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.
Package required but not available: 'animation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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
Packages required but not available: 'ctsem', 'RPushbullet', 'scholar'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'colordistance'

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: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 128392 marked UTF-8 strings
Package required but not available: 'dataRetrieval'

Package suggested but not available for checking: 'hurricaneexposure'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'choroplethr'
Error(s) in re-building vignettes:
  ...
--- re-building 'countytimezones.Rmd' using rmarkdown
Quitting from lines 111-123 (countytimezones.Rmd) 
Error: processing vignette 'countytimezones.Rmd' failed with diagnostics:
there is no package called 'choroplethr'
--- failed re-building 'countytimezones.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'gstat'
  All declared Imports should be used.
Package suggested but not available for checking: 'plotly'
Namespaces in Imports field not imported from:
  'colourpicker' 'dplyr' 'markdown' 'shinyjs' 'table1' 'tidyr'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rentrez', '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: 'httr', 'rio'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'lubridate'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'devtools'

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

Packages suggested but not available for checking: 'rvest', 'pointblank'

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

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: 'curl', 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Package suggested but not available for checking: 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'projmgr', 'httr'

Package suggested but not available for checking: 'tidyverse'

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 required but not available: 'httr'

Packages suggested but not available for checking:
  'pkgdown', 'rvest', 'usethis'

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

Package suggested but not available for checking: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'Rcpp' 'gsl'
  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:
  'ggplot2' 'misc3d'
  All declared Imports should be used.
Packages suggested but not available for checking: 'covr', 'magick'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'curl'
'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.
'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: 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
coxr: no visible global function definition for 'model.extract'
coxr: no visible global function definition for 'model.matrix'
coxr.draw: no visible global function definition for 'lines'
coxr.draw: no visible global function definition for 'points'
coxr.fit: no visible global function definition for 'quantile'
gen_data: no visible global function definition for 'rnorm'
gen_data: no visible global function definition for 'rexp'
plot.coxr: no visible global function definition for 'quantile'
plot.coxr: no visible global function definition for 'par'
plot.coxr: no visible global function definition for 'mtext'
plot.coxr: no visible global function definition for 'title'
plot.coxr: no visible global function definition for 'split.screen'
plot.coxr: no visible global function definition for 'screen'
plot.coxr: no visible global function definition for 'close.screen'
print.coxr: no visible global function definition for 'pnorm'
print.coxr: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  close.screen lines model.extract model.matrix mtext par pchisq pnorm
  points quantile rexp rnorm screen split.screen title
Consider adding
  importFrom("graphics", "close.screen", "lines", "mtext", "par",
             "points", "screen", "split.screen", "title")
  importFrom("stats", "model.extract", "model.matrix", "pchisq", "pnorm",
             "quantile", "rexp", "rnorm")
to your NAMESPACE file.
'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
'LazyData' is specified without a 'data' directory
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cplexAPI/cplexAPI.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'RcppProgress'
  All declared Imports should be used.
Package required but not available: 'car'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' 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
Package required but not available: 'rvest'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
crantastic.submitInstalledPackages: no visible global function
  definition for 'installed.packages'
postData: no visible global function definition for 'make.socket'
postData: no visible global function definition for 'write.socket'
postData: no visible global function definition for 'read.socket'
postData: no visible global function definition for 'close.socket'
Undefined global functions or variables:
  close.socket installed.packages make.socket read.socket write.socket
Consider adding
  importFrom("utils", "close.socket", "installed.packages",
             "make.socket", "read.socket", "write.socket")
to your NAMESPACE file.
Package required but not available: 'rmapshaper'

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: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
cm.CVaR: no visible global function definition for 'quantile'
cm.hist: no visible global function definition for 'hist'
cm.quantile: no visible global function definition for 'qnorm'
cm.rnorm: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  hist qnorm quantile rnorm
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BSgenome.Scerevisiae.UCSC.sacCer2'
Namespaces in Imports field not imported from:
  'DT' 'gbm'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'R6' 'igraph'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'crul', 'pdftools'

Packages suggested but not available for checking: 'rcrossref', 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'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.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
get.plan: no visible global function definition for 'menu'
Undefined global functions or variables:
  menu
Consider adding
  importFrom("utils", "menu")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
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.
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.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'openVA'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'using-crossva-and-openva.Rmd' using rmarkdown
Quitting from lines 14-17 (using-crossva-and-openva.Rmd) 
Error: processing vignette 'using-crossva-and-openva.Rmd' failed with diagnostics:
there is no package called 'openVA'
--- failed re-building 'using-crossva-and-openva.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'R6' 'dplyr' 'r6extended'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'crunch', 'httptest'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'FSA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
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.
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
Packages suggested but not available for checking:
  'mapboxapi', 'tigris', 'tidycensus'
'LazyData' is specified without a 'data' directory
Package required but not available: 'curl'

Package suggested but not available for checking: 'webmockr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'httr', 'httpcache'

Packages suggested but not available for checking:
  'covr', 'crunchy', 'devtools', 'httptest', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'crunch', 'httpcache'

Packages suggested but not available for checking:
  'covr', 'httptest', 'shinytest'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'qte'

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

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: 'plotly'
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
Packages required but not available: 'FactoMineR', 'randomcoloR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rmapshaper'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 3 marked Latin-1 strings
  Note: found 55 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.
Package in Depends field not imported from: 'compiler'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
csSAM: no visible binding for global variable 'quantile'
csSAM: no visible global function definition for 'median'
csfit: no visible global function definition for 'lsfit'
csfit: no visible global function definition for 'ls.diag'
plotCsSAM: no visible global function definition for 'pdf'
plotCsSAM: no visible global function definition for 'par'
plotCsSAM: no visible global function definition for 'title'
plotCsSAM: no visible global function definition for 'dev.off'
runSAM: no visible binding for global variable 'median'
runSAM: no visible global function definition for 'quantile'
Undefined global functions or variables:
  dev.off ls.diag lsfit median par pdf quantile title
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "title")
  importFrom("stats", "ls.diag", "lsfit", "median", "quantile")
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  file.exists(tmp_metadata) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  -- 2. Error (test-metadata.R:48:5): External metadata loads automatically ------
  Error: invalid 'description' argument
  Backtrace:
   1. testthat::expect_identical(...) test-metadata.R:48:4
   4. base::readLines(dir(dirname(tmp), pattern = ".yaml", full.names = TRUE))
   5. base::file(con, "r")
  
  == DONE ========================================================================
  Error: Test failures
  Execution halted
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
Package suggested but not available for checking: 'crawl'
Package suggested but not available for checking: 'move'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
Package suggested but not available for checking: 'car'
Packages required but not available: 'httr', 'curl', 'rvest'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ctsem'

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.
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
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'pspearman'
  All declared Imports should be used.
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'webutils'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/curl/curl.Rcheck/00install.out' for details.
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
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
Package which this enhances but not available for checking: 'covr'
Packages required but not available: 'set', 'do'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Package suggested but not available for checking: 'covr'
ci.cvAUC: no visible global function definition for 'qnorm'
ci.pooled.cvAUC: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
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.
Package required but not available: 'ggpubr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'pkgdown'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'ggimage'
Package unavailable to check Rd xrefs: 'ggimage'
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').
Package suggested but not available for checking: 'covr'
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.
Package suggested but not available for checking: 'covr'

Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
Packages required but not available: 'curl', 'RcppCWB', 'httr', 'zen4R'

Package suggested but not available for checking: 'aws.s3'

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

Packages suggested but not available for checking: 'stplanr', 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'CytobankAPI'

Packages suggested but not available for checking: 'httr', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'CytobankAPI'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'httr', 'usethis'

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.
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
Package suggested but not available for checking: 'httr'

Package which this enhances but not available for checking: 'V8'
'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
Namespaces in Imports field not imported from:
  'plyr' 'simpleboot'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Note: found 4 marked Latin-1 strings
  Note: found 21 marked UTF-8 strings
Package required but not available: 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 's20x'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'dagitty'
Packages required but not available:
  'curl', 'gargle', 'googleCloudStorageR', 'httr', 'magick', 'pdftools'

Packages suggested but not available for checking:
  'covr', 'qpdf', 'usethis'

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

Package which this enhances but not available for checking: 'doMC'
Packages required but not available: 'car', 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'lintr', 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'basic_cea.Rmd' using rmarkdown
Quitting from lines 81-86 (basic_cea.Rmd) 
Error: processing vignette 'basic_cea.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'basic_cea.Rmd'

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'crul'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'TTR', 'quantmod', 'rtweet'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'kableExtra'

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: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
drawAimSpot: no visible global function definition for 'points'
drawBoard: no visible global function definition for 'par'
drawBoard: no visible global function definition for 'points'
drawBoard: no visible global function definition for 'text'
drawHeatmap: no visible global function definition for 'heat.colors'
drawHeatmap: no visible global function definition for 'par'
drawHeatmap: no visible global function definition for 'image'
drawHeatmap: no visible global function definition for 'rect'
generalExpScores: no visible global function definition for 'fft'
simpleExpScores: no visible global function definition for 'mvfft'
simpleExpScores: no visible global function definition for 'fft'
Undefined global functions or variables:
  fft heat.colors image mvfft par points rect text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "par", "points", "rect", "text")
  importFrom("stats", "fft", "mvfft")
to your NAMESPACE file.
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.
Packages suggested but not available for checking: 'lintr', 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'dash', 'plotly'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dash'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dash'
Packages required but not available: 'fiery', 'routr', 'plotly', 'reqres'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'aws.s3', 'ssh'
Package suggested but not available for checking: 'ProjectionBasedClustering'
Packages required but not available: 'summarytools', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'miniUI'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'curl', 'httr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package in Depends field not imported from: 'DBI'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.onLoad : <anonymous>: no visible global function definition for
  'read.table'
.onLoad : <anonymous>: no visible global function definition for
  'dbConnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbListTables'
.onLoad : <anonymous>: no visible global function definition for
  'dbExistsTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbReadTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbWriteTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbDisconnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbRemoveTable'
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Package required but not available: 'rio'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonvalidate', 'tableschema.r', 'V8'

Packages suggested but not available for checking:
  'covr', 'curl', 'devtools', 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'devtools', 'usethis'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'httr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kableExtra'
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'whoami'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'curl'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Package suggested but not available for checking: 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Packages required but not available: 'Rlabkey', 'curl', 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'EML'

Package suggested but not available for checking: 'kableExtra'

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: 'covr'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'lintr'
Package suggested but not available for checking: 'curl'
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'R6' 'rmarkdown' 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ggmap', 'choroplethr', 'plotly'
Package unavailable to check Rd xrefs: 'plotly'
Package suggested but not available for checking: 'rstanarm'
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Note: found 54337 marked UTF-8 strings
Packages suggested but not available for checking: 'covr', 'devtools'
Note: found 1 marked Latin-1 string
  Note: found 360 marked UTF-8 strings
Package suggested but not available for checking: 'lintr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'devtools'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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

Package suggested but not available for checking: 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking: 'devtools', 'lintr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'pkgdown'
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
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
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
Packages required but not available: 'rumidas', 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'golem'

Packages suggested but not available for checking: 'covr', 'jsonvalidate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'commonmark' 'htmltools' 'shinyhelper'
  All declared Imports should be used.
Package required but not available: 'dnet'

Package suggested but not available for checking: 'doMC'

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

Package suggested but not available for checking: 'BRugs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Package suggested but not available for checking: 'INLA'
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'CDM'
  All declared Imports should be used.
Package required but not available: 'dclone'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
test.LM: no visible global function definition for 'lm'
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
Package required but not available: 'qpdf'

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: 'ggalt'

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.
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.
Package required but not available: '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: 'devtools'
Package suggested but not available for checking: 'covr'
'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.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'chillR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'AER'
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 46826 marked UTF-8 strings
Packages required but not available: 'PSF', 'forecast', 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyverse'
DeconCPdf: no visible global function definition for 'bw.nrd0'
DeconCPdf: no visible global function definition for 'bw.nrd'
DeconCPdf: no visible global function definition for 'bw.ucv'
DeconCPdf: no visible global function definition for 'bw.bcv'
DeconCPdf: no visible global function definition for 'bw.SJ'
DeconCPdf: no visible global function definition for 'density'
DeconCPdf: no visible global function definition for 'dnorm'
bw.dboot2 : suppL2: no visible global function definition for 'density'
bw.dboot2 : suppL2: no visible global function definition for 'rnorm'
bw.dboot2 : gaussL2: no visible global function definition for
  'density'
bw.dboot2 : gaussL2: no visible global function definition for 'rnorm'
bw.dmise: no visible global function definition for 'var'
plot.Decon: no visible global function definition for 'plot.default'
plot.Decon: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv density dnorm plot.default
  rnorm var
Consider adding
  importFrom("graphics", "abline", "plot.default")
  importFrom("stats", "bw.SJ", "bw.bcv", "bw.nrd", "bw.nrd0", "bw.ucv",
             "density", "dnorm", "rnorm", "var")
to your NAMESPACE file.
Package suggested but not available for checking: 'VariantAnnotation'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'Deducer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Deducer'

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.

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 required but not available: 'Deducer'

Depends: includes the non-default packages:
  'JavaGD', 'Deducer', 'sp', 'maptools', 'OpenStreetMap', 'scales',
  'rgdal'
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: 'Deducer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Deducer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cranlogs', 'httr'

Packages suggested but not available for checking:
  'covr', 'devtools', 'miniCRAN', 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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
Packages suggested but not available for checking: 'covr', 'kableExtra'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'overview.Rmd' using rmarkdown
--- finished re-building 'overview.Rmd'

--- re-building 'predict.Rmd' using rmarkdown
Quitting from lines 54-61 (predict.Rmd) 
Error: processing vignette 'predict.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'predict.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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: 'covr'
Namespace in Imports field not imported from: 'assertthat'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'rstan'

Package suggested but not available for checking: 'knitcitations'

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
bootbagg: no visible global function definition for 'runif'
bootworpl: no visible global function definition for 'runif'
des12: no visible global function definition for 'rnorm'
des12: no visible global function definition for 'runif'
eval.stage.gauss: no visible global function definition for 'var'
plotparti: no visible global function definition for 'lines'
plotpartilev: no visible global function definition for 'polygon'
plotpartilev: no visible global function definition for 'points'
simesi: no visible global function definition for 'runif'
simesi3d: no visible global function definition for 'runif'
simfssk: no visible global function definition for 'rnorm'
simfssk: no visible global function definition for 'runif'
simmix.delt: no visible global function definition for 'rnorm'
simmix.delt: no visible global function definition for 'runif'
simpp: no visible global function definition for 'rnorm'
simpp: no visible global function definition for 'runif'
simutree: no visible global function definition for 'runif'
stage.gaussR: no visible global function definition for 'var'
unidis: no visible global function definition for 'runif'
Undefined global functions or variables:
  lines points polygon rnorm runif var
Consider adding
  importFrom("graphics", "lines", "points", "polygon")
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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

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: 'heatmaply', 'covr'
Package required but not available: 'forecast'

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.
Malformed Description field: should contain one or more complete sentences.
DendSer: no visible global function definition for 'getFromNamespace'
crit2cost : <anonymous>: no visible global function definition for
  'as.dist'
dser.dist: no visible global function definition for 'hclust'
dser.matrix: no visible global function definition for 'dist'
plotAsColor: no visible global function definition for 'image'
plotAsColor: no visible global function definition for 'box'
plotAsColor: no visible global function definition for 'axis'
seriation_method_dist_dser: no visible global function definition for
  'hclust'
seriation_method_dist_dser: no visible global function definition for
  'modifyList'
seriation_method_leafsort: no visible global function definition for
  'modifyList'
Undefined global functions or variables:
  as.dist axis box dist getFromNamespace hclust image modifyList
Consider adding
  importFrom("graphics", "axis", "box", "image")
  importFrom("stats", "as.dist", "dist", "hclust")
  importFrom("utils", "getFromNamespace", "modifyList")
to your NAMESPACE file.
Package required but not available: 'drc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'FactoMineR'

Package suggested but not available for checking: 'missMDA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'mvtnorm'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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 suggested but not available for checking: 'usethis', 'devtools'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'telegram.bot', 'usethis'

Package suggested but not available for checking: 'covr'

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: 'Rdonlp2'
Package suggested but not available for checking: 'Rdonlp2'
Namespace in Imports field not imported from: 'grDevices'
  All declared Imports should be used.
Packages suggested but not available for checking: 'covr', 'lintr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'whoami', 'gh'
'LazyData' is specified without a 'data' directory
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Backtrace:
    1. testthat::with_mock(...) test-non-oo.R:26:2
    2. testthat:::extract_mocks(mock_funs, .env = .env)
    3. base::lapply(...)
    4. testthat:::FUN(X[[i]], ...)
    5. base::asNamespace(pkg_name)
    6. base::getNamespace(ns)
    7. base::loadNamespace(name)
    8. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
    9. base:::withOneRestart(expr, restarts[[1L]])
   10. base:::doWithOneRestart(return(expr), restart)
  
  == DONE ========================================================================
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lintr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'curl'
Note: found 5764 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
Package required but not available: 'kableExtra'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RDCOMClient'
Packages unavailable to check Rd xrefs: 'car', 'forecast'
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.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
Package suggested but not available for checking: 'afex'
Note: found 47 marked UTF-8 strings
Error(s) in re-building vignettes:
--- re-building 'design-to-dataframe.Rmd' using rmarkdown
--- finished re-building 'design-to-dataframe.Rmd'

--- re-building 'power-analyses.Rmd' using rmarkdown
Loading required package: lme4
Loading required package: Matrix

Attaching package: 'lmerTest'

The following object is masked from 'package:lme4':

    lmer

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

    step

Quitting from lines 25-32 (power-analyses.Rmd) 
Error: processing vignette 'power-analyses.Rmd' failed with diagnostics:
there is no package called 'afex'
--- failed re-building 'power-analyses.Rmd'

SUMMARY: processing the following file failed:
  'power-analyses.Rmd'

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
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
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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: 'dclone', 'dcmle'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'covr', 'AER', 'ROI.plugin.neos'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(testthat)
  > library(detectseparation)
  > 
  > test_check("detectseparation")
  == Failed tests ================================================================
  -- Error (test-separator_lpSolveAPI.R:31:1): (code run outside of `test_that()`) --
  Error: object 'settings' not found
  Backtrace:
      x
   1. \-base::nrow(settings) test-separator_lpSolveAPI.R:31:0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 18 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: 'dplR'
  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:
  '.get' 'InteractiveDetrending' 'RemoveTrend'
Package suggested but not available for checking: 'covr'
GNU make is a SystemRequirements.
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
Packages required but not available: 'usethis', 'httr', 'rversions'

Packages suggested but not available for checking:
  'covr', 'curl', 'foghorn', 'gh', 'gmailr', 'lintr', 'pkgdown', 'rhub'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'MVN'

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
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.
Package suggested but not available for checking: 'AER'
Running examples in 'dfidx-Ex.R' failed
The error most likely occurred in:

> ### Name: dfidx
> ### Title: Data frames with indexes
> ### Aliases: dfidx
> 
> ### ** Examples
> 
> 
> data("TravelMode", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'AER'
Calls: data -> find.package
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'dfidx.Rmd' using rmarkdown

Attaching package: 'dfidx'

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

    filter

Quitting from lines 60-62 (dfidx.Rmd) 
Error: processing vignette 'dfidx.Rmd' failed with diagnostics:
there is no package called 'AER'
--- failed re-building 'dfidx.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 1 marked UTF-8 string
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.
Package required but not available: 'plotly'

Package suggested but not available for checking: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MLInterfaces', 'genefilter'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'GOstats', 'doMC'
Package suggested but not available for checking: 'biomaRt'
Package required but not available: 'sva'

Packages suggested but not available for checking:
  'canvasXpress', 'biomaRt'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'rlang'
  All declared Imports should be used.
Packages suggested but not available for checking: 'covr', 'DiagrammeRsvg'
Note: found 1 marked UTF-8 string
Package required but not available: 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 294851 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Note: found 7880 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
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.
'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: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'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').
Package required but not available: 'rfishbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Packages suggested but not available for checking: 'devtools', 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'diffenrich_vignette.Rmd' using rmarkdown
Loading required package: kableExtra
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'kableExtra'
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'kableExtra'
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'kableExtra'
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'kableExtra'
Quitting from lines 339-342 (diffenrich_vignette.Rmd) 
Error: processing vignette 'diffenrich_vignette.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'diffenrich_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' 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
'LazyData' is specified without a 'data' directory
Package required but not available: 'systemfit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'Quandl'
Package suggested but not available for checking: 'Quandl'
Package suggested but not available for checking: 'Quandl'
Package suggested but not available for checking: 'lintr'
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ShinyItemAnalysis'
Running examples in 'difNLR-Ex.R' failed
The error most likely occurred in:

> ### Name: difORD
> ### Title: DIF detection among ordinal data.
> ### Aliases: difORD
> ### Keywords: DIF
> 
> ### ** Examples
> 
> # Loading data
> data(dataMedicalgraded, package = "ShinyItemAnalysis")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'ShinyItemAnalysis'
Calls: data -> find.package
Execution halted
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  digest.c:207:25: warning: too many arguments for format [-Wformat-extra-args]
  digest.c:432:25: warning: too many arguments for format [-Wformat-extra-args]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/digest/digest.Rcheck/00install.out' for details.
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.
Package required but not available: 'httr'

Package suggested but not available for checking: 'bibliometrix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'FactoMineR'
Package required but not available: 'forecast'

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: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'usethis'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'EdSurvey'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
nullTest: no visible global function definition for 'rmultinom'
rdirichlet: no visible global function definition for 'rgamma'
simPop: no visible global function definition for 'rnorm'
simPop: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  rgamma rmultinom rnorm
Consider adding
  importFrom("stats", "rgamma", "rmultinom", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'INLA'
Namespaces in Imports field not imported from:
  'rgdal' 'rgeos' 'splancs' 'utils'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'shinytest'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Package suggested but not available for checking: 'Seurat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'crul'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
rdisclap: 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: 'psych'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'dplyr' 'readr'
  All declared Imports should be used.
Packages required but not available: 'golem', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'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.
Package suggested but not available for checking: 'FactoMineR'
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: 'covr'
Running examples in 'disdat-Ex.R' failed
The error most likely occurred in:

> ### Name: AWT
> ### Title: Australian Wet Tropics species distribution data
> ### Aliases: AWT
> ### Keywords: datasets
> 
> ### ** Examples
> 
> awt_po <- disPo("AWT")
> awt_bg <- disBg("AWT")
> 
> awt_pa_plant <- disPa("AWT", "plant")
> awt_env_plant <- disEnv("AWT", "plant")
> awt_pa_bird <- disPa("AWT", "bird")
> awt_env_bird <- disEnv("AWT", "bird")
> 
> 
> # Or all in one list
> awt <- disData("AWT")
Error in rbind(deparse.level, ...) : 
  numbers of columns of arguments do not match
Calls: disData -> do.call -> <Anonymous> -> rbind
Execution halted
Package which this enhances but not available for checking: 'INLA'
Package required but not available: 'systemfit'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Note: found 106 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'car'
Package unavailable to check Rd xrefs: 'car'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'devtools', 'kableExtra'
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking: 'opencpu', 'covr'

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: 'rsconnect'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    8.   \-distill:::render_website(dir, "blog")
    9.     \-rmarkdown::render_site(dir)
   10.       \-generator$render(...)
   11.         \-distill:::render_collections(input, config, collections, quiet)
   12.           \-base::lapply(...)
   13.             \-distill:::FUN(X[[i]], ...)
   14.               \-distill:::render_collection(...)
   15.                 \-base::lapply(...)
   16.                   \-distill:::FUN(X[[i]], ...)
   17.                     \-distill:::render_collection_article(...)
   18.                       \-base::file.copy(...)
  
  [ FAIL 1 | WARN 1 | SKIP 1 | PASS 3 ]
  Error: Test failures
  Execution halted
Package required but not available: 'factoextra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'plotly'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    2. | \-testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. |   +-testthat:::.capture(...)
    4. |   | +-withr::with_output_sink(...)
    5. |   | | \-base::force(code)
    6. |   | +-base::withCallingHandlers(...)
    7. |   | \-base::withVisible(code)
    8. |   \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. +-base::plot(dist, fun = "pdf", npoints = 10)
   10. \-distr6:::plot.Distribution(dist, fun = "pdf", npoints = 10)
   11.   \-distr6:::.plot_multivariate(x, fun, npoints)
   12.     \-distr6:::assert_pkgload("plotly")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4202 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking:
  'httr', 'plumberDeploy', 'analogsea'
Running examples in 'distribglm-Ex.R' failed
The error most likely occurred in:

> ### Name: api_url
> ### Title: API Functions and wrappers
> ### Aliases: api_url api_set_url api_available_models api_get_current_beta
> ###   api_model_trace api_model_specification api_submit_gradient
> ###   api_model_converged api_setup_model api_clear_model
> ###   api_estimate_model
> 
> ### ** Examples
> 
> api_url()
[1] "https://rsconnect.biostat.jhsph.edu/distribglm"
> api_set_url(api_url())
[1] "https://rsconnect.biostat.jhsph.edu/distribglm"
> api_available_models()
Error in api_dep_check() : Need httr and jsonlite to run api functions
Calls: api_available_models -> api_dep_check
Execution halted
Package suggested but not available for checking: 'covr'
'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: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tidyverse'
'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: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'lintr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'ggmulti' 'loon' 'loon.data' 'loon.ggplot' 'zenplots'
  All declared Imports should be used.
Package suggested but not available for checking: 'entropart'
Package required but not available: 'ggpubr'

Package suggested but not available for checking: 'BOLTSSIRR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'sendplot', 'HWxtest'
Package suggested but not available for checking: 'covr'
Packages required but not available: 'tidyverse', 'plotly', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'lintr'
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking: 'covr', 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'nardl', 'dynlm', 'AER'

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: 'magick'
Packages required but not available: 'kableExtra', 'RcmdrMisc'

Package suggested but not available for checking: 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rgraphviz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'MplusAutomation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'ggrepel'
  All declared Imports should be used.
Package required but not available: 'EML'

Packages suggested but not available for checking: 'covr', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'covr', 'DiagrammeRsvg', 'tidyverse'
Package unavailable to check Rd xrefs: 'DiagrammeRsvg'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'quantmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthis'
GNU make is a SystemRequirements.
Package required but not available: 'Rgraphviz'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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
Package suggested but not available for checking: 'OutliersO3'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'dobin.Rmd' using rmarkdown
Quitting from lines 22-34 (dobin.Rmd) 
Error: processing vignette 'dobin.Rmd' failed with diagnostics:
Package OutliersO3 is needed for the vignette. Please install it.
--- failed re-building 'dobin.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Note: found 9796 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'magick', 'pdftools'

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'
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.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'devtools'
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'osmdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'skpr'
Package unavailable to check Rd xrefs: 'skpr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'car', 'covr', 'dynlm'
Running examples in 'dominanceanalysis-Ex.R' failed
The error most likely occurred in:

> ### Name: mlmWithCov
> ### Title: Uses covariance/correlation matrix to calculate multivariate
> ###   index of fit
> ### Aliases: mlmWithCov
> 
> ### ** Examples
> 
> library(car)
Error in library(car) : there is no package called 'car'
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == Failed tests ================================================================
  -- Error (test-dominanceanalysis-with-dynlm.R:3:1): (code run outside of `test_that()`) --
  Error: there is no package called 'dynlm'
  Backtrace:
      x
   1. \-base::library(dynlm) test-dominanceanalysis-with-dynlm.R:3:0
  -- Error (test-lmWithCovsMlm.R:3:1): (code run outside of `test_that()`) -------
  Error: there is no package called 'car'
  Backtrace:
      x
   1. \-base::library(car) test-lmWithCovsMlm.R:3:0
  
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 192 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'RcmdrMisc'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rvest', 'usethis'
Note: found 100 marked UTF-8 strings
Error(s) in re-building vignettes:
--- re-building 'Intro.Rmd' using rmarkdown
--- finished re-building 'Intro.Rmd'

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

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

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

--- re-building 'make_lookup_df.Rmd' using rmarkdown
Quitting from lines 18-26 (make_lookup_df.Rmd) 
Error: processing vignette 'make_lookup_df.Rmd' failed with diagnostics:
there is no package called 'usethis'
--- failed re-building 'make_lookup_df.Rmd'

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

--- re-building 'parse_lookup.Rmd' using rmarkdown

Attaching package: 'DOPE'

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

    parse


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

Your search matched multiple categories. Please choose one 
from the following list and refine your search. Example: 
lookup_syn('mushrooms') or lookup_syn('psilocybin')
--- finished re-building 'parse_lookup.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'rvest', 'httr', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
Namespace in Imports field not imported from: 'gridExtra'
  All declared Imports should be used.
Packages suggested but not available for checking: 'doRedis', 'devtools'
Package required but not available: 'dagitty'

Package suggested but not available for checking: 'DOT'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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').
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'V8'

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: 'covr', 'AER'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Packages suggested but not available for checking: 'covr', 'devtools'
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'forecast'
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Note: found 4 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'rio'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'drc', 'devtools'
Running examples in 'dr4pl-Ex.R' failed
The error most likely occurred in:

> ### Name: print.summary.dr4pl
> ### Title: Print the dr4pl object summary to screen.
> ### Aliases: print.summary.dr4pl
> 
> ### ** Examples
> 
> library(drc)  # Needed for the data set 'ryegras'
Error in library(drc) : there is no package called 'drc'
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'walk_through_in_R.Rmd' using rmarkdown
Quitting from lines 21-24 (walk_through_in_R.Rmd) 
Error: processing vignette 'walk_through_in_R.Rmd' failed with diagnostics:
there is no package called 'drc'
--- failed re-building 'walk_through_in_R.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'golem', 'rvest', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 78 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'curl', 'disk.frame', 'usethis'
Package required but not available: 'httr'

Package suggested but not available for checking: 'highcharter'

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
DRaWR: no visible global function definition for 'write.table'
DRaWR: no visible global function definition for 'read.table'
DRaWR: no visible global function definition for 'aggregate'
DRaWR: no visible global function definition for 'slot'
Undefined global functions or variables:
  aggregate read.table slot write.table
Consider adding
  importFrom("methods", "slot")
  importFrom("stats", "aggregate")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Namespaces in Imports field not imported from:
  'magrittr' 'purrr' 'rlang'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'rstan'

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 suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'drc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: 'spatstat.core'
  All declared Imports should be used.
Packages required but not available:
  'modelsummary', 'summarytools', 'tidyverse', 'car', 'kableExtra'

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

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.
Package suggested but not available for checking: 'devtools'
Package required but not available: 'SmartEDA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GenomicFeatures', 'TxDb.Hsapiens.UCSC.hg19.knownGene'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
cdfDRM: no visible global function definition for 'tail'
densityDRM: no visible binding for global variable 'density'
drmdel: no visible binding for global variable 'optim'
drmdel: no visible global function definition for 'pchisq'
quantEst: no visible global function definition for 'tail'
quantileCompWald: no visible global function definition for 'pchisq'
quantileCompWald: no visible global function definition for 'p.adjust'
quantileDRM: no visible global function definition for 'tail'
quantileDRM: no visible global function definition for 'density'
Undefined global functions or variables:
  density optim p.adjust pchisq tail
Consider adding
  importFrom("stats", "density", "optim", "p.adjust", "pchisq")
  importFrom("utils", "tail")
to your NAMESPACE file.
Package required but not available: 'DESeq2'

See section 'The DESCRIPTION file' 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'userGuide.Rmd' using rmarkdown
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
Quitting from lines 433-435 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
replacement has 2 rows, data has 3
--- failed re-building 'userGuide.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

Packages suggested but not available for checking:
  'covr', 'devtools', 'pkgdown'

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

Packages suggested but not available for checking:
  'covr', 'devtools', 'pkgdown'

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

Package suggested but not available for checking: 'stR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'start.Rmd' using rmarkdown
Quitting from lines 136-140 (start.Rmd) 
Error: processing vignette 'start.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'start.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Note: found 149 marked UTF-8 strings
Note: found 4891 marked UTF-8 strings
Package suggested but not available for checking: 'resourcer'
Package suggested but not available for checking: 'covr'
Packages required but not available: 'MolgenisAuth', 'httr'

Package suggested but not available for checking: 'dsBaseClient'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'opalr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'Rcpp'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
DStree: no visible global function definition for 'model.frame'
DStree: no visible global function definition for 'model.matrix'
DStree: no visible global function definition for 'model.response'
DStree: no visible global function definition for 'as.formula'
bag: no visible global function definition for 'model.frame'
bag: no visible global function definition for 'model.response'
plot.DStree: no visible global function definition for 'par'
plot.DStree: no visible global function definition for 'rainbow'
plot.DStree: no visible global function definition for 'lines'
plot.DStree: no visible global function definition for 'legend'
predict.DStree: no visible global function definition for 'predict'
print.DStree: no visible global function definition for 'naprint'
prune.DStree: no visible global function definition for 'median'
prune.DStree: no visible global function definition for 'predict'
prune.DStree: no visible binding for global variable 'var'
summ.MAE: no visible global function definition for 'predict'
summary.DStree: no visible global function definition for 'naprint'
Undefined global functions or variables:
  as.formula legend lines median model.frame model.matrix
  model.response naprint par predict rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.formula", "median", "model.frame",
             "model.matrix", "model.response", "naprint", "predict",
             "var")
to your NAMESPACE file.
Package required but not available: 'sva'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Note: found 1 marked Latin-1 string
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
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.
DTMC: 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
Package suggested but not available for checking: 'covr'
'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: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'digest' 'dplyr'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'Seurat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'arrow'
Package required but not available: 'crul'

Package suggested but not available for checking: 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
dummy: no visible global function definition for 'model.matrix'
dummy: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  model.frame model.matrix
Consider adding
  importFrom("stats", "model.frame", "model.matrix")
to your NAMESPACE file.
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.
Package required but not available: 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'DT'
  All declared Imports should be used.
Package required but not available: 'tsDyn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'ncdf4' 'rgdal'
  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
Package suggested but not available for checking: 'httr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'ari'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'maptools' 'tools'
  All declared Imports should be used.
MultiTestH0 : MultiTestOneColumn: no visible global function definition
  for 'pchisq'
RunClustering : CheckClusterNew: no visible global function definition
  for 'qchisq'
RunClustering: no visible global function definition for 'qchisq'
RunDenoising: no visible binding for global variable 'var'
RunDenoising: no visible global function definition for 'qchisq'
RunDenoising: no visible binding for global variable 'median'
RunDenoising: no visible global function definition for 'var'
RunDenoising : buildEstimate: no visible global function definition for
  'qchisq'
Undefined global functions or variables:
  median pchisq qchisq var
Consider adding
  importFrom("stats", "median", "pchisq", "qchisq", "var")
to your NAMESPACE file.
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'smacof'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'magrittr'
  All declared Imports should be used.
Packages suggested but not available for checking: 'covr', 'Seurat'
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.
Package required but not available: 'car'

Package suggested but not available for checking: 'TSA'

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
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tseries'
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
Namespace in Imports field not imported from: 'hms'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
GNU make is a SystemRequirements.
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: 'plotly', 'shinytest'

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

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.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'pkgdown'
Namespace in Imports field not imported from: 'progress'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'FSA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'ggplot2' 'reshape2' 'scales' 'xtable'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'base64enc' 'knitr' 'markdown'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.file_attachment: no visible global function definition for
  'base64encode'
.plot_attachment: no visible global function definition for 'dev.off'
.update_list: no visible global function definition for 'modifyList'
easyHtmlReport: no visible global function definition for 'knit'
easyHtmlReport: no visible global function definition for
  'markdownToHTML'
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'
simpleHtmlReport : <anonymous>: no visible global function definition
  for 'write.table'
Undefined global functions or variables:
  base64encode dev.off knit markdownToHTML 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
Package required but not available: 'devtools'

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: 'pdftools'
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 suggested but not available for checking: 'covr'

Package which this enhances but not available for checking: 'gurobi'
Namespace in Imports field not imported from: 'RSQLite'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking:
  'kableExtra', 'usethis', 'devtools'
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
Packages required but not available: 'car', 'EffectLiteR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package unavailable to check Rd xrefs: 'car'
'LazyData' is specified without a 'data' directory
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
Package required but not available: 'car'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Package required but not available: 'drc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'INLA'
Packages required but not available: 'curl', 'rsdmx', 'httr'

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 unavailable to check Rd xrefs: 'systemfit'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'car', 'kableExtra'
Packages unavailable to check Rd xrefs: 'drc', 'car'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Error: package or namespace load failed for 'echarty':
 .onLoad failed in loadNamespace() for 'echarty', details:
  call: loadNamespace(x)
  error: there is no package called 'shiny'
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
Package required but not available: 'animation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'ggspatial', 'httptest', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'geouy'

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: 'factoextra'
Namespace in Imports field not imported from: 'pander'
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building 'eclust.Rmd' using rmarkdown
See example usage at http://sahirbhatnagar.com/eclust/
Quitting from lines 142-168 (eclust.Rmd) 
Error: processing vignette 'eclust.Rmd' failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building 'eclust.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'curl'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'rvest', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'EML', 'emld', 'httr', 'neonUtilities'

Packages suggested but not available for checking:
  'ritis', 'taxize', 'worrms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
Note: found 8 marked UTF-8 strings
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
GNU make is a SystemRequirements.
Package required but not available: 'biomod2'

Package suggested but not available for checking: 'qpdf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'smacof'
Error(s) in re-building vignettes:
  ...
--- re-building 'IntroductionETA.Rmd' using rmarkdown
Quitting from lines 201-211 (IntroductionETA.Rmd) 
Error: processing vignette 'IntroductionETA.Rmd' failed with diagnostics:
there is no package called 'smacof'
--- failed re-building 'IntroductionETA.Rmd'

--- re-building 'Transformation.Rmd' using rmarkdown
Quitting from lines 154-157 (Transformation.Rmd) 
Error: processing vignette 'Transformation.Rmd' failed with diagnostics:
there is no package called 'smacof'
--- failed re-building 'Transformation.Rmd'

SUMMARY: processing the following files failed:
  'IntroductionETA.Rmd' 'Transformation.Rmd'

Error: Vignette re-building failed.
Execution halted
plot.ETdiagnosis: no visible global function definition for 'par'
plot.ETdiagnosis: no visible global function definition for 'lines'
plot.ETdiagnosis: no visible global function definition for 'legend'
plot.ETmain: no visible global function definition for 'par'
plot.ETmain: no visible global function definition for 'polygon'
plot.ETmain: no visible global function definition for 'axis'
plot.ETmain: no visible global function definition for 'legend'
plot.ETmain: no visible global function definition for 'lines'
plot.Transpose: no visible global function definition for 'par'
plot.Transpose: no visible global function definition for 'polygon'
plot.Transpose: no visible global function definition for 'axis'
plot.Transpose: no visible global function definition for 'legend'
plot.smooth: no visible global function definition for 'lines'
plot_ETdiagnosis_isopleth: no visible global function definition for
  'par'
plot_ETdiagnosis_isopleth: no visible global function definition for
  'rainbow'
plot_ETdiagnosis_isopleth: no visible global function definition for
  'filled.contour'
regPB: no visible global function definition for 'coef'
regPB: no visible global function definition for 'lm'
regPB.ac: no visible global function definition for 'coef'
regPB.ac: no visible global function definition for 'lm'
regPB.ctsa: no visible global function definition for 'coef'
regPB.ctsa: no visible global function definition for 'lm'
Undefined global functions or variables:
  axis coef filled.contour legend lines lm par polygon rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "filled.contour", "legend", "lines",
             "par", "polygon")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
Note: found 5 marked UTF-8 strings
Package required but not available: 'smoof'

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 suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'tidyverse'

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

Packages suggested but not available for checking:
  'covr', 'lintr', 'httptest', 'devtools', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'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
Package required but not available: 'rio'

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

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 required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package required but not available: 'plotly'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rstanarm'

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

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.
'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.
Package suggested but not available for checking: 'animation'
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'rmarkdown'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'afex', 'brms', 'car', 'covr', 'rstanarm'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'heplots', 'car', 'alr4'
Package unavailable to check Rd xrefs: 'car'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'methods-supported-by-effects.Rnw' using knitr
kpsewhich: major issue: So far, you have not checked for updates as a MiKTeX user.
--- finished re-building 'methods-supported-by-effects.Rnw'

--- re-building 'partial-residuals.Rnw' using knitr
--- finished re-building 'partial-residuals.Rnw'

--- re-building 'predictor-effects-gallery.Rnw' using knitr
Quitting from lines 96-101 (predictor-effects-gallery.Rnw) 
Error: processing vignette 'predictor-effects-gallery.Rnw' failed with diagnostics:
there is no package called 'car'
--- failed re-building 'predictor-effects-gallery.Rnw'

SUMMARY: processing the following file failed:
  'predictor-effects-gallery.Rnw'

Error: Vignette re-building failed.
Execution halted
Malformed Title field: should not end in a period.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'kableExtra', 'ggpubr'
Running examples in 'EGAnet-Ex.R' failed
The error most likely occurred in:

> ### Name: dimStability
> ### Title: Dimension Stability Statistics from 'bootEGA'
> ### Aliases: dimStability
> 
> ### ** Examples
> 
> # Load data
> wmt <- wmt2[,7:24]
> 
> 
> # Estimate item stability statistics
> res <- dimStability(boot.wmt, orig.wc = ega.wmt$wc, item.stability = TRUE)
Computing results...Error in loadNamespace(x) : there is no package called 'ggpubr'
Calls: dimStability ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'tseries', 'quantmod'

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

Package suggested but not available for checking: 'eggCountsExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'EGRET'

Packages suggested but not available for checking: 'pkgdown', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dataRetrieval'

Packages suggested but not available for checking:
  'EGRETci', 'pkgdown', 'covr'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'snow'
  All declared Imports should be used.
Packages required but not available: 'wru', 'censusxy'

Packages suggested but not available for checking: 'opencage', 'tigris'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
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').
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'mathjaxr'
  All declared Imports should be used.
Packages required but not available: 'httr', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'curl', 'crul'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'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
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'usethis'
'LazyData' is specified without a 'data' directory
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

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 suggested but not available for checking:
  'covr', 'devtools', 'pkgdown'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'datasets'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'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: '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').
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'curl', 'httr'

Package suggested but not available for checking: 'hexSticker'

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: 'move'
Packages suggested but not available for checking: 'rstanarm', 'covr'
Package unavailable to check Rd xrefs: 'rstanarm'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'Matrix' 'Rtsne' 'uwot'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'car'
Note: found 62 marked UTF-8 strings
Package which this enhances but not available for checking: 'PPtree'
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'MASS' 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages required but not available: 'nnfor', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 50 marked Latin-1 strings
License components which are templates and need '+ file LICENSE':
  MIT
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'jsonld'

Packages suggested but not available for checking: 'covr', 'rdflib'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'emld'

Packages suggested but not available for checking: 'taxadb', 'covr', 'EML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' calls to packages already attached by Depends:
  'clusterSim' 'earth'
  Please remove these calls from your code.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'clusterSim' 'earth'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
distance: no visible global function definition for
  'data.Normalization'
emmatn: no visible global function definition for 'runif'
estimateModel: no visible global function definition for 'as.formula'
estimateModel: no visible global function definition for 'earth'
estimateModel: no visible global function definition for 'plotmo'
estimateModel: no visible global function definition for 'predict'
mutation: no visible global function definition for 'runif'
plot.emma: no visible global function definition for 'colorRampPalette'
plot.emma: no visible global function definition for 'par'
plot.emma: no visible global function definition for 'persp'
plot.emma: no visible global function definition for 'points'
plot.emma: no visible global function definition for 'trans3d'
Undefined global functions or variables:
  as.formula colorRampPalette data.Normalization earth par persp plotmo
  points predict runif trans3d
Consider adding
  importFrom("grDevices", "colorRampPalette", "trans3d")
  importFrom("graphics", "par", "persp", "points")
  importFrom("stats", "as.formula", "predict", "runif")
to your NAMESPACE file.
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
Packages suggested but not available for checking: 'brms', 'car'

Package which this enhances but not available for checking: 'rstanarm'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'DESeq2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 23639 marked Latin-1 strings
Package required but not available: 'sampleSelection'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ExactMultinomialTest: no visible global function definition for
  'dmultinom'
ExactMultinomialTest : <anonymous>: no visible global function
  definition for 'dmultinom'
ExactMultinomialTestChisquare : <anonymous>: no visible global function
  definition for 'dmultinom'
MonteCarloMultinomialTest: no visible global function definition for
  'rmultinom'
MonteCarloMultinomialTest: no visible global function definition for
  'flush.console'
MonteCarloMultinomialTestChisquare: no visible global function
  definition for 'rmultinom'
MonteCarloMultinomialTestChisquare: no visible global function
  definition for 'flush.console'
multinomial.test: no visible global function definition for
  'flush.console'
plotMultinom: no visible global function definition for 'barplot'
plotMultinom: no visible global function definition for 'mtext'
Undefined global functions or variables:
  barplot dmultinom flush.console mtext rmultinom
Consider adding
  importFrom("graphics", "barplot", "mtext")
  importFrom("stats", "dmultinom", "rmultinom")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Packages required but not available: 'httr', 'V8'

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
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rgdal' 'rgeos'
  All declared Imports should be used.
Package required but not available: 'rangeModelMetadata'

Packages suggested but not available for checking: 'spocc', 'devtools'

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

Package suggested but not available for checking: 'ecospat'

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 required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'EnsemblePCReg-Ex.R' failed
The error most likely occurred in:

> ### Name: epcreg.save
> ### Title: Custom Functions for Disk I/O in 'EnsemblePCReg' Package
> ### Aliases: epcreg.save epcreg.load
> 
> ### ** Examples
> 
> data(servo)
> myformula <- class~motor+screw+pgain+vgain
> perc.train <- 0.7
> index.train <- sample(1:nrow(servo), size = round(perc.train*nrow(servo)))
> data.train <- servo[index.train,]
> data.predict <- servo[-index.train,]
> est <- epcreg(myformula, data.train, ncores=2
+   , baselearner.control=epcreg.baselearner.control(
+     baselearners="knn"
+     , baselearner.configs = make.configs("knn"
+       , config.df = expand.grid(kernel = "rectangular"
+         , k = c(5, 10)))), filemethod = TRUE)
running in parallel mode, using 2 cores
CV training of base learners...
binding predictions from all base learners...finished
finished CV training of base learners
processing fold 1 of 5 
processing fold 2 of 5 
processing fold 3 of 5 
processing fold 4 of 5 
processing fold 5 of 5 
> epcreg.save(est, "somefile")
> rm(est) # alternatively, exit and re-launch R session
> est.loaded <- epcreg.load("somefile")
Error in epcreg.load("somefile") : 
  unexpected multiple directories in tar filepaths
Execution halted
Package required but not available: 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'RCurl' 'bitops' 'rjson'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'ggpubr'

Package suggested but not available for checking: 'pkgdown'

See section 'The DESCRIPTION file' 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
Package required but not available: 'drc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'animation'

Packages suggested but not available for checking:
  'xcms', 'MSnbase', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'concaveman'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'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'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  report.c:1466:31: warning: '%02d' directive writing between 2 and 11 bytes into a region of size between 1 and 8 [-Wformat-overflow=]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/epanet2toolkit/epanet2toolkit.Rcheck/00install.out' for details.
Package required but not available: 'tidyverse'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'colorspace'
  All declared Imports should be used.
'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
Packages required but not available: 'httr', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
Package required but not available: 'ggmap'

Package suggested but not available for checking: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'devtools', 'usethis', 'pkgdown', 'lintr', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'kableExtra'
Packages suggested but not available for checking: 'epidict', 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'forecast', 'imputeTS', 'statnet'
Packages required but not available: 'tergm', 'tergmLite'

Package suggested but not available for checking: 'ndtv'

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

Packages suggested but not available for checking:
  'EpiSoon', 'forecastHybrid', 'kableExtra', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages unavailable to check Rd xrefs: 'ilc', 'demography'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dagitty', 'ggdag'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'DT' 'ggplot2' 'knitr' 'pander'
  All declared Imports should be used.
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
Package required but not available: 'kableExtra'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Packages suggested but not available for checking: 'covr', 'pkgdown'
Packages suggested but not available for checking: 'usethis', 'covr'
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
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'FSA', 'covr'
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.
'library' or 'require' call to 'qtl' which was already attached by Depends.
  Please remove these calls from your code.
Unexported objects imported by ':::' calls:
  'qtl:::c.scanone' 'qtl:::plot.scanone'
  See the note in ?`:::` about the use of this operator.
The following files contain a license that requires
distribution of original sources:
  'upgreek.sty'
Please ensure that you have complied with it.
Packages suggested but not available for checking:
  'texPreview', 'covr', 'forecast'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  boundary (singular) fit: see ?isSingular
  boundary (singular) fit: see ?isSingular
  == Skipped tests ===============================================================
  * On CRAN (21)
  
  == Failed tests ================================================================
  -- Error (test-forecast-arima.R:1:1): (code run outside of `test_that()`) ------
  Error: there is no package called 'forecast'
  Backtrace:
      x
   1. \-base::library(forecast) test-forecast-arima.R:1:0
  
  [ FAIL 1 | WARN 0 | SKIP 21 | PASS 15 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'forecast-arima.Rmd' using rmarkdown
Quitting from lines 29-37 (forecast-arima.Rmd) 
Error: processing vignette 'forecast-arima.Rmd' failed with diagnostics:
there is no package called 'forecast'
--- failed re-building 'forecast-arima.Rmd'

--- re-building 'intro-equatiomatic.Rmd' using rmarkdown
--- finished re-building 'intro-equatiomatic.Rmd'

--- re-building 'lme4-lmer.Rmd' using rmarkdown
--- finished re-building 'lme4-lmer.Rmd'

--- re-building 'plotting-integration.Rmd' using rmarkdown
`geom_smooth()` using formula 'y ~ x'
Warning: Removed 2 rows containing non-finite values (stat_smooth).
Warning: Removed 2 rows containing missing values (geom_point).
`geom_smooth()` using formula 'y ~ x'
Warning: Removed 2 rows containing non-finite values (stat_smooth).
Warning: Removed 2 rows containing missing values (geom_point).
`geom_smooth()` using formula 'y ~ x'
Warning: Removed 2 rows containing non-finite values (stat_smooth).
Warning: Removed 2 rows containing missing values (geom_point).
Warning in is.na(x) :
  is.na() applied to non-(list or vector) of type 'expression'
--- finished re-building 'plotting-integration.Rmd'

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

SUMMARY: processing the following file failed:
  'forecast-arima.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
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
Package suggested but not available for checking: 'mzR'
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'systemfit', 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'statnet', 'btergm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Running 'testthat.R'
Package required but not available: 'texreg'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Subdirectory 'ergm.rank/src' contains apparent object files/libraries
  include_stubs.o init.o wtMHproposals.o
Object files/libraries should no OK
Package has no Sweave vignette sources and no VignetteBuilder field.
Packages suggested but not available for checking: 'tergm', 'covr'
Package unavailable to check Rd xrefs: 'tergm'
Namespace in Imports field not imported from: 'signal'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'R6' 'rlang'
  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: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'parallel'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

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

Package suggested but not available for checking: 'covr'

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

Package suggested but not available for checking: 'covr'

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
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').
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'datamods'

Package suggested but not available for checking: 'rio'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'brms'

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: 'covr'
Namespace in Imports field not imported from: 'matrixStats'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'AER', 'ivpack', 'modelsummary', 'car'

Package which this enhances but not available for checking: 'texreg'
Packages unavailable to check Rd xrefs: 'car', 'texreg'
Running examples in 'estimatr-Ex.R' failed
The error most likely occurred in:

> ### Name: lh_robust
> ### Title: Linear Hypothesis for Ordinary Least Squares with Robust
> ###   Standard Errors
> ### Aliases: lh_robust
> 
> ### ** Examples
> 
> 
> library(fabricatr)
> dat <- fabricate(
+   N = 40,
+   y = rpois(N, lambda = 4),
+   x = rnorm(N),
+   z = rbinom(N, 1, prob = 0.4),
+   clusterID = sample(1:4, 40, replace = TRUE)
+ )
> 
> # Default variance estimator is HC2 robust standard errors
> lhro <- lh_robust(y ~ x + z, data = dat, linear_hypothesis = "z + 2x = 0")
Loading required namespace: car
Failed with error:  'there is no package called 'car''
Error in loadNamespace(x) : there is no package called 'car'
Calls: lh_robust ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'sleep.R'
  Comparing 'sleep.Rout' to 'sleep.Rout.save' ... OK
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   2.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     \-base:::withOneRestart(expr, restarts[[1L]])
   4.       \-base:::doWithOneRestart(return(expr), restart)
  -- Error (test-stata-output.R:97:3): iv_robust matches stata -------------------
  Error: there is no package called 'AER'
  Backtrace:
      x
   1. \-base::loadNamespace(x) test-stata-output.R:97:2
   2.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     \-base:::withOneRestart(expr, restarts[[1L]])
   4.       \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 11 | WARN 0 | SKIP 8 | PASS 1007 ]
  Error: Test failures
  Execution halted
'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.
Package required but not available: 'quantmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
etc.diff: no visible global function definition for 'model.frame'
etc.diff: no visible binding for global variable 'sd'
etc.diff: no visible global function definition for 'qt'
etc.diff: no visible global function definition for 'pt'
etc.diff: no visible global function definition for 'wilcox.test'
etc.rat: no visible global function definition for 'model.frame'
etc.rat: no visible binding for global variable 'sd'
etc.rat: no visible global function definition for 'qt'
etc.rat: no visible global function definition for 'pt'
Undefined global functions or variables:
  model.frame pt qt sd wilcox.test
Consider adding
  importFrom("stats", "model.frame", "pt", "qt", "sd", "wilcox.test")
to your NAMESPACE file.
Package required but not available: 'httr'

Package suggested but not available for checking: 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rvest', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'rvest'

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: 'covr'
Namespace in Imports field not imported from: 'RSQLite'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'rvest', 'pdftools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'httr', 'RefManageR'

Packages suggested but not available for checking:
  'covr', 'rvest', 'usethis'

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

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:
  'covr', 'ggalt', 'shinytest'
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == Failed tests ================================================================
  -- Error (test-explore-scenarios.R:4:1): (code run outside of `test_that()`) ---
  Error: there is no package called 'shinytest'
  Backtrace:
      x
   1. \-base::library(shinytest) test-explore-scenarios.R:4:0
  -- Error (test-openfair-example.R:3:1): (code run outside of `test_that()`) ----
  Error: there is no package called 'shinytest'
  Backtrace:
      x
   1. \-base::library(shinytest) test-openfair-example.R:3:0
  
  [ FAIL 2 | WARN 1 | SKIP 3 | PASS 138 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: 'EnvStats'
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
powerSet : <anonymous>: no visible global function definition for
  'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
mposterior: no visible global function definition for 'optim'
rl.pred: no visible global function definition for 'matplot'
rl.pst: no visible binding for global variable 'quantile'
rl.pst: no visible global function definition for 'matplot'
Undefined global functions or variables:
  matplot optim quantile
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
Packages required but not available: 'EventDetectR', 'plotly'

Packages suggested but not available for checking: 'shinytest', 'devtools'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rio'
Error(s) in re-building vignettes:
  ...
--- re-building 'example-analysis.Rmd' using rmarkdown
Quitting from lines 302-313 (example-analysis.Rmd) 
Error: processing vignette 'example-analysis.Rmd' failed with diagnostics:
there is no package called 'rio'
--- failed re-building 'example-analysis.Rmd'

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

--- re-building 'stata-sas-comparason.Rmd' using rmarkdown
--- finished re-building 'stata-sas-comparason.Rmd'

SUMMARY: processing the following file failed:
  'example-analysis.Rmd'

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

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

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
evolvabilityBetaMCMC : <anonymous>: no visible binding for global
  variable 'median'
evolvabilityBetaMCMC: no visible binding for global variable 'median'
evolvabilityBetaMCMC2: no visible binding for global variable 'median'
evolvabilityMeans: no visible global function definition for 'var'
evolvabilityMeansMCMC : <anonymous>: no visible global function
  definition for 'var'
evolvabilityMeansMCMC: no visible binding for global variable 'median'
randomBeta: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  median rnorm var
Consider adding
  importFrom("stats", "median", "rnorm", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: 'evd'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DPOT: no visible global function definition for 'optim'
mop.rho: no visible global function definition for 'median'
Undefined global functions or variables:
  median optim
Consider adding
  importFrom("stats", "median", "optim")
to your NAMESPACE file.
'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.
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.
'LazyData' is specified without a 'data' directory
Package required but not available: 'usethis'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'magick'
plot.pgrid: no visible global function definition for 'image'
statistic.cv: no visible global function definition for 'quantile'
statistic.sim: no visible global function definition for 'contourLines'
Undefined global functions or variables:
  contourLines image quantile
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "image")
  importFrom("stats", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'js'
Package suggested but not available for checking: 'INLA'
Package required but not available: 'brms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking: 'covr', 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gage'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'kableExtra', 'rio'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'polynom'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'smoof'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of 'env' to 'envir'
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of 'env' to 'envir'
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  'wid' to 'width'
MS: 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'FactoMineR', 'GDAtools'
Packages unavailable to check Rd xrefs: 'FactoMineR', 'GDAtools'
Package required but not available: 'repmis'

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.
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
Package suggested but not available for checking: 'covr'
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.
exbio: no visible global function definition for 'as.formula'
exbio: no visible global function definition for 'glm'
exbio: no visible binding for global variable 'gaussian'
exbio: no visible global function definition for 'Gamma'
exbio: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  Gamma as.formula gaussian glm pchisq
Consider adding
  importFrom("stats", "Gamma", "as.formula", "gaussian", "glm", "pchisq")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
font_install: no visible global function definition for
  'installed.packages'
font_install: no visible global function definition for
  'install.packages'
fonttable_add: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  install.packages installed.packages write.csv
Consider adding
  importFrom("utils", "install.packages", "installed.packages",
             "write.csv")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'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').
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.
Packages suggested but not available for checking: 'covr', 'exuberdata'
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'drc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  p$labels$y not identical to "count".
  Attributes: < Modes: list, NULL >
  Attributes: < Lengths: 1, 0 >
  Attributes: < names for target but not for current >
  Attributes: < current is not list-like >
  -- Failure (test_two_category_tally.R:19:3): y axis is labeled 'count' ---------
  p$labels$y not identical to "count".
  Attributes: < Modes: list, NULL >
  Attributes: < Lengths: 1, 0 >
  Attributes: < names for target but not for current >
  Attributes: < current is not list-like >
  
  [ FAIL 8 | WARN 1 | SKIP 0 | PASS 79 ]
  Error: Test failures
  Execution halted
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'textreadr'

Packages suggested but not available for checking: 'rvest', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'tsibble'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

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.
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.
'LazyData' is specified without a 'data' directory
Package required but not available: 'prophet'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'forecast'
Package unavailable to check Rd xrefs: 'forecast'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   2.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     \-base:::withOneRestart(expr, restarts[[1L]])
   4.       \-base:::doWithOneRestart(return(expr), restart)
  -- Error (test-rw.R:79:3): SNAIVE ----------------------------------------------
  Error: there is no package called 'forecast'
  Backtrace:
      x
   1. \-base::loadNamespace(x) test-rw.R:79:2
   2.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     \-base:::withOneRestart(expr, restarts[[1L]])
   4.       \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 5 | WARN 10 | SKIP 1 | PASS 53 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'animation'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'FactoMineR'

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

Packages suggested but not available for checking: 'missMDA', 'Factoshiny'

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

Package suggested but not available for checking: 'survminer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'car'
Package unavailable to check Rd xrefs: 'car'
Note: found 5 marked Latin-1 strings
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'FactoMineR', 'FactoInvestigate', 'missMDA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  'RCurl' 'RJSONIO' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createFactualConnection: no visible global function definition for
  'new'
factualGetSchema: no visible global function definition for 'fromJSON'
factualRead: no visible global function definition for 'curlEscape'
factualRead: no visible global function definition for 'fromJSON'
processFactualReadJSON: no visible global function definition for 'new'
processFactualSchemaJSON: no visible global function definition for
  'new'
Undefined global functions or variables:
  curlEscape fromJSON 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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Skipping vignette re-building
Packages suggested but not available for checking:
  'covr', 'devtools', 'lintr', 'packager', 'rasciidoc', 'usethis'

VignetteBuilder package required for checking but not installed: 'rasciidoc'
Namespace in Imports field not imported from: 'fritools'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running 'runit.R'
Running the tests in 'tests/runit.R' failed.
Last 13 lines of output:
  --------------------------- 
  Test file: C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fakemake/fakemake.Rcheck/fakemake/runit_tests/runit-throw.R 
  test_exception: (1 checks) ... OK (0 seconds)
  --------------------------- 
  Test file: C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fakemake/fakemake.Rcheck/fakemake/runit_tests/runit-xmake.R 
  test_make_full_tree: (5 checks) ... OK (0.08 seconds)
  test_make_missing: (2 checks) ... OK (0.04 seconds)
  test_make_newer: (2 checks) ... OK (1.05 seconds)
  test_make_phony: (3 checks) ... OK (2.07 seconds)
  test_make_prerequisite: (3 checks) ... OK (1.06 seconds)
  test_make_sink: (2 checks) ... OK (0.03 seconds)
  test_make_source_files: (0 checks) ... OK (0 seconds)
  test_make_unconditionally: (1 checks) ... OK (0.02 seconds)
  Error: RUnit failed.
  Execution halted
Errors in running code in vignettes:
when running code in 'Building_Packages.Rmd'
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'rasciidoc' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  'Building_Packages.Rmd' using 'UTF-8'... failed to complete the test
File 'fame/R/windows/zzz.R':
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section 'Good practice' in '?.onAttach'.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Note: found 179 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'OpenML'
'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
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'tidyhydat'

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

Package suggested but not available for checking: 'curl'

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: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'RobustGaSP'
  All declared Imports should be used.
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.
Package suggested but not available for checking: 'coxKM'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'rgdal'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File 'fastmatch/libs/x64/fastmatch.dll':
  Found non-API call to R: 'match5'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'car', 'alr3'
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'magrittr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
.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
Found the following file(s) containing GNU extensions:
  inst/Rcgi/Makefile
  src/Rcgi/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section 'Writing portable
packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Packages required but not available: 'set', 'do', 'car', 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'DESeq2'
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking: 'crul', 'curl', 'httr'
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  > test_check("fauxpas")
  Loading required package: fauxpas
  == Skipped tests ===============================================================
  * On CRAN (8)
  
  == Failed tests ================================================================
  -- Error (test-http_star.R:4:1): (code run outside of `test_that()`) -----------
  Error: there is no package called 'crul'
  Backtrace:
      x
   1. \-base::library("crul") test-http_star.R:4:0
  
  [ FAIL 1 | WARN 0 | SKIP 8 | PASS 0 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'httr'
Package suggested but not available for checking: 'curl'
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'httr'
'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 suggested but not available for checking: 'covr', 'hasseDiagram'
Package suggested but not available for checking: 'covr'
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.
PTSingleAssetBarrierOption2: no visible global function definition for
  'new'
newton: no visible global function definition for 'abline'
probInRange: no visible global function definition for 'pnorm'
shortfall_risk: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline new pnorm
Consider adding
  importFrom("graphics", "abline")
  importFrom("methods", "new")
  importFrom("stats", "pnorm")
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
Packages suggested but not available for checking:
  'plotly', 'ProjectionBasedClustering', 'smacof', 'CEC'
Package unavailable to check Rd xrefs: 'plotly'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Note: found 75 marked UTF-8 strings
Namespace in Imports field not imported from: 'fdapace'
  All declared Imports should be used.
Note: found 76 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required but not available: 'usethis'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'randomcoloR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
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
Package suggested but not available for checking: 'covr'
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
Package suggested but not available for checking: 'usethis'
Note: found 20 marked UTF-8 strings
Packages required but not available: 'devtools', 'curl', 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rvest', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'texreg'
Package unavailable to check Rd xrefs: 'texreg'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > test_check("feisr")
  == Failed tests ================================================================
  -- Error (test_EstimationResults.R:221:3): extract feis (for texreg) -----------
  Error: there is no package called 'texreg'
  Backtrace:
      x
   1. +-feisr:::extract.feis(feis1.mod) test_EstimationResults.R:221:2
   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 168 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'feisr-vignette.Rmd' using rmarkdown
Quitting from lines 118-124 (feisr-vignette.Rmd) 
Error: processing vignette 'feisr-vignette.Rmd' failed with diagnostics:
there is no package called 'texreg'
--- failed re-building 'feisr-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: 'curl'

Package suggested but not available for checking: 'covr'

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 suggested but not available for checking: 'covr', 'pkgdown'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'rvest'

See section 'The DESCRIPTION file' 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.
Package suggested but not available for checking: 'car'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'covr', 'curl', 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'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.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'kableExtra'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  'mvtnorm' 'numDeriv'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dmymvnorm: no visible global function definition for 'dmvnorm'
dmymvt: no visible global function definition for 'dmvt'
gof.test: no visible global function definition for 'quantile'
gof.test : ecdf: no visible global function definition for 'mecdf'
gof.test: no visible global function definition for 'jacobian'
gof.test: no visible global function definition for 'var'
gradCdfT: no visible global function definition for 'dt'
gradCdfT: no visible global function definition for 'pt'
gradCdfT: no visible global function definition for 'pmvt'
influFun: no visible global function definition for 'jacobian'
mult.sim: no visible global function definition for 'rnorm'
plackettFormula: no visible global function definition for 'pt'
plackettFormula: no visible global function definition for 'pmvt'
pmymvnorm: no visible global function definition for 'GenzBretz'
pmymvnorm: no visible global function definition for 'TVPACK'
pmymvnorm : <anonymous>: no visible global function definition for
  'pmvnorm'
pmymvt: no visible global function definition for 'GenzBretz'
pmymvt: no visible global function definition for 'TVPACK'
pmymvt : <anonymous>: no visible global function definition for 'pmvt'
rmymvnorm: no visible global function definition for 'rmvnorm'
rmymvt: no visible global function definition for 'rmvt'
Undefined global functions or variables:
  GenzBretz TVPACK dmvnorm dmvt dt jacobian mecdf pmvnorm pmvt pt
  quantile rmvnorm rmvt rnorm var
Consider adding
  importFrom("stats", "dt", "pt", "quantile", "rnorm", "var")
to your NAMESPACE file.
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.
Found the following significant warnings:
  fgsg.h:96:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:202:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:347:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:460:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:516:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:636:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:717:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:852:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:996:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FGSG/FGSG.Rcheck/00install.out' for details.
Package required but not available: 'httr'

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.
Namespace in Imports field not imported from: 'numDeriv'
  All declared Imports should be used.
Packages required but not available: 'golem', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'concaveman'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Package required but not available: 'reqres'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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').
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rstan', 'survminer'
Package unavailable to check Rd xrefs: 'survminer'
Running examples in 'finalfit-Ex.R' failed
The error most likely occurred in:

> ### Name: surv_plot
> ### Title: Plot survival curves with number-at-risk table
> ### Aliases: surv_plot
> 
> ### ** Examples
> 
> library(finalfit)
> 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

> 
> # Survival plot
> data(colon_s)
> explanatory = c("perfor.factor")
> dependent = "Surv(time, status)"
> colon_s %>%
+   surv_plot(dependent, explanatory, xlab="Time (days)", pval=TRUE, legend="none")
Error in loadNamespace(x) : there is no package called 'survminer'
Calls: %>% ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Backtrace:
      x
   1. +-testthat::expect_is(...) test_plots.R:23:8
   2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
   3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
   4. +-finalfit::surv_plot(colon_s, "Surv(time, status)", "age.factor")
   5. | \-base::do.call(survminer::ggsurvplot, args)
   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 1 | WARN 10 | SKIP 0 | PASS 130 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'quantmod', 'TTR'

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

Package suggested but not available for checking: 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'EML'

Package suggested but not available for checking: 'crul'

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

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: 'covr'
Namespace in Imports field not imported from: 'yardstick'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcmdr', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'rvest', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tseries'
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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.
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'DiagrammeRsvg'
'library' or 'require' call to 'tkrplot' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'methods' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages required but not available:
  'rstan', 'fishualize', 'rfishbase', 'httr', 'curl'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Note: found 7 marked UTF-8 strings
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
Package suggested but not available for checking: 'rfishbase'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'community-analysis.Rmd' using rmarkdown
--- finished re-building 'community-analysis.Rmd'

--- re-building 'comparative-analysis.Rmd' using rmarkdown
Quitting from lines 41-48 (comparative-analysis.Rmd) 
Error: processing vignette 'comparative-analysis.Rmd' failed with diagnostics:
there is no package called 'rfishbase'
--- failed re-building 'comparative-analysis.Rmd'

SUMMARY: processing the following file failed:
  'comparative-analysis.Rmd'

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

Packages suggested but not available for checking: 'rfishbase', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package in Depends field not imported from: 'FitAR'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
FitARMA: no visible global function definition for 'PacfDL'
FitARMA: no visible global function definition for 'GetARMeanMLE'
FitARMA: no visible global function definition for
  'BackcastResidualsAR'
FitARMA: no visible global function definition for 'LjungBoxTest'
GetFitARMA: no visible global function definition for 'LoglikelihoodAR'
GetFitARMA: no visible global function definition for 'ChampernowneD'
GetFitARMA : EntropyARMA: no visible global function definition for
  'PacfToAR'
GetFitARMA : EntropyARMA: no visible global function definition for
  'PacfDL'
GetFitARMA : EntropyARMA: no visible global function definition for
  'FastLoglikelihoodAR'
GetFitARMA: no visible global function definition for 'PacfToAR'
InformationMatrixARMA: no visible global function definition for
  'InvertibleQ'
TacvfARMA: no visible global function definition for 'InvertibleQ'
Undefined global functions or variables:
  BackcastResidualsAR ChampernowneD FastLoglikelihoodAR GetARMeanMLE
  InvertibleQ LjungBoxTest LoglikelihoodAR PacfDL PacfToAR
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.
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'varian', 'exactextractr'

Package suggested but not available for checking: 'magick'

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: 'devtools', 'covr'
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'MASS' 'XML' 'gglasso' 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ihs'
Packages suggested but not available for checking: 'doMC', '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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'rstudioapi'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'rvest'

Packages suggested but not available for checking: 'covr', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'fivethirtyeightdata'
Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
Note: found 584 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'pkgdown'
Package required but not available: 'curl'

Package suggested but not available for checking: 'NFCP'

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', 'plotly', 'smoof'
Running examples in 'flacco-Ex.R' failed
The error most likely occurred in:

> ### Name: plotBarrierTree2D
> ### Title: Plot Barrier Tree in 2D
> ### Aliases: plotBarrierTree2D
> 
> ### ** Examples
> 
> # create a feature object
> X = createInitialSample(n.obs = 900, dim = 2)
> f = smoof::makeAckleyFunction(dimensions = 2)
Error in loadNamespace(x) : there is no package called 'smoof'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'test-features.R'
  Running 'test-general.R'
Running the tests in 'tests/test-general.R' failed.
Last 13 lines of output:
  > test_check("flacco", filter = "^base")
  Loading required package: flacco
  == Failed tests ================================================================
  -- Error (test-base-printFeatureObject.R:68:3): Usage of regular and smoof functions --
  Error: there is no package called 'smoof'
  Backtrace:
      x
   1. \-base::loadNamespace(x) test-base-printFeatureObject.R:68:2
   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 152 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'eurostat'
Namespaces in Imports field not imported from:
  'dplyr' 'evaluate' 'ggplot2'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'paletteer'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: 'tidyr'
  All declared Imports should be used.
Note: found 82 marked UTF-8 strings
Package required but not available: 'httr'

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: 'covr'
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'magick'
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
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'devtools', 'multipanelfigure'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'covr', 'tidyverse', 'plotly'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'alternative.Rmd' using rmarkdown
--- finished re-building 'alternative.Rmd'

--- re-building 'exactness.Rmd' using rmarkdown
Quitting from lines 12-18 (exactness.Rmd) 
Error: processing vignette 'exactness.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'exactness.Rmd'

--- re-building 'flipr.Rmd' using rmarkdown
Quitting from lines 20-31 (flipr.Rmd) 
Error: processing vignette 'flipr.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'flipr.Rmd'

--- re-building 'pvalue-function.Rmd' using rmarkdown
Quitting from lines 20-43 (pvalue-function.Rmd) 
Error: processing vignette 'pvalue-function.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'pvalue-function.Rmd'

SUMMARY: processing the following files failed:
  'exactness.Rmd' 'flipr.Rmd' 'pvalue-function.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'BiodiversityR'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'kableExtra'

Package suggested but not available for checking: 'covr'

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

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: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'stats' 'utils'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'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.
Packages required but not available: 'FactoMineR', 'factoextra'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'curl', 'httr', 'rvest'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Note: found 41 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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
'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.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Note: found 234 marked UTF-8 strings
Packages suggested but not available for checking: 'devtools', 'covr'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'footprint.Rmd' using rmarkdown
Quitting from lines 21-25 (footprint.Rmd) 
Error: processing vignette 'footprint.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'footprint.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'doMC'
Package required but not available: 'forecast'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'dtplyr'
  All declared Imports should be used.
Package required but not available: 'tseries'

Package suggested but not available for checking: 'forecTheta'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'PSF', 'decomposedPSF', 'imputeTestbench', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'mathjaxr'
  All declared Imports should be used.
Packages required but not available: 'forecast', 'tseries'

See section 'The DESCRIPTION file' 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:
  '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.
Namespace in Imports field not imported from: 'RColorBrewer'
  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:
  'blockCV' 'patchwork' 'proxy'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'systemfit', 'car'

Package suggested but not available for checking: 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Package suggested but not available for checking: 'FactoMineR'
Error(s) in re-building vignettes:
  ...
--- re-building 'Overview.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 25-33 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
there is no package called 'FactoMineR'
--- failed re-building 'Overview.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'devtools'
Namespace in Imports field not imported from: 'spatstat'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without 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.
GenObs: no visible global function definition for 'rnorm'
GenObs.T: no visible global function definition for 'rt'
MeasL: no visible global function definition for 'rbeta'
OutDet: no visible global function definition for 'median'
RanCur: no visible global function definition for 'rnorm'
init: no visible global function definition for 'prcomp'
Undefined global functions or variables:
  median prcomp rbeta rnorm rt
Consider adding
  importFrom("stats", "median", "prcomp", "rbeta", "rnorm", "rt")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'pdftools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2', 'mvoutlier'
Packages required but not available: 'expsmooth', 'fma', 'forecast'

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

See section 'The DESCRIPTION file' 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.
Packages required but not available:
  'forecast', 'fma', 'expsmooth', 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'forecast'
'library' or 'require' calls in package code:
  'pcaPP' 'snowFT' 'wavelets'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ComputeDCT2FFT: no visible global function definition for 'fft'
ComputeSemipgramFFT: no visible global function definition for 'fft'
WaveVarFD: no visible global function definition for 'modwt'
do.fd.estimate: no visible global function definition for
  'performParallel'
do.fd.estimate2d.simple: no visible global function definition for
  'median'
fd.Genton: no visible global function definition for 'qn'
fd.estimate.matrix: no visible global function definition for
  'performParallel'
fd.plot.legend: no visible global function definition for 'legend'
fd.plot.loglog: no visible global function definition for 'points'
fd.plot.loglog: no visible global function definition for 'abline'
summary.FractalDim: no visible binding for global variable 'sd'
Undefined global functions or variables:
  abline fft legend median modwt performParallel points qn sd
Consider adding
  importFrom("graphics", "abline", "legend", "points")
  importFrom("stats", "fft", "median", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'plotly'
'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: '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.
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'smacof'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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
Packages required but not available: 'httr', 'rvest'

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: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'survminer'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: 'FrF2'
  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
Note: found 50 marked UTF-8 strings
Packages suggested but not available for checking:
  'devtools', 'packager', 'whoami'
Package unavailable to check Rd xrefs: 'devtools'
Package required but not available: 'ggpubr'

Packages suggested but not available for checking:
  'covr', 'dggrids', 'INLA'

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

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.
Package unavailable to check Rd xrefs: 'FSA'
Package required but not available: 'car'

Packages suggested but not available for checking:
  'marked', 'pkgdown', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'car', 'foba', 'rrlda'
Packages suggested but not available for checking:
  'covr', 'RTCGA.rnaseq', 'lintr', 'pkgdown'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(entropy)
  
  Attaching package: 'entropy'
  
  The following object is masked from 'package:FSelectorRcpp':
  
      discretize
  
  > library(lintr)
  Error in library(lintr) : there is no package called 'lintr'
  Execution halted
Namespaces in Imports field not imported from:
  'class' 'mlbench' 'neuralnet' 'rpart'
  All declared Imports should be used.
Packages required but not available: 'googlesheets', 'readtext'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'plotly'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lintr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > # required packages
  > library(testthat)
  > library(fstcore)
  > library(lintr)
  Error in library(lintr) : there is no package called 'lintr'
  Execution halted
Package suggested but not available for checking: 'lintr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'meboot'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'crul', 'rplos', 'rcrossref', 'microdemic', 'aRxiv', 'rentrez',
  'pdftools'

Packages suggested but not available for checking: 'pubchunks', 'vcr'

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.
Package required but not available: 'ggpubr'

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: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'geometry'
  All declared Imports should be used.
.FunFEM.main: no visible global function definition for 'kmeans'
.FunFEM.main: no visible global function definition for 'rmultinom'
.FunFEM.main: no visible global function definition for 'cutree'
.FunFEM.main: no visible global function definition for 'hclust'
.FunFEM.main: no visible global function definition for 'dist'
.FunFEM.main: no visible global function definition for 'par'
.mstep: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov cutree dist hclust kmeans par rmultinom
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "cov", "cutree", "dist", "hclust", "kmeans",
             "rmultinom")
to your NAMESPACE file.
Note: found 120 marked UTF-8 strings
Note: found 1 marked UTF-8 string
'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.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'pROC' 'reshape2' 'survival'
  All declared Imports should be used.
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  'd' to 'digits'
probRejTies: no visible binding for global variable 'nn'
Undefined global functions or variables:
  nn
Packages suggested but not available for checking: 'rvest', 'covr'
'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.
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking: 'covr', 'modelsummary'
Error(s) in re-building vignettes:
  ...
--- re-building 'fwildclusterboot.Rmd' using rmarkdown
fixest 0.9.0, BREAKING changes! (Permanently remove this message with fixest_startup_msg(FALSE).) 
- In i():
    + the first two arguments have been swapped! Now it's i(factor_var, continuous_var) for interactions. 
    + argument 'drop' has been removed (put everything in 'ref' now).
- In feglm(): 
    + the default family becomes 'gaussian' to be in line with glm(). Hence, for Poisson estimations, please use fepois() instead.
Loading required package: Matrix
Quitting from lines 87-97 (fwildclusterboot.Rmd) 
Error: processing vignette 'fwildclusterboot.Rmd' failed with diagnostics:
there is no package called 'modelsummary'
--- failed re-building 'fwildclusterboot.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'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.
Package required but not available: 'KEGGREST'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'cgdsr'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
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.
Packages required but not available:
  'rosm', 'ggmap', 'ggspatial', 'prettymapr'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' 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.
Packages required but not available: 'crul', 'httr'

Packages suggested but not available for checking: 'covr', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'DT' 'webshot'
  All declared Imports should be used.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Packages suggested but not available for checking: 'forecast', 'car'
Error(s) in re-building vignettes:
  ...
--- re-building 'AirbagEffectiveness.Rmd' using rmarkdown
--- finished re-building 'AirbagEffectiveness.Rmd'

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

--- re-building 'resampling.Rmd' using rmarkdown
Quitting from lines 126-142 (resampling.Rmd) 
Error: processing vignette 'resampling.Rmd' failed with diagnostics:
there is no package called 'car'
--- failed re-building 'resampling.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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
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').
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'googleAnalyticsR', 'rvest'

Packages suggested but not available for checking: 'devtools', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'kableExtra'
Note: found 2 marked UTF-8 strings
Package suggested but not available for checking: 'plotly'
Packages suggested but not available for checking:
  'tidyverse', 'modeltime', 'timetk', 'covr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Loading required package: parsnip
  Loading required package: rugarch
  Loading required package: parallel
  
  Attaching package: 'rugarch'
  
  The following object is masked from 'package:stats':
  
      sigma
  
  Loading required package: rmgarch
  > 
  > library(timetk)
  Error in library(timetk) : there is no package called 'timetk'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'getting-started.Rmd' using rmarkdown
Loading required package: parsnip
Loading required package: rugarch
Loading required package: parallel

Attaching package: 'rugarch'

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

    sigma

Loading required package: rmgarch
Quitting from lines 43-47 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
there is no package called 'timetk'
--- failed re-building 'getting-started.Rmd'

--- re-building 'tuning_univariate_algorithms.Rmd' using rmarkdown
Loading required package: parsnip
Loading required package: rugarch
Loading required package: parallel

Attaching package: 'rugarch'

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

    sigma

Loading required package: rmgarch
Quitting from lines 43-47 (tuning_univariate_algorithms.Rmd) 
Error: processing vignette 'tuning_univariate_algorithms.Rmd' failed with diagnostics:
there is no package called 'timetk'
--- failed re-building 'tuning_univariate_algorithms.Rmd'

SUMMARY: processing the following files failed:
  'getting-started.Rmd' 'tuning_univariate_algorithms.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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

Package suggested but not available for checking: 'tidyverse'

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

Package suggested but not available for checking: 'covr'

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
'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.
Packages required but not available: 'curl', 'httr', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'curl'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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.
Packages suggested but not available for checking:
  'classGraph', 'Rgraphviz'
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.
Namespace in Imports field not imported from: 'raster'
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
Packages required but not available: 'httr', 'rvest'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'gcmr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

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

See section 'The DESCRIPTION file' 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.
DownloadGdelt: no visible global function definition for
  'packageVersion'
DownloadGdelt: no visible global function definition for
  'download.file'
GdeltZipToDataframe: no visible global function definition for
  'read.delim'
GdeltZipToDataframe: no visible global function definition for 'unzip'
GetSizeOfGDELT: no visible global function definition for 'read.delim'
IsValidGDELT: no visible global function definition for 'read.delim'
IsValidGDELT: no visible global function definition for 'md5sum'
NormEventCounts: no visible global function definition for
  'download.file'
NormEventCounts: no visible global function definition for 'read.csv'
Undefined global functions or variables:
  download.file md5sum packageVersion read.csv read.delim unzip
Consider adding
  importFrom("utils", "download.file", "packageVersion", "read.csv",
             "read.delim", "unzip")
to your NAMESPACE file.
Packages required but not available: 'rgbif', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magick', 'pdftools'

Packages suggested but not available for checking: 'ssh', 'stevedore'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'badger'

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: 'curl'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gdxrrw'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'AER', 'ivpack', 'covr'
Namespace in Imports field not imported from: 'rootSolve'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
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: 'sp'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
plot.rbga: no visible global function definition for 'par'
plot.rbga: no visible global function definition for 'hist'
plot.rbga: no visible global function definition for 'lines'
rbga: no visible global function definition for 'runif'
rbga: no visible global function definition for 'dnorm'
rbga.bin: no visible global function definition for 'dnorm'
rbga.bin: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm hist lines par runif
Consider adding
  importFrom("graphics", "hist", "lines", "par")
  importFrom("stats", "dnorm", "runif")
to your NAMESPACE file.
genmvnorm: 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: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking: 'genderdata', 'covr'

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: 'repmis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'annotate', 'GEOquery'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Packages required but not available: 'rentrez', 'httr', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Packages required but not available: 'Rgraphviz', 'gRain'

Package suggested but not available for checking: 'RHugin'

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

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: 'plotly'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: 'shinytest'
Namespace in Imports field not imported from: 'htmlwidgets'
  All declared Imports should be used.
Package required but not available: 'httr'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'exactextractr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'httr', 'rvest'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'geno2proteo-Ex.R' failed
The error most likely occurred in:

> ### Name: generatingCDSaaFile
> ### Title: Generating a file containing the DNA and AA sequences of all the
> ###   protein coding regions (CDSs) in a genome
> ### Aliases: generatingCDSaaFile
> 
> ### ** Examples
> 
>     # the data folder in this package
>     dataFolder = system.file("extdata", package="geno2proteo") 
> 
>     geneticCodeFile_line = file.path(dataFolder, 
+                                     "geneticCode_standardTable_lines.txt")
>     gtfFile = file.path(dataFolder, 
+                 "Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz")
>     DNAfastaFile =  file.path(dataFolder, 
+             "Homo_sapiens.GRCh37.74.dna.chromosome.16.fa_theFirst3p5M.txt.gz")
>     
>     outputFolder = tempdir(); # using the current folder as output folder
>     # calling the function.
>     generatingCDSaaFile(geneticCodeFile_line=geneticCodeFile_line, 
+         gtfFile=gtfFile, DNAfastaFile=DNAfastaFile, outputFolder=outputFolder)
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 2 did not have 7 elements
Calls: generatingCDSaaFile -> read.table -> scan
Execution halted
Running 'runTests.R'
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  ERROR in test_generatingCDSaaFile: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
    line 2 did not have 7 elements
  ERROR in test_genomicLocsToWholeDNASequence: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
    line 2 did not have 13 elements
  
  Test files with failing tests
  
     test_functionsInGeno2proteo.R 
       test_generatingCDSaaFile 
       test_genomicLocsToWholeDNASequence 
  
  
  Error in BiocGenerics:::testPackage("geno2proteo") : 
    unit tests failed for package geno2proteo
  Execution halted
Errors in running code in vignettes:
when running code in 'geno2proteoIntroduction.Rnw'
  ...

> tmpFolder = tempdir()

> generatingCDSaaFile(geneticCodeFile_line = geneticCodeFile, 
+     gtfFile = gtfFile_chr16, DNAfastaFile = DNAfastaFile_chr16, 
+     outputFolder = .... [TRUNCATED] 

  When sourcing 'geno2proteoIntroduction.R':
Error: line 2 did not have 7 elements
Execution halted

  'geno2proteoIntroduction.Rnw'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'geno2proteoIntroduction.Rnw' using Sweave

Error: processing vignette 'geno2proteoIntroduction.Rnw' failed with diagnostics:
 chunk 3 (label = example_generatingCDSaaFile) 
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 2 did not have 7 elements

--- failed re-building 'geno2proteoIntroduction.Rnw'

SUMMARY: processing the following file failed:
  'geno2proteoIntroduction.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'rio'

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: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'colorspace'
  All declared Imports should be used.
Package required but not available: 'car'

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
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.
Packages required but not available: 'curl', 'httr'

Packages suggested but not available for checking: 'covr', 'crul'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'threewords'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'car', 'ggpubr', 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'adjustinconsistency.Rmd' using rmarkdown
Loading required package: sp
Loading required package: spData
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
Loading required package: sf
Linking to GEOS 3.6.2, GDAL 3.0.4, PROJ 7.0.0
--- finished re-building 'adjustinconsistency.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 56-79 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'ggpubr'
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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.
Package suggested but not available for checking: 'covr'
Error(s) in re-building vignettes:
  ...
--- re-building 'inspection.Rmd' using rmarkdown
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
Packages suggested but not available for checking:
  'tidyverse', 'ggmap', 'factoextra', 'rfigshare'
Namespaces in Imports field not imported from:
  'phonTools' 'rgdal' 'rgeos'
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building 'geodiv_vignette.Rmd' using rmarkdown
Quitting from lines 86-104 (geodiv_vignette.Rmd) 
Error: processing vignette 'geodiv_vignette.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'geodiv_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'imguR'

Packages suggested but not available for checking: 'covr', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'httpcache', 'httr'

Packages suggested but not available for checking:
  'covr', 'geofacet', 'ggtern', 'httptest', 'pxweb', 'tricolore'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'lintr', 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'crul', 'V8'

Package suggested but not available for checking: 'gistr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'crul', 'jsonvalidate', 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'geojsonlint'
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Packages required but not available: 'httr', 'curl'

Package suggested but not available for checking: 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidycensus', 'tigris'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking: 'EML', 'emld'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'Rcpp' 'readr' 'spatstat'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'pander' 'rgdal' 'snakecase' 'stringr'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Component "geometry": Attributes: < Component 3: Attributes: < target is NULL, current is list > >
  Component "geometry": Attributes: < Component 3: target is character, current is crs >
  Component "geometry": Attributes: < Component 4: Modes: list, numeric >
  ...
  -- Failure (test-get_empty_geoinstances.R:19:3): get_empty_geoinstances works --
  `empty` not equal to structure(...).
  Component "geometry": Attributes: < Component "bbox": Attributes: < Length mismatch: comparison on first 1 components > >
  Component "geometry": Attributes: < Component "class": 1 string mismatch >
  Component "geometry": Component 1: Modes: list, numeric
  Component "geometry": Component 1: Attributes: < Component "class": 1 string mismatch >
  Component "geometry": Component 1: Length mismatch: comparison on first 0 components
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 19 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'geomultistar.Rmd' using rmarkdown
Quitting from lines 296-298 (geomultistar.Rmd) 
Error: processing vignette 'geomultistar.Rmd' failed with diagnostics:
Evaluation error: Found 1 feature with invalid spherical geometry.
[1] Loop 4 is not valid: Edge 76 is degenerate (duplicate vertex).
--- failed re-building 'geomultistar.Rmd'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'devtools', 'ggmap'
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'ggmap'
Namespace in Imports field not imported from: 'velociraptr'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'car'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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
Package required but not available: 'sparklyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'INLA'
Note: found 4 marked Latin-1 strings
Package suggested but not available for checking: 'DESeq2'
Malformed Description field: should contain one or more complete sentences.
Namespaces in Imports field not imported from:
  'iterators' 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'curl', 'ggspatial'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

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: 'gsheet', 'inti'
Error(s) in re-building vignettes:
  ...
--- re-building 'GerminaQuant.Rmd' using rmarkdown
Quitting from lines 16-17 (GerminaQuant.Rmd) 
Error: processing vignette 'GerminaQuant.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building 'GerminaQuant.Rmd'

--- re-building 'GerminaR.Rmd' using rmarkdown
Quitting from lines 16-17 (GerminaR.Rmd) 
Error: processing vignette 'GerminaR.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building 'GerminaR.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 16-17 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building 'introduction.Rmd'

SUMMARY: processing the following files failed:
  'GerminaQuant.Rmd' 'GerminaR.Rmd' 'introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'httr'
Error(s) in re-building vignettes:
  ...
--- re-building 'Introduction.Rmd' using rmarkdown_notangle
Quitting from lines 128-153 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
object 'VerHistory' not found
--- 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: 'credentials'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rio', 'RSelenium'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'rvest'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'devtools'
Packages required but not available: 'curl', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'crul'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'pipeR' 'rlang'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyverse'
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.
Package suggested but not available for checking: 'covr'
Packages required but not available: 'curl', 'rvest'

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.
'library' or 'require' call to 'multtest' which was already attached by Depends.
  Please remove these calls from your code.
Package suggested but not available for checking: 'curl'
'LazyData' is specified without a 'data' directory
Package required but not available: 'animation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'survminer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'rvest', 'httr', 'V8', 'googlesheets', 'gsheet'

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: 'car'
Error(s) in re-building vignettes:
  ...
--- re-building 'the-gfilmm-package.Rmd' using rmarkdown
Quitting from lines 139-149 (the-gfilmm-package.Rmd) 
Error: processing vignette 'the-gfilmm-package.Rmd' failed with diagnostics:
there is no package called 'car'
--- failed re-building 'the-gfilmm-package.Rmd'

SUMMARY: processing the following file failed:
  'the-gfilmm-package.Rmd'

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

Packages suggested but not available for checking: 'vcr', 'covr'

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
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 suggested but not available for checking: 'magick', 'covr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  == Failed tests ================================================================
  -- Error (test-anim_save.R:21:3): anim_save overwrites existing files ----------
  Error: there is no package called 'magick'
  Backtrace:
      x
   1. +-base::nrow(magick::image_info(magick::image_read(tf))) test-anim_save.R:21:2
   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 1 | PASS 5 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lintr'
'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: 'dagitty'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'do', 'set', 'base.rms'

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: 'covr', 'pkgdown'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'GGEBiplotGUI' 'gge' 'utils'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'magrittr'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'AER', 'brms', 'httr', 'rstanarm'
Package required but not available: '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: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
Namespaces in Imports field not imported from:
  'R6' 'grDevices' 'scales' 'utils'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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 suggested but not available for checking: 'concaveman', 'covr'
Namespace in Imports field not imported from: 'withr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking:
  'forecast', 'lintr', 'tseries'
Running examples in 'ggfortify-Ex.R' failed
The error most likely occurred in:

> ### Name: autoplot.forecast
> ### Title: Autoplot 'forecast::forecast'
> ### Aliases: autoplot.forecast
> 
> ### ** Examples
> 
> d.arima <- forecast::auto.arima(AirPassengers)
Error in loadNamespace(x) : there is no package called 'forecast'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: 'magick'

Package suggested but not available for checking: 'covr'

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: 'animation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'gridExtra' 'lazyeval' 'readr'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'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
Packages required but not available: 'factoextra', 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package required but not available: 'magick'

Package suggested but not available for checking: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'knitr' 'reshape2'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
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.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'graph'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'tidyverse', 'covr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   1. \-base::library(tidyverse) test_position.R:2:0
  -- Error (test_serialaxes.R:2:1): (code run outside of `test_that()`) ----------
  Error: there is no package called 'tidyverse'
  Backtrace:
      x
   1. \-base::library(tidyverse) test_serialaxes.R:2:0
  -- Error (test_stat.R:2:1): (code run outside of `test_that()`) ----------------
  Error: there is no package called 'tidyverse'
  Backtrace:
      x
   1. \-base::library(tidyverse) test_stat.R:2:0
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'sna' 'utils'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ggnetwork)
  Loading required package: ggplot2
  > 
  > test_check("ggnetwork")
  == Failed tests ================================================================
  -- Failure (test-ggnetwork.R:57:3): ggnetwork works ----------------------------
  `ggnetwork(n)` did not produce any warnings.
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 42 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'dplyr' 'grid' 'scales'
  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: 'covr'
Package suggested but not available for checking: 'AER'
Namespace in Imports field not imported from: 'survival'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in 'ggparty-Ex.R' failed
The error most likely occurred in:

> ### Name: geom_node_label
> ### Title: Draw (multi-line) labels at nodes
> ### Aliases: geom_node_label geom_node_info geom_node_splitvar
> 
> ### ** Examples
> 
> library(ggparty)
> data("WeatherPlay", package = "partykit")
> sp_o <- partysplit(1L, index = 1:3)
> sp_h <- partysplit(3L, breaks = 75)
> sp_w <- partysplit(4L, index = 1:2)
> pn <- partynode(1L, split = sp_o, kids = list(
+   partynode(2L, split = sp_h, kids = list(
+     partynode(3L, info = "yes"),
+     partynode(4L, info = "no"))),
+   partynode(5L, info = "yes"),
+   partynode(6L, split = sp_w, kids = list(
+     partynode(7L, info = "yes"),
+     partynode(8L, info = "no")))))
> py <- party(pn, WeatherPlay)
> 
> ggparty(py) +
+   geom_edge() +
+   geom_edge_label() +
+   geom_node_label(aes(label = splitvar),
+                   ids = "inner") +
+   geom_node_label(aes(label = info),
+                   ids = "terminal")
> 
> ######################################
> 
> data("TeachingRatings", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'AER'
Calls: data -> find.package
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'ggparty-graphic-partying.Rmd' using rmarkdown
Quitting from lines 42-122 (ggparty-graphic-partying.Rmd) 
Error: processing vignette 'ggparty-graphic-partying.Rmd' failed with diagnostics:
there is no package called 'AER'
--- failed re-building 'ggparty-graphic-partying.Rmd'

--- re-building 'on-the-edge.Rmd' using rmarkdown
Loading required package: ggplot2
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
--- finished re-building 'on-the-edge.Rmd'

SUMMARY: processing the following file failed:
  'ggparty-graphic-partying.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'mgcv'
  All declared Imports should be used.
Packages required but not available: 'tidyverse', 'editData'

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: 'ggimage'
Error(s) in re-building vignettes:
  ...
--- re-building 'ggplotify.Rmd' using rmarkdown
Quitting from lines 27-37 (ggplotify.Rmd) 
Error: processing vignette 'ggplotify.Rmd' failed with diagnostics:
there is no package called 'ggimage'
--- failed re-building 'ggplotify.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: '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: 'magick'
Namespaces in Imports field not imported from:
  'MASS' 'dplyr' 'glue' 'gridExtra' 'xts' 'zoo'
  All declared Imports should be used.
'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
Package suggested but not available for checking: 'magick'
Namespaces in Imports field not imported from:
  'generics' 'plyr' 'polynom'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'grammar-extensions.Rmd' using rmarkdown
Loading required package: ggplot2

Attaching package: 'ggpp'

The following object is masked from 'package:ggplot2':

    annotate


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 594-613 (grammar-extensions.Rmd) 
Error: processing vignette 'grammar-extensions.Rmd' failed with diagnostics:
there is no package called 'magick'
--- failed re-building 'grammar-extensions.Rmd'

SUMMARY: processing the following file failed:
  'grammar-extensions.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'covr', 'rstatix'
Error(s) in re-building vignettes:
  ...
--- re-building 'axes.Rmd' using rmarkdown
--- finished re-building 'axes.Rmd'

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

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

--- re-building 'pvalues.Rmd' using rmarkdown
Quitting from lines 259-265 (pvalues.Rmd) 
Error: processing vignette 'pvalues.Rmd' failed with diagnostics:
there is no package called 'rstatix'
--- failed re-building 'pvalues.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'rstatix'

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
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggpubr', 'plotly', 'survminer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggmap', 'pkgdown'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'randomForest'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Package required but not available: 'bgmm'

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'
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gRbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Note: found 6242 marked UTF-8 strings
Packages required but not available:
  'do', 'set', 'cutoff', 'fastStat', 'nomogramFormula'

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

Packages suggested but not available for checking: 'covr', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'devtools'
Running examples in 'ggseg-Ex.R' failed
The error most likely occurred in:

> ### Name: geom_brain
> ### Title: Brain geom
> ### Aliases: geom_brain GeomBrain
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> ggplot() +
+  geom_brain(atlas = dk)
Error: stat_sf requires the following missing aesthetics: geometry
Backtrace:
     x
  1. +-(function (x, ...) ...
  2. \-ggplot2:::print.ggplot(x)
  3.   +-ggplot2::ggplot_build(x)
  4.   \-ggplot2:::ggplot_build.ggplot(x)
  5.     \-ggplot2:::by_layer(function(l, d) l$compute_statistic(d, layout))
  6.       \-ggplot2:::f(l = layers[[i]], d = data[[i]])
  7.         \-l$compute_statistic(d, layout)
  8.           \-ggplot2:::f(..., self = self)
  9.             \-self$stat$compute_layer(data, self$computed_stat_params, layout)
 10.               \-ggplot2:::f(..., self = self)
 11.                 \-ggproto_parent(Stat, self)$compute_layer(data, params, layout)
 12.                   \-ggplot2:::f(..., self = self)
 13.                     \-ggplot2:::check_required_aesthetics(...)
Execution halted
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    7.         +-ggplot2::ggplot_build(x)
    8.         \-ggplot2:::ggplot_build.ggplot(x)
    9.           \-ggplot2:::by_layer(function(l, d) l$compute_statistic(d, layout))
   10.             \-ggplot2:::f(l = layers[[i]], d = data[[i]])
   11.               \-l$compute_statistic(d, layout)
   12.                 \-ggplot2:::f(..., self = self)
   13.                   \-self$stat$compute_layer(data, self$computed_stat_params, layout)
   14.                     \-ggplot2:::f(..., self = self)
   15.                       \-ggproto_parent(Stat, self)$compute_layer(data, params, layout)
   16.                         \-ggplot2:::f(..., self = self)
   17.                           \-ggplot2:::check_required_aesthetics(...)
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 108 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'externalData.Rmd' using rmarkdown
--- finished re-building 'externalData.Rmd'

--- re-building 'freesurfer_files.Rmd' using rmarkdown
Quitting from lines 11-20 (freesurfer_files.Rmd) 
Error: processing vignette 'freesurfer_files.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'freesurfer_files.Rmd'

--- re-building 'geom-sf.Rmd' using rmarkdown
Quitting from lines 45-46 (geom-sf.Rmd) 
Error: processing vignette 'geom-sf.Rmd' failed with diagnostics:
stat_sf requires the following missing aesthetics: geometry
--- failed re-building 'geom-sf.Rmd'

--- re-building 'ggseg.Rmd' using rmarkdown
Quitting from lines 54-55 (ggseg.Rmd) 
Error: processing vignette 'ggseg.Rmd' failed with diagnostics:
stat_sf requires the following missing aesthetics: geometry
--- failed re-building 'ggseg.Rmd'

SUMMARY: processing the following files failed:
  'freesurfer_files.Rmd' 'geom-sf.Rmd' 'ggseg.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'pkgdown'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'ggmap'
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Package required but not available: 'rosm'

Packages suggested but not available for checking: 'prettymapr', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'dplyr' 'tibble'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'afex', 'metaBMA'
Namespace in Imports field not imported from: 'tidyr'
  All declared Imports should be used.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ggtern/ggtern.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'lintr'
Note: found 138 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Package suggested but not available for checking: 'ggmap'

VignetteBuilder package required for checking but not installed: 'ggmap'
Errors in running code in vignettes:
when running code in 'ggvoronoi.Rmd'
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder 'ggmap' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  'ggvoronoi.Rmd' using 'UTF-8'... failed to complete the test
Package suggested but not available for checking: 'covr'
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
Namespace in Imports field not imported from: 'class'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'refund'
  All declared Imports should be used.
Package required but not available: 'gh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'codemetar'
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
Package required but not available: 'crul'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
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.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'GIFTr_tutorial.Rmd' using rmarkdown
Quitting from lines 34-39 (GIFTr_tutorial.Rmd) 
Error: processing vignette 'GIFTr_tutorial.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'GIFTr_tutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'tibble'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'MIIVsem', 'imputeTS'

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

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: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'lwgeom'
  All declared Imports should be used.
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').
Packages required but not available: 'crul', 'httr'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'devtools', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Package suggested but not available for checking: 'devtools'

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

Package suggested but not available for checking: 'qpdf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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

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

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'car', 'texreg'
Package unavailable to check Rd xrefs: 'car'
Error(s) in re-building vignettes:
--- re-building 'covstruct.rmd' using rmarkdown
--- finished re-building 'covstruct.rmd'

--- re-building 'mcmc.rmd' using rmarkdown
--- finished re-building 'mcmc.rmd'

--- re-building 'miscEx.rmd' using rmarkdown
--- finished re-building 'miscEx.rmd'

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

--- re-building 'sim.rmd' using rmarkdown
--- finished re-building 'sim.rmd'

--- re-building 'troubleshooting.rmd' using rmarkdown
--- finished re-building 'troubleshooting.rmd'

--- re-building 'glmmTMB.Rnw' using knitr
Loading required package: stats4
Warning in qt((1 - level)/2, df) : NaNs produced
Warning in max(ids, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
--- finished re-building 'glmmTMB.Rnw'

--- re-building 'model_evaluation.Rnw' using knitr
Quitting from lines 95-113 (model_evaluation.Rnw) 
Error: processing vignette 'model_evaluation.Rnw' failed with diagnostics:
there is no package called 'car'
--- failed re-building 'model_evaluation.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package required but not available: 'AER'

Packages suggested but not available for checking: 'schlegel', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'purrr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'FactoMineR', 'covr'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'glmtree.Rmd' using rmarkdown
Quitting from lines 32-53 (glmtree.Rmd) 
Error: processing vignette 'glmtree.Rmd' failed with diagnostics:
there is no package called 'FactoMineR'
--- failed re-building 'glmtree.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'AER'
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.
Package suggested but not available for checking: 'fxregime'
Unavailable namespace imported from by a ':::' call: 'fxregime'
  See the note in ?`:::` about the use of this operator.
Package unavailable to check Rd xrefs: 'fxregime'
Package suggested but not available for checking: 'magick'
Namespace in Imports field not imported from: 'scales'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
ScoreTest: no visible global function definition for 'pchisq'
Var1: no visible global function definition for 'runif'
gLRT1: no visible global function definition for 'pchisq'
gLRT2: no visible global function definition for 'pchisq'
gLRT3: no visible global function definition for 'pchisq'
gLRT4: no visible global function definition for 'pf'
Undefined global functions or variables:
  pchisq pf runif
Consider adding
  importFrom("stats", "pchisq", "pf", "runif")
to your NAMESPACE file.
Packages suggested but not available for checking: 'covr', 'httr', 'rvest'
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   1. \-base::library(rvest) test-6.8-autolinks.R:3:0
  -- Error (test-generic-functions.R:4:1): (code run outside of `test_that()`) ---
  Error: there is no package called 'rvest'
  Backtrace:
      x
   1. \-base::library(rvest) test-generic-functions.R:4:0
  -- Error (test-github-issue.R:4:1): (code run outside of `test_that()`) --------
  Error: there is no package called 'rvest'
  Backtrace:
      x
   1. \-base::library(rvest) test-github-issue.R:4:0
  
  [ FAIL 26 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'github-spec.Rmd' using rmarkdown
Quitting from lines 21-24 (github-spec.Rmd) 
Error: processing vignette 'github-spec.Rmd' failed with diagnostics:
there is no package called 'rvest'
--- failed re-building 'github-spec.Rmd'

--- re-building 'literal-programming.Rmd' using rmarkdown
Quitting from lines 20-24 (literal-programming.Rmd) 
Error: processing vignette 'literal-programming.Rmd' failed with diagnostics:
there is no package called 'rvest'
--- failed re-building 'literal-programming.Rmd'

SUMMARY: processing the following files failed:
  'github-spec.Rmd' 'literal-programming.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'gargle', 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'RcmdrMisc'

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 required but not available: 'gRbase'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'Deducer'
Package required but not available: '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
Note: found 2629 marked UTF-8 strings
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'doMC'
Package suggested but not available for checking: 'car'
Error(s) in re-building vignettes:
  ...
--- re-building 'gmm_with_R.rnw' using knitr
Warning in nlminb(P$t0, .obj1, x = x, w = w, ...) :
  NA/NaN function evaluation
Warning in nlminb(P$t0, .obj1, x = x, w = w, ...) :
  NA/NaN function evaluation
Quitting from lines 352-354 (gmm_with_R.rnw) 
Error: processing vignette 'gmm_with_R.rnw' failed with diagnostics:
there is no package called 'car'
--- failed re-building 'gmm_with_R.rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'AER', 'car'
Running examples in 'gmnl-Ex.R' failed
The error most likely occurred in:

> ### Name: AIC.gmnl
> ### Title: Akaike's Information Criterion
> ### Aliases: AIC.gmnl BIC.gmnl
> 
> ### ** Examples
> 
> 
> ## Estimate MNL model
> data("TravelMode", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'AER'
Calls: data -> find.package
Execution halted
Packages suggested but not available for checking: 'tidyverse', 'pdftools'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'bi-objective_2x.Rmd' using rmarkdown
Warning: ggrepel: 70 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 70 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 70 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 70 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building 'bi-objective_2x.Rmd'

--- re-building 'bi-objective_3x_ex1.Rmd' using rmarkdown
--- finished re-building 'bi-objective_3x_ex1.Rmd'

--- re-building 'intro.Rmd' using rmarkdown
Quitting from lines 15-29 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'intro.Rmd'

--- re-building 'polytope_2d.Rmd' using rmarkdown
--- finished re-building 'polytope_2d.Rmd'

--- re-building 'polytope_3d_ex1.Rmd' using rmarkdown
--- finished re-building 'polytope_3d_ex1.Rmd'

--- re-building 'tri-objective.Rmd' using rmarkdown
Quitting from lines 15-29 (tri-objective.Rmd) 
Error: processing vignette 'tri-objective.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'tri-objective.Rmd'

SUMMARY: processing the following files failed:
  'intro.Rmd' 'tri-objective.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'curl'
Packages required but not available: 'nonlinearTseries', 'tseries'

Package suggested but not available for checking: 'quantmod'

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: 'qrmtools'
Package required but not available: 'kableExtra'

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'
Note: found 3 marked UTF-8 strings
Package suggested but not available for checking: 'BiodiversityR'
Namespace in Imports field not imported from: 'Hmisc'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'BiodiversityR'
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
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'fGarch' 'fastICA'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
UprodR: no visible global function definition for 'combn'
goinit: no visible global function definition for 'as.formula'
ccor,GoGARCH : <anonymous>: no visible global function definition for
  'cov2cor'
ccor,Gopredict : <anonymous>: no visible global function definition for
  'cov2cor'
goest,Goestica: no visible global function definition for 'fastICA'
goest,Goestml: no visible global function definition for 'nlminb'
goest,Goestmm : <anonymous>: no visible global function definition for
  'combn'
goest,Goestnls: no visible global function definition for 'optim'
show,Goinit: no visible global function definition for 'head'
show,Gopredict: no visible global function definition for 'head'
update,GoGARCH: no visible global function definition for
  'update.formula'
update,Goestica: no visible global function definition for
  'update.formula'
update,Goestml: no visible global function definition for
  'update.formula'
update,Goestmm: no visible global function definition for
  'update.formula'
update,Goestnls: no visible global function definition for
  'update.formula'
Undefined global functions or variables:
  as.formula combn cov2cor fastICA head nlminb optim update.formula
Consider adding
  importFrom("stats", "as.formula", "cov2cor", "nlminb", "optim",
             "update.formula")
  importFrom("utils", "combn", "head")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking: 'covr', 'pdftools'
Package required but not available: 'usethis'

Packages suggested but not available for checking:
  'covr', 'devtools', 'pkgdown', 'rsconnect'

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: 'car'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'GoodmanKruskal.Rmd' using rmarkdown
Loading required package: GoodmanKruskal
Loading required package: MASS
Loading required package: car
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'car'
Quitting from lines 148-151 (GoodmanKruskal.Rmd) 
Error: processing vignette 'GoodmanKruskal.Rmd' failed with diagnostics:
object 'Greene' not found
--- failed re-building 'GoodmanKruskal.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'covr', 'lintr', 'whoami'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'googleAuthR', 'httr', 'measurementProtocol', 'usethis'

Packages suggested but not available for checking:
  'bigQueryR', 'covr', 'ganalytics', 'googleCloudStorageR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gargle', 'httr'

Packages suggested but not available for checking:
  'bigQueryR', 'covr', 'devtools', 'googleAnalyticsR', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'googleAuthR', 'googleCloudStorageR', 'httr', 'plumber',
  'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'googleAuthR', 'httr'

Packages suggested but not available for checking:
  'googleComputeEngineR', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'googleAuthR'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'googleAuthR', 'httr'

Packages suggested but not available for checking:
  'covr', 'googleCloudStorageR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'gargle', 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'googleAuthR'

Package suggested but not available for checking: 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Packages required but not available: 'googleAuthR', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'curl', 'gargle', 'googledrive', 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'googleAuthR', 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Random.Start: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
.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.
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'AER'

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: '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.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Package suggested but not available for checking: 'plumber'
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
Package required but not available: 'usethis'

Package suggested but not available for checking: 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package required but not available: 'covr'

Package suggested but not available for checking: 'hexSticker'

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.
Package required but not available: 'car'

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

Packages suggested but not available for checking:
  'kableExtra', 'summarytools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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
Namespaces in Imports field not imported from:
  'Rdpack' 'knitr' 'rmarkdown' 'spatstat.core'
  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
Package required but not available: 'sparklyr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

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: 'FactoMineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
Package suggested but not available for checking: 'rtweet'
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'rtweet'
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.
Packages suggested but not available for checking: 'devtools', 'covr'
Namespaces in Imports field not imported from:
  'methods' 'quadmesh'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'graticule.Rmd' using rmarkdown
Loading required package: sp
rgdal: version: 1.5-23, (SVN revision 1121)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.0.4, released 2020/01/28
Path to GDAL shared files: C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/lib/rgdal/gdal
GDAL binary built with GEOS: FALSE 
Loaded PROJ runtime: Rel. 7.0.0, March 1st, 2020, [PJ_VERSION: 700]
Path to PROJ shared files: C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/lib/rgdal/proj
PROJ CDN enabled: FALSE
Linking to sp version:1.4-5
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading rgdal.
Overwritten PROJ_LIB was C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/lib/rgdal/proj
### Welcome to rworldmap ###
For a short introduction type : 	 vignette('rworldmap')
Loading required package: gsw
Loading required package: testthat
Quitting from lines 301-302 (graticule.Rmd) 
Error: processing vignette 'graticule.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'graticule.Rmd'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'forecast'

Packages suggested but not available for checking:
  'curl', 'rsdmx', 'taxstats', 'taxstats1516', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package required but not available: 'Rgraphviz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gRbase'

Package suggested but not available for checking: 'Rgraphviz'

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.
Packages suggested but not available for checking: 'swirlify', 'swirl'
'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
Package suggested but not available for checking: 'tidyverse'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'texreg'

Packages suggested but not available for checking: 'smooth', 'doMC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'gridGraphviz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'magick', 'pdftools'
Package required but not available: 'Rgraphviz'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'BiasedUrn'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Running 'testpage.R'
Running the tests in 'tests/testpage.R' failed.
Last 13 lines of output:
  > 
  > 
  > #######################################
  > # Now import testpage.ps and draw it in various ways
  > #######################################
  > 
  > require(grImport)
  Loading required package: grImport
  Loading required package: XML
  > 
  > PostScriptTrace("testpage.ps", "testpage.xml")
  Error in system(command, as.integer(flag), f, stdout, stderr, timeout) : 
    character string expected as first argument
  Calls: PostScriptTrace -> system
  Execution halted
Errors in running code in vignettes:
when running code in 'import.Rnw'
  ...
+   .... [TRUNCATED] 

> library("grImport")
Loading required package: XML

> PostScriptTrace("chess_game_01.fromInkscape.eps")

  When sourcing 'import.R':
Error: character string expected as first argument
Execution halted
when running code in 'importText.Rnw'
  ...
+     grid .... [TRUNCATED] 

> library(grImport)
Loading required package: XML

> PostScriptTrace("hello.ps", "hello.xml")

  When sourcing 'importText.R':
Error: character string expected as first argument
Execution halted

  'import.Rnw'... failed
  'importText.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'import.Rnw' using Sweave
Loading required package: XML

Error: processing vignette 'import.Rnw' failed with diagnostics:
 chunk 5 (label = chesspiece) 
Error in system(command, as.integer(flag), f, stdout, stderr, timeout) : 
  character string expected as first argument

--- failed re-building 'import.Rnw'

--- re-building 'importText.Rnw' using Sweave
Loading required package: XML

Error: processing vignette 'importText.Rnw' failed with diagnostics:
 chunk 4 (label = simpleimport) 
Error in system(command, as.integer(flag), f, stdout, stderr, timeout) : 
  character string expected as first argument

--- failed re-building 'importText.Rnw'

SUMMARY: processing the following files failed:
  'import.Rnw' 'importText.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'gRbase', 'Rgraphviz', 'gRain'

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 required but not available: 'usethis'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'snplist'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'MASS' 'rjags'
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'Rcpp'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
PCgamma : <anonymous>: no visible global function definition for
  'prcomp'
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for 'glm'
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for 'update'
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for 'pchisq'
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for 'lm'
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for 'anova'
PCgamma: no visible global function definition for 'qgamma'
PCgamma: no visible global function definition for 'pgamma'
RNAgamma : rnafunc: no visible global function definition for
  'model.matrix'
RNAgamma : rnafunc: no visible global function definition for
  'as.formula'
RNAgamma: no visible global function definition for 'qgamma'
RNAgamma: no visible global function definition for 'pgamma'
STTtoShapeParameter : f: no visible global function definition for
  'qgamma'
STTtoShapeParameter: no visible global function definition for
  'optimize'
Undefined global functions or variables:
  anova as.formula glm lm model.matrix optimize pchisq pgamma prcomp
  qgamma update
Consider adding
  importFrom("stats", "anova", "as.formula", "glm", "lm", "model.matrix",
             "optimize", "pchisq", "pgamma", "prcomp", "qgamma",
             "update")
to your NAMESPACE file.
.gsa.assignGATKTableToEnvironment: no visible global function
  definition for 'type.convert'
Undefined global functions or variables:
  type.convert
Consider adding
  importFrom("utils", "type.convert")
to your NAMESPACE file.
'library' or 'require' call to 'impute' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
GSA: no visible global function definition for 'impute.knn'
Undefined global functions or variables:
  impute.knn
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'gsDesign'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- Error (test_spending.R:10:12): OBF spending function matches gsdesign -------
  Error: there is no package called 'gsDesign'
  Backtrace:
      x
   1. +-testthat::expect_equal(...) test_spending.R:10:11
   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 6 | WARN 0 | SKIP 0 | PASS 17 ]
  Error: Test failures
  Execution halted
binding: no visible global function definition for 'rnorm'
binding: no visible binding for global variable 'var'
binding: no visible global function definition for 'uniroot'
equivonly: no visible global function definition for 'rnorm'
equivonly: no visible binding for global variable 'var'
equivonly: no visible global function definition for 'uniroot'
figureE: no visible global function definition for 'rgb'
figureEF: no visible global function definition for 'rgb'
nfix : f: no visible global function definition for 'pnorm'
nfix : f: no visible global function definition for 'qnorm'
nfix: no visible global function definition for 'uniroot'
nonbinding: no visible global function definition for 'rnorm'
nonbinding: no visible binding for global variable 'var'
nonbinding: no visible global function definition for 'uniroot'
oc: no visible global function definition for 'rnorm'
oc: no visible global function definition for 'var'
Undefined global functions or variables:
  pnorm qnorm rgb rnorm uniroot var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "pnorm", "qnorm", "rnorm", "uniroot", "var")
to your NAMESPACE file.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package unavailable to check Rd xrefs: 'nflfastR'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'curl', 'httr'

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
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
gte: no visible global function definition for 'model.extract'
gte: no visible global function definition for 'model.matrix'
gte: no visible binding for global variable 'sd'
gte: no visible global function definition for 'dnorm'
plot.gte: no visible global function definition for 'par'
plot.gte: no visible global function definition for 'polygon'
plot.gte: no visible global function definition for 'gray'
plot.gte: no visible global function definition for 'lines'
plot.gte: no visible global function definition for 'legend'
Undefined global functions or variables:
  dnorm gray legend lines model.extract model.matrix par polygon sd
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "legend", "lines", "par", "polygon")
  importFrom("stats", "dnorm", "model.extract", "model.matrix", "sd")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'readr'
  All declared Imports should be used.
Package suggested but not available for checking: 'dodgr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'car', 'SGP', 'taxize'
Found the following possibly unsafe calls:
File 'gtools/R/unByteCode.R':
  unlockBinding(name, env = env)
Packages unavailable to check Rd xrefs: 'taxize', 'SGP', 'car'
Package required but not available: 'hts'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'rvest'
Note: found 116 marked UTF-8 strings
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
       x
    1. +-`%>%`(...) test-text_transform.R:346:2
    2. +-testthat::expect_equal(...)
    3. | \-testthat::quasi_label(enquo(object), label, arg = "object")
    4. |   \-rlang::eval_bare(expr, quo_get_env(quo))
    5. +-gt:::selection_text(., "[class='gt_row gt_left gt_stub']")
    6. | \-html %>% rvest::html_nodes(selection) %>% rvest::html_text() test-text_transform.R:23:2
    7. \-base::loadNamespace(x)
    8.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
    9.     \-base:::withOneRestart(expr, restarts[[1L]])
   10.       \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 20 | WARN 0 | SKIP 31 | PASS 1976 ]
  Error: Test failures
  Execution halted
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'car', 'covr', 'kableExtra'
Note: found 8177 marked UTF-8 strings
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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: 'Rgraphviz'

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: 'covr'
Package suggested but not available for checking: 'curl'
Note: found 13617 marked UTF-8 strings
Package suggested but not available for checking: 'drc'
Package required but not available: 'tsDyn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'eda4treeR'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
simCCCent : <anonymous>: no visible global function definition for
  'simulate.formula'
Undefined global functions or variables:
  simulate.formula
'LazyData' is specified without a 'data' directory
calculate.threshold: no visible global function definition for 'pchisq'
gwerAM: no visible global function definition for 'rnorm'
gwerAM: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  pchisq quantile rnorm
Consider adding
  importFrom("stats", "pchisq", "quantile", "rnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'Matrix'
  All declared Imports should be used.
normalweight: no visible binding for global variable 'NW_above'
normalweight: no visible binding for global variable 'NW_below'
obese: no visible global function definition for 'data'
obese: no visible binding for global variable 'OB_above'
obese: no visible binding for global variable 'OB_below'
overweight: no visible global function definition for 'data'
overweight: no visible binding for global variable 'OW_above'
overweight: no visible binding for global variable 'OW_below'
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'doParallel' 'foreach' 'spgwr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'mvoutlier'
Namespace in Imports field not imported from: 'sf'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'golem', 'plotly'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' calls to packages already attached by Depends:
  'fields' 'lars'
  Please remove these calls from your code.
Package in Depends field not imported from: 'lars'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gwl.beta: no visible global function definition for 'lars'
gwl.cv.err: no visible global function definition for 'lars'
gwl.est: no visible global function definition for 'lm'
gwr.bw.est: no visible global function definition for 'lm'
gwr.est: no visible global function definition for 'lm'
gwr.rsquare: no visible global function definition for 'cor'
gwrr.est: no visible global function definition for 'lm'
Undefined global functions or variables:
  cor lars lm
Consider adding
  importFrom("stats", "cor", "lm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'curl'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
GxMestimator: no visible global function definition for 'na.omit'
initialization_chol: no visible global function definition for 'cov'
initialization_corr: no visible global function definition for 'cov'
initialization_nlmain: no visible global function definition for
  'lm.fit'
print.summaryGxMclass: no visible global function definition for
  'pnorm'
print.summaryGxMclass: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  cov lm.fit na.omit pnorm printCoefmat
Consider adding
  importFrom("stats", "cov", "lm.fit", "na.omit", "pnorm",
             "printCoefmat")
to your NAMESPACE file.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'plotly'
Package required but not available: 'V8'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
hf.bt: 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
Package required but not available: 'httr'

Packages suggested but not available for checking: 'covr', 'httptest'

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: 'covr'
Namespaces in Imports field not imported from:
  'DT' 'gsubfn' 'stringr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
       x
    1. +-testthat::expect_silent(read_hdx("https://raw.githubusercontent.com/hadexversum/HDX-data/master/lysenin.csv"))
    2. | \-testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. |   +-testthat:::.capture(...)
    4. |   | +-withr::with_output_sink(...)
    5. |   | | \-base::force(code)
    6. |   | +-base::withCallingHandlers(...)
    7. |   | \-base::withVisible(code)
    8. |   \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. \-HaDeX::read_hdx("https://raw.githubusercontent.com/hadexversum/HDX-data/master/lysenin.csv")
   10.   \-data.table::fread(filename)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 14 ]
  Error: Test failures
  Execution halted
hsTableReader: no visible global function definition for 'object.size'
hsWriteTable: no visible global function definition for 'write.table'
Undefined global functions or variables:
  object.size write.table
Consider adding
  importFrom("utils", "object.size", "write.table")
to your NAMESPACE file.
Package suggested but not available for checking: 'rhdf5'
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'jsonld'

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: 'covr'
Package unavailable to check Rd xrefs: 'mnis'
EMvar: no visible global function definition for 'model.matrix'
RecodeHaplos: no visible global function definition for 'na.omit'
RecodeHaplos: no visible global function definition for 'tail'
anova.hapassoc: no visible global function definition for 'pchisq'
handleMissings: no visible global function definition for 'na.omit'
hapassoc: no visible global function definition for 'binomial'
hapassoc: no visible global function definition for 'formula'
hapassoc: no visible global function definition for 'glm'
hapassoc : <anonymous>: no visible global function definition for 'glm'
hapassoc: no visible global function definition for 'model.frame'
hapassoc: no visible global function definition for 'model.matrix'
hapassoc: no visible binding for global variable 'contrasts'
hapassoc: no visible global function definition for 'glm.control'
hapassoc : <anonymous>: no visible global function definition for
  'glm.control'
probY: no visible global function definition for 'dbinom'
probY: no visible global function definition for 'dpois'
probY: no visible global function definition for 'dnorm'
probY: no visible global function definition for 'dgamma'
summary.hapassoc: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  binomial contrasts dbinom dgamma dnorm dpois formula glm glm.control
  model.frame model.matrix na.omit pchisq tail
Consider adding
  importFrom("stats", "binomial", "contrasts", "dbinom", "dgamma",
             "dnorm", "dpois", "formula", "glm", "glm.control",
             "model.frame", "model.matrix", "na.omit", "pchisq")
  importFrom("utils", "tail")
to your NAMESPACE file.
allele.marq: no visible global function definition for 'na.omit'
depart.LDL: no visible global function definition for 'aov'
freq.all: no visible global function definition for 'na.omit'
hapim.LD.add: no visible global function definition for 'optim'
hapim.LDL.add: no visible global function definition for 'optim'
obj.haplomax.HS.add: no visible global function definition for 'aov'
obj.haplomax.add: no visible global function definition for 'aov'
vrais.LD.add: no visible global function definition for 'dnorm'
vrais.LDL.add.pere: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  aov dnorm na.omit optim
Consider adding
  importFrom("stats", "aov", "dnorm", "na.omit", "optim")
to your NAMESPACE file.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
AssignQTL : <anonymous>: no visible global function definition for
  'rgamma'
AssignSingleQTL: no visible global function definition for 'rgamma'
ListQTL : <anonymous>: no visible global function definition for
  'rgamma'
SampleBaseHaplotype: no visible global function definition for 'runif'
SampleHaplotype: no visible global function definition for 'rpois'
SampleHaplotype: no visible global function definition for 'runif'
SampleHaplotype: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  rbinom rgamma rpois runif
Consider adding
  importFrom("stats", "rbinom", "rgamma", "rpois", "runif")
to your NAMESPACE file.
Package required but not available: 'gh'

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:
  'covr', 'devtools', 'usethis'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Expected match: "must not contain any spaces"
  Actual message: "The `usethis` package must be installed for this functionality."
  Backtrace:
      x
   1. +-testthat::expect_error(...) test-use.R:94:2
   2. | \-testthat:::quasi_capture(...)
   3. |   +-testthat:::.capture(...)
   4. |   | \-base::withCallingHandlers(...)
   5. |   \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. \-hardhat::create_modeling_package(model = "model with space")
   7.   \-hardhat:::validate_installed("usethis")
  
  [ FAIL 23 | WARN 0 | SKIP 0 | PASS 642 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'Seurat'
Packages suggested but not available for checking: 'covr', 'httr'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'Basic_use.Rmd' using rmarkdown
Quitting from lines 67-70 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
Required package curl not found. Please run: install.packages('curl')
--- failed re-building 'Basic_use.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Package required but not available: 'Rgraphviz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Found the following significant warnings:
  readstat/sas/readstat_sas.c:319:21: warning: too many arguments for format [-Wformat-extra-args]
  readstat/sas/readstat_sas7bdat_read.c:1009:66: warning: too many arguments for format [-Wformat-extra-args]
  readstat/sas/readstat_sas7bdat_read.c:1045:25: warning: too many arguments for format [-Wformat-extra-args]
  readstat/sas/readstat_sas7bdat_read.c:1071:66: warning: too many arguments for format [-Wformat-extra-args]
  readstat/sas/readstat_sas7bdat_read.c:1111:25: warning: too many arguments for format [-Wformat-extra-args]
  readstat/sas/readstat_sas7bdat_read.c:1144:25: warning: too many arguments for format [-Wformat-extra-args]
  readstat/sas/readstat_sas7bdat_read.c:1248:62: warning: too many arguments for format [-Wformat-extra-args]
  readstat/spss/readstat_por_read.c:129:52: warning: too many arguments for format [-Wformat-extra-args]
  readstat/spss/readstat_por_read.c:140:52: warning: too many arguments for format [-Wformat-extra-args]
  readstat/spss/readstat_por_write.c:64:52: warning: too many arguments for format [-Wformat-extra-args]
  readstat/spss/readstat_sav_write.c:1307:66: warning: '%d' directive output may be truncated writing between 1 and 10 bytes into a region of size 8 [-Wformat-truncation=]
  readstat/stata/readstat_dta_read.c:190:25: warning: too many arguments for format [-Wformat-extra-args]
  readstat/stata/readstat_dta_read.c:407:62: warning: too many arguments for format [-Wformat-extra-args]
  readstat/stata/readstat_dta_read.c:704:62: warning: too many arguments for format [-Wformat-extra-args]
  readstat/stata/readstat_dta_read.c:981:62: warning: too many arguments for format [-Wformat-extra-args]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/haven/haven.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
extract_hazus_functions: no visible global function definition for
  'data'
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
detect.movement: no visible global function definition for 't.test'
generate.random.conf: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm t.test
Consider adding
  importFrom("stats", "rnorm", "t.test")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Note: found 3 marked UTF-8 strings
Note: found 104392 marked UTF-8 strings
PoincarePlot: no visible global function definition for 'lines'
PoincarePlot: no visible global function definition for 'lowess'
hctest: no visible global function definition for 'cor.test'
rdplot: no visible global function definition for 'lines'
rdplot: no visible global function definition for 'lowess'
rdplot: no visible global function definition for 'rgb'
simer: no visible global function definition for 'runif'
simer: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  cor.test lines lowess rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines")
  importFrom("stats", "cor.test", "lowess", "rnorm", "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
'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: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  H5ls.c:78:73: warning: too many arguments for format [-Wformat-extra-args]
  H5ls.c:88:84: warning: too many arguments for format [-Wformat-extra-args]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/hdf5r/hdf5r.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Promax.only: no visible global function definition for 'lm.fit'
factor.pa.ginv: no visible binding for global variable 'median'
factor.pa.ginv: no visible global function definition for 'cor'
factor.pa.ginv: no visible global function definition for 'varimax'
factor.pa.ginv: no visible global function definition for 'pchisq'
pairwise.mahalanobis: no visible global function definition for 'cor'
pairwise.mahalanobis: no visible global function definition for
  'mahalanobis'
Undefined global functions or variables:
  cor lm.fit mahalanobis median pchisq varimax
Consider adding
  importFrom("stats", "cor", "lm.fit", "mahalanobis", "median", "pchisq",
             "varimax")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'FactoMineR'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 42 marked UTF-8 strings
coef.HDtweedie: no visible global function definition for 'rbind2'
coef.cv.HDtweedie: no visible global function definition for 'coef'
cv.tweediegrppath: no visible global function definition for 'predict'
cv.tweediegrppath: no visible binding for global variable
  'weighted.mean'
cvcompute: no visible binding for global variable 'weighted.mean'
error.bars: no visible global function definition for 'segments'
lambda.interp: no visible global function definition for 'approx'
plot.HDtweedie: no visible global function definition for 'par'
plot.HDtweedie: no visible binding for global variable 'plot.default'
plot.HDtweedie: no visible global function definition for 'gray.colors'
plot.HDtweedie: no visible global function definition for 'abline'
plot.cv.HDtweedie: no visible global function definition for 'points'
plot.cv.HDtweedie: no visible global function definition for 'axis'
plot.cv.HDtweedie: no visible global function definition for 'abline'
predict.HDtweedie: no visible global function definition for 'rbind2'
predict.HDtweedie: no visible global function definition for 'cbind2'
predict.cv.HDtweedie: no visible global function definition for
  'predict'
Undefined global functions or variables:
  abline approx axis cbind2 coef gray.colors par plot.default points
  predict rbind2 segments weighted.mean
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "abline", "axis", "par", "plot.default",
             "points", "segments")
  importFrom("methods", "cbind2", "rbind2")
  importFrom("stats", "approx", "coef", "predict", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages suggested but not available for checking: 'covr', 'lintr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'timetk'

Package suggested but not available for checking: 'tidyquant'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'timetk', 'modeltime', 'modeltime.ensemble', 'modeltime.resample',
  'tidyquant', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'healthyR', 'healthyR.ts'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'covr', 'ggpubr', 'rerddap'
Package required but not available: 'sampleSelection'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rgho'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'devtools', 'covr'
Note: found 1 marked Latin-1 string
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rvest', 'httr', 'taxize'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'httpcache'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'Rgraphviz'
Package required but not available: 'car'

Packages suggested but not available for checking:
  'candisc', 'animation', 'mvinfluence'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'crul', 'curl'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
hergm: no visible global function definition for 'ergm.Cprepare'
hergm.getnetwork: no visible global function definition for
  'ergm.Cprepare'
hergm.mcmc: no visible global function definition for 'ergm.Cprepare'
hergm.preprocess: no visible global function definition for
  'ergm.Cprepare'
hergm.set.mcmc: no visible global function definition for
  'ergm.Cprepare'
Undefined global functions or variables:
  ergm.Cprepare
Package suggested but not available for checking: 'synbreed'
Package required but not available: 'DESeq2'

Package suggested but not available for checking: 'glmmADMB'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
Packages suggested but not available for checking: 'covr', 'kableExtra'
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'cea.Rmd' using rmarkdown
--- finished re-building 'cea.Rmd'

--- re-building 'intro.Rmd' using rmarkdown
Quitting from lines 29-37 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'intro.Rmd'

--- re-building 'markov-cohort.Rmd' using rmarkdown
--- finished re-building 'markov-cohort.Rmd'

--- re-building 'markov-inhomogeneous-cohort.Rmd' using rmarkdown
Quitting from lines 84-96 (markov-inhomogeneous-cohort.Rmd) 
Error: processing vignette 'markov-inhomogeneous-cohort.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'markov-inhomogeneous-cohort.Rmd'

--- re-building 'markov-inhomogeneous-indiv.Rmd' using rmarkdown
Quitting from lines 38-43 (markov-inhomogeneous-indiv.Rmd) 
Error: processing vignette 'markov-inhomogeneous-indiv.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'markov-inhomogeneous-indiv.Rmd'

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

--- re-building 'mstate.Rmd' using rmarkdown
Loading required package: survival
--- finished re-building 'mstate.Rmd'

--- re-building 'psm.Rmd' using rmarkdown
Loading required package: survival
Warning: Survival curves crossed 0.06 percent of the time.
--- finished re-building 'psm.Rmd'

SUMMARY: processing the following files failed:
  'intro.Rmd' 'markov-inhomogeneous-cohort.Rmd'
  'markov-inhomogeneous-indiv.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'MASS' 'Matrix'
  All declared Imports should be used.
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package required but not available: 'processmapR'

Package suggested but not available for checking: 'DiagrammeRsvg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'affy'
Package required but not available: 'ggimage'

Package suggested but not available for checking: 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
HubNetwork: no visible global function definition for 'rbinom'
HubNetwork: no visible global function definition for 'runif'
HubNetwork: no visible global function definition for 'cov2cor'
binaryMCMC: no visible global function definition for 'rbinom'
image.hbn: no visible global function definition for 'col2rgb'
image.hbn: no visible global function definition for 'rgb'
image.hbn: no visible global function definition for 'dev.new'
image.hbn: no visible global function definition for 'par'
image.hbn: no visible global function definition for 'image'
image.hcov: no visible global function definition for 'col2rgb'
image.hcov: no visible global function definition for 'rgb'
image.hcov: no visible global function definition for 'dev.new'
image.hcov: no visible global function definition for 'par'
image.hcov: no visible global function definition for 'image'
image.hglasso: no visible global function definition for 'col2rgb'
image.hglasso: no visible global function definition for 'rgb'
image.hglasso: no visible global function definition for 'dev.new'
image.hglasso: no visible global function definition for 'par'
image.hglasso: no visible global function definition for 'image'
plot.hbn: no visible global function definition for 'rgb'
plot.hcov: no visible global function definition for 'rgb'
plot.hglasso: no visible global function definition for 'rgb'
Undefined global functions or variables:
  col2rgb cov2cor dev.new image par rbinom rgb runif
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rgb")
  importFrom("graphics", "image", "par")
  importFrom("stats", "cov2cor", "rbinom", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'rmarkdown'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'car', 'Rcmdr', 'RcmdrPlugin.HH'
Package unavailable to check Rd xrefs: 'Rcmdr'
Namespace in Imports field not imported from: 'spatstat.linnet'
  All declared Imports should be used.
Packages suggested but not available for checking: 'covr', 'devtools'
Namespace in Imports field not imported from: 'MCMCpack'
  All declared Imports should be used.
':::' call which should be '::': 'ggplot2:::guide_axis'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'ggplot2:::build_guides' 'ggplot2:::scales_list'
  See the note in ?`:::` about the use of this operator.
banded: no visible global function definition for 'toeplitz'
gpband: no visible global function definition for 'toeplitz'
hierband.cv: no visible global function definition for 'cov'
hierband.cv: no visible binding for global variable 'sd'
subdiag.thresh: no visible global function definition for 'uniroot'
subdiag.thresh: no visible global function definition for 'toeplitz'
Undefined global functions or variables:
  cov sd toeplitz uniroot
Consider adding
  importFrom("stats", "cov", "sd", "toeplitz", "uniroot")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: 'entropart'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'XMLRPC'
calcPower: no visible global function definition for 'pchisq'
calcPower: no visible global function definition for 'qchisq'
delta2 : K1: no visible global function definition for 'qnorm'
delta2: no visible global function definition for 'qnorm'
delta2: no visible global function definition for 'pnorm'
delta2: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm")
to your NAMESPACE file.
compute.contrasts: no visible binding for global variable 'sd'
compute.contrasts: no visible global function definition for 'cor'
compute.contrasts: no visible global function definition for 'sd'
plot.hiertest: no visible global function definition for 'legend'
Undefined global functions or variables:
  cor legend sd
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'library' or 'require' calls to packages already attached by Depends:
  'nnet' 'stats'
  Please remove these calls from your code.
Package in Depends field not imported from: 'nnet'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: 'quantmod'

Packages suggested but not available for checking:
  'httr', 'forecast', 'geojsonio', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
CLX.sim.Covtest: no visible global function definition for 'cov'
CLX.sim.equalcov: no visible global function definition for 'cov'
CLX.sim.unequalcov: no visible global function definition for 'cov'
CLX.test.equalcov: no visible global function definition for 'cov'
CLX.test.unequalcov: no visible global function definition for 'cov'
ChenQin.sim: no visible global function definition for 'pnorm'
ChenQin.test: no visible global function definition for 'pnorm'
GCT.sim: no visible binding for global variable 'var'
GCT.sim: no visible global function definition for 'acf'
GCT.sim: no visible global function definition for 'pnorm'
GCT.test: no visible binding for global variable 'var'
GCT.test: no visible global function definition for 'acf'
GCT.test: no visible global function definition for 'pnorm'
GCT.test.missing: no visible binding for global variable 'var'
GCT.test.missing: no visible global function definition for 'acf'
GCT.test.missing: no visible global function definition for 'pnorm'
SK.sim: no visible global function definition for 'cov'
SK.sim: no visible global function definition for 'pnorm'
SK.test: no visible global function definition for 'cov'
SK.test: no visible global function definition for 'pnorm'
build2popData : <anonymous>: no visible global function definition for
  'rnorm'
build2popData: no visible global function definition for 'arima.sim'
build2popData_muYafunction : <anonymous>: no visible global function
  definition for 'rnorm'
build2popData_muYafunction: no visible global function definition for
  'arima.sim'
innovate: no visible binding for global variable 'rnorm'
rdblepareto: no visible global function definition for 'runif'
rgammashift: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  acf arima.sim cov pnorm rgamma rnorm runif var
Consider adding
  importFrom("stats", "acf", "arima.sim", "cov", "pnorm", "rgamma",
             "rnorm", "runif", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: 'quantmod'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
BenjaminiHochberg: no visible global function definition for 'p.adjust'
CaoKosorok : CKfunc: no visible global function definition for 'pnorm'
CaoKosorok : <anonymous>: no visible global function definition for
  'pnorm'
StoreyTibshirani: no visible global function definition for
  'smooth.spline'
plotI_Lines: no visible global function definition for 'par'
plotI_Lines: no visible global function definition for 'lines'
plotI_Lines: no visible global function definition for 'legend'
plotI_Points: no visible global function definition for 'points'
plotI_Points: no visible global function definition for 'legend'
tStatistic : <anonymous>: no visible global function definition for
  't.test'
venn2: no visible global function definition for 'plot.new'
venn3: no visible global function definition for 'plot.new'
Undefined global functions or variables:
  legend lines p.adjust par plot.new pnorm points smooth.spline t.test
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot.new", "points")
  importFrom("stats", "p.adjust", "pnorm", "smooth.spline", "t.test")
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
Packages required but not available: 'ggpubr', 'FSA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
occupancy: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
data_simu: no visible global function definition for 'runif'
data_simu: no visible global function definition for 'rbinom'
data_simu: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rbinom rnorm runif
Consider adding
  importFrom("stats", "rbinom", "rnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
overlay.sim: no visible global function definition for 'points'
plotDistr: no visible global function definition for 'dev.hold'
plotDistr: no visible global function definition for 'dev.flush'
plotDistr: no visible global function definition for 'segments'
Undefined global functions or variables:
  dev.flush dev.hold points segments
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold")
  importFrom("graphics", "points", "segments")
to your NAMESPACE file.
'library' or 'require' call to 'rgl' which was already attached by Depends.
  Please remove these calls from your code.
PlotOptPower: no visible global function definition for 'bmp'
PlotOptPower: no visible global function definition for
  'filled.contour'
PlotOptPower: no visible global function definition for 'title'
PlotOptPower: no visible global function definition for 'grey.colors'
PlotOptPower: no visible global function definition for 'axis'
PlotOptPower: no visible global function definition for 'polygon'
PlotOptPower: no visible global function definition for 'legend'
PlotOptPower: no visible global function definition for 'mtext'
PlotOptPower: no visible global function definition for 'dev.off'
PlotOptPower: no visible global function definition for
  'terrain.colors'
ShowOptDesign: no visible global function definition for 'head'
diffVariantError: no visible global function definition for 'pbinom'
predictPoolNCP: no visible global function definition for 'data'
probDetEqual3: no visible global function definition for 'dbinom'
probDetEqual3: no visible global function definition for 'pbinom'
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
arms: no visible global function definition for 'rnorm'
rballunif: no visible global function definition for 'rnorm'
rballunif: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Packages suggested but not available for checking: 'car', 'heplots'
Package unavailable to check Rd xrefs: 'alr4'
Running examples in 'HistData-Ex.R' failed
The error most likely occurred in:

> ### Name: CushnyPeebles
> ### Title: Cushny-Peebles Data: Soporific Effects of Scopolamine
> ###   Derivatives
> ### Aliases: CushnyPeebles CushnyPeeblesN
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(CushnyPeebles)
> # quick looks at the data
> plot(CushnyPeebles)
> boxplot(CushnyPeebles, ylab="Hours of Sleep", xlab="Treatment")
> 
> ##########################
> # Repeated measures MANOVA
> 
> CPmod <- lm(cbind(Control, L_hyoscyamine, L_hyoscine, DL_hyoscine) ~ 1, data=CushnyPeebles)
> 
> # Assign within-S factor and contrasts
> Treatment <- factor(colnames(CushnyPeebles), levels=colnames(CushnyPeebles))
> contrasts(Treatment) <- matrix(
+ 	c(-3, 1, 1, 1,
+ 	   0,-2, 1, 1,
+ 	   0, 0,-1, 1), ncol=3)
> colnames(contrasts(Treatment)) <- c("Control.Drug", "L.DL", "L_hy.DL_hy")
> 
> Treats <- data.frame(Treatment)
> if (require(car)) {
+ (CPaov <- Anova(CPmod, idata=Treats, idesign= ~Treatment))
+ }
Loading required package: car
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'car'
> summary(CPaov, univariate=FALSE)
Error in summary(CPaov, univariate = FALSE) : object 'CPaov' not found
Execution halted
Package required but not available: 'FactoMineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 5002 marked UTF-8 strings
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'FGN'
Packages required but not available: 'devtools', 'usethis', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'curl', 'usethis'

Packages suggested but not available for checking: 'covr', 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'car'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'Rcpp' 'methods' 'rgl'
  All declared Imports should be used.
Package suggested but not available for checking: 'plotly'
Running examples in 'Hmisc-Ex.R' failed
The error most likely occurred in:

> ### Name: combplotp
> ### Title: Combination Plot
> ### Aliases: combplotp
> 
> ### ** Examples
> 
> g <- function() sample(0:1, n, prob=c(1 - p, p), replace=TRUE)
> set.seed(2); n <- 100; p <- 0.5
> x1 <- g(); label(x1) <- 'A long label for x1 that describes it'
> x2 <- g()
> x3 <- g(); label(x3) <- 'This is<br>a label for x3'
> x4 <- g()
> combplotp(~ x1 + x2 + x3 + x4, showno=TRUE, includenone=TRUE)
Error in loadNamespace(x) : there is no package called 'plotly'
Calls: combplotp ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'Rgraphviz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
baumwelchcont: no visible global function definition for 'dnorm'
hmmcontSimul: no visible global function definition for 'rnorm'
hmmcontSimul: no visible global function definition for 'rbinom'
plot.ContObservHMM: no visible global function definition for 'lines'
statesDistributionsPlot: no visible global function definition for
  'dnorm'
statesDistributionsPlot: no visible global function definition for 'sd'
statesDistributionsPlot: no visible global function definition for
  'lines'
statesDistributionsPlot: no visible global function definition for
  'legend'
summary.ContObservHMM: no visible global function definition for 'sd'
Undefined global functions or variables:
  dnorm legend lines rbinom rnorm sd
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "dnorm", "rbinom", "rnorm", "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
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
dishonestCasino: no visible global function definition for 'axis'
dishonestCasino: no visible global function definition for 'text'
dishonestCasino: no visible global function definition for 'rect'
dishonestCasino: no visible global function definition for 'rgb'
dishonestCasino: no visible global function definition for 'points'
Undefined global functions or variables:
  axis points rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "points", "rect", "text")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'usethis'
Namespace in Imports field not imported from: 'Matrix'
  All declared Imports should be used.
Package required but not available: 'quantmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
hornpa: no visible global function definition for 'rnorm'
hornpa: no visible global function definition for 'cor'
hornpa: no visible global function definition for 'quantile'
Undefined global functions or variables:
  cor quantile rnorm
Consider adding
  importFrom("stats", "cor", "quantile", "rnorm")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  'MASS' 'Rdpack'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'survival'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'FactoMineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'sampleSelection'
Malformed Description field: should contain one or more complete sentences.
hpbayes.plot: no visible global function definition for 'par'
hpbayes.plot: no visible global function definition for 'points'
postpri.plot: no visible global function definition for 'par'
postpri.plot: no visible global function definition for 'points'
postpri.plot: no visible global function definition for 'segments'
postpri.plot: no visible global function definition for 'boxplot'
Undefined global functions or variables:
  boxplot par points segments
Consider adding
  importFrom("graphics", "boxplot", "par", "points", "segments")
to your NAMESPACE file.
ApproxC: no visible global function definition for 'convolve'
DMC: no visible global function definition for 'median'
DMC: no visible global function definition for 'ecdf'
ToSWF: no visible global function definition for 'write.table'
Undefined global functions or variables:
  convolve ecdf median write.table
Consider adding
  importFrom("stats", "convolve", "ecdf", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages required but not available: 'imputeTS', 'forecast'

Package suggested but not available for checking: 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
bracket: no visible global function definition for 'segments'
Undefined global functions or variables:
  segments
Consider adding
  importFrom("graphics", "segments")
to your NAMESPACE file.
Package suggested but not available for checking: 'tidyverse'
Error(s) in re-building vignettes:
--- re-building 'PropertiesAthens.Rmd' using knitr
Linking to GEOS 3.6.2, GDAL 3.0.4, PROJ 7.0.0
Quitting from lines 15-19 (PropertiesAthens.Rmd) 
Error: processing vignette 'PropertiesAthens.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'PropertiesAthens.Rmd'

--- re-building 'hsar.Rmd' using knitr
Checking rgeos availability: TRUE
rgdal: version: 1.5-23, (SVN revision 1121)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.0.4, released 2020/01/28
Path to GDAL shared files: C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/lib/rgdal/gdal
GDAL binary built with GEOS: FALSE 
Loaded PROJ runtime: Rel. 7.0.0, March 1st, 2020, [PJ_VERSION: 700]
Path to PROJ shared files: C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/lib/rgdal/proj
PROJ CDN enabled: FALSE
Linking to sp version:1.4-5
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading rgdal.
Overwritten PROJ_LIB was C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/lib/rgdal/proj
rgeos version: 0.5-5, (SVN revision 640)
 GEOS runtime version: 3.6.2-CAPI-1.10.2 
 Linking to sp version: 1.4-5 
 Polygon checking: TRUE 

Loading required package: spData
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
Loading required package: sf
Linking to GEOS 3.6.2, GDAL 3.0.4, PROJ 7.0.0
--- finished re-building 'hsar.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
hsicCCA: no visible global function definition for 'median'
hsicCCA: no visible global function definition for 'dist'
hsicCCAfunc: no visible global function definition for 'rnorm'
hsicCCAfunc: no visible global function definition for 'runif'
hsicCCAfunc: no visible global function definition for 'optim'
ktaCCA: no visible global function definition for 'median'
ktaCCA: no visible global function definition for 'dist'
ktaCCAfunc: no visible global function definition for 'rnorm'
ktaCCAfunc: no visible global function definition for 'runif'
ktaCCAfunc: no visible global function definition for 'optim'
Undefined global functions or variables:
  dist median optim rnorm runif
Consider adding
  importFrom("stats", "dist", "median", "optim", "rnorm", "runif")
to your NAMESPACE file.
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.
get.d: no visible global function definition for 'dgeom'
get.d: no visible global function definition for 'dnbinom'
get.d: no visible global function definition for 'dpois'
get.pdf: no visible global function definition for 'dnorm'
get.pdf: no visible global function definition for 'dpois'
get.pdf: no visible global function definition for 'dmvnorm'
hsmm: no visible global function definition for 'uniroot'
hsmm.sim: no visible global function definition for 'rbinom'
hsmm.sim: no visible global function definition for 'rnorm'
hsmm.sim: no visible global function definition for 'rpois'
hsmm.sim: no visible global function definition for 'rmvnorm'
loggeom.update: no visible global function definition for 'plogis'
rmt: no visible global function definition for 'rt'
rmt: no visible global function definition for 'rnorm'
rmt: no visible global function definition for 'rchisq'
rvm: no visible global function definition for 'runif'
Undefined global functions or variables:
  dgeom dmvnorm dnbinom dnorm dpois plogis rbinom rchisq rmvnorm rnorm
  rpois rt runif uniroot
Consider adding
  importFrom("stats", "dgeom", "dnbinom", "dnorm", "dpois", "plogis",
             "rbinom", "rchisq", "rnorm", "rpois", "rt", "runif",
             "uniroot")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

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
'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: 'httr', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'httr', 'rvest'
'LazyData' is specified without a 'data' directory
BasicHTML: no visible global function definition for 'png'
BasicHTML: no visible global function definition for 'dev.list'
BasicHTML: no visible global function definition for 'dev.off'
FramedHTML: no visible global function definition for 'graphics.off'
Undefined global functions or variables:
  dev.list dev.off graphics.off png
Consider adding
  importFrom("grDevices", "dev.list", "dev.off", "graphics.off", "png")
to your NAMESPACE file.
Package suggested but not available for checking: 'HTSFilter'
Package required but not available: 'forecast'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'editData'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DESeq2', 'phyloseq'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Package suggested but not available for checking: 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
getToHost: no visible global function definition for 'make.socket'
getToHost: no visible global function definition for 'write.socket'
getToHost: no visible global function definition for 'read.socket'
getToHost: no visible global function definition for 'close.socket'
postToHost: no visible global function definition for 'runif'
simplePostToHost: no visible global function definition for
  'make.socket'
simplePostToHost: no visible global function definition for
  'write.socket'
simplePostToHost: no visible global function definition for
  'read.socket'
simplePostToHost: no visible global function definition for
  'close.socket'
Undefined global functions or variables:
  close.socket make.socket read.socket runif write.socket
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "close.socket", "make.socket", "read.socket",
             "write.socket")
to your NAMESPACE file.
Packages required but not available: 'curl', 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'curl'
GNU make is a SystemRequirements.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(httpuv)
  > 
  > test_check("httpuv")
  Error in library(curl) : there is no package called 'curl'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Package required but not available: 'curl'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: 'testthat'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Calculate3D: no visible global function definition for 'persp'
CalculateHUM_Ex: no visible global function definition for 'combn'
CalculateHUM_Plot: no visible global function definition for 'polygon'
CalculateHUM_Plot: no visible global function definition for 'text'
CalculateHUM_Plot: no visible global function definition for 'points'
CalculateHUM_Plot: no visible global function definition for 'lines'
Undefined global functions or variables:
  combn lines persp points polygon text
Consider adding
  importFrom("graphics", "lines", "persp", "points", "polygon", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package suggested but not available for checking: 'pdftools'
Package required but not available: 'rvest'

Packages suggested but not available for checking: 'covr', 'devtools'

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

Package suggested but not available for checking: 'hurricaneexposuredata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking:
  'AER', 'covr', 'devtools', 'httr'
Namespaces in Imports field not imported from:
  'R6' 'xml2'
  All declared Imports should be used.
Malformed Title field: should not end in a period.
HWEImportSamp: no visible global function definition for 'dnorm'
HWEImportSamp: no visible global function definition for 'rnorm'
HWEmodelsMLE: no visible global function definition for 'optim'
HWEsimdat: no visible global function definition for 'rmultinom'
LambdaOptim: no visible global function definition for 'rnorm'
LambdaOptim : LambdaPriorChoice: no visible global function definition
  for 'quantile'
LambdaOptim: no visible global function definition for 'optim'
SinglefPrior: no visible global function definition for 'rnorm'
SinglefReject: no visible global function definition for 'runif'
TriangNormHWE: no visible global function definition for 'pbeta'
Undefined global functions or variables:
  dnorm optim pbeta quantile rmultinom rnorm runif
Consider adding
  importFrom("stats", "dnorm", "optim", "pbeta", "quantile", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  'colourpicker' 'shiny' 'wordcloud2'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
HW.plain: 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.
getHwriterVersion: no visible global function definition for
  'sessionInfo'
hmapRowCol: no visible global function definition for 'na.omit'
hwriteImage: no visible global function definition for 'dev.print'
hwriteImage: no visible binding for global variable 'png'
showExample: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL dev.print na.omit png sessionInfo
Consider adding
  importFrom("grDevices", "dev.print", "png")
  importFrom("stats", "na.omit")
  importFrom("utils", "browseURL", "sessionInfo")
to your NAMESPACE file.
Checking should be performed on sources prepared by 'R CMD build'.
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.
hybridMC: no visible global function definition for 'txtProgressBar'
hybridMC : pbFun: no visible global function definition for
  'setTxtProgressBar'
hybridMC: no visible global function definition for 'mcmc'
Undefined global functions or variables:
  mcmc setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'graph'
  All declared Imports should be used.
ARPIEM2012.Lmom.sample: no visible global function definition for 'var'
ARPIEM2012.freq: no visible binding for global variable 'quantile'
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.Qind_camp: no visible global
  function definition for 'rnorm'
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.Qind_reg_moltiplicativo: no
  visible global function definition for 'rnorm'
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.LCV_camp.LCA_camp: no visible
  global function definition for 'rnorm'
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.LCV_camp.LCA_reg_additivo: no
  visible global function definition for 'rnorm'
ARPIEM2012.sim.Lmoments :
  ARPIEM2012.sim.LCV_reg_moltiplicativo.LCA_reg_additivo: no visible
  global function definition for 'rnorm'
Undefined global functions or variables:
  quantile rnorm var
Consider adding
  importFrom("stats", "quantile", "rnorm", "var")
to your NAMESPACE file.
Note: found 3026 marked UTF-8 strings
Package required but not available: 'plotly'

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: 'flowCore'
'LazyData' is specified without a 'data' directory
Package required but not available: 'matlib'

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: 'magick'
Packages in Depends field not imported from:
  'R.utils' 'ape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
requiprobable: no visible global function definition for 'extract'
requiprobable : make.tree: no visible global function definition for
  'extract'
requiprobable : make.tree: no visible global function definition for
  'runif'
rgenetree: no visible global function definition for 'dbinom'
rgenetree: no visible global function definition for 'dnbinom'
rgenetree: no visible global function definition for 'runif'
rgenetree: no visible global function definition for 'rbinom'
rgenetree: no visible global function definition for 'rnbinom'
Undefined global functions or variables:
  dbinom dnbinom extract rbinom rnbinom runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "rbinom", "rnbinom", "runif")
to your NAMESPACE file.
conint: no visible global function definition for 'sd'
findroot: no visible global function definition for 'integrate'
hypothesis: no visible global function definition for 'sd'
hypothesis: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate sd
Consider adding
  importFrom("stats", "integrate", "sd")
to your NAMESPACE file.
Package required but not available: 'httr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages in Depends field not imported from:
  'MCMCpack' 'coda' 'foreach'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: 'ymlthis'

Packages suggested but not available for checking: 'plotly', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Package required but not available: 'kableExtra'

Packages suggested but not available for checking:
  'tidyverse', 'rvest', 'pdftools', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
ibdhap.barplot: no visible global function definition for 'rect'
ibdhap.compare.loci: no visible global function definition for 'hist'
ibdhap.compare.segs: no visible global function definition for 'tail'
ibdhap.make.calls: no visible global function definition for
  'count.fields'
ibdhap.make.calls: no visible global function definition for
  'read.table'
ibdhap.make.true: no visible global function definition for
  'read.table'
ibdhap.names: no visible global function definition for 'count.fields'
ibdhap.names: no visible global function definition for 'read.table'
ibdhap.reduce.states: no visible global function definition for
  'read.table'
ibdhap.reduce.states: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  count.fields hist read.table rect tail write.table
Consider adding
  importFrom("graphics", "hist", "rect")
  importFrom("utils", "count.fields", "read.table", "tail",
             "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
CreateVoronoi: no visible global function definition for 'slot'
CreateVoronoi : <anonymous>: no visible global function definition for
  'slot'
CreateVoronoi: no visible global function definition for 'chull'
ExtractIMFi2D: no visible global function definition for 'par'
LocatedAtBoundary: no visible global function definition for
  'txtProgressBar'
LocatedAtBoundary: no visible global function definition for
  'setTxtProgressBar'
PlotFit: no visible global function definition for 'par'
iBEEMD: no visible global function definition for 'is'
iBEEMD: no visible global function definition for 'sd'
iBEEMD: no visible global function definition for 'txtProgressBar'
iBEEMD: no visible global function definition for 'rnorm'
iBEEMD: no visible global function definition for 'setTxtProgressBar'
iBEEMD: no visible global function definition for 'terrain.colors'
rbfcreate: no visible global function definition for 'is'
rbfcreate : rbfAssemble: no visible global function definition for
  'dist'
rbfinterp: no visible global function definition for 'is'
rbfinterp: no visible global function definition for 'dist'
Undefined global functions or variables:
  chull dist is par rnorm sd setTxtProgressBar slot terrain.colors
  txtProgressBar
Consider adding
  importFrom("grDevices", "chull", "terrain.colors")
  importFrom("graphics", "par")
  importFrom("methods", "is", "slot")
  importFrom("stats", "dist", "rnorm", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package required but not available: 'httr'

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: 'magick'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Iboot: 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
Package suggested but not available for checking: 'covr'
..placeOrder: no visible global function definition for 'str'
.reqMktData.vignette: no visible global function definition for
  'flush.console'
e_portfolio_value: no visible global function definition for 'str'
print.eventPortfolioValue: no visible global function definition for
  'str'
print.twsContract: no visible global function definition for 'str'
print.twsContractDetails: no visible global function definition for
  'str'
print.twsOrder: no visible global function definition for 'str'
print.twsOrderState: no visible global function definition for 'str'
print.twsScannerSubscription: no visible global function definition for
  'str'
reqAccountUpdates: no visible binding for global variable 'timestamp'
reqContractDetails: no visible binding for global variable 'timestamp'
reqHistoricalData: no visible global function definition for
  'flush.console'
reqHistoricalData: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  flush.console str timestamp write.table
Consider adding
  importFrom("utils", "flush.console", "str", "timestamp", "write.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'tcltk' which was already attached by Depends.
  Please remove these calls from your code.
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.
ICA: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package required but not available: 'V8'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ICCbare: no visible global function definition for 'na.omit'
ICCbare: no visible global function definition for 'formula'
ICCbare: no visible global function definition for 'replications'
ICCbare: no visible global function definition for 'aggregate'
ICCbare: no visible global function definition for 'anova'
ICCbare: no visible global function definition for 'aov'
ICCbareF: no visible global function definition for 'aggregate'
ICCest: no visible global function definition for 'na.omit'
ICCest: no visible global function definition for 'anova'
ICCest: no visible global function definition for 'aov'
ICCest: no visible global function definition for 'aggregate'
ICCest: no visible global function definition for 'qf'
ICCest: no visible global function definition for 'qnorm'
Nest: no visible global function definition for 'qnorm'
effort : CIW: no visible global function definition for 'qf'
effort: no visible global function definition for 'axis'
effort: no visible global function definition for 'lines'
effort: no visible global function definition for 'legend'
Undefined global functions or variables:
  aggregate anova aov axis formula legend lines na.omit qf qnorm
  replications
Consider adding
  importFrom("graphics", "axis", "legend", "lines")
  importFrom("stats", "aggregate", "anova", "aov", "formula", "na.omit",
             "qf", "qnorm", "replications")
to your NAMESPACE file.
Package suggested but not available for checking: 'rvest'
Note: found 303398 marked UTF-8 strings
Package suggested but not available for checking: 'icd'
Note: found 55 marked UTF-8 strings
Namespace in Imports field not imported from: 'coda'
  All declared Imports should be used.
Packages required but not available: 'plotly', 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'KernSmooth' which was already attached by Depends.
  Please remove these calls from your code.
bickde: no visible global function definition for 'optimize'
iclocpoly: no visible global function definition for 'approx'
iclocpoly: no visible global function definition for 'sd'
iclocpoly: no visible global function definition for 'dnorm'
iclocpoly: no visible global function definition for 'pnorm'
iclocpoly: no visible global function definition for 'var'
inmost: no visible global function definition for 'stack'
Undefined global functions or variables:
  approx dnorm optimize pnorm sd stack var
Consider adding
  importFrom("stats", "approx", "dnorm", "optimize", "pnorm", "sd",
             "var")
  importFrom("utils", "stack")
to your NAMESPACE file.
Package suggested but not available for checking: 'plotly'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  ---------------------  "----------"                        
  Direction              "short"                             
  Start                  2020-04-02                          
  End                    2020-09-29                          
  Ticker                 "TKR"                               
  ichimoku: cannot create an ichimoku object from a 'ggggplot' object
  == Failed tests ================================================================
  -- Failure (test-ichimoku.R:22:3): ichimoku plot functions pass ----------------
  `iplot` inherits from 'gg'/'ggplot' not 'plotly'.
  -- Failure (test-ichimoku.R:23:3): ichimoku plot functions pass ----------------
  `iplot` inherits from 'gg'/'ggplot' not 'htmlwidget'.
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 26 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Depends: includes the non-default packages:
  'lattice', 'caTools', 'gdata', 'gtools', 'gplots', 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'caTools' 'gdata' 'gplots' 'gtools' 'lattice' 'parallel'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: 'magick'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rvest', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'magrittr' 'tidyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
PH.ICsurv.EM: no visible global function definition for 'quantile'
PH.ICsurv.EM: no visible global function definition for 'optim'
fast.PH.ICsurv.EM: no visible global function definition for 'quantile'
fast.PH.ICsurv.EM: no visible global function definition for 'optim'
Undefined global functions or variables:
  optim quantile
Consider adding
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

idbg.interact: no visible global function definition for
  'capture.output'
idbg.interact: no visible global function definition for 'timestamp'
idbg.print_breakpoints: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output timestamp
Consider adding
  importFrom("utils", "capture.output", "timestamp")
to your NAMESPACE file.
Package required but not available: 'httr'

Package suggested but not available for checking: 'plotly'

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: 'rggobi'
Package required but not available: 'FRK'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Packages suggested but not available for checking:
  'rentrez', 'ggpubr', 'kableExtra', 'badger'

VignetteBuilder packages required for checking but not installed:
  'kableExtra', 'badger', 'rentrez'
Errors in running code in vignettes:
when running code in 'AVignette.Rmd'
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'kableExtra' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in 'index.Rmd'
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'kableExtra' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  'AVignette.Rmd' using 'UTF-8'... failed to complete the test
  'index.Rmd' using 'UTF-8'... failed to complete the test
Package suggested but not available for checking: 'pkgnet'
Package required but not available: 'animation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
comp.uri: no visible global function definition for 'quantile'
est.IDR: no visible global function definition for 'ecdf'
get.pseudo.mix: no visible global function definition for 'pnorm'
get.uri.2d: no visible global function definition for 'smooth.spline'
get.uri.2d: no visible global function definition for 'predict'
Undefined global functions or variables:
  ecdf pnorm predict quantile smooth.spline
Consider adding
  importFrom("stats", "ecdf", "pnorm", "predict", "quantile",
             "smooth.spline")
to your NAMESPACE file.
Packages required but not available: 'GD', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mzR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages in Depends field not imported from:
  'XML' 'vegan'
  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
Packages suggested but not available for checking:
  'ie2miscdata', 'rvest', 'qdap'
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: 'testit'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 40 marked UTF-8 strings
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'expm' 'rlecuyer'
  All declared Imports should be used.
ROC_plot: no visible global function definition for 'pdf'
ROC_plot: no visible global function definition for 'par'
ROC_plot: no visible global function definition for 'dev.off'
Ymean_compare: no visible binding for global variable 'sd'
Ymean_compare: no visible global function definition for 'pdf'
Ymean_compare: no visible global function definition for 'par'
Ymean_compare: no visible global function definition for 'dev.off'
data_simulation: no visible global function definition for 'rnorm'
gibbs_sampling: no visible global function definition for 'rnorm'
mcmc_trace_plot: no visible global function definition for 'pdf'
mcmc_trace_plot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off par pdf rnorm sd
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "rnorm", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

ifa.em: no visible global function definition for 'runif'
ifa.init.pca: no visible global function definition for 'var'
ifa.init.pca: no visible global function definition for 'cor'
ifa.init.pca: no visible global function definition for 'runif'
ifa.init.random: no visible global function definition for 'runif'
ifa.init.random: no visible global function definition for 'var'
Undefined global functions or variables:
  cor runif var
Consider adding
  importFrom("stats", "cor", "runif", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
  'LazyDataCompression' is specified without a 'data' directory
Package suggested but not available for checking: 'IFCdata'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'forecast', 'timetk'
Running examples in 'iForecast-Ex.R' failed
The error most likely occurred in:

> ### Name: iForecast
> ### Title: Extract predictions and class probabilities from train objects
> ### Aliases: iForecast
> 
> ### ** Examples
> 
> # Cross-validation takes time, example below is commented.
> ## Machine Learning by library(caret)
> #Case 1. Low frequency, regression type
> data("macrodata")
> dep <- macrodata[569:669,"unrate",drop=FALSE]
> ind <- macrodata[569:669,-1,drop=FALSE]
> train.end <- "2018-12-01"# Choosing the end dating of train
> 
> models <- c("svm","rf","rpart","gamboost","BstLm","bstSm","blackboost")[1]
> type <- c("none","trend","season","both")[1]
> Caret <- ttsCaret(y=dep, x=ind, arOrder=c(1), xregOrder=c(1),
+  method=models, tuneLength =1, train.end, type=type,
+  trControl= trainControl(method = "cv"))
Error in loadNamespace(x) : there is no package called 'forecast'
Calls: ttsCaret ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 160 marked UTF-8 strings
Namespace in Imports field not imported from: 'reticulate'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: 'covr'
Packages required but not available: 'curl', 'httr', 'rvest'

Package suggested but not available for checking: 'covr'

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: 'covr'
Packages required but not available: 'demography', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'magick'
Package suggested but not available for checking: 'magick'
Running examples in 'image.ContourDetector-Ex.R' failed
The error most likely occurred in:

> ### Name: image_contour_detector
> ### Title: Unsupervised Smooth Contour Lines Detection in an image
> ### Aliases: image_contour_detector
> 
> ### ** Examples
> 
> library(pixmap)
> imagelocation <- system.file("extdata", "image.pgm", package="image.ContourDetector")
> image <- read.pnm(file = imagelocation, cellres = 1)
Read 262144 items
> x <- image@grey * 255
> contourlines <- image_contour_detector(x)
> contourlines
Contour Lines Detector
  found 192 contour lines
> plot(image)
> plot(contourlines, add = TRUE, col = "red")
> 
> ##
> ## line_segment_detector expects a matrix as input
> ##  if you have a jpg/png/... convert it to pgm first or take the r/g/b channel
> library(magick)
Error in library(magick) : there is no package called 'magick'
Execution halted
Package suggested but not available for checking: 'magick'
Running examples in 'image.CornerDetectionF9-Ex.R' failed
The error most likely occurred in:

> ### Name: image_detect_corners
> ### Title: Find Corners in Digital Images with FAST-9.
> ### Aliases: image_detect_corners
> 
> ### ** Examples
> 
> library(pixmap)
> imagelocation <- system.file("extdata", "chairs.pgm", package="image.CornerDetectionF9")
> image   <- read.pnm(file = imagelocation, cellres = 1)
Read 262144 items
> x       <- image@grey * 255
> corners <- image_detect_corners(x, 80)
> plot(image)
> points(corners$x, corners$y, col = "red", pch = 20, lwd = 0.5)
> 
> ##
> ## image_detect_corners expects a matrix as input
> ##  if you have a jpg/png/... convert it to pgm first or take the r/g/b channel
> library(magick)
Error in library(magick) : there is no package called 'magick'
Execution halted
Package suggested but not available for checking: 'magick'
Running examples in 'image.CornerDetectionHarris-Ex.R' failed
The error most likely occurred in:

> ### Name: image_harris
> ### Title: Find Corners using Harris Corner Detection
> ### Aliases: image_harris
> 
> ### ** Examples
> 
> library(magick)
Error in library(magick) : there is no package called 'magick'
Execution halted
Package suggested but not available for checking: 'magick'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/image.dlib/image.dlib.Rcheck/00install.out' for details.
Package required but not available: 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'magick'
Running examples in 'image.libfacedetection-Ex.R' failed
The error most likely occurred in:

> ### Name: image_detect_faces
> ### Title: Detect faces in images using the libfacedetection CNN
> ### Aliases: image_detect_faces
> 
> ### ** Examples
> 
> library(magick)
Error in library(magick) : there is no package called 'magick'
Execution halted
Package suggested but not available for checking: 'magick'
Running examples in 'image.LineSegmentDetector-Ex.R' failed
The error most likely occurred in:

> ### Name: image_line_segment_detector
> ### Title: Line Segments Detection (LSD) in an image
> ### Aliases: image_line_segment_detector
> 
> ### ** Examples
> 
> library(pixmap)
> imagelocation <- system.file("extdata", "chairs.pgm", package="image.LineSegmentDetector")
> image <- read.pnm(file = imagelocation, cellres = 1)
Read 262144 items
> x <- image@grey * 255
> 
> linesegments <- image_line_segment_detector(x)
> linesegments
Line Segment Detector
  found 700 line segments
> plot(image)
> plot(linesegments, add = TRUE, col = "red")
> 
> 
> ##
> ## image_line_segment_detector expects a matrix as input
> ##  if you have a jpg/png/... convert it to pgm first or take the r/g/b channel
> library(magick)
Error in library(magick) : there is no package called 'magick'
Execution halted
Package suggested but not available for checking: 'magick'
Running examples in 'image.Otsu-Ex.R' failed
The error most likely occurred in:

> ### Name: image_otsu
> ### Title: Image segmentation using Otsu
> ### Aliases: image_otsu
> 
> ### ** Examples
> 
> library(magick)
Error in library(magick) : there is no package called 'magick'
Execution halted
Package suggested but not available for checking: 'tesseract'
Package suggested but not available for checking: 'magick'
Package required but not available: 'Rgraphviz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'jpeg'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'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: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'magick'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'magick', 'usethis', 'rtweet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'keras'
  All declared Imports should be used.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GSEABase', 'GSVA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'repmis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'missMDA'

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: 'compareGroups'
Namespaces in Imports field not imported from:
  'data.table' 'dplyr' 'haven'
  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
generate.ExpressionData: no visible global function definition for
  'rnorm'
impute.MinDet: no visible binding for global variable 'quantile'
impute.MinProb: no visible binding for global variable 'quantile'
impute.MinProb: no visible binding for global variable 'sd'
impute.MinProb: no visible global function definition for 'median'
impute.MinProb: no visible global function definition for 'rnorm'
impute.QRILC: no visible global function definition for 'qnorm'
impute.QRILC: no visible global function definition for 'quantile'
impute.QRILC: no visible global function definition for 'lm'
insertMVs: no visible global function definition for 'rnorm'
model.Selector: no visible global function definition for 'qnorm'
model.Selector: no visible global function definition for 'quantile'
model.Selector: no visible global function definition for 'lm'
model.Selector: no visible global function definition for 'ecdf'
model.Selector: no visible global function definition for 'pnorm'
pep2prot: no visible binding for global variable 'median'
Undefined global functions or variables:
  ecdf lm median pnorm qnorm quantile rnorm sd
Consider adding
  importFrom("stats", "ecdf", "lm", "median", "pnorm", "qnorm",
             "quantile", "rnorm", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
impute.mdr: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'DBI'
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'count_compare'
Package required but not available: 'PSF'

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

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.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- Failure (test_doIMRMCfromFile.R:45:7): doIMRMC given fileName does not change --
  `saveResult` not equal to `result`.
  Component "perReader": Component "readerID": 'current' is not a factor
  Component "perReader": Component "modalityA": 'current' is not a factor
  Component "perReader": Component "modalityB": 'current' is not a factor
  Component "Ustat": Component "modalityA": 'current' is not a factor
  Component "Ustat": Component "modalityB": 'current' is not a factor
  Component "Ustat": Component "UstatOrMLE": 'current' is not a factor
  Component "MLEstat": Component "modalityA": 'current' is not a factor
  Component "MLEstat": Component "modalityB": 'current' is not a factor
  Component "MLEstat": Component "UstatOrMLE": 'current' is not a factor
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 12 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'lme4' 'reshape2'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package required but not available: 'genefilter'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: 'testthat'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'dplyr' 'rgeos'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Package required but not available: 'gfonts'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'pkgdown'
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'API.Rmd' using rmarkdown
Quitting from lines 22-36 (API.Rmd) 
Error: processing vignette 'API.Rmd' failed with diagnostics:
there is no package called 'pkgdown'
--- failed re-building 'API.Rmd'

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

--- re-building 'Performance.Rmd' using rmarkdown
Quitting from lines 22-30 (Performance.Rmd) 
Error: processing vignette 'Performance.Rmd' failed with diagnostics:
there is no package called 'pkgdown'
--- failed re-building 'Performance.Rmd'

--- re-building 'Tutorial.Rmd' using rmarkdown
Quitting from lines 22-32 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
there is no package called 'pkgdown'
--- failed re-building 'Tutorial.Rmd'

SUMMARY: processing the following files failed:
  'API.Rmd' 'Performance.Rmd' 'Tutorial.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'car', 'RcmdrMisc'
Note: found 2 marked UTF-8 strings
Malformed Title field: should not end in a period.
IDM.bootCI: no visible global function definition for 'cov'
IDM.bootCI: no visible global function definition for 'cor'
IDM.bootCI: no visible global function definition for 'quantile'
Undefined global functions or variables:
  cor cov quantile
Consider adding
  importFrom("stats", "cor", "cov", "quantile")
to your NAMESPACE file.
Package in Depends field not imported from: 'sandwich'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
infer,coxph: no visible global function definition for 'coef'
infer,coxph: no visible global function definition for 'vcov'
infer,coxph: no visible global function definition for 'sandwich'
infer,coxph: no visible global function definition for 'pnorm'
infer,coxph: no visible global function definition for 'qnorm'
infer,gee: no visible global function definition for 'coef'
infer,gee: no visible global function definition for 'pnorm'
infer,gee: no visible global function definition for 'qnorm'
infer,glm: no visible global function definition for 'coef'
infer,glm: no visible global function definition for 'sandwich'
infer,glm: no visible global function definition for 'vcov'
infer,glm: no visible global function definition for 'pnorm'
infer,glm: no visible global function definition for 'qnorm'
infer,lm: no visible global function definition for 'coef'
infer,lm: no visible global function definition for 'sandwich'
infer,lm: no visible global function definition for 'vcov'
infer,lm: no visible global function definition for 'pnorm'
infer,lm: no visible global function definition for 'qnorm'
infer,lme: no visible global function definition for 'coef'
infer,lme: no visible global function definition for 'fixed.effects'
infer,lme: no visible global function definition for 'vcov'
infer,lme: no visible global function definition for 'pnorm'
infer,lme: no visible global function definition for 'qnorm'
infer,mer: no visible global function definition for 'coef'
infer,mer: no visible global function definition for 'vcov'
infer,mer: no visible global function definition for 'pnorm'
infer,mer: no visible global function definition for 'qnorm'
infer,mer: no visible binding for global variable 'fm1'
Undefined global functions or variables:
  coef fixed.effects fm1 pnorm qnorm sandwich vcov
Consider adding
  importFrom("stats", "coef", "pnorm", "qnorm", "vcov")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
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.
contrib: no visible global function definition for 'aggregate'
est.expDeath : surv_p: no visible global function definition for
  'survfit'
est.expDeath : surv_p: no visible global function definition for
  'approx'
function1: no visible global function definition for 'coxph.detail'
inference.SMR: no visible global function definition for 'qnorm'
var.expDeath : surv_p: no visible global function definition for
  'survfit'
var.expDeath : surv_p: no visible global function definition for
  'approx'
Undefined global functions or variables:
  aggregate approx coxph.detail qnorm survfit
Consider adding
  importFrom("stats", "aggregate", "approx", "qnorm")
to your NAMESPACE file.
Packages suggested but not available for checking: 'covr', 'devtools'
Package suggested but not available for checking: 'covr'
Package unavailable to check Rd xrefs: 'minfi'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Note: found 151 marked UTF-8 strings
Namespace in Imports field not imported from: 'optimr'
  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
Package suggested but not available for checking: 'NNS'
Package unavailable to check Rd xrefs: 'NNS'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
BugReports field should be the URL of a single webpage
gen.intercepts: no visible global function definition for 'contr.SAS'
Undefined global functions or variables:
  contr.SAS
Consider adding
  importFrom("stats", "contr.SAS")
to your NAMESPACE file.
entropy: no visible global function definition for 'na.omit'
interinformation: no visible global function definition for 'na.omit'
multiinformation: no visible global function definition for 'na.omit'
mutinformation: 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.
Package suggested but not available for checking: 'rNOMADS'
Malformed Description field: should contain one or more complete sentences.
getInfra: no visible global function definition for 'txtProgressBar'
getInfra: no visible global function definition for 'download.file'
getInfra: no visible global function definition for 'setTxtProgressBar'
getInfra : <anonymous>: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "download.file", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Unexported object imported by a ':::' call: 'ltm:::crf.GPCM'
  See the note in ?`:::` about the use of this operator.
Jeffreys: no visible global function definition for 'integrate'
Jeffreys: no visible global function definition for 'splinefun'
count.rows: no visible global function definition for 'tail'
count.rows: no visible global function definition for 'head'
cprobs : <anonymous>: no visible global function definition for
  'plogis'
inf.func.ltm : f: no visible global function definition for 'plogis'
iota: no visible global function definition for 'integrate'
iota: no visible global function definition for 'optimize'
iota: no visible global function definition for 'pchisq'
iota.c : rirm: no visible global function definition for 'coef'
iota.c: no visible global function definition for 'integrate'
iota.c: no visible global function definition for 'sd'
iota.u: no visible global function definition for 'integrate'
iprobs : <anonymous>: no visible global function definition for
  'plogis'
logL.ltm : logL: no visible global function definition for 'dbinom'
logL.ltm : logL: no visible global function definition for 'plogis'
logL.ltm : logL : <anonymous>: no visible global function definition
  for 'plogis'
rJeffreys : Jpinv.min: no visible global function definition for
  'integrate'
rJeffreys : Jpinv: no visible global function definition for 'nlminb'
rJeffreys : Jpinv: no visible global function definition for 'qnorm'
rJeffreys: no visible global function definition for 'runif'
Undefined global functions or variables:
  coef dbinom head integrate nlminb optimize pchisq plogis qnorm runif
  sd splinefun tail
Consider adding
  importFrom("stats", "coef", "dbinom", "integrate", "nlminb",
             "optimize", "pchisq", "plogis", "qnorm", "runif", "sd",
             "splinefun")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Packages suggested but not available for checking: 'covr', 'ggmap', 'INLA'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'dataRetrieval'
Namespaces in Imports field not imported from:
  'raster' 'sp'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
  'LazyDataCompression' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'entropart'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'tidyverse', 'kableExtra', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'AER', 'afex', 'blavaan', 'brms', 'httr', 'ivreg', 'metaBMA',
  'rstanarm'
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  VGLM    linear loop  4 :  deviance = 5.129141
  == Skipped tests ===============================================================
  * On CRAN (6)
  
  == Failed tests ================================================================
  -- Error (test-fixest.R:24:3): (code run outside of `test_that()`) -------------
  Error: Not any single variable with a positive variance was found after the weighted-OLS stage. (If possible, could you send a replicable example to fixest's author? He's curious about when that actually happens, since in theory it should never happen.)
  Backtrace:
      x
   1. \-fixest::feglm(...) test-fixest.R:24:2
   2.   \-fixest::feglm.fit(env = env)
  
  [ FAIL 1 | WARN 28 | SKIP 6 | PASS 1815 ]
  Error: Test failures
  Execution halted
Package required but not available: 'InterVA5'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package required but not available: 'missMDA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'curl', 'devtools'
Package unavailable to check Rd xrefs: 'curl'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'DiagrammeRsvg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking: 'covr', 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'grDevices'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'biomaRt', 'DESeq2'

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 which this enhances but not available for checking:
  'brms', 'rstanarm'
Packages unavailable to check Rd xrefs: 'brms', 'pequod'
'LazyData' is specified without a 'data' directory
Running examples in 'interactions-Ex.R' failed
The error most likely occurred in:

> ### Name: probe_interaction
> ### Title: Probe interaction effects via simple slopes and plotting
> ### Aliases: probe_interaction
> 
> ### ** Examples
> 
> 
> # Using a fitted model as formula input
> fiti <- lm(Income ~ Frost + Murder * Illiteracy,
+   data=as.data.frame(state.x77))
> probe_interaction(model = fiti, pred = Murder, modx = Illiteracy,
+                   modx.values = "plus-minus")
JOHNSON-NEYMAN INTERVAL 

When Illiteracy is OUTSIDE the interval [0.68, 2.20], the slope of Murder
is p < .05.

Note: The range of observed values of Illiteracy is [0.50, 2.80]

SIMPLE SLOPES ANALYSIS 

Error in prettyNum(.Internal(format(x, trim, digits, nsmall, width, 3L,  : 
  invalid value 0 for 'digits' argument
Calls: <Anonymous> ... print.sim_slopes -> format -> format.default -> prettyNum
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'categorical.Rmd' using rmarkdown
--- finished re-building 'categorical.Rmd'

--- re-building 'interactions.Rmd' using rmarkdown
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
Quitting from lines 372-373 (interactions.Rmd) 
Error: processing vignette 'interactions.Rmd' failed with diagnostics:
invalid value 0 for 'digits' argument
--- failed re-building 'interactions.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Malformed Title field: should not end in a period.
ClearBottomMenuPlot: no visible global function definition for 'rect'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertX'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertX'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'polygon'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertX'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertY'
InteractiveIGraph : keybd: no visible global function definition for
  'readClipboard'
InteractiveIGraph : keybd: no visible global function definition for
  'par'
PlotRegionGeneral: no visible global function definition for 'polygon'
plot.InteractiveIGraph: no visible global function definition for 'par'
plot.Menu: no visible global function definition for 'par'
plot.Menu: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'strwidth'
plot.MenuItem: no visible binding for global variable 'strheight'
plot.MenuItem: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'text'
plot.MenuLine: no visible binding for global variable 'rect'
Undefined global functions or variables:
  grconvertX grconvertY par polygon readClipboard rect strheight
  strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "polygon",
             "rect", "strheight", "strwidth", "text")
  importFrom("utils", "readClipboard")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
interact: no visible global function definition for 'cor'
standardize.matrix: no visible binding for global variable 'var'
standardize.matrix: no visible binding for global variable 'sd'
Undefined global functions or variables:
  cor sd var
Consider adding
  importFrom("stats", "cor", "sd", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
HH: no visible global function definition for 'var'
HH: no visible global function definition for 'qnorm'
exactCI: no visible global function definition for 'quantile'
sample.n: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  qnorm quantile rbinom var
Consider adding
  importFrom("stats", "qnorm", "quantile", "rbinom", "var")
to your NAMESPACE file.
Package required but not available: 'AER'

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: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'Case_studies.Rmd' using rmarkdown
--- finished re-building 'Case_studies.Rmd'

--- re-building 'interlineaR.Rmd' using rmarkdown
Quitting from lines 16-23 (interlineaR.Rmd) 
Error: processing vignette 'interlineaR.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'interlineaR.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  'chron' 'date'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Mo.Th.Ra.: no visible global function definition for 'aggregate'
daily_mean: no visible global function definition for 'aggregate'
date.time: no visible global function definition for 'chron'
date.time: no visible global function definition for 'years'
date.time: no visible global function definition for 'days'
date.time: no visible global function definition for 'hours'
par_calibration: no visible global function definition for 'date.mdy'
par_calibration: no visible global function definition for 'as.date'
par_calibration: no visible global function definition for 'aggregate'
plot_meas_sim: no visible global function definition for 'as.date'
plot_meas_sim: no visible global function definition for 'date.mdy'
plot_meas_sim: no visible global function definition for 'par'
plot_meas_sim: no visible global function definition for 'legend'
shape_calibration: no visible global function definition for 'date.mdy'
shape_calibration: no visible global function definition for 'as.date'
shape_calibration: no visible global function definition for
  'aggregate'
Undefined global functions or variables:
  aggregate as.date chron date.mdy days hours legend par years
Consider adding
  importFrom("graphics", "legend", "par")
  importFrom("stats", "aggregate")
to your NAMESPACE file.
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
interventionEffects: no visible binding for global variable 'sd'
interventionEffects: no visible global function definition for 'pt'
interventionEffects: no visible global function definition for 'sd'
interventionalInference: no visible global function definition for 'sd'
interventionalInferenceAdvanced: no visible global function definition
  for 'sd'
linesROC: no visible global function definition for 'segments'
plotMaxML: no visible global function definition for 'segments'
Undefined global functions or variables:
  pt sd segments
Consider adding
  importFrom("graphics", "segments")
  importFrom("stats", "pt", "sd")
to your NAMESPACE file.
Package required but not available: 'FactoMineR'

Package suggested but not available for checking: 'gsheet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'maxLik' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'maxLik'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ILik : rbern: no visible global function definition for 'runif'
ILik : q: no visible global function definition for 'dnorm'
ILik : SlambdaG: no visible global function definition for 'rnorm'
ILik : Pi_hat: no visible global function definition for 'rnorm'
ILik : q: no visible global function definition for 'dgamma'
ILik : SlambdaG: no visible global function definition for 'rgamma'
ILik : Pi_hat: no visible global function definition for 'rgamma'
ILik: no visible global function definition for 'maxLik'
ILik: no visible global function definition for 'coef'
ILik: no visible global function definition for 'hessian'
Undefined global functions or variables:
  coef dgamma dnorm hessian maxLik rgamma rnorm runif
Consider adding
  importFrom("stats", "coef", "dgamma", "dnorm", "rgamma", "rnorm",
             "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'mgcv'
  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: 'graphics'
  All declared Imports should be used.
Note: found 11653 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
f.B: no visible global function definition for 'pnorm'
f.B.neglog.deriv: no visible global function definition for 'pnorm'
f.B.neglog.deriv: no visible global function definition for 'dnorm'
f.grovest3 : f.est: no visible global function definition for 'survfit'
f.grovest3 : f.est: no visible global function definition for 'lines'
f.grovest3: no visible global function definition for 'model.frame'
f.grovest3: no visible global function definition for 'model.extract'
invGauss: no visible global function definition for 'model.frame'
invGauss: no visible global function definition for 'model.extract'
invGauss: no visible global function definition for 'model.matrix'
predict.invGauss: no visible global function definition for
  'model.frame'
predict.invGauss: no visible global function definition for
  'model.extract'
predict.invGauss: no visible global function definition for
  'model.matrix'
predict.invGauss: no visible binding for global variable 'formula'
predict.invGauss: no visible binding for global variable 'data'
summary.invGauss: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  data dnorm formula lines model.extract model.frame model.matrix pnorm
  survfit
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "dnorm", "formula", "model.extract", "model.frame",
             "model.matrix", "pnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking:
  'covr', 'ggmosaic', 'plotly'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- Error (test_ftplots.R:35:5): Plots can be rotated ---------------------------
  Error: is.character(act$val) is not TRUE
  Backtrace:
      x
   1. \-testthat::expect_match(attr(p1, "code"), "coord_flip") test_ftplots.R:35:4
   2.   \-base::stopifnot(is.character(act$val))
  -- Failure (test_interaction.R:30:5): FT plots return the correct response -----
  can.interact(...) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  
  [ FAIL 10 | WARN 12 | SKIP 9 | PASS 286 ]
  Error: Test failures
  Execution halted
Package required but not available: 'car'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Packages required but not available: 'plotly', 'kableExtra', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
flowsRandom: no visible global function definition for 'dmultinom'
readBed: no visible global function definition for 'read.table'
Undefined global functions or variables:
  dmultinom read.table
Consider adding
  importFrom("stats", "dmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rhdf5'
Packages required but not available: 'eurostat', 'kableExtra'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'stringr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'stringr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'Matrix' 'expm'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'kableExtra'

Package suggested but not available for checking: 'covr'

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: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'seqinr'
  All declared Imports should be used.
Note: found 12 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'MplusAutomation', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'coda' 'lattice'
  All declared Imports should be used.
Running examples in 'IRATER-Ex.R' failed
The error most likely occurred in:

> ### Name: clean.admb
> ### Title: delete IRATE (ADMB) run files
> ### Aliases: clean.admb clean.IRATE
> 
> ### ** Examples
> 
> example.setup <- IRATE.examples()
> new.setup <- new.setup.path <- example.setup[1] # select old IRATE setup to reparameterize
> print(new.setup) # print setup name to be run
[1] "HoenigNonMixing"
> old.setup.path <- system.file(paste0("IRATE.examples/",new.setup,".dat"), package = "IRATER")
> 
> system(paste("mkdir -p ",new.setup.path)) # create run folder for new setup
[1] 0
> system(paste("cp",old.setup.path, new.setup.path)) # copy old setup in new run folder
[1] 0
> setwd(new.setup.path)
> 
> run.IRATE(new.setup) # compile and run setup
Error in R2admb::compile_admb(setup.file, safe = safe, re = re, verbose = verbose,  : 
  base admb command failed: run setup_admb(), or check ADMB installation
Calls: run.IRATE -> <Anonymous>
Execution halted
Namespaces in Imports field not imported from:
  'Rdpack' 'glmnet'
  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
Package required but not available: 'gsheet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'irr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
dendrify: no visible binding for global variable 'item'
dendrify: no visible binding for global variable 'node'
dendrify: no visible binding for global variable 'value'
exogenize: no visible binding for global variable 'item'
Undefined global functions or variables:
  item node value
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
isbf: no visible global function definition for 'var'
isbf: no visible global function definition for 'qnorm'
isbfReg: no visible global function definition for 'var'
isbfReg: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
residualplot: no visible global function definition for 'predict'
residualplot: no visible global function definition for 'rstandard'
residualplot: no visible global function definition for
  'complete.cases'
residualplot: no visible global function definition for 'points'
residualplot: no visible global function definition for 'lines'
residualplot: no visible global function definition for 'smooth.spline'
residualplot: no visible global function definition for 'sd'
residualplot: no visible global function definition for 'rgb'
residualplot: no visible global function definition for 'polygon'
Undefined global functions or variables:
  complete.cases lines points polygon predict rgb rstandard sd
  smooth.spline
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "points", "polygon")
  importFrom("stats", "complete.cases", "predict", "rstandard", "sd",
             "smooth.spline")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  'colorRamps' 'virtualspecies'
  All declared Imports should be used.
Note: found 104 marked UTF-8 strings
Package suggested but not available for checking: 'BRugs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'magick'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'isoband1.Rmd' using rmarkdown
--- finished re-building 'isoband1.Rmd'

--- re-building 'isoband2.Rmd' using rmarkdown
Quitting from lines 56-97 (isoband2.Rmd) 
Error: processing vignette 'isoband2.Rmd' failed with diagnostics:
there is no package called 'magick'
--- failed re-building 'isoband2.Rmd'

--- re-building 'isoband3.Rmd' using rmarkdown
--- finished re-building 'isoband3.Rmd'

SUMMARY: processing the following file failed:
  'isoband2.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'isocat.Rmd' using rmarkdown
Quitting from lines 16-33 (isocat.Rmd) 
Error: processing vignette 'isocat.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'isocat.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Malformed Title field: should not end in a period.
C.cal: no visible global function definition for 'as.stepfun'
bandwidth.choose.cv: no visible global function definition for 'isoreg'
g.density: no visible global function definition for 'as.stepfun'
g.density: no visible global function definition for 'dnorm'
h.density: no visible global function definition for 'dnorm'
iso.bt.unit: no visible global function definition for 'quantile'
iso.bt.unit.sub: no visible global function definition for 'isoreg'
iso.bt.unit.sub: no visible global function definition for 'as.stepfun'
iso.bt.wald.unit: no visible global function definition for 'var'
iso.ci: no visible global function definition for 'isoreg'
iso.ci.transform.unit: no visible global function definition for
  'as.stepfun'
Undefined global functions or variables:
  as.stepfun dnorm isoreg quantile var
Consider adding
  importFrom("stats", "as.stepfun", "dnorm", "isoreg", "quantile", "var")
to your NAMESPACE file.
ACO : bordacircular: no visible global function definition for
  'medianCircular'
Undefined global functions or variables:
  medianCircular
Note: found 7418 marked UTF-8 strings
Namespace in Imports field not imported from: 'Rcpp'
  All declared Imports should be used.
Package required but not available: 'affy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'proxy' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
isopam : core: no visible global function definition for 'dist'
isopam : core: no visible global function definition for 'write.table'
isopam : core: no visible global function definition for 'as.dist'
isopam : core: no visible global function definition for
  'txtProgressBar'
isopam : core: no visible global function definition for
  'setTxtProgressBar'
isopam : core: no visible global function definition for 'aggregate'
isopam: no visible binding for global variable 'var'
isopam: no visible global function definition for 'na.omit'
isopam: no visible global function definition for 'write.table'
isopam: no visible global function definition for 'bmp'
isopam: no visible global function definition for 'dev.off'
isotab: no visible global function definition for 'aggregate'
isotab : fshtest: no visible global function definition for 'dhyper'
isotab : fshtest : pnhyper: no visible global function definition for
  'phyper'
Undefined global functions or variables:
  aggregate as.dist bmp dev.off dhyper dist na.omit phyper
  setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "bmp", "dev.off")
  importFrom("stats", "aggregate", "as.dist", "dhyper", "dist",
             "na.omit", "phyper", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'devtools', 'rhdf5', 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'magick'
'LazyData' is specified without a 'data' directory
Package required but not available: 'ibd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

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 required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Depends: includes the non-default packages:
  'partitions', 'VGAM', 'MASS', 'ape', 'apTreeshape', 'geiger',
  'gtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'MASS' 'VGAM' 'apTreeshape' 'ape' 'geiger' 'gtools' 'partitions'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'Rgraphviz'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'vignette.Rmd' using rmarkdown
Loading required package: pkgmaker
Loading required package: registry
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 47/48
Loading required namespace: Rgraphviz
Failed with error:  'there is no package called 'Rgraphviz''
Quitting from lines 94-99 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
Package 'Rgraphviz' (from Bioconductor) must be installed for plotting graphs!
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'chemometrics'
  All declared Imports should be used.
Packages required but not available: 'car', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages in Depends field not imported from:
  'Matching' 'R2jags' 'boot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bpsm: no visible global function definition for 'glm'
bpsm: no visible global function definition for 'binomial'
bpsm: no visible global function definition for 'Match'
bpsm: no visible global function definition for 'cov'
bpsm: no visible global function definition for 'vcov'
bpsm : inits: no visible global function definition for 'runif'
bpsm: no visible global function definition for 'jags'
bpsr: no visible global function definition for 'glm'
bpsr: no visible global function definition for 'binomial'
bpsr: no visible global function definition for 'lm'
bpsr : inits: no visible global function definition for 'runif'
bpsr: no visible global function definition for 'jags'
modelpsm: no visible binding for global variable 'D'
modelpsr: no visible binding for global variable 'D'
Undefined global functions or variables:
  D Match binomial cov glm jags lm runif vcov
Consider adding
  importFrom("stats", "D", "binomial", "cov", "glm", "lm", "runif",
             "vcov")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: 'AER'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Package required but not available: 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
ivFixed.formula: no visible global function definition for
  'model.matrix'
ivFixed.formula: no visible global function definition for
  'model.response'
summary.ivFixed: no visible global function definition for 'coef'
summary.ivFixed: 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.
Package suggested but not available for checking: 'locClass'
Packages suggested but not available for checking:
  'gurobi', 'cplexAPI', 'AER'
Error(s) in re-building vignettes:
  ...
--- re-building 'ivmte.Rmd' using rmarkdown
Quitting from lines 130-132 (ivmte.Rmd) 
Error: processing vignette 'ivmte.Rmd' failed with diagnostics:
there is no package called 'AER'
--- failed re-building 'ivmte.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
hausman: no visible global function definition for 'pchisq'
ivbe: no visible global function definition for 'cor'
ivbe: no visible global function definition for 'pt'
ivfixed: no visible global function definition for 'cor'
ivfixed: no visible global function definition for 'pt'
ivpan.formula: no visible global function definition for 'model.matrix'
ivpan.formula: no visible global function definition for
  'model.response'
ivrandom: no visible global function definition for 'cor'
ivrandom: no visible global function definition for 'pt'
summary.ivpan: no visible global function definition for 'printCoefmat'
Undefined global functions or variables:
  cor model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response", "pchisq",
             "printCoefmat", "pt")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package required but not available: 'AER'

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

Packages suggested but not available for checking: 'AER', 'modelsummary'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'timereg'
  All declared Imports should be used.
Packages suggested but not available for checking: 'covr', 'forecast'

Package which this enhances but not available for checking: 'texreg'
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   6.       \-base:::doWithOneRestart(return(expr), restart)
  -- Error (test-ivx-ar.R:24:3): ar estimation is identical ----------------------
  Error: there is no package called 'forecast'
  Backtrace:
      x
   1. +-ivx::ivx_ar(...) test-ivx-ar.R:24:2
   2. | \-ivx::ivx_ar_fit(...)
   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 2 | WARN 0 | SKIP 0 | PASS 35 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
histw: no visible global function definition for 'plot.new'
histw: no visible global function definition for 'plot.window'
histw: no visible global function definition for 'axis'
histw: no visible global function definition for 'rect'
histw: no visible global function definition for 'lines'
Undefined global functions or variables:
  axis lines plot.new plot.window rect
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  'Rcpp' 'dplyr' 'magrittr'
  All declared Imports should be used.
'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:
  'fBasics' 'reshape' 'tidyr' 'utils'
  All declared Imports should be used.
Note: found 2261 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
boxplot.james: no visible global function definition for 'mtext'
getBestSolutionValues.james : <anonymous>: no visible global function
  definition for 'tail'
isMinimizing: no visible global function definition for 'head'
isMinimizing: no visible global function definition for 'tail'
mergeJAMES.james: no visible global function definition for 'glob2rx'
plotConvergence.james : <anonymous> : <anonymous>: no visible global
  function definition for 'tail'
plotConvergence.james: no visible global function definition for 'tail'
plotConvergence.james: no visible global function definition for 'head'
plotConvergence.james : <anonymous>: no visible global function
  definition for 'tail'
plotConvergence.james: no visible global function definition for
  'matplot'
plotConvergence.james: no visible global function definition for
  'mtext'
summary.james: no visible global function definition for 'sd'
summary.james: no visible global function definition for 'median'
summary.james: no visible global function definition for 'IQR'
Undefined global functions or variables:
  IQR glob2rx head matplot median mtext sd tail
Consider adding
  importFrom("graphics", "matplot", "mtext")
  importFrom("stats", "IQR", "median", "sd")
  importFrom("utils", "glob2rx", "head", "tail")
to your NAMESPACE file.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Package required but not available: 'crul'

Package suggested but not available for checking: 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'MASS' 'ggExtra' 'ggplot2' 'grid' 'gridExtra' 'mcmcplots'
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'gtools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

make_template: no visible global function definition for 'invalid'
Undefined global functions or variables:
  invalid
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Namespace in Imports field not imported from: 'GA'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'ids'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kableExtra'
Packages suggested but not available for checking:
  'forecast', 'iClick', 'quantmod', 'timetk'
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'pkgdown'
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
powerLongSurv: no visible global function definition for 'qnorm'
powerLongSurv: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
'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
JBTest: no visible global function definition for 'pchisq'
generateSignificance: no visible global function definition for 'pnorm'
packages: no visible global function definition for 'install.packages'
shift: no visible global function definition for 'tail'
shift: no visible global function definition for 'head'
splitBy: no visible global function definition for 'head'
Undefined global functions or variables:
  head install.packages pchisq pnorm tail
Consider adding
  importFrom("stats", "pchisq", "pnorm")
  importFrom("utils", "head", "install.packages", "tail")
to your NAMESPACE file.
Package required but not available: 'httr'

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

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

Attaching package: 'jmvReadWrite'

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

    ToothGrowth

Quitting from lines 69-80 (jmvReadWrite.Rmd) 
Error: processing vignette 'jmvReadWrite.Rmd' failed with diagnostics:
there is no package called 'jmv'
--- failed re-building 'jmvReadWrite.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
RE.ADT: no visible global function definition for 'sd'
RE.ADT: no visible global function definition for 'pnorm'
RE.Johnson: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm sd
Consider adding
  importFrom("stats", "pnorm", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
Packages which this enhances but not available for checking:
  'MRCE', 'remMap'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'ggpubr', 'covr'
'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.
binteg: no visible global function definition for 'contourLines'
binteg: no visible global function definition for 'approx'
binteg: no visible global function definition for 'par'
plot1: no visible global function definition for 'par'
plot1: no visible global function definition for 'rect'
plot1: no visible global function definition for 'axis'
plot1: no visible global function definition for 'contour'
plot1: no visible global function definition for 'contourLines'
plot1: no visible binding for global variable 'approx'
plot1: no visible global function definition for 'lines'
plot1: no visible global function definition for 'text'
plot2: no visible global function definition for 'abline'
plot2: no visible global function definition for 'lines'
plot2: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline approx axis contour contourLines legend lines par rect text
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "abline", "axis", "contour", "legend", "lines",
             "par", "rect", "text")
  importFrom("stats", "approx")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'MASS' 'boot' 'fds' 'rpart'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'doParallel'
  All declared Imports should be used.
Packages suggested but not available for checking: 'badger', 'covr'
Package suggested but not available for checking: 'lintr'
Note: found 176 marked UTF-8 strings
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  NULL
  NULL
  NULL
  == Skipped tests ===============================================================
  * On CRAN (5)
  
  == Failed tests ================================================================
  -- Failure (test-internal.R:53:5): validate ------------------------------------
  nrow(df_check) not equal to 1L.
  1/1 mismatches
  [1] 10 - 1 == 9
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 175 ]
  Error: Test failures
  Execution halted
Package required but not available: 'V8'

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: 'covr'
Packages required but not available: 'jstable', 'ggpubr'

Package suggested but not available for checking: 'shinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
sonarCSV: 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.
Package suggested but not available for checking: 'covr'
Packages required but not available: 'V8', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'httr', 'curl'
Package suggested but not available for checking: 'curl'
Package required but not available: 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'V8'

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 suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Note: found 17 marked UTF-8 strings
Package suggested but not available for checking: 'kableExtra'

Packages which this enhances but not available for checking:
  'brms', 'rstanarm'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == Failed tests ================================================================
  -- Failure (test-jsumm.R:97:3): summ: knit_print works -------------------------
  jtools:::knit_print.summ.lm(summ(fit)) inherits from `'NULL'` not `'character'`.
  -- Failure (test-jsumm.R:98:3): summ: knit_print works -------------------------
  jtools:::knit_print.summ.glm(summ(fitgf)) inherits from `'NULL'` not `'character'`.
  -- Failure (test-jsumm.R:100:5): summ: knit_print works ------------------------
  jtools:::knit_print.summ.merMod(summ(mv)) inherits from `'NULL'` not `'character'`.
  -- Failure (test-jsumm.R:103:5): summ: knit_print works ------------------------
  jtools:::knit_print.summ.svyglm(summ(regmodel)) inherits from `'NULL'` not `'character'`.
  -- Failure (test-quantreg.R:25:3): summ.rq works -------------------------------
  jtools:::knit_print.summ.rq(summ(rfit)) inherits from `'NULL'` not `'character'`.
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 343 ]
  Error: Test failures
  Execution halted
qtls: no visible global function definition for 'quantile'
qtls: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm quantile
Consider adding
  importFrom("stats", "pnorm", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'pdftools', 'rvest', 'SwimmeR'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rvest'

Package suggested but not available for checking: 'magick'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
KappaV: no visible global function definition for 'over'
KappaV: no visible global function definition for 'layout'
KappaV: no visible global function definition for 'terrain.colors'
KappaV: no visible global function definition for 'as'
Undefined global functions or variables:
  as layout over terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "layout")
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages required but not available:
  'MVN', 'tseries', 'forecast', 'nonlinearTseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
ikcirt.fun.mss.eta: no visible global function definition for 'var'
ikcirt.fun.mss.eta: no visible global function definition for 'pnorm'
ikcirt.fun.mss.lambda: no visible global function definition for 'var'
ikcirt.fun.mss.lambda: no visible global function definition for
  'pnorm'
ikcirt.fun.mss.mu: no visible global function definition for 'pnorm'
kcirt.fitEE: no visible binding for global variable 'sd'
kcirt.fitEE: no visible global function definition for 'var'
kcirt.fitEE: no visible global function definition for 'cor'
kcirt.fitMSS: no visible global function definition for 'var'
kcirt.fitMSS: no visible global function definition for 'pnorm'
kcirt.fitMSS: no visible global function definition for 'sfInit'
kcirt.fitMSS: no visible global function definition for 'sfExport'
kcirt.fitMSS: no visible global function definition for 'rnorm'
kcirt.fitMSS: no visible global function definition for
  'txtProgressBar'
kcirt.fitMSS: no visible global function definition for 'sfIsRunning'
kcirt.fitMSS: no visible global function definition for 'sfStop'
kcirt.fitMSS: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor pnorm rnorm sd sfExport sfInit sfIsRunning sfStop txtProgressBar
  var
Consider adding
  importFrom("stats", "cor", "pnorm", "rnorm", "sd", "var")
  importFrom("utils", "txtProgressBar")
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: 'covr'
Namespaces in Imports field not imported from:
  'EQL' 'univariateML'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
as.matrix.multiPhylo : tip2tip: no visible global function definition
  for 'cophenetic'
bw.nn : <anonymous>: no visible global function definition for
  'quantile'
dist.diss: no visible binding for global variable 'median'
dist.diss: no visible global function definition for 'dist'
hist.kdetrees: no visible binding for global variable 'density'
kdetrees : cutoff: no visible global function definition for 'quantile'
kdetrees.complete: no visible global function definition for 'hist'
kdetrees.complete: no visible global function definition for
  'write.csv'
plot.kdetrees: no visible binding for global variable 'density'
Undefined global functions or variables:
  cophenetic density dist hist median quantile write.csv
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cophenetic", "density", "dist", "median",
             "quantile")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
SeasonalMannKendall: no visible global function definition for 'is.ts'
SeasonalMannKendall: no visible global function definition for
  'frequency'
SeasonalMannKendall: no visible global function definition for 'cycle'
SeasonalMannKendall: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  cycle frequency is.ts pnorm
Consider adding
  importFrom("stats", "cycle", "frequency", "is.ts", "pnorm")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  'lme4' 'metafor' 'nlme'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Packages required but not available: 'plotly', 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Checking should be performed on sources prepared by 'R CMD build'.
Packages in Depends field not imported from:
  'chron' 'date' 'evir'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ALbw: no visible global function definition for 'sd'
ALbw: no visible global function definition for 'quantile'
CVbw: no visible global function definition for 'quantile'
PBbw: no visible global function definition for 'sd'
PBbw: no visible global function definition for 'IQR'
kernel_function: no visible global function definition for 'dnorm'
kernel_function_distribution: no visible global function definition for
  'pnorm'
simp_int: no visible global function definition for 'approx'
Undefined global functions or variables:
  IQR approx dnorm pnorm quantile sd
Consider adding
  importFrom("stats", "IQR", "approx", "dnorm", "pnorm", "quantile",
             "sd")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'inline'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Package required but not available: 'benchmarkme'

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: 'readtext'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'shiny'
  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
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'RcppProgress'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Packages required but not available: 'rio', 'elastic'

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.
kissmigDummyS: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
Package required but not available: 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'rkward'
distrct.analysis : <anonymous> : <anonymous>: no visible global
  function definition for 'cor'
grand.table: no visible global function definition for 'write.csv2'
grand.table: no visible global function definition for 'write.csv'
klausur: no visible global function definition for 'sd'
klausur: no visible global function definition for 'na.omit'
klausur.gen.marks : suggestion : <anonymous>: no visible global
  function definition for 'qnorm'
klausur.mufo: no visible global function definition for 'sd'
klausur.report: no visible global function definition for 'dev.off'
klausur.report : tabellenbau: no visible global function definition for
  'capture.output'
plot,klausuR-missing: no visible global function definition for
  'na.omit'
plot,klausuR-missing: no visible global function definition for 'sd'
plot,klausuR-missing : <anonymous>: no visible global function
  definition for 'dnorm'
Undefined global functions or variables:
  capture.output cor dev.off dnorm na.omit qnorm sd write.csv
  write.csv2
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "cor", "dnorm", "na.omit", "qnorm", "sd")
  importFrom("utils", "capture.output", "write.csv", "write.csv2")
to your NAMESPACE file.
Note: found 8 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'Rcpp' 'SnowballC' 'stringi'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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.
comp.npci: no visible global function definition for 'qnorm'
epband.fun: no visible global function definition for 'data'
epband.fun: no visible binding for global variable
  'critical.value.nair.90'
epband.fun: no visible binding for global variable
  'critical.value.nair.95'
epband.fun: no visible binding for global variable
  'critical.value.nair.99'
hall.wellner.fun: no visible global function definition for 'data'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.90'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.95'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.99'
lrt.confints: no visible global function definition for 'qchisq'
rothman.fun: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
dscore: no visible global function definition for 'glm'
dscore: no visible binding for global variable 'binomial'
dscore: no visible global function definition for 'pnorm'
pearson.group: no visible global function definition for 'cor'
spearman.group: no visible global function definition for 'cor'
sscore: no visible global function definition for 'glm'
sscore: no visible binding for global variable 'binomial'
sscore: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  binomial cor glm pnorm
Consider adding
  importFrom("stats", "binomial", "cor", "glm", "pnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
C_zero : <anonymous>: no visible global function definition for 'runif'
get_extra_centroid_index: no visible global function definition for
  'head'
get_within_cluster_ss: no visible global function definition for
  'aggregate'
kmod: no visible global function definition for 'head'
kmod: no visible global function definition for 'tail'
Undefined global functions or variables:
  aggregate head runif tail
Consider adding
  importFrom("stats", "aggregate", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'covr', 'devtools', 'usethis'
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'RefManageR', 'httr'

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: 'gpg'
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'gpg'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'magick', 'httr'
Package unavailable to check Rd xrefs: 'magick'
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for 'rbeta'
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for 'runif'
calculate.power : <anonymous>: no visible binding for global variable
  'quantile'
generate.benchmark.data: no visible global function definition for
  'runif'
generate.benchmark.data: no visible global function definition for
  'rnorm'
generate.benchmark.data: no visible global function definition for
  'rbinom'
generate.patchwork.copula: no visible global function definition for
  'rbeta'
generate.patchwork.copula: no visible global function definition for
  'runif'
novelTest.chisq: no visible global function definition for 'pchisq'
novelTest.chisq4nn: no visible global function definition for 'pchisq'
optimise.copula.mi : <anonymous>: no visible global function definition
  for 'optimize'
power.plot: no visible global function definition for 'axis'
power.plot : <anonymous>: no visible global function definition for
  'points'
power.plot: no visible global function definition for 'legend'
roc.plot: no visible global function definition for 'colorRampPalette'
roc.plot : <anonymous> : <anonymous>: no visible global function
  definition for 'points'
run.tests : <anonymous> : <anonymous>: no visible global function
  definition for 'runif'
Undefined global functions or variables:
  axis colorRampPalette legend optimize pchisq points quantile rbeta
  rbinom rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "legend", "points")
  importFrom("stats", "optimize", "pchisq", "quantile", "rbeta",
             "rbinom", "rnorm", "runif")
to your NAMESPACE file.
Package required but not available: 'forecast'

Package suggested but not available for checking: 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'FNN' 'caret' 'datasets' 'dplyr' 'e1071' 'psycho' 'rhandsontable'
  'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rgbif'
Note: found 9 marked Latin-1 strings
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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: 'devtools', 'covr'
Namespaces in Imports field not imported from:
  'mice' 'tibble'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rgraphviz'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'kpcalg_tutorial.Rnw' using knitr
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Quitting from lines 61-65 (kpcalg_tutorial.Rnw) 
Error: processing vignette 'kpcalg_tutorial.Rnw' failed with diagnostics:
package required but not installed: 'Rgraphviz'
--- failed re-building 'kpcalg_tutorial.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'gmp'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'dplyr' 'tibble'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
image.kriging: no visible global function definition for 'heat.colors'
image.kriging: no visible global function definition for 'image'
kriging: no visible global function definition for 'lm'
plot.kriging: no visible global function definition for 'curve'
Undefined global functions or variables:
  curve heat.colors image lm
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "curve", "image")
  importFrom("stats", "lm")
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
kselection: no visible global function definition for 'txtProgressBar'
kselection: no visible global function definition for
  'setTxtProgressBar'
plot.Kselection: no visible global function definition for 'lines'
plot.Kselection: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend lines setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rgraphviz'
Error(s) in re-building vignettes:
--- re-building 'kst.Rnw' using Sweave
Loading required package: proxy

Attaching package: 'proxy'

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

    as.dist, dist

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

    as.matrix

Loading required package: relations
Loading required package: sets
Loading required namespace: Rgraphviz
Failed with error:  'there is no package called 'Rgraphviz''
Loading required namespace: Rgraphviz
Failed with error:  'there is no package called 'Rgraphviz''
Loading required namespace: Rgraphviz
Failed with error:  'there is no package called 'Rgraphviz''
Loading required namespace: Rgraphviz
Failed with error:  'there is no package called 'Rgraphviz''
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "kst.tex" --max-iterations=20 -I "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/rinst/share/texmf/tex/latex" -I "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/rinst/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'kst.Rnw' failed with diagnostics:
running 'texi2dvi' on 'kst.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex (file ./kst-012.pdf): PDF inclusion: required page does
 not exist <0>
 ==> Fatal error occurred, no output PDF file produced!

--- failed re-building 'kst.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'XML' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
auc: no visible global function definition for 'approx'
kulife.colors: no visible global function definition for 'palette'
rootonorm: no visible global function definition for 'sd'
rootonorm: no visible global function definition for 'hist'
rootonorm: no visible global function definition for 'pnorm'
rootonorm: no visible global function definition for 'dnorm'
rootonorm: no visible global function definition for 'rect'
rootonorm: no visible global function definition for 'lines'
rootonorm: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline approx dnorm hist lines palette pnorm rect sd
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "hist", "lines", "rect")
  importFrom("stats", "approx", "dnorm", "pnorm", "sd")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'RUnit'
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
kztp: warning in rowMeans(kztp, dim = 2): partial argument match of
  'dim' to 'dims'
'LazyData' is specified without 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: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rcmdr'
Package unavailable to check Rd xrefs: 'factoextra'
Package required but not available: 'httr'

Package suggested but not available for checking: 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
LDuncan.aov : prob: no visible global function definition for 'qtukey'
LDuncan.aov: no visible global function definition for 'qtukey'
LScottKnott.aov : sk: no visible global function definition for
  'pchisq'
LScottKnott.aov: no visible global function definition for 'read.table'
LTukey.aov: no visible global function definition for 'qtukey'
Undefined global functions or variables:
  pchisq qtukey read.table
Consider adding
  importFrom("stats", "pchisq", "qtukey")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Package required but not available: 'curl'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Errors in running code in vignettes:
when running code in 'laGP.Rnw'
  ...
+     big.nn.nomle =  .... [TRUNCATED] 

> for (t in 1:T) {
+     x <- randomLHS(N + Npred, dim)
+     y <- apply(x, 1, borehole)
+     ypred.0 <- y[-(1:N)]
+     y <- y[1:N]
+     xpred <- x .... [TRUNCATED] 

... incomplete output.  Crash?

  'laGP.Rnw'... failed to complete the test
Error(s) in re-building vignettes:
  ...
--- re-building 'laGP.Rnw' using Sweave
Package suggested but not available for checking: 'car'
Malformed Title field: should not end in a period.
'library' or 'require' calls in package code:
  'GPArotation' 'mice'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
angoff: no visible global function definition for 'cov2cor'
angoff: no visible global function definition for 'runif'
cov.lambda4: no visible global function definition for 'cov2cor'
cov.lambda4: no visible global function definition for 'median'
guttman: no visible global function definition for 'cov2cor'
impute.cov: no visible global function definition for 'cov'
impute.cov: no visible global function definition for 'complete'
impute.cov: no visible global function definition for 'mice'
kristof: no visible global function definition for 'cov2cor'
kristof: no visible global function definition for 'runif'
lambda1: no visible global function definition for 'cov2cor'
lambda2: no visible global function definition for 'cov2cor'
lambda3: no visible global function definition for 'cov2cor'
lambda3: no visible binding for global variable 'sd'
lambda5: no visible global function definition for 'cov2cor'
lambda6: no visible global function definition for 'cov2cor'
omega.tot: no visible global function definition for 'cov2cor'
omega.tot: no visible global function definition for 'factanal'
quant.lambda4: no visible global function definition for 'cov2cor'
quant.lambda4: no visible global function definition for 'runif'
quant.lambda4: no visible global function definition for 'quantile'
raju: no visible global function definition for 'cov2cor'
raju: no visible global function definition for 'runif'
user.lambda4: no visible global function definition for 'runif'
user.lambda4: no visible binding for global variable 'sd'
Undefined global functions or variables:
  complete cov cov2cor factanal median mice quantile runif sd
Consider adding
  importFrom("stats", "cov", "cov2cor", "factanal", "median", "quantile",
             "runif", "sd")
to your NAMESPACE file.
Packages required but not available: 'bestNormalize', 'imputeTS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
GNU make is a SystemRequirements.
Package required but not available: 'GOstats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 23 marked UTF-8 strings
Kern.FUN: no visible global function definition for 'dnorm'
Prob.Covariate.ShortEvent: no visible global function definition for
  'bw.nrd'
optimize.mse.BW: no visible global function definition for 'optimize'
Undefined global functions or variables:
  bw.nrd dnorm optimize
Consider adding
  importFrom("stats", "bw.nrd", "dnorm", "optimize")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Packages required but not available: 'httr', 'curl'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lintr'

Package suggested but not available for checking: 'covr'

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: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
Error(s) in re-building vignettes:
  ...
--- re-building 'Vignette_for_LA.Rmd' using rmarkdown
Quitting from lines 25-27 (Vignette_for_LA.Rmd) 
Error: processing vignette 'Vignette_for_LA.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'Vignette_for_LA.Rmd'

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

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

Packages suggested but not available for checking:
  'forecast', 'googleAuthR', 'googlesheets4', 'quantmod', 'plotly',
  'rdrop2', 'rtweet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 6 marked UTF-8 strings
betabreaker: no visible global function definition for 'predict'
coef.lars: no visible global function definition for 'predict'
cv.lars: no visible global function definition for 'predict'
cv.lars: no visible binding for global variable 'var'
error.bars: no visible global function definition for 'segments'
plot.lars: no visible global function definition for 'matplot'
plot.lars: no visible global function definition for 'title'
plot.lars: no visible global function definition for 'abline'
plot.lars: no visible global function definition for 'axis'
predict.lars: no visible global function definition for 'approx'
Undefined global functions or variables:
  abline approx axis matplot predict segments title var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "segments",
             "title")
  importFrom("stats", "approx", "predict", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covTest'
glassoscore: no visible global function definition for 'var'
glassoscore: no visible global function definition for 'pchisq'
lassoscore: no visible global function definition for 'txtProgressBar'
lassoscore: no visible global function definition for
  'setTxtProgressBar'
lassoscore: no visible global function definition for 'pchisq'
plot.glassoscore: no visible global function definition for 'legend'
plot.lassoscore: no visible global function definition for 'legend'
plot.mbscore: no visible global function definition for 'legend'
qqpval: no visible global function definition for 'ppoints'
qqpval: no visible global function definition for 'qbeta'
qqpval: no visible global function definition for 'points'
qqpval: no visible global function definition for 'abline'
qqpval: no visible global function definition for 'polygon'
Undefined global functions or variables:
  abline legend pchisq points polygon ppoints qbeta setTxtProgressBar
  txtProgressBar var
Consider adding
  importFrom("graphics", "abline", "legend", "points", "polygon")
  importFrom("stats", "pchisq", "ppoints", "qbeta", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Package suggested but not available for checking: 'heplots'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
Namespace in Imports field not imported from: 'sf'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rgraphviz', 'gof', 'lava.tobit'
Package unavailable to check Rd xrefs: 'tseries'
Package suggested but not available for checking: 'forecast'
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without 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: 'covr'
plotcorr.lba.3d: warning in pch3d(colcoordi[, dim], pch = pch.budget,
  col = col.budget, ...): partial argument match of 'col' to 'color'
lbfgs: no visible global function definition for 'hasArg'
Undefined global functions or variables:
  hasArg
Consider adding
  importFrom("methods", "hasArg")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'doParallel'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Malformed Description field: should contain one or more complete sentences.
cclcda.default: no visible global function definition for 'as.formula'
cclcda.default: no visible global function definition for 'chisq.test'
cclcda.formula: no visible global function definition for 'model.frame'
cclcda2.default: no visible global function definition for 'runif'
cclcda2.default: no visible global function definition for 'chisq.test'
cclcda2.formula: no visible global function definition for
  'model.frame'
lcda.default: no visible global function definition for 'as.formula'
lcda.formula: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  as.formula chisq.test model.frame runif
Consider adding
  importFrom("stats", "as.formula", "chisq.test", "model.frame", "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
Namespaces in Imports field not imported from:
  'data.table' 'utf8'
  All declared Imports should be used.
Packages required but not available: 'quantmod', 'TTR'

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 suggested but not available for checking: 'tosca'
Package unavailable to check Rd xrefs: 'tosca'
Packages required but not available: 'highcharter', '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: 'pkgdown'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gistr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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.
Malformed Title field: should not end in a period.
multistart : <anonymous>: no visible global function definition for
  'runif'
plot.FreD.x: no visible global function definition for 'modifyList'
plot.FreD.x: no visible global function definition for 'abline'
plot.FreD.x: no visible global function definition for 'points'
Undefined global functions or variables:
  abline modifyList points runif
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("stats", "runif")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
ARConfIntEst: no visible global function definition for 'sd'
PTLinkFunc: no visible global function definition for 'pnorm'
PTLinkFunc: no visible global function definition for 'qnorm'
PTMultiPeriodPD: no visible global function definition for 'uniroot'
PTOnePeriodPD : f: no visible global function definition for 'pbinom'
PTOnePeriodPD: no visible global function definition for 'uniroot'
QMMGetRLogitPD: no visible global function definition for 'ecdf'
QMMPDlinkFunc: no visible global function definition for 'qnorm'
QMMPlot: no visible global function definition for 'lines'
QMMPlot: no visible global function definition for 'legend'
VDBCalibratePD: no visible global function definition for 'ecdf'
VDBGetK: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  ecdf legend lines pbinom pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "ecdf", "pbinom", "pnorm", "qnorm", "sd",
             "uniroot")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'covr', 'VariantAnnotation'
Packages suggested but not available for checking: 'covr', 'shinytest'
Namespaces in Imports field not imported from:
  'R6' 'shiny' 'shinyjs'
  All declared Imports should be used.
Note: found 75 marked UTF-8 strings
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   1. \-base::library(shinytest) test-drilling.R:1:0
  -- Error (test-initialize.R:1:1): (code run outside of `test_that()`) ----------
  Error: there is no package called 'shinytest'
  Backtrace:
      x
   1. \-base::library(shinytest) test-initialize.R:1:0
  -- Error (test-selection.R:1:1): (code run outside of `test_that()`) -----------
  Error: there is no package called 'shinytest'
  Backtrace:
      x
   1. \-base::library(shinytest) test-selection.R:1:0
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 7 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'rgeos'
  All declared Imports should be used.
Note: found 1096 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- Error (test-velocity.R:7:3): velocity ---------------------------------------
  Error: Required package curl not found. Please run: install.packages('curl')
  Backtrace:
      x
   1. \-jsonlite::fromJSON(content) test-velocity.R:7:2
   2.   \-jsonlite:::loadpkg("curl")
   3.     \-base::tryCatch(...)
   4.       \-base:::tryCatchList(expr, classes, parentenv, handlers)
   5.         \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6.           \-value[[3L]](cond)
   7.             \-jsonlite:::stop(...)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 165 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'V8'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'httr'
Package which this enhances but not available for checking: 'geojsonio'
Namespaces in Imports field not imported from:
  'dplyr' 'htmlwidgets' 'jsonlite' 'sf'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'leaflet'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'geojsonio'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'doMC'
BEAPFrOG: no visible global function definition for 'jags.model'
BEAPFrOG: no visible global function definition for 'coda.samples'
LEAPFrOG_EM: no visible global function definition for 'write.table'
LEAPFrOG_EM: no visible global function definition for 'constrOptim'
LEAPFrOG_plot: no visible global function definition for 'par'
LEAPFrOG_plot: no visible global function definition for 'barplot'
LEAPFrOG_plot: no visible global function definition for 'legend'
constrOptim2: no visible global function definition for 'optim'
Undefined global functions or variables:
  barplot coda.samples constrOptim jags.model legend optim par
  write.table
Consider adding
  importFrom("graphics", "barplot", "legend", "par")
  importFrom("stats", "constrOptim", "optim")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package required but not available: 'sva'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'opencpu'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'magick'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 78 marked UTF-8 strings
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Package required but not available: 'Rcmdr'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking: 'curl', 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'greybox', 'smooth'

Packages suggested but not available for checking: 'Mcomp', 'doMC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'covr', 'devtools'
Found the following significant warnings:
  Warning: Python 'C:\Users\tomas\AppData\Local\basilisk\1.0.2\0\envs\r-reticulate\python.exe' was requested but 'C:/Users/tomas/AppData/Local/basilisk/1.0.2/0/python.exe' was loaded instead (see reticulate::py_config() for more information)
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/leiden/leiden.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: 'covr'
Package suggested but not available for checking: 'covr'
'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: 'devtools'
Package suggested but not available for checking: 'pkgdown'
Namespaces in Imports field not imported from:
  'cli' 'glue' 'stringr'
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
Packages suggested but not available for checking:
  'covr', 'kableExtra', 'pdftools'
Error(s) in re-building vignettes:
  ...
--- re-building 'demo.Rmd' using rmarkdown
Quitting from lines 13-18 (demo.Rmd) 
Error: processing vignette 'demo.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'demo.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'HMDHFDplus'
Package suggested but not available for checking: 'covr'
Packages required but not available: 'forecast', 'tseries'

Package suggested but not available for checking: 'doMC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'spatstat'
  All declared Imports should be used.
Package required but not available: 'rstan'

Package suggested but not available for checking: 'covr'

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:
  'covr', 'gmailr', 'RPushbullet', 'rsyslog'
Packages unavailable to check Rd xrefs: 'gmailr', 'RPushbullet', 'rsyslog'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'whoami'
Package unavailable to check Rd xrefs: 'whoami'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
Error(s) in re-building vignettes:
  ...
--- re-building 'Vignette_for_LHD.Rmd' using rmarkdown
Quitting from lines 26-28 (Vignette_for_LHD.Rmd) 
Error: processing vignette 'Vignette_for_LHD.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'Vignette_for_LHD.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'biomaRt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

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: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'concaveman', 'covr'
Package unavailable to check Rd xrefs: 'concaveman'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Loading required package: raster
  Loading required package: sp
  > test_check("lidR")
  == Skipped tests ===============================================================
  * On CRAN (25)
  * empty test (1)
  
  == Failed tests ================================================================
  -- Failure (test-grid_canopy.R:101:3): grid_canopy pit-free works both with LAS and LAScatalog --
  `x` not equal to `y`.
  Attributes: < Component "data": Attributes: < Component "values": Mean relative difference: 0.02083333 > >
  
  [ FAIL 1 | WARN 0 | SKIP 26 | PASS 1246 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking:
  'demography', 'forecast', 'StMoMo'
Errors in running code in vignettes:
when running code in 'mortality_projection.Rnw'
  ...

> options(width = 80, prompt = "R>")

> library(demography)

  When sourcing 'mortality_projection.R':
Error: there is no package called 'demography'
Execution halted

  'an_introduction_to_lifecontingencies_package.Rnw' using 'UTF-8'... OK
  'mortality_projection.Rnw' using 'UTF-8'... failed
  'PensionPlanVal.Rmd' using 'UTF-8'... OK
  'compute-detail.Rmd' using 'UTF-8'... OK
  'introToLifecontingencies.Rmd' using 'UTF-8'... OK
  'pensionfunding.Rmd' using 'UTF-8'... OK
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'using-the-lifeinsurancecontracts-package.Rmd' using rmarkdown
Quitting from lines 24-47 (using-the-lifeinsurancecontracts-package.Rmd) 
Error: processing vignette 'using-the-lifeinsurancecontracts-package.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'using-the-lifeinsurancecontracts-package.Rmd'

SUMMARY: processing the following file failed:
  'using-the-lifeinsurancecontracts-package.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'fitbitScraper'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2'
Packages required but not available: 'curl', 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'pavo'
Package unavailable to check Rd xrefs: 'pavo'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'RSelenium', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Depends: includes the non-default packages:
  'sn', 'moments', 'BB', 'Bolstad2', 'optimx', 'Rmpfr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'BB' 'Bolstad2' 'Rmpfr' 'moments' 'optimx' 'sn'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
Note: found 7 marked UTF-8 strings
Packages required but not available: 'car', 'pathview', 'RCy3', 'survminer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'ddpcr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'SnowballC' 'data.table' 'e1071' 'fastmatch'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'magick'
Package unavailable to check Rd xrefs: 'magick'
Running examples in 'lime-Ex.R' failed
The error most likely occurred in:

> ### Name: plot_superpixels
> ### Title: Test super pixel segmentation
> ### Aliases: plot_superpixels
> 
> ### ** Examples
> 
> image <- system.file('extdata', 'produce.png', package = 'lime')
> 
> # plot with default settings
> plot_superpixels(image)
Error: The magick package is required for image explanation
Execution halted
Package suggested but not available for checking: 'covr'
plotBox: no visible global function definition for 'sd'
plotBox: no visible global function definition for 'rect'
plotBox: no visible global function definition for 'qnorm'
plotBox: no visible global function definition for 'segments'
plotInit: no visible global function definition for 'runif'
plotInit: no visible global function definition for 'mtext'
plotInit: no visible global function definition for 'segments'
plotStack: no visible global function definition for 'points'
Undefined global functions or variables:
  mtext points qnorm rect runif sd segments
Consider adding
  importFrom("graphics", "mtext", "points", "rect", "segments")
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Plotranges.double: no visible global function definition for 'strwidth'
Plotranges.double: no visible global function definition for
  'strheight'
Plotranges.double: no visible global function definition for 'plot.new'
Plotranges.double: no visible global function definition for 'par'
Plotranges.double: no visible global function definition for
  'plot.window'
Plotranges.double: no visible global function definition for 'mtext'
Plotranges.double: no visible global function definition for 'abline'
Plotranges.double: no visible global function definition for 'points'
Plotranges.double: no visible global function definition for 'segments'
Plotranges.double: no visible global function definition for 'text'
Plotranges.double: no visible global function definition for 'axis'
Plotranges.double: no visible global function definition for 'box'
Plotranges.double: no visible global function definition for 'title'
Undefined global functions or variables:
  abline axis box mtext par plot.new plot.window points segments
  strheight strwidth text title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "mtext", "par",
             "plot.new", "plot.window", "points", "segments",
             "strheight", "strwidth", "text", "title")
to your NAMESPACE file.
class.calib: no visible global function definition for 'lm'
class.calib: no visible global function definition for 'coef'
class.calib: no visible global function definition for 'qt'
hoad.calib: no visible global function definition for 'lm'
hoad.calib: no visible global function definition for 'anova'
hoad.calib: no visible global function definition for 'qt'
hoad.calib: no visible global function definition for 'rnorm'
huntlam.calib: no visible global function definition for 'lm'
huntlam.calib: no visible global function definition for 'anova'
huntlam.calib: no visible global function definition for 'rnorm'
huntlam.calib: no visible global function definition for 'qnorm'
inver.calib: no visible global function definition for 'lm'
inver.calib: no visible global function definition for 'coef'
inver.calib: no visible global function definition for 'anova'
inver.calib: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  anova coef lm qnorm qt rnorm
Consider adding
  importFrom("stats", "anova", "coef", "lm", "qnorm", "qt", "rnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'factoextra'

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

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: 'covr'
Package suggested but not available for checking: 'devtools'
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Note: found 58573 marked UTF-8 strings
Package suggested but not available for checking: 'pkgdown'
'LazyData' is specified without a 'data' directory
Package required but not available: 'devtools'

Package suggested but not available for checking: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'RColorBrewer'
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
gcomb: no visible global function definition for 'complete.cases'
linkim: no visible global function definition for 'runif'
missing.dist: no visible global function definition for
  'complete.cases'
pgdata1: no visible global function definition for 'barplot'
pgdata1: no visible global function definition for 'layout'
pgdata1: no visible global function definition for 'par'
pgdata1: no visible global function definition for 'rainbow'
singim: no visible global function definition for 'complete.cases'
singim: no visible global function definition for 'runif'
Undefined global functions or variables:
  barplot complete.cases layout par rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "barplot", "layout", "par")
  importFrom("stats", "complete.cases", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
gen.lms: no visible global function definition for 'na.omit'
plot.idf: no visible global function definition for 'mtext'
plot.idf: no visible global function definition for 'points'
plot.idf: no visible global function definition for 'segments'
plot.idf: no visible global function definition for 'ftable'
plot.idf: no visible global function definition for 'image'
plot.idf: no visible global function definition for 'gray'
plot.idf: no visible global function definition for 'abline'
plot.s.linlir: no visible global function definition for 'mtext'
plot.s.linlir: no visible global function definition for 'polygon'
plot.s.linlir: no visible global function definition for 'points'
plot.s.linlir: no visible global function definition for 'curve'
s.linlir: no visible global function definition for 'na.omit'
s.linlir: no visible global function definition for 'dbinom'
s.linlir: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline curve dbinom ftable gray image mtext na.omit pchisq points
  polygon segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "curve", "image", "mtext", "points",
             "polygon", "segments")
  importFrom("stats", "dbinom", "ftable", "na.omit", "pchisq")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to 'lpSolve' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'lpSolve'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
solveLP: no visible global function definition for 'lp'
Undefined global functions or variables:
  lp
Package suggested but not available for checking: 'AER'
Package required but not available: 'httr'

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: 'covr'
Note: found 32 marked UTF-8 strings
last: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
getMatrix : <anonymous>: 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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'workflowr'
'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: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kableExtra'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'litteR-installation.Rmd' using rmarkdown
--- finished re-building 'litteR-installation.Rmd'

--- re-building 'litteR-manual.Rmd' using rmarkdown
Quitting from lines 19-29 (litteR-manual.Rmd) 
Error: processing vignette 'litteR-manual.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'litteR-manual.Rmd'

SUMMARY: processing the following file failed:
  'litteR-manual.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'e1071'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'caret' 'knitr' 'pROC' 'utils'
  All declared Imports should be used.
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'scatterplot3d' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'rgl' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
lm.beta: no visible global function definition for 'coef'
lm.beta: no visible global function definition for 'model.matrix'
lm.beta: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  coef model.frame model.matrix
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'Matrix'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'car'
Package unavailable to check Rd xrefs: 'car'
'library' or 'require' call to 'mvtnorm' which was already attached by Depends.
  Please remove these calls from your code.
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: no visible global function definition for 'lm'
lmec: no visible global function definition for 'pnorm'
lmec: no visible global function definition for 'dnorm'
lmec : vtrnorm2: no visible global function definition for 'runif'
lmec : vtrnorm2: no visible global function definition for 'qnorm'
lmec : vtrnorm2: no visible global function definition for 'pnorm'
lmec: no visible global function definition for 'rnorm'
lmec: no visible global function definition for 'ar'
Undefined global functions or variables:
  ar dnorm lm pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "ar", "dnorm", "lm", "pnorm", "qnorm", "rnorm",
             "runif")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
mq.diagnostics : mq_missinggenotype_plot: no visible global function
  definition for 'plot.missing'
Undefined global functions or variables:
  plot.missing
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'nlme'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
approx.Z : <anonymous>: no visible global function definition for
  'approx'
smspline: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  approx model.frame
Consider adding
  importFrom("stats", "approx", "model.frame")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
HTest: no visible global function definition for 'is.owin'
HTest: no visible global function definition for 'inside.owin'
HTest: no visible global function definition for 'area.owin'
HTest: no visible global function definition for 'union.owin'
HTest: no visible global function definition for 'intersect.owin'
HTest: no visible global function definition for 'erosion.owin'
HTest: no visible global function definition for 'dilation.owin'
area_esh: no visible global function definition for 'area.owin'
detectability_cps: no visible global function definition for 'disc'
detectability_cps: no visible global function definition for
  'intersect.owin'
detectability_cps: no visible global function definition for 'edges'
detectability_cps: no visible global function definition for
  'lengths.psp'
detectability_cps: no visible global function definition for
  'union.owin'
detectability_cps: no visible global function definition for 'erosion'
detectability_cps: no visible global function definition for 'dilation'
gg_wind: no visible global function definition for 'disc'
gg_wind: no visible global function definition for 'union.owin'
shades: no visible global function definition for 'owin'
shades: no visible global function definition for 'union.owin'
shades: no visible global function definition for 'disc'
visibility_thinning_cps: no visible global function definition for
  'disc'
visibility_thinning_cps: no visible global function definition for
  'intersect.owin'
visibility_thinning_cps: no visible global function definition for
  'inside.owin'
visibility_thinning_cps: no visible global function definition for
  'union.owin'
visibility_thinning_cps: no visible global function definition for
  'erosion'
visibility_thinning_cps: no visible global function definition for
  'dilation'
Undefined global functions or variables:
  area.owin dilation dilation.owin disc edges erosion erosion.owin
  inside.owin intersect.owin is.owin lengths.psp owin union.owin
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'mnormt'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'genefilter'

Package suggested but not available for checking: 'devtools'

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 suggested but not available for checking: 'car', 'dynlm', 'AER'
Package unavailable to check Rd xrefs: 'car'
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'R6' 'nnls' 'utils'
  All declared Imports should be used.
Package suggested but not available for checking: 'plotly'
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'pkgdown'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'checkmate'
  All declared Imports should be used.
'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 suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Running examples in 'localsolver-Ex.R' failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
Error in ls.problem(model.text.lsp) : 
  has.localsolver(ls.path) is not TRUE
Calls: ls.problem -> stopifnot
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'localsolver.Rmd' using knitr
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
--- failed re-building 'localsolver.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
AnalyticalOptim: no visible global function definition for 'optim'
LLConstructor : LL: no visible global function definition for 'dpois'
MixtureDensity: no visible global function definition for 'glm'
MixtureDensity : f_hat: no visible global function definition for
  'predict'
NullDensity : f0: no visible global function definition for 'dpois'
Undefined global functions or variables:
  dpois glm optim predict
Consider adding
  importFrom("stats", "dpois", "glm", "optim", "predict")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Note: found 23 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'kableExtra', 'devtools'
Error(s) in re-building vignettes:
  ...
--- re-building 'quickstart.Rmd' using rmarkdown
Quitting from lines 32-35 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'quickstart.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'modules'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: 'distr'
  All declared Imports should be used.
Package in Depends field not imported from: 'logcondens'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages suggested but not available for checking:
  'slackr', 'RPushbullet', 'telegram', 'covr', 'devtools', 'rsyslog'
Package unavailable to check Rd xrefs: 'rsyslog'
Note: found 12 marked UTF-8 strings
Malformed Title field: should not end in a period.
EstimateProbability: no visible global function definition for
  'predict'
LOGICOIL: no visible binding for global variable 'pssm'
LOGICOIL: no visible binding for global variable 'LOGICOILfit'
LOGICOIL: no visible binding for global variable 'Model_Parameters'
plot_LOGICOIL: no visible global function definition for 'png'
plot_LOGICOIL: no visible global function definition for 'par'
plot_LOGICOIL: no visible global function definition for 'lines'
plot_LOGICOIL: no visible global function definition for 'axis'
plot_LOGICOIL: no visible global function definition for 'mtext'
plot_LOGICOIL: no visible global function definition for 'legend'
plot_LOGICOIL: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  LOGICOILfit Model_Parameters axis dev.off legend lines mtext par png
  predict pssm
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par")
  importFrom("stats", "predict")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
LogitNet.weight: no visible global function definition for 'lowess'
LogitNet.weight: no visible global function definition for 'median'
Undefined global functions or variables:
  lowess median
Consider adding
  importFrom("stats", "lowess", "median")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
rloglognorm: 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
LogrankA: no visible global function definition for 'is.Surv'
LogrankA: no visible global function definition for 'na.omit'
LogrankA: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  is.Surv na.omit pchisq
Consider adding
  importFrom("stats", "na.omit", "pchisq")
to your NAMESPACE file.
Packages suggested but not available for checking: 'plumber', 'covr'
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'plumber'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'ggplot2'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'survminer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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
Note: found 994 marked Latin-1 strings
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking:
  'Rgraphviz', 'RDRToolbox', 'covr'
Packages suggested but not available for checking: 'tidyverse', 'covr'
Packages suggested but not available for checking: 'tidyverse', 'covr'
Error(s) in re-building vignettes:
  ...
--- re-building 'classification.Rmd' using rmarkdown
Quitting from lines 67-93 (classification.Rmd) 
Error: processing vignette 'classification.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'classification.Rmd'

--- re-building 'tours.Rmd' using rmarkdown
Quitting from lines 68-94 (tours.Rmd) 
Error: processing vignette 'tours.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'tours.Rmd'

SUMMARY: processing the following files failed:
  'classification.Rmd' 'tours.Rmd'

Error: Vignette re-building failed.
Execution halted
fplot: no visible global function definition for 'rnorm'
fplot: no visible global function definition for 'segments'
fplot: no visible global function definition for 'points'
fplot: no visible global function definition for 'text'
fplot.foodweb: no visible global function definition for 'segments'
fplot.foodweb: no visible global function definition for 'points'
fplot.foodweb: no visible global function definition for 'text'
gplot: no visible global function definition for 'runif'
groupplot: no visible global function definition for 'rnorm'
groupplot: no visible global function definition for 'segments'
groupplot: no visible global function definition for 'points'
groupplot: no visible global function definition for 'text'
groupplot.foodweb: no visible global function definition for 'rnorm'
groupplot.foodweb: no visible global function definition for 'segments'
groupplot.foodweb: no visible global function definition for 'points'
groupplot.foodweb: no visible global function definition for 'text'
Undefined global functions or variables:
  points rnorm runif segments text
Consider adding
  importFrom("graphics", "points", "segments", "text")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'brms', 'rstan', 'rstanarm'
Package required but not available: 'httr'

Package suggested but not available for checking: 'biomaRt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'scio'
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'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: 'doMC'
Checking should be performed on sources prepared by 'R CMD build'.
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
lpint : <anonymous>: no visible global function definition for
  'integrate'
lpint: no visible global function definition for 'integrate'
lpint : lpint : <anonymous>: no visible global function definition for
  'integrate'
lplikint : lplikint.fun : <anonymous>: no visible global function
  definition for 'integrate'
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'LPGraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'Rsymphony' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
mipSolve.Rsymphony: no visible global function definition for
  'Rsymphony_solve_LP'
Undefined global functions or variables:
  Rsymphony_solve_LP
'LazyData' is specified without a 'data' directory
Package required but not available: 'LPGraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
learnPattern.default: no visible global function definition for 'runif'
plot.learnPattern: no visible global function definition for 'matplot'
plotMDS: no visible global function definition for 'par'
plotMDS: no visible global function definition for 'rainbow'
plotMDS: no visible global function definition for 'pairs'
visualizePattern: no visible global function definition for 'par'
visualizePattern: no visible global function definition for 'points'
visualizePattern: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend matplot pairs par points rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "matplot", "pairs", "par", "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
LP.comoment: no visible global function definition for 'cor'
LP.comoment: no visible global function definition for 'cov'
LP.moment: no visible global function definition for 'cor'
LPTrans: no visible global function definition for 'ecdf'
VAR: no visible global function definition for 'embed'
VAR: no visible global function definition for 'lm'
Undefined global functions or variables:
  cor cov ecdf embed lm
Consider adding
  importFrom("stats", "cor", "cov", "ecdf", "embed", "lm")
to your NAMESPACE file.
Packages suggested but not available for checking: 'pkgdown', 'devtools'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'car'
Note: found 55 marked UTF-8 strings
Running examples in 'LSAmitR-Ex.R' failed
The error most likely occurred in:

> ### Encoding: UTF-8
> 
> ### Name: Kapitel  1
> ### Title: Kapitel 1: Testkonstruktion
> ### Aliases: 'Kapitel 1'
> 
> ### ** Examples
> 
> library(TAM)
Loading required package: CDM
Loading required package: mvtnorm
**********************************
** CDM 7.5-15 (2020-03-10 14:19:21)      
** Cognitive Diagnostic Models  **
**********************************

* TAM 3.6-45 (2021-04-22 14:35:52)
> library(miceadds)
Loading required package: mice

Attaching package: 'mice'

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

    filter

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

    cbind, rbind

* miceadds 3.11-6 (2021-01-21 11:48:47)
> library(irr)
Loading required package: lpSolve
> library(gtools)
> library(car)
Error in library(car) : there is no package called 'car'
Execution halted
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
Namespace in Imports field not imported from: 'Matrix'
  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
Packages required but not available: 'tseries', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Lsdv.formula: no visible global function definition for 'model.frame'
Lsdv.formula: no visible global function definition for 'model.matrix'
Lsdv.formula: no visible global function definition for
  'model.response'
lsdv: no visible global function definition for 'pf'
summary.Lsdv: no visible global function definition for 'coef'
summary.Lsdv: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.frame model.matrix model.response pf pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pf", "pt")
to your NAMESPACE file.
legend.lshorth: no visible global function definition for 'legend'
legend.lshorth: no visible global function definition for 'strwidth'
legend.lshorth: no visible global function definition for 'text'
plot.lshorth: no visible global function definition for 'plot.new'
plot.lshorth: no visible global function definition for 'plot.window'
plot.lshorth: no visible global function definition for 'axis'
plot.lshorth: no visible global function definition for 'title'
plot.lshorth: no visible global function definition for 'box'
plot.lshorth: no visible global function definition for 'lines'
plot.lshorth: no visible global function definition for 'legend'
plot.lshorth: no visible global function definition for 'strwidth'
plot.lshorth: no visible global function definition for 'text'
Undefined global functions or variables:
  axis box legend lines plot.new plot.window strwidth text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot.new",
             "plot.window", "strwidth", "text", "title")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'lavaan'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'NFCP'
Namespace in Imports field not imported from: 'lifecycle'
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building 'LSMRealOptions.Rmd' using rmarkdown
Warning: position_stack requires non-overlapping x intervals
Quitting from lines 394-395 (LSMRealOptions.Rmd) 
Error: processing vignette 'LSMRealOptions.Rmd' failed with diagnostics:
there is no package called 'NFCP'
--- failed re-building 'LSMRealOptions.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
Note: found 2096 marked UTF-8 strings
OC : Lnapprox: no visible global function definition for 'pnorm'
OC : Lnapprox: no visible global function definition for 'qnorm'
OC : Lt: no visible global function definition for 'pt'
OC : Lt: no visible global function definition for 'qnorm'
OC : OC_emwa2: no visible global function definition for 'pnorm'
OC : OC_emwa2: no visible global function definition for 'qnorm'
OC: no visible global function definition for 'pnorm'
OC: no visible global function definition for 'qnorm'
cmBE : LAtHy: no visible global function definition for 'phyper'
cmBE: no visible global function definition for 'uniroot'
planAOQL : Gderivacex: no visible global function definition for
  'pnorm'
planAOQL : Mnk: no visible global function definition for 'uniroot'
planAOQL : k0AOQL : delta: no visible global function definition for
  'pnorm'
planAOQL : alpha0: no visible global function definition for 'pnorm'
planAOQL : alpha0: no visible global function definition for 'qnorm'
planAOQL : fMSmodq2: no visible global function definition for
  'optimize'
planAOQL : kAOQL: no visible global function definition for 'uniroot'
planLTPD : nAPPROXL : k0L : g: no visible global function definition
  for 'qnorm'
planLTPD : nAPPROXL : k0L : h: no visible global function definition
  for 'qnorm'
planLTPD : nAPPROXL : k0L: no visible global function definition for
  'qnorm'
planLTPD : nAPPROXL : alpha0: no visible global function definition for
  'pnorm'
planLTPD : nAPPROXL : alpha0: no visible global function definition for
  'qnorm'
planLTPD : nAPPROXL: no visible global function definition for
  'uniroot'
planLTPD : kEWMA: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  optimize phyper pnorm pt qnorm uniroot
Consider adding
  importFrom("stats", "optimize", "phyper", "pnorm", "pt", "qnorm",
             "uniroot")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  'Icens' 'interval'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'robustbase'
  Please remove these calls from your code.
ltsbase: no visible global function definition for 'lm'
ltsbase: no visible global function definition for 'lines'
ltsbase: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend lines lm
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "lm")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'rpostgis'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'ncdf4' 'raster'
  All declared Imports should be used.
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'RLumShiny', 'plotly', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
terrestrial.season: 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').
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'fs' 'progress'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'covr', 'devtools', 'usethis'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   2. | \-base::withCallingHandlers(...)
   3. \-lvmisc::create_proj(proj_dir)
   4.   \-lvmisc::abort_package_not_installed(c("withr", "git2r", "usethis"))
  -- Error (test-create_proj.R:80:3): create_proj() writes a README.md file ------
  Error: Package "usethis" is needed for this function to work. Please install it.
  Backtrace:
      x
   1. +-base::suppressMessages(create_proj(proj_dir)) test-create_proj.R:80:2
   2. | \-base::withCallingHandlers(...)
   3. \-lvmisc::create_proj(proj_dir)
   4.   \-lvmisc::abort_package_not_installed(c("withr", "git2r", "usethis"))
  
  [ FAIL 5 | WARN 0 | SKIP 7 | PASS 231 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'gWQS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  lxb.c:62:25: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
  lxb.c:62:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 4 [-Wformat-overflow=]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/lxb/lxb.Rcheck/00install.out' for details.
generate.clonal.data : pcr.rpareto.func: no visible global function
  definition for 'runif'
generate.clonal.data : get.readcount.given.cellcount: no visible global
  function definition for 'rlnorm'
generate.clonal.data: no visible global function definition for
  'rmultinom'
generate.clonal.data: no visible global function definition for 'rpois'
infer.clonality: no visible global function definition for 'cov'
infer.clonality: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output cov rlnorm rmultinom rpois runif
Consider adding
  importFrom("stats", "cov", "rlnorm", "rmultinom", "rpois", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'moveHMM'
Namespaces in Imports field not imported from:
  'e1071' 'utils'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'moveHMM'
Running examples in 'm2b-Ex.R' failed
The error most likely occurred in:

> ### Name: xytb2hmm
> ### Title: xytb object conversion to moveHMM object
> ### Aliases: xytb2hmm
> 
> ### ** Examples
> 
> #track_CAGA_005 is a dataset
> xytb<-xytb(track_CAGA_005,"a track",3,.5)
[1] "Compute 13 indicators on 1 moving windows"
[1] "Compute indicators on 3 points"
[1] "Done"
> xyhmm <-xytb2hmm(xytb)
Error: moveHMM needed for this function to work. Please install it.
Execution halted
Package required but not available: 'usethis'

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
project.M3.1.to.M3.2: no visible global function definition for
  'coordinates<-'
project.M3.1.to.M3.2: no visible global function definition for
  'proj4string<-'
project.M3.1.to.M3.2: no visible global function definition for 'CRS'
project.M3.1.to.M3.2: no visible global function definition for
  'spTransform'
project.M3.1.to.M3.2: no visible global function definition for
  'coordinates'
Undefined global functions or variables:
  CRS coordinates coordinates<- proj4string<- spTransform
Package required but not available: 'GenomicFeatures'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
maboost.default: no visible global function definition for
  'flush.console'
maboost.default: no visible binding for global variable 'na.pass'
maboost.default : predict.type: no visible global function definition
  for 'predict'
maboost.formula: no visible global function definition for
  'model.extract'
maboost.machine.bin: no visible global function definition for 'runif'
maboost.machine.bin: no visible binding for global variable 'na.pass'
maboost.machine.multi: no visible global function definition for
  'runif'
maboost.machine.multi: no visible binding for global variable 'na.pass'
projsplx_k: no visible global function definition for 'tail'
varplot.maboost: no visible global function definition for 'dotchart'
Undefined global functions or variables:
  dotchart flush.console model.extract na.pass predict runif tail
Consider adding
  importFrom("graphics", "dotchart")
  importFrom("stats", "model.extract", "na.pass", "predict", "runif")
  importFrom("utils", "flush.console", "tail")
to your NAMESPACE file.
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

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

--- re-building 'UsersGuide.Rmd' using rmarkdown
Quitting from lines 22-24 (UsersGuide.Rmd) 
Error: processing vignette 'UsersGuide.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'UsersGuide.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'machina'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'etl'

Package suggested but not available for checking: 'clifro'

VignetteBuilder packages required for checking but not installed:
  'etl', 'clifro'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
logistic_z: no visible global function definition for 'glm'
logistic_z: no visible binding for global variable 'binomial'
logistic_z: no visible global function definition for 'predict'
plsrf_x: no visible global function definition for 'qnorm'
plsrf_x: no visible global function definition for 'predict'
plsrf_x_pv: no visible global function definition for 'qnorm'
plsrf_x_pv: no visible global function definition for 'predict'
plsrf_xz: no visible global function definition for 'qnorm'
plsrf_xz: no visible global function definition for 'predict'
plsrf_xz_pv: no visible global function definition for 'qnorm'
plsrf_xz_pv: no visible global function definition for 'predict'
rf_z: no visible global function definition for 'qnorm'
rf_z: no visible global function definition for 'predict'
simuldata_list: no visible global function definition for 'rnorm'
simuldatacluster_list: no visible global function definition for
  'rnorm'
svm_x: no visible global function definition for 'predict'
Undefined global functions or variables:
  binomial glm predict qnorm rnorm
Consider adding
  importFrom("stats", "binomial", "glm", "predict", "qnorm", "rnorm")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'R2wd' 'ggplot2' 'metafor'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'mathjaxr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rlang' 'torch'
  All declared Imports should be used.
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' calls in package code:
  'R2wd' 'ggplot2' 'metafor'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'TCGAbiolinks', 'plotly', 'canvasXpress'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'doMC'
Package required but not available: 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

Packages suggested but not available for checking: 'pdftools', 'tesseract'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'crul'

Packages suggested but not available for checking:
  'dittoSeq', 'vcr', 'webmockr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package required but not available: 'Rgraphviz'

Packages suggested but not available for checking:
  'convert', 'GEOquery', 'GEOmetadb', 'KEGGREST', 'pdInfoBuilder',
  'lumi', 'oligo', 'affy', 'genefilter', 'simpleaffy', 'GOstats',
  'globaltest', 'Category', 'annotate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gmailr', 'googledrive', 'googlesheets4'

Package suggested but not available for checking: 'covr'

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
'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
Packages suggested but not available for checking: 'rstan', 'INLA'
Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown' 'testthat'
  All declared Imports should be used.
Packages unavailable to check Rd xrefs: 'INLA', 'rstan'
Package suggested but not available for checking: 'curl'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'curl', 'httr'

Package suggested but not available for checking: 'rdhs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package in Depends field not imported from: 'rJava'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MalletLDA: no visible global function definition for '.jnew'
mallet.doc.topics: no visible global function definition for
  '.jevalArray'
mallet.import: no visible global function definition for 'J'
mallet.import: no visible global function definition for '.jnew'
mallet.import: no visible global function definition for '.jcast'
mallet.subset.topic.words: no visible global function definition for
  '.jevalArray'
mallet.topic.hclust: no visible global function definition for 'hclust'
mallet.topic.hclust: no visible global function definition for 'dist'
mallet.topic.words: no visible global function definition for
  '.jevalArray'
mallet.word.freqs: no visible global function definition for
  '.jevalArray'
Undefined global functions or variables:
  .jcast .jevalArray .jnew J dist hclust
Consider adding
  importFrom("stats", "dist", "hclust")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'tibble'
  All declared Imports should be used.
Note: found 328 marked UTF-8 strings
Package required but not available: 'plotly'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

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: 'plotly', 'covr'
Note: found 55 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'rentrez'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'gtools' 'reshape'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'forecast', 'smooth'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'curl', 'aws.s3', 'magick'

Packages suggested but not available for checking: 'tigris', 'tidycensus'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
Note: found 3058 marked UTF-8 strings
Note: found 11396 marked UTF-8 strings
Packages suggested but not available for checking: 'covr', 'googleway'
Package which this enhances but not available for checking: 'geojsonio'
'LazyData' is specified without a 'data' directory
cf1.sample: no visible global function definition for 'rexp'
cf1.sample: no visible global function definition for 'rmultinom'
dherlang : <anonymous> : <anonymous>: no visible global function
  definition for 'dgamma'
erhmm.param.kmeans: no visible global function definition for 'kmeans'
erhmm.param.kmeans: no visible global function definition for 'var'
erhmm.param.kmeans: no visible global function definition for 'runif'
gmmpp.param.kmeans: no visible global function definition for 'kmeans'
gmmpp.param.kmeans: no visible global function definition for 'runif'
herlang.param.kmeans: no visible global function definition for
  'kmeans'
herlang.param.kmeans: no visible global function definition for 'var'
map.param.kmeans: no visible global function definition for 'kmeans'
map.param.kmeans: no visible global function definition for 'runif'
ph.param.random: no visible global function definition for 'runif'
ph.sample: no visible global function definition for 'rmultinom'
ph.sample: no visible global function definition for 'rexp'
pherlang : <anonymous> : <anonymous>: no visible global function
  definition for 'pgamma'
rherlang: no visible global function definition for 'rmultinom'
rherlang : <anonymous>: no visible global function definition for
  'rgamma'
Undefined global functions or variables:
  dgamma kmeans pgamma rexp rgamma rmultinom runif var
Consider adding
  importFrom("stats", "dgamma", "kmeans", "pgamma", "rexp", "rgamma",
             "rmultinom", "runif", "var")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  'dplyr' 'rgdal' 'rlang' 'testthat'
  All declared Imports should be used.
'library' or 'require' call to 'mgcv' which was already attached by Depends.
  Please remove these calls from your code.
ageprofile: no visible global function definition for 'model.frame'
ageprofile: no visible binding for global variable 'poisson'
ageprofile: no visible global function definition for 'predict.gam'
ageprofile: no visible global function definition for 'as.formula'
ageprofile: no visible global function definition for 'summary.gam'
ageprofile: no visible global function definition for 'contrasts<-'
ageprofile: no visible global function definition for 'anova.gam'
plotap: no visible global function definition for 'dev.new'
plotap: no visible global function definition for 'lines'
plotap: no visible global function definition for 'points'
plotap: no visible global function definition for 'legend'
splitter: no visible global function definition for 'reshape'
tabm: no visible global function definition for 'coef'
tabm: no visible global function definition for 'AIC'
Undefined global functions or variables:
  AIC anova.gam as.formula coef contrasts<- dev.new legend lines
  model.frame points poisson predict.gam reshape summary.gam
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "points")
  importFrom("stats", "AIC", "as.formula", "coef", "contrasts<-",
             "model.frame", "poisson", "reshape")
to your NAMESPACE file.
Packages required but not available:
  'cartography', 'httr', 'curl', 'geojsonio'

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

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

Packages suggested but not available for checking:
  'taxize', 'rgbif', 'scrubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 55 marked UTF-8 strings
Note: found 16 marked Latin-1 strings
  Note: found 980 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
Note: found 13084 marked UTF-8 strings
calcStats: no visible global function definition for 'as.formula'
calcStats: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  as.formula na.omit
Consider adding
  importFrom("stats", "as.formula", "na.omit")
to your NAMESPACE file.
Package required but not available: 'curl'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'betareg'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'AER'
Package unavailable to check Rd xrefs: 'AER'
'LazyData' is specified without a 'data' directory
Package required but not available: 'kableExtra'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
negbin.rel.clust: no visible global function definition for 'kmeans'
negbin.rel.clust: no visible global function definition for 'matplot'
negbin.rel.pca: no visible global function definition for 'princomp'
negbin.rel.pca: no visible global function definition for 'biplot'
pois.rel.clust: no visible global function definition for 'kmeans'
pois.rel.clust: no visible global function definition for 'matplot'
pois.rel.pca: no visible global function definition for 'princomp'
pois.rel.pca: no visible global function definition for 'biplot'
sim.negbin: no visible global function definition for 'rnbinom'
sim.pois: no visible global function definition for 'rpois'
wt.rel.negbin: no visible global function definition for 'var'
wt.rel.negbin: no visible global function definition for 'optimize'
wt.rel.negbin: no visible global function definition for 'integrate'
wt.rel.pois: no visible global function definition for 'optimize'
wt.rel.pois: no visible global function definition for 'integrate'
Undefined global functions or variables:
  biplot integrate kmeans matplot optimize princomp rnbinom rpois var
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "biplot", "integrate", "kmeans", "optimize",
             "princomp", "rnbinom", "rpois", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
mAr.pca: no visible binding for global variable 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'forecast'
Running examples in 'MARSS-Ex.R' failed
The error most likely occurred in:

> ### Name: accuracy.marssMLE
> ### Title: Return accuracy metrics
> ### Aliases: accuracy.marssMLE accuracy.marssPredict
> 
> ### ** Examples
> 
> dat <- t(harborSeal)
> dat <- dat[c(2, 11, 12),]
> train.dat <- dat[,1:12]
> fit <- MARSS(train.dat, model = list(Z = factor(c("WA", "OR", "OR"))))
Success! abstol and log-log tests passed at 79 iterations.
Alert: conv.test.slope.tol is 0.5.
Test with smaller values (<0.1) to ensure convergence.

MARSS fit is
Estimation method: kem 
Convergence test: conv.test.slope.tol = 0.5, abstol = 0.001
Estimation converged in 79 iterations. 
Log-likelihood: 14.98234 
AIC: -13.96467   AICc: -2.887748   
 
                Estimate
A.OR.SouthCoast   0.8952
R.diag            0.0087
U.WA              0.1043
U.OR              0.0569
Q.(WA,WA)         0.0112
Q.(OR,OR)         0.0000
x0.WA             7.3171
x0.OR             6.2970
Initial states (x0) defined at t=0

Standard errors have not been calculated. 
Use MARSSparamCIs to compute CIs and bias estimates.

> 
> library(forecast)
Error in library(forecast) : there is no package called 'forecast'
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'FactoMineR', 'factoextra', 'GOