‘aggregate’
SI4: no visible global function definition for ‘sd’
fCV: no visible global function definition for ‘sd’
Undefined global functions or variables:
  aggregate cor pairs sd
Consider adding
  importFrom("graphics", "pairs")
  importFrom("stats", "aggregate", "cor", "sd")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
GCV: no visible global function definition for ‘lm’
GCV: no visible global function definition for ‘resid’
ffplot: no visible global function definition for ‘par’
ffplot: no visible global function definition for ‘points’
ffplot: no visible global function definition for ‘legend’
flowfield: no visible global function definition for ‘write.table’
gpr: no visible global function definition for ‘quantile’
gpr: no visible global function definition for ‘var’
smoothp: no visible global function definition for ‘lm’
smoothp: no visible global function definition for ‘predict’
smoothp: no visible global function definition for ‘resid’
smoothp: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  legend lm optimize par points predict quantile resid var write.table
Consider adding
  importFrom("graphics", "legend", "par", "points")
  importFrom("stats", "lm", "optimize", "predict", "quantile", "resid",
             "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Undeclared package ‘Kendall’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
GNU make is a SystemRequirements.
export: no visible global function definition for ‘write.table’
flux.odae : <anonymous>: no visible global function definition for
  ‘combn’
mf.flux: no visible global function definition for ‘runsd’
plot.fluss: no visible global function definition for ‘dev.new’
plot.fluss: no visible global function definition for ‘pdf’
plot.fluss: no visible global function definition for ‘dev.off’
plot.fluxes: no visible global function definition for ‘dev.new’
plot.fluxes: no visible global function definition for ‘devAskNewPage’
plot.fluxes: no visible global function definition for ‘pdf’
plot.fluxes: no visible global function definition for ‘dev.off’
plot.fluxxes: no visible global function definition for ‘dev.new’
plot.fluxxes: no visible global function definition for ‘devAskNewPage’
plot.fluxxes: no visible global function definition for ‘pdf’
plot.fluxxes: no visible global function definition for ‘dev.off’
reco.bulk : get.out: no visible global function definition for
  ‘boxplot.stats’
Undefined global functions or variables:
  boxplot.stats combn dev.new dev.off devAskNewPage pdf runsd
  write.table
Consider adding
  importFrom("grDevices", "boxplot.stats", "dev.new", "dev.off",
             "devAskNewPage", "pdf")
  importFrom("utils", "combn", "write.table")
to your NAMESPACE file.
Undeclared package ‘HMR’ in Rd xrefs
Found the following files/directories:
  ‘flux.CH4.txt’
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘neurobase’
Error(s) in re-building vignettes:
--- re-building ‘projection_scrubbing.rmd’ using rmarkdown
Quitting from lines 84-86 (projection_scrubbing.rmd) 
Error: processing vignette 'projection_scrubbing.rmd' failed with diagnostics:
there is no package called 'neurobase'
--- failed re-building ‘projection_scrubbing.rmd’

SUMMARY: processing the following file failed:
  ‘projection_scrubbing.rmd’

Error: Vignette re-building failed.
Execution halted
BSOptionValue: no visible global function definition for ‘pnorm’
ImpliedVol: no visible global function definition for ‘uniroot’
callFMstable: no visible global function definition for ‘integrate’
fitGivenQuantile: no visible global function definition for ‘uniroot’
matchQuartiles: no visible global function definition for ‘optim’
putFMstable: no visible global function definition for ‘integrate’
standardStableQuantile: no visible global function definition for
  ‘qnorm’
tailsGstable: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate optim pnorm qnorm uniroot
Consider adding
  importFrom("stats", "integrate", "optim", "pnorm", "qnorm", "uniroot")
to your NAMESPACE file.
File ‘FMStable/libs/FMStable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (7) KL.dist.Rd:35: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) KL.divergence.Rd:36: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) crossentropy.Rd:27: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) entropy.Rd:19: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) get.knn.Rd:43: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) knn.Rd:30: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) knn.cv.Rd:33: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) knn.dist.Rd:28: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) knn.index.Rd:28: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) knn.reg.Rd:49: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) mutual_information.Rd:28: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) ownn.rd:27: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) print.knnRegCV.Rd:19: invalid email address: lishengqiao@yahoo.com.
'LazyData' is specified without a 'data' directory
File ‘fNonlinear/libs/fNonlinear.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘XICOR’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 32.0Mb
  sub-directories of 1Mb or more:
    libs  31.0Mb
Note: found 41 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
checkRd: (7) analyse.list.Rd:32: \item in \value must have non-empty label
checkRd: (7) analyse.list.Rd:33: \item in \value must have non-empty label
checkRd: (7) analyse.list.Rd:34: \item in \value must have non-empty label
checkRd: (7) analyse.seq.Rd:29: \item in \value must have non-empty label
checkRd: (7) analyse.seq.Rd:30: \item in \value must have non-empty label
checkRd: (7) analyse.seq.Rd:31: \item in \value must have non-empty label
'LazyData' is specified without a 'data' directory
Note: found 234 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘ForecastCombinations’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘decomposedPSF’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  ‘combinat’ ‘genetics’
  Please remove these calls from your code.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘forensic/R/zzz.R’:
  .First.lib calls:
    cat("## Statistical Methods in Forensic Genetics \n")
    cat("## The work was supported by the project 1M06014 of the Ministry of \n        Education, Youth and Sports of the Czech Republic. \n")
    require(genetics, quietly = TRUE)
    require(combinat, quietly = TRUE)

Package startup functions should not change the search path.
Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
Malformed Description field: should contain one or more complete sentences.
File ‘forensim/libs/forensim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘sim.txt’
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘blockCV’ ‘patchwork’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rgeos’ ‘viridis’
  All declared Imports should be used.
Undeclared package ‘rgdal’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgKitten’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tibble’ ‘viridis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
ForImp: no visible global function definition for ‘head’
ForImp: no visible global function definition for ‘tail’
ForImp: no visible global function definition for ‘dist’
medianimp: no visible global function definition for ‘quantile’
rancatmat: no visible global function definition for ‘runif’
transfmatcat: no visible global function definition for ‘qnorm’
transfmatcat: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dist head qnorm quantile runif sd tail
Consider adding
  importFrom("stats", "dist", "qnorm", "quantile", "runif", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
INFCvpe: no visible binding for global variable ‘INFCstats’
INFCvpe: no visible binding for global variable ‘INFCdomain’
Undefined global functions or variables:
  INFCdomain INFCstats
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ForwardSearch.fit: no visible global function definition for ‘glm.fit’
ForwardSearch.plot: no visible global function definition for ‘lines’
ForwardSearch.pointwise.asymptotics: no visible global function
  definition for ‘qnorm’
ForwardSearch.pointwise.asymptotics: no visible global function
  definition for ‘dnorm’
Undefined global functions or variables:
  dnorm glm.fit lines qnorm
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "dnorm", "glm.fit", "qnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘spatstat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘LaplacesDemon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
File ‘fpow/libs/fpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘fable’ ‘fabletools’ ‘feasts’ ‘ggplot2’ ‘lubridate’ ‘tibble’
  ‘tidyr’ ‘tsibble’ ‘tsibbledata’ ‘urca’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘fractional/libs/fractional.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    help   2.2Mb
    libs   6.4Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'library' or 'require' calls to packages already attached by Depends:
  ‘CCP’ ‘MASS’ ‘calibrate’ ‘corpcor’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘CCP’ ‘MASS’ ‘calibrate’ ‘corpcor’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
custom.draw.circle: no visible global function definition for ‘lines’
frcc: no visible binding for global variable ‘sd’
frcc: no visible global function definition for ‘cor.shrink’
frcc: no visible global function definition for ‘cor’
frcc: no visible global function definition for ‘p.asym’
generate_multivariate_normal_sample: no visible global function
  definition for ‘mvrnorm’
plot_units: no visible binding for global variable ‘sd’
plot_units: no visible global function definition for ‘points’
plot_units: no visible global function definition for ‘textxy’
plot_variables: no visible global function definition for ‘points’
plot_variables: no visible global function definition for ‘textxy’
plot_variables: no visible global function definition for ‘segments’
Undefined global functions or variables:
  cor cor.shrink lines mvrnorm p.asym points sd segments textxy
Consider adding
  importFrom("graphics", "lines", "points", "segments")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Undeclared package ‘DoE.wrapper’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘frictionless.Rmd’ using rmarkdown
Quitting from lines 36-37 (frictionless.Rmd) 
Error: processing vignette 'frictionless.Rmd' failed with diagnostics:
Can't find file at `https://zenodo.org/record/5879096/files/datapackage.json`.
--- failed re-building ‘frictionless.Rmd’

SUMMARY: processing the following file failed:
  ‘frictionless.Rmd’

Error: Vignette re-building failed.
Execution halted
Note: found 50 marked UTF-8 strings
Undeclared package ‘covr’ in Rd xrefs
Package suggested but not available for checking: ‘dggrids’
installed size is 65.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.7Mb
    libs  57.7Mb
Undeclared packages ‘frm’, ‘frmpd’ in Rd xrefs
Undeclared packages ‘frm’, ‘frmhet’ in Rd xrefs
Packages in Depends field not imported from:
  ‘Rmpfr’ ‘partitions’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Bell : nways: no visible global function definition for ‘setparts’
Bell: no visible global function definition for ‘restrictedparts’
CalIncLapInt : Deriv: no visible global function definition for ‘D’
CalIncLapInt: no visible global function definition for ‘is.whole’
CalIncLapInt: no visible global function definition for ‘mpfr’
CalIncLapInt: no visible global function definition for ‘chooseMpfr’
derivErfc : Deriv: no visible global function definition for ‘D’
derivErfc : Erfc: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  D chooseMpfr is.whole mpfr pnorm restrictedparts setparts
Consider adding
  importFrom("stats", "D", "pnorm")
to your NAMESPACE file.
Undeclared packages ‘frmhet’, ‘frmpd’ in Rd xrefs
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  29.8Mb
ROCscore: no visible global function definition for ‘par’
ROCscore: no visible global function definition for ‘axis’
ROCscore: no visible global function definition for ‘mtext’
ROCscore: no visible global function definition for ‘legend’
alphafrontier.2d: no visible global function definition for ‘par’
alphafrontier.2d: no visible global function definition for ‘polygon’
alphafrontier.2d: no visible global function definition for ‘lines’
alphafrontier.2d: no visible global function definition for ‘points’
alphafrontier.3d: no visible global function definition for ‘layout’
alphafrontier.3d: no visible global function definition for ‘barplot’
alphafrontier.3d: no visible global function definition for ‘axis’
alphafrontier.3d: no visible global function definition for ‘lines’
alphafrontier.3d: no visible global function definition for ‘na.omit’
ordermfrontier.2d: no visible global function definition for ‘par’
ordermfrontier.2d: no visible global function definition for ‘polygon’
ordermfrontier.2d: no visible global function definition for ‘lines’
ordermfrontier.2d: no visible global function definition for ‘points’
ordermscore.boot: no visible global function definition for ‘sd’
Undefined global functions or variables:
  axis barplot layout legend lines mtext na.omit par points polygon sd
Consider adding
  importFrom("graphics", "axis", "barplot", "layout", "legend", "lines",
             "mtext", "par", "points", "polygon")
  importFrom("stats", "na.omit", "sd")
to your NAMESPACE file.
File ‘frontiles/libs/frontiles.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘chillR’ in Rd xrefs
Undeclared package ‘FSA’ in Rd xrefs
Packages suggested but not available for checking: 'foba', 'rrlda'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’ ‘neuralnet’ ‘rpart’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 39 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘fts/libs/fts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘snowfall’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fugeR.evo: no visible global function definition for ‘runif’
fugeR.sfRun: no visible global function definition for ‘sfInit’
fugeR.sfRun: no visible global function definition for ‘sfLibrary’
fugeR.sfRun: no visible global function definition for ‘sfExport’
fugeR.sfRun: no visible global function definition for ‘sfLapply’
fugeR.sfRun: no visible global function definition for ‘sfStop’
Undefined global functions or variables:
  runif sfExport sfInit sfLapply sfLibrary sfStop
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘fugeR/libs/fugeR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Undeclared package ‘future’ in Rd xrefs
Note: found 120 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘fUnitRoots/libs/fUnitRoots.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FNN’ ‘igraph’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  ‘RUnit’ ‘futile.options’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.validateGuardExpression: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'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’
Undeclared package ‘globals’ in Rd xrefs
File ‘futureheatwaves/libs/futureheatwaves.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
NeedsCompilation field must take value ‘yes’ or ‘no’
'library' or 'require' call to ‘splines’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gensurf: no visible global function definition for ‘persp’
gensurf: no visible global function definition for ‘rainbow’
plotMF: no visible global function definition for ‘plot.new’
plotMF: no visible global function definition for ‘plot.window’
plotMF: no visible global function definition for ‘runif’
plotMF: no visible global function definition for ‘predict’
plotMF: no visible global function definition for ‘interpSpline’
plotMF: no visible global function definition for ‘lines’
plotMF: no visible global function definition for ‘text’
plotMF: no visible global function definition for ‘title’
plotMF: no visible global function definition for ‘axis’
plotMF: no visible global function definition for ‘box’
Undefined global functions or variables:
  axis box interpSpline lines persp plot.new plot.window predict
  rainbow runif text title
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "persp", "plot.new",
             "plot.window", "text", "title")
  importFrom("stats", "predict", "runif")
to your NAMESPACE file.
Rd file 'newFIS.Rd':
  \usage lines wider than 90 characters:
     newFIS(FISName, FISType = "mamdani", version = "1.0", andMethod = "min", orMethod = "max", impMethod = "min", aggMethod = "max", defuzz ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Undeclared package ‘cffdrs’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘MASS’ ‘igraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DBNScoreStep1: no visible global function definition for ‘lm’
DBNScoreStep1: no visible global function definition for ‘rlm’
DBNScoreStep1: no visible global function definition for ‘pt’
DBNScoreStep2: no visible global function definition for ‘lm’
DBNScoreStep2: no visible global function definition for ‘rlm’
DBNScoreStep2: no visible global function definition for ‘pt’
SimulGeneExpressionAR1: no visible global function definition for
  ‘rnorm’
SimulGeneExpressionAR1: no visible global function definition for ‘ts’
SimulNetworkAdjMatrix: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  lm pt rlm rnorm runif ts
Consider adding
  importFrom("stats", "lm", "pt", "rnorm", "runif", "ts")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ArrayBin’
crossover: no visible global function definition for ‘runif’
exchangeSols: no visible global function definition for ‘runif’
fps: no visible global function definition for ‘runif’
mutation: no visible global function definition for ‘runif’
plotBicluster: no visible global function definition for ‘gray’
plotBicluster: no visible global function definition for ‘heatmap’
reproduction: no visible global function definition for ‘runif’
Undefined global functions or variables:
  gray heatmap runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("stats", "heatmap", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  proglikelihood.cc:279:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  proglikelihood.cc:368:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  proglikelihood.cc:371:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/gadget2.Rcheck/00install.out’ for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    bin   7.2Mb
FPTsimul: no visible global function definition for ‘runif’
histplot: no visible global function definition for ‘dev.new’
histplot: no visible global function definition for ‘hist’
histplot: no visible global function definition for ‘par’
histplot: no visible global function definition for ‘legend’
mdt: no visible binding for global variable ‘deltat’
plot.FPTdensity: no visible global function definition for ‘dev.new’
res_summary: no visible global function definition for ‘write.table’
res_summary: no visible global function definition for ‘sd’
res_summary: no visible global function definition for ‘median’
vdt: no visible binding for global variable ‘deltat’
Undefined global functions or variables:
  deltat dev.new hist legend median par runif sd write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "legend", "par")
  importFrom("stats", "deltat", "median", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘results_Wiener1.out’
Note: found 19 marked UTF-8 strings
File ‘gafit/libs/gafit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘maptools’
  All declared Imports should be used.
CI.RMSEA: no visible global function definition for ‘qchisq’
CI.RMSEA: no visible global function definition for ‘pchisq’
GAIPE.RMSEA: no visible global function definition for ‘par’
GAIPE.RMSEA: no visible global function definition for ‘abline’
GAIPE.RMSEA: no visible global function definition for ‘colors’
GAIPE.RMSEA: no visible global function definition for ‘text’
GAIPE.RMSEA: no visible global function definition for ‘arrows’
GAIPE.RMSEA: no visible global function definition for ‘points’
GAIPE.RMSEA: no visible global function definition for ‘axis’
GAIPE.RMSEA: no visible global function definition for ‘lines’
GAIPE.RMSEA: no visible global function definition for ‘legend’
GAIPE.RMSEA: no visible global function definition for ‘pchisq’
GAIPE.RMSEA: no visible global function definition for ‘qchisq’
GAIPE.RMSEA: no visible global function definition for ‘mtext’
GAIPE.RMSEA: no visible global function definition for ‘title’
PA.RMSEA: no visible global function definition for ‘pchisq’
PA.RMSEA: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  abline arrows axis colors legend lines mtext par pchisq points qchisq
  text title
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "abline", "arrows", "axis", "legend", "lines",
             "mtext", "par", "points", "text", "title")
  importFrom("stats", "pchisq", "qchisq")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘gargle’ ‘getProxy’ ‘rappsflyer’ ‘rfacebookstat’ ‘rgoogleads’
  ‘rmytarget’ ‘rvkstat’ ‘ryandexdirect’ ‘rym’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘webshot’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
cvriskMSM: no visible global function definition for ‘predict’
plotcvriskMSM: no visible binding for global variable ‘lines’
plotcvriskMSM: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines predict
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "predict")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘gamlss’ in Rd xrefs
Undeclared packages ‘gamlss.dist’, ‘gamlss.add’ in Rd xrefs
Package in Depends field not imported from: ‘gamlss’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘gamlss:::.gamlss.bi.list’
  See the note in ?`:::` about the use of this operator.
finterp.data.frame: no visible global function definition for
  ‘as.formula’
finterp.data.frame: no visible global function definition for ‘terms’
finterp.data.frame: no visible global function definition for
  ‘model.matrix’
finterp.data.frame: no visible global function definition for
  ‘model.frame’
finterp.default: no visible global function definition for ‘terms’
finterp.default: no visible global function definition for
  ‘model.matrix’
finterp.default: no visible global function definition for
  ‘model.frame’
gamlss.nl: no visible global function definition for ‘nlm’
nl: no visible global function definition for ‘is’
nlgamlss: no visible global function definition for ‘NO’
nlgamlss: no visible global function definition for ‘as.gamlss.family’
nlgamlss: no visible global function definition for ‘nlm’
nlgamlss: no visible global function definition for ‘cov2cor’
summary.nlgamlss: no visible global function definition for ‘coef’
summary.nlgamlss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Undeclared package ‘gamlss.dist’ in Rd xrefs
Undeclared package ‘hyperSpec’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   4.0Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Found the following significant warnings:
  genope.cpp:963:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  genope.cpp:1400:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/GA.Rcheck/00install.out’ for details.
installed size is 47.7Mb
  sub-directories of 1Mb or more:
    doc   44.4Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.9Mb
installed size is 57.5Mb
  sub-directories of 1Mb or more:
    libs  57.0Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 64.7Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     61.3Mb
Undeclared package ‘RcppEigen’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'flowWorkspaceData', 'ncdfFlow'
Namespace in Imports field not imported from: ‘tools’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
File ‘gausscov/libs/gausscov.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘fortunes’, ‘rmsfact’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘orthopolynom’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘orthopolynom’ ‘polynom’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
contindic.gb2: no visible global function definition for ‘contour’
contindic.gb2: no visible global function definition for ‘box’
contindic.gb2: no visible global function definition for ‘mtext’
contprof.gb2: no visible global function definition for ‘image’
contprof.gb2: no visible global function definition for ‘heat.colors’
contprof.gb2: no visible global function definition for ‘contour’
contprof.gb2: no visible global function definition for ‘text’
contprof.gb2: no visible global function definition for ‘box’
dplot.cavgb2: no visible global function definition for ‘par’
dplot.cavgb2: no visible global function definition for ‘curve’
dplot.cavgb2: no visible global function definition for ‘legend’
dplot.cavgb2: no visible global function definition for ‘lines’
dplot.cgb2: no visible global function definition for ‘curve’
dplot.cgb2: no visible global function definition for ‘lines’
dplot.cgb2: no visible global function definition for ‘legend’
plotsML.gb2: no visible global function definition for ‘par’
plotsML.gb2: no visible global function definition for ‘abline’
plotsML.gb2: no visible global function definition for ‘curve’
plotsML.gb2: no visible global function definition for ‘legend’
saveplot : <local>: no visible global function definition for ‘dev.set’
saveplot : <local>: no visible global function definition for
  ‘dev.print’
saveplot : <local>: no visible binding for global variable ‘pdf’
Undefined global functions or variables:
  abline box contour curve dev.print dev.set heat.colors image legend
  lines mtext par pdf text
Consider adding
  importFrom("grDevices", "dev.print", "dev.set", "heat.colors", "pdf")
  importFrom("graphics", "abline", "box", "contour", "curve", "image",
             "legend", "lines", "mtext", "par", "text")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Found the following files/directories:
  ‘checkdata.csv’ ‘gbmforest.sas’
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  12.0Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘gbp/libs/gbp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package 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.
coeplot: no visible global function definition for ‘axis’
coeplot: no visible global function definition for ‘lines’
coeplot: no visible global function definition for ‘title’
coeplot: no visible global function definition for ‘legend’
corplot: no visible global function definition for ‘par’
corplot: no visible global function definition for ‘pairs’
corplot: no visible global function definition for ‘strwidth’
lm.estimate: no visible global function definition for ‘as.formula’
lm.estimate: no visible global function definition for ‘glm’
panel.cor: no visible global function definition for ‘par’
panel.cor: no visible global function definition for ‘cor’
panel.cor: no visible global function definition for ‘strwidth’
panel.cor: no visible global function definition for ‘text’
panel.smooth.r: no visible global function definition for ‘par’
panel.smooth.r: no visible global function definition for ‘points’
panel.smooth.r: no visible global function definition for ‘lines’
posplot: no visible global function definition for ‘par’
posplot: no visible global function definition for ‘barplot’
posplot: no visible global function definition for ‘points’
Undefined global functions or variables:
  as.formula axis barplot cor glm legend lines pairs par points
  strwidth text title
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "pairs",
             "par", "points", "strwidth", "text", "title")
  importFrom("stats", "as.formula", "cor", "glm")
to your NAMESPACE file.
gcat.test: no visible global function definition for ‘pnorm’
generate_sub: no visible global function definition for ‘runif’
pfcn: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm runif
Consider adding
  importFrom("stats", "pnorm", "runif")
to your NAMESPACE file.
File ‘gCat/libs/gCat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘gputools’
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gcmr’
Unknown package ‘gcmr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘arm’ ‘usethis’
  All declared Imports should be used.
File ‘GCPM/libs/GCPM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    libs    26.3Mb
checkRd: (7) rename.vars.Rd:50: invalid email address: macq\@llnl.gov
Undeclared package ‘reshape’ in Rd xrefs
Running examples in ‘gdata-Ex.R’ failed
The error most likely occurred in:

> ### Name: is.what
> ### Title: Run Multiple is.* Tests on a Given Object
> ### Aliases: is.what
> ### Keywords: classes NA programming error utilities
> 
> ### ** Examples
> 
> is.what(pi)
[1] "is.atomic"  "is.double"  "is.finite"  "is.numeric" "is.vector" 
> is.what(NA, verbose=TRUE)
                    is
is.array             .
is.atomic            T
is.call              .
is.character         .
is.complex           .
is.data.frame        .
is.double            .
is.environment       .
is.expression        .
is.factor            .
is.finite            .
is.function          .
is.hashtab           .
is.infinite          .
is.integer           .
is.language          .
is.leaf              .
is.levelsMap         .
is.list              .
is.listLevelsMap     .
is.logical           T
is.matrix            .
is.mts               .
is.na                T
is.na.POSIXlt        T
is.na.data.frame     T
is.name              .
is.nan               .
is.null              .
is.numeric           .
is.numeric.Date      .
is.numeric.POSIXt    .
is.numeric.difftime  .
is.numeric_version   .
is.object            .
is.object_sizes      .
is.ordered           .
is.package_version   .
is.pairlist          .
is.primitive         .
is.qr                .
is.raster            .
is.raw               .
is.recursive         .
is.relistable        .
is.stepfun           .
is.symbol            .
is.table             .
is.ts                .
is.tskernel          .
is.unsorted          .
is.vector            T
> is.what(lm(1~1))
Error in !is.logical(result) || is.na(result) : 
  'length = 11' in coercion to 'logical(1)'
Calls: is.what
Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Undeclared package ‘nloptr’ in Rd xrefs
Note: found 1 marked UTF-8 string
Found the following significant warnings:
  gdpc_auxfunc.cpp:79:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/gdpc.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘badger’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lifecycle’
  All declared Imports should be used.
File ‘GEEaSPU/libs/GEEaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (7) genZcor.Rd:22: \item in \value must have non-empty label
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
Undeclared package ‘TreeSim’ in Rd xrefs
Namespace in Imports field not imported from: ‘survAUC’
  All declared Imports should be used.
File ‘gelnet/libs/gelnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.5Mb
    libs      1.1Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘pracma’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Undeclared package ‘poibin’ in Rd xrefs
genmvnorm: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘genderdata’
Undeclared package ‘mmap’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘R.utils’ ‘markdown’
  All declared Imports should be used.
t1p1: no visible global function definition for ‘var’
t1p1: no visible global function definition for ‘pt’
t1p2: no visible global function definition for ‘pt’
Undefined global functions or variables:
  pt var
Consider adding
  importFrom("stats", "pt", "var")
to your NAMESPACE file.
Rd file 'flexorhtest.Rd':
  \examples lines wider than 100 characters:
          plot(x,y, main="Location and Strong Order Restrictions",cex.axis=1.5, cex.lab=1.5, cex.main=1.5, cex=1.5)

These lines will be truncated in the PDF manual.
Note: found 123 marked UTF-8 strings
load.genelist: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
Rd file 'geneListPie-package.Rd':
  \examples lines wider than 100 characters:
     glist<-c("ABCB7","ABCF1","ABHD2","ACAD9","ACIN1","AMOTL1","ANLN","ANXA4","APBA2","APBA3","BAI3","BCLAF1","BEST1")

Rd file 'geneListProfile.Rd':
  \examples lines wider than 100 characters:
     glist<-c("ABCB7","ABCF1","ABHD2","ACAD9","ACIN1","AMOTL1","ANLN","ANXA4","APBA2","APBA3","BAI3","BCLAF1","BEST1")

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
File ‘genepi/libs/genepi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘tune’ in Rd xrefs
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’ ‘reshape2’
  All declared Imports should be used.
Undeclared package ‘bootstrap’ in Rd xrefs
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
ForImp.Mahala: no visible global function definition for ‘combn’
ForImp.Mahala: no visible global function definition for ‘var’
ForImp.Mahala: no visible global function definition for ‘quantile’
ForImp.Mahala : <anonymous>: no visible global function definition for
  ‘var’
ForImp.Mahala : <anonymous> : <anonymous>: no visible global function
  definition for ‘var’
ForImp.Mahala : <anonymous> : <anonymous>: no visible global function
  definition for ‘quantile’
ForImp.PCA: no visible global function definition for ‘cov’
ForImp.PCA: no visible global function definition for ‘princomp’
ForImp.PCA: no visible global function definition for ‘combn’
ForImp.PCA: no visible global function definition for ‘quantile’
ForImp.PCA : <anonymous> : <anonymous>: no visible global function
  definition for ‘quantile’
Undefined global functions or variables:
  combn cov princomp quantile var
Consider adding
  importFrom("stats", "cov", "princomp", "quantile", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package suggested but not available for checking: ‘GLDEX’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘KernSmooth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
KernSec: no visible global function definition for ‘na.omit’
KernSur: no visible global function definition for ‘na.fail’
KernSur: no visible global function definition for ‘na.omit’
bandwidthselect: no visible global function definition for ‘na.omit’
bandwidthselect: no visible global function definition for ‘dpik’
correlationselect: no visible global function definition for ‘cor’
nearest: no visible global function definition for ‘na.fail’
nearest: no visible global function definition for ‘na.omit’
per: no visible global function definition for ‘na.fail’
Undefined global functions or variables:
  cor dpik na.fail na.omit
Consider adding
  importFrom("stats", "cor", "na.fail", "na.omit")
to your NAMESPACE file.
File ‘GenKern/libs/GenKern.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  MatingPrograms.cpp:31:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  MatingPrograms.cpp:36:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  MatingPrograms.cpp:42:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  MatingPrograms.cpp:47:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  MatingPrograms.cpp:52:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  MatingPrograms.cpp:57:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  MatingPrograms.cpp:62:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  MatingPrograms.cpp:67:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  MatingPrograms.cpp:72:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/GenomicMating.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Found the following significant warnings:
  mdr.cpp:684:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:686:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:688:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:690:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:719:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:721:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:723:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:725:16: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:755:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:757:18: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:759:18: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:761:18: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:791:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:793:18: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:795:18: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  mdr.cpp:797:18: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/GenomicTools.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Found the following files/directories:
  ‘test.csv’ ‘test_temp_cross.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
splineAnalyze: no visible global function definition for ‘var’
splineAnalyze: no visible global function definition for ‘par’
splineAnalyze: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines par var
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    1.9Mb
    libs   2.9Mb
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
PAEA : <anonymous>: no visible global function definition for
  ‘integrate’
PAEAAnalysis: no visible global function definition for
  ‘txtProgressBar’
PAEAAnalysis : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
PAEAAnalysis: no visible global function definition for ‘par’
PAEAAnalysis: no visible global function definition for ‘barplot’
chdirSig: no visible global function definition for ‘prcomp’
chdirSig: no visible global function definition for ‘rchisq’
chdirSig: no visible global function definition for ‘txtProgressBar’
chdirSig : <anonymous> : <anonymous>: no visible global function
  definition for ‘setTxtProgressBar’
chdirplots : <anonymous>: no visible global function definition for
  ‘par’
chdirplots : <anonymous>: no visible global function definition for
  ‘arrows’
chdirplots : <anonymous>: no visible global function definition for
  ‘barplot’
multigmtPAEAAnalysis: no visible global function definition for
  ‘txtProgressBar’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘setTxtProgressBar’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘data’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘write.table’
Undefined global functions or variables:
  arrows barplot data integrate par prcomp rchisq setTxtProgressBar
  txtProgressBar write.table
Consider adding
  importFrom("graphics", "arrows", "barplot", "par")
  importFrom("stats", "integrate", "prcomp", "rchisq")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘PAEA_p_values-Cancer_Cell_Line_Encyclopedia.gmt.txt’
  ‘PAEA_p_values-ChEA.gmt.txt’
Namespaces in Imports field not imported from:
  ‘maptools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘pander’ ‘readr’ ‘tidyr’
  All declared Imports should be used.
Note: found 80 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘phonTools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘RiemBase’ in Rd xrefs
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Note: found 646 marked UTF-8 strings
Note: found 76726 marked UTF-8 strings
installed size is 75.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  74.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   4.3Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
Malformed Description field: should contain one or more complete sentences.
Rd file 'fujitopo.Rd':
  \examples lines wider than 100 characters:
     PLOC=list(LON=range(fujitopo$lon), x=range(fujitopo$lon), LAT=range(fujitopo$lat), y=range(fujitopo$lat))

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R         9.0Mb
    extdata   1.7Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘ggmap’ in Rd xrefs
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
Undeclared package ‘car’ in Rd xrefs
geoscaleBox: no visible global function definition for ‘boxplot’
geoscaleBox: no visible global function definition for ‘par’
geoscaleBox: no visible global function definition for ‘text’
geoscaleBox: no visible global function definition for ‘segments’
geoscaleBox: no visible global function definition for ‘rect’
geoscaleBox: no visible global function definition for ‘rgb’
geoscaleBox: no visible global function definition for ‘polygon’
geoscaleBox: no visible global function definition for ‘points’
geoscaleBox: no visible global function definition for ‘axis’
geoscalePlot: no visible global function definition for ‘par’
geoscalePlot: no visible global function definition for ‘text’
geoscalePlot: no visible global function definition for ‘segments’
geoscalePlot: no visible global function definition for ‘rect’
geoscalePlot: no visible global function definition for ‘rgb’
geoscalePlot: no visible global function definition for ‘points’
geoscalePlot: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis boxplot par points polygon rect rgb segments text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "boxplot", "par", "points", "polygon",
             "rect", "segments", "text")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘nloptr’ in Rd xrefs
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  32.5Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
Undeclared package ‘loo’ in Rd xrefs
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’.
Namespaces in Imports field not imported from:
  ‘iterators’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 64 marked Latin-1 strings
  Note: found 25 marked UTF-8 strings
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘GWmodel’ ‘beepr’ ‘cartography’ ‘dplyr’ ‘raster’ ‘readxl’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinybusy’ ‘shinyjs’ ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    libs  31.0Mb
GESTr: no visible global function definition for ‘rnorm’
GESTr: no visible global function definition for ‘sd’
GESTr : <anonymous>: no visible global function definition for ‘pnorm’
TranSAM : magChange: no visible global function definition for ‘median’
TranSAM : dstat: no visible global function definition for ‘sd’
TranSAM: no visible binding for global variable ‘sd’
TranSAM: no visible global function definition for ‘quantile’
findReplicateGroups: no visible global function definition for ‘qnorm’
findReplicateGroups: no visible global function definition for ‘sd’
fitGMM : simulateData: no visible global function definition for
  ‘rnorm’
fitGMM : simulateData: no visible global function definition for ‘sd’
fitGMM: no visible global function definition for ‘median’
fitGMM: no visible global function definition for ‘ks.test’
fitRockeDurbin: no visible global function definition for ‘dist’
fitRockeDurbin : findLowGenes: no visible global function definition
  for ‘median’
fitRockeDurbin : findLowGenes: no visible global function definition
  for ‘mad’
fitRockeDurbin: no visible binding for global variable ‘sd’
getMonotonicConfidences_multiclass: no visible global function
  definition for ‘pnorm’
getMonotonicConfidences_multiclass: no visible global function
  definition for ‘sd’
Undefined global functions or variables:
  dist ks.test mad median pnorm qnorm quantile rnorm sd
Consider adding
  importFrom("stats", "dist", "ks.test", "mad", "median", "pnorm",
             "qnorm", "quantile", "rnorm", "sd")
to your NAMESPACE file.
Rd file 'TranSAM.Rd':
  \usage lines wider than 90 characters:
     TranSAM(x,samples1,samples2,minChange=0.2,var_filter=0.01,maxFDR=1,changeStep=0.1,scoreFun="magChange")
  \examples lines wider than 100 characters:
     selected.columns <- sort(c(sample(1:ncol(ABIdata),30),which(colnames(ABIdata) %in% c("GSM194513","GSM194514","GSM194515","GSM194516","G ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘lubridate’ ‘readr’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pipeR’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘scales’ ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘party’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘party’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gTree: no visible global function definition for ‘ctree’
gTree: no visible global function definition for ‘ctree_control’
guttmanErrors: no visible global function definition for ‘runif’
Undefined global functions or variables:
  ctree ctree_control runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘multtest’ which was already attached by Depends.
  Please remove these calls from your code.
Rd file 'gexmap.Rd':
  \usage lines wider than 90 characters:
     gexmap(genome = "homosapiens", scale = "", source = "", res = "", isGO = FALSE, isMAP = TRUE, lim_chi = 5, global_test_choice = 4, pcor ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘googlesheets4’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    libs  30.5Mb
'LazyData' is specified without a 'data' directory
Undeclared packages ‘glue’, ‘magrittr’ in Rd xrefs
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘do’ ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘gge’ in Rd xrefs
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 2356 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘grDevices’ ‘scales’ ‘utils’
  All declared Imports should be used.
Found the following assignments to the global environment:
File ‘ggExtra/R/ggMarginalGadget.R’:
  assign(plotname, eval(parse(text = origPlot)), envir = .GlobalEnv)
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  16.2Mb
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘quantreg’ 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
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘gtable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘rlang’ in Rd xrefs
Undeclared package ‘rlang’ in Rd xrefs
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mathjaxr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘productplots’ ‘scales’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graph’
  All declared Imports should be used.
Undeclared package ‘dwlm’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘sna’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grid’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘scales’, ‘labeling’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggOceanMapsData’
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.1Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘RPostgres’ ‘colourpicker’ ‘dplyr’
  ‘ggpmisc’ ‘ggpubr’ ‘ggrepel’ ‘gridExtra’ ‘markdown’ ‘plotly’
  ‘quantreg’ ‘rlang’ ‘shinyFiles’ ‘shinyjqui’ ‘shinyjs’ ‘survival’
  ‘survminer’ ‘table1’ ‘tidyr’ ‘zoo’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.0Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Found the following significant warnings:
  repel_boxes.cpp:183:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  repel_boxes.cpp:193:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/ggrepel.Rcheck/00install.out’ for details.
Note: found 6242 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘nomogramFormula’ ‘survival’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ggplot2’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ggroc: no visible global function definition for ‘ggplot’
ggroc: no visible global function definition for ‘aes’
ggroc: no visible global function definition for ‘geom_point’
ggroc: no visible global function definition for ‘geom_line’
ggroc: no visible global function definition for ‘theme’
ggroc: no visible global function definition for ‘element_text’
ggroc: no visible global function definition for ‘labs’
ggroc: no visible global function definition for ‘ggsave’
Undefined global functions or variables:
  aes element_text geom_line geom_point ggplot ggsave labs theme
Found the following files/directories:
  ‘roc.pdf’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘utils’
  All declared Imports should be used.
Package suggested but not available for checking: ‘freesurfer’
Undeclared package ‘RColorBrewer’ 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
Undeclared package ‘rlang’ in Rd xrefs
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘hexbin’
  All declared Imports should be used.
Undeclared packages ‘chemometrics’, ‘rlang’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 138 marked UTF-8 strings
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc  10.2Mb
Note: found 203 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘graphics’ ‘refund’ ‘stats’ ‘utils’
  All declared Imports should be used.
Undeclared package ‘usethis’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/ghyp.Rcheck/00install.out’ for details.
acovamcmc: no visible global function definition for ‘rnorm’
acovamcmc: no visible global function definition for ‘rgamma’
acovamcmc: no visible binding for global variable ‘quantile’
acovamcmc: no visible global function definition for ‘quantile’
acovamcmc: no visible global function definition for ‘var’
plot.acovamcmc: no visible global function definition for ‘dev.new’
plot.acovamcmc: no visible global function definition for ‘par’
plot.acovamcmc: no visible global function definition for ‘density’
plot.acovamcmc: no visible global function definition for ‘acf’
plot.acovamcmc: no visible global function definition for ‘contour’
plot.acovamcmc: no visible global function definition for ‘image’
plot.acovamcmc: no visible global function definition for ‘persp’
Undefined global functions or variables:
  acf contour density dev.new image par persp quantile rgamma rnorm var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "contour", "image", "par", "persp")
  importFrom("stats", "acf", "density", "quantile", "rgamma", "rnorm",
             "var")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘gibbs.met/R/firstlib.R’:
  .First.lib calls:
    cat("Naive Gibbs Sampling with Metropolis steps(gibbs.met) loaded\n",     "COPYRIGHT 2008 (c) Longhai Li (http://math.usask.ca/~longhai)\n",     "Type ?begin.gibbs.met for help to this package\n", sep = "")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.

met_gaussian : one_transition: no visible global function definition
  for ‘rnorm’
met_gaussian : one_transition: no visible global function definition
  for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘mc_mvn_closemix.eps’ ‘mc_mvn_farmix_met.eps’ ‘mc_mvn_lowcor.eps’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘Runuran’, ‘ghyp’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
'LazyData' is specified without a 'data' directory
Undeclared packages ‘ineq’, ‘IC2’ in Rd xrefs
Unknown package ‘IC2’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘GiRaF/libs/GiRaF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1178 marked UTF-8 strings
choro.legend: no visible global function definition for ‘strwidth’
choro.legend: no visible global function definition for ‘legend’
choro.legend: no visible global function definition for ‘text’
jitter.points: no visible global function definition for ‘rnorm’
level.plot: no visible global function definition for ‘.filled.contour’
map.scale: no visible global function definition for ‘par’
map.scale: no visible global function definition for ‘rect’
map.scale: no visible global function definition for ‘lines’
map.scale: no visible global function definition for ‘text’
map.scale: no visible global function definition for ‘strheight’
north.arrow: no visible global function definition for ‘polygon’
north.arrow: no visible global function definition for ‘text’
north.arrow: no visible global function definition for ‘strheight’
poly.labels: no visible global function definition for ‘slot’
poly.labels : <anonymous>: no visible global function definition for
  ‘slot’
quantileCuts: no visible global function definition for ‘quantile’
sdCuts: no visible global function definition for ‘sd’
Undefined global functions or variables:
  .filled.contour legend lines par polygon quantile rect rnorm sd slot
  strheight strwidth text
Consider adding
  importFrom("graphics", ".filled.contour", "legend", "lines", "par",
             "polygon", "rect", "strheight", "strwidth", "text")
  importFrom("methods", "slot")
  importFrom("stats", "quantile", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MCMCpack’ ‘ggplot2’ ‘moments’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
fptcdf: no visible global function definition for ‘dnorm’
fptcdf: no visible global function definition for ‘pnorm’
fptpdf: no visible global function definition for ‘pnorm’
fptpdf: no visible global function definition for ‘dnorm’
lba: no visible global function definition for ‘as.formula’
lba: no visible global function definition for ‘model.frame’
lba : logl: no visible global function definition for ‘head’
lba: no visible global function definition for ‘optim’
pmod: no visible global function definition for ‘model.frame’
pmod: no visible global function definition for ‘model.matrix’
rlba: no visible global function definition for ‘pnorm’
rlba: no visible global function definition for ‘rnorm’
rlba: no visible global function definition for ‘runif’
tablba: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula dnorm head model.frame model.matrix optim pnorm rnorm
  runif
Consider adding
  importFrom("stats", "as.formula", "dnorm", "model.frame",
             "model.matrix", "optim", "pnorm", "rnorm", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
File ‘gllm/libs/gllm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 85.2Mb
  sub-directories of 1Mb or more:
    libs  84.4Mb
File ‘GLMaSPU/libs/GLMaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 36.4Mb
  sub-directories of 1Mb or more:
    libs  35.7Mb
GNU make is a SystemRequirements.
Undeclared package ‘GMMBoost’ in Rd xrefs
Undeclared package ‘lme4’ in Rd xrefs
installed size is 41.8Mb
  sub-directories of 1Mb or more:
    libs  40.8Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
installed size is 45.8Mb
  sub-directories of 1Mb or more:
    libs           41.0Mb
    test_data       2.2Mb
    vignette_data   1.1Mb
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    libs  29.3Mb
Namespaces in Imports field not imported from:
  ‘AER’ ‘MASS’ ‘Matrix’ ‘censReg’ ‘effects’ ‘foreign’ ‘lme4’ ‘lmtest’
  ‘nnet’ ‘pBrackets’ ‘plm’ ‘pscl’ ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
.nPerms: no visible global function definition for ‘terms’
expr.dev.test: no visible global function definition for ‘terms’
expr.dev.test: no visible global function definition for ‘model.matrix’
expr.dev.test: no visible global function definition for ‘pchisq’
lancaster: no visible global function definition for ‘pgamma’
liptak: no visible global function definition for ‘pnorm’
summary.dev.test : ci: no visible global function definition for
  ‘qnorm’
varwiselogLik : <anonymous>: no visible global function definition for
  ‘deviance’
varwiselogLik.regression: no visible global function definition for
  ‘glm.fit’
Undefined global functions or variables:
  deviance glm.fit model.matrix pchisq pgamma pnorm qnorm terms
Consider adding
  importFrom("stats", "deviance", "glm.fit", "model.matrix", "pchisq",
             "pgamma", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
Package suggested but not available for checking: ‘cplexAPI’
Malformed Title field: should not end in a period.
CreateFormula: no visible global function definition for ‘as.formula’
GeneratePvalues: no visible binding for global variable ‘binomial’
globalARTP: no visible binding for global variable ‘binomial’
globalFisher: no visible binding for global variable ‘binomial’
globalFisher: no visible global function definition for ‘pchisq’
globalSimes: no visible binding for global variable ‘binomial’
pvalFmla: no visible binding for global variable ‘binomial’
pvalFmla: no visible global function definition for ‘glm’
pvalFmla: no visible global function definition for ‘anova’
runPermut: no visible binding for global variable ‘binomial’
runPvalues: no visible binding for global variable ‘binomial’
Undefined global functions or variables:
  anova as.formula binomial glm pchisq
Consider adding
  importFrom("stats", "anova", "as.formula", "binomial", "glm", "pchisq")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
File ‘globalOptTests/libs/globalOptTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rnaturalearthdata’
  All declared Imports should be used.
Note: found 1191 marked UTF-8 strings
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   8.5Mb
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Undeclared package ‘caret’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 2629 marked UTF-8 strings
checkRd: (7) param_learn.Rd:47-48: \item in \value must have non-empty label
checkRd: (7) param_learn.Rd:49-52: \item in \value must have non-empty label
checkRd: (7) struct_learn.Rd:66-67: \item in \value must have non-empty label
checkRd: (7) struct_learn.Rd:68-71: \item in \value must have non-empty label
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Undeclared package ‘glmmLasso’ in Rd xrefs
Undeclared package ‘sandwich’ in Rd xrefs
checkRd: (7) estimable.Rd:97: invalid email address: bxc\@novonordisk.com
Undeclared package ‘rms’ in Rd xrefs
Package suggested but not available for checking: ‘webshot2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘repeated’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Undeclared package ‘gdata’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘base’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Undeclared package ‘goftest’ in Rd xrefs
Note: found 1352 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rhandsontable’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GANPA’ ‘WGCNA’
A package should be listed in only one of these fields.
'library' or 'require' calls to packages already attached by Depends:
  ‘GANPA’ ‘WGCNA’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘GANPA’ ‘WGCNA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GOGANPA: no visible global function definition for ‘GSE.Test.Main’
selectRho: no visible global function definition for
  ‘scaleFreeFitIndex’
Undefined global functions or variables:
  GSE.Test.Main scaleFreeFitIndex
Found the following files/directories:
  ‘GOGANPAResult.MeanAbs.MultiW.csv’ ‘GOGANPAResult.MeanAbs.NoW.csv’
  ‘GOGANPAResult.MeanAbs.OrigW.csv’
Undeclared package ‘fBasics’ in Rd xrefs
Namespace in Imports field not imported from: ‘brio’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘rcmdcheck’, ‘covr’, ‘devtools’, ‘pkgdown’ 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
Undeclared package ‘jsonlite’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘future’ ‘httr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘BradleyTerry2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
Undeclared package ‘DiceOptim’ in Rd xrefs
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
installed size is 105.4Mb
  sub-directories of 1Mb or more:
    libs  104.5Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘utils’
  All declared Imports should be used.
checkRd: (7) trait.posterior.Rd:23: \item in \value must have non-empty label
.r1: no visible global function definition for ‘cor’
.r2: no visible global function definition for ‘cor’
rgp: no visible global function definition for ‘runif’
rgp: no visible global function definition for ‘rexp’
Undefined global functions or variables:
  cor rexp runif
Consider adding
  importFrom("stats", "cor", "rexp", "runif")
to your NAMESPACE file.
checkRd: (7) nsgpr.Rd:94: \item in \describe must have non-empty label
checkRd: (7) nsgpr.Rd:95: \item in \describe must have non-empty label
checkRd: (7) nsgpr.Rd:95-96: \item in \describe must have non-empty label
checkRd: (7) nsgpr.Rd:98: \item in \describe must have non-empty label
checkRd: (7) nsgpr.Rd:98-99: \item in \describe must have non-empty label
checkRd: (7) nsgpr.Rd:99: \item in \describe must have non-empty label
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   4.4Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘gplm/libs/gplm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    3.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Found the following significant warnings:
  U_NZentries.cpp:27:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/GPvecchia.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  ‘mgcv’ ‘rgl’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘PairedData’ ‘RColorBrewer’ ‘agricolae’ ‘corrplot’ ‘desplot’
  ‘dplyr’ ‘ggplot2’ ‘ggpubr’ ‘gridGraphics’ ‘gtools’ ‘kableExtra’
  ‘knitr’ ‘magrittr’ ‘pastecs’ ‘reshape2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘summarytools’
  All declared Imports should be used.
KL: no visible global function definition for ‘complete.cases’
MergeNodes: no visible global function definition for ‘colors’
cross.validate: no visible global function definition for ‘runif’
fit.APFA: no visible global function definition for ‘complete.cases’
fit.APFA: no visible global function definition for ‘aggregate’
select.beagle: no visible global function definition for ‘write.table’
select.beagle: no visible global function definition for ‘aggregate’
select.beagle: no visible global function definition for ‘colors’
simulateAPFA: no visible global function definition for ‘runif’
st: no visible global function definition for ‘colors’
Undefined global functions or variables:
  aggregate colors complete.cases runif write.table
Consider adding
  importFrom("grDevices", "colors")
  importFrom("stats", "aggregate", "complete.cases", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    help   2.4Mb
    libs   2.5Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cubature’ ‘magicaxis’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘Matrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GrassmannOptim: no visible global function definition for ‘rnorm’
GrassmannOptim: no visible global function definition for ‘runif’
GrassmannOptim : <anonymous>: no visible global function definition for
  ‘expm’
GrassmannOptim : <anonymous>: no visible global function definition for
  ‘Matrix’
Undefined global functions or variables:
  Matrix expm rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Undeclared package ‘mapproj’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘methods’ ‘quadmesh’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Namespaces in Imports field not imported from:
  ‘Rtsne’ ‘cowplot’ ‘ggpubr’ ‘ggrepel’
  All declared Imports should be used.
Found the following significant warnings:
  SimpleIclCoModel.cpp:219:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  SimpleIclCoModel.cpp:223:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/data/gannet/ripley/R/packages/tests-clang/greed.Rcheck/00install.out’ for details.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
Note: found 989 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mclust’
  All declared Imports should be used.
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
bestcut2: no visible global function definition for ‘pchisq’
cov.func: no visible global function definition for ‘rbinom’
cov.func: no visible global function definition for ‘cov’
cov.func: no visible global function definition for ‘pnorm’
cox.summary: no visible global function definition for ‘predict’
em.func: no visible global function definition for ‘quantile’
genSurvData: no visible global function definition for ‘rweibull’
greyzone.func: no visible global function definition for ‘points’
greyzone.func: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cov pchisq pnorm points predict quantile rbinom rweibull
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("stats", "cov", "pchisq", "pnorm", "predict", "quantile",
             "rbinom", "rweibull")
to your NAMESPACE file.
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘msm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
File ‘groupRemMap/libs/groupRemMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘rjags’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
Malformed Description field: should contain one or more complete sentences.
Undeclared packages ‘repeated’, ‘gnlm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [17s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(grpSLOPE)
  > 
  > test_check("grpSLOPE")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 321 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_grpSLOPE.R:24:3): when the groups are consecutive blocks ──────
  result$c not equal to `sol.c`.
  2/10 mismatches (average diff: 13.3)
  [3]  2.98 - 17.0 == -14.0
  [4] 17.46 -  4.9 ==  12.6
  ── Failure (test_grpSLOPE.R:328:3): when the groups are consecutive blocks ─────
  result$c not equal to `sol.c`.
  2/10 mismatches (average diff: 13.3)
  [3]  2.98 - 17.0 == -14.0
  [4] 17.46 -  4.9 ==  12.6
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 321 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
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’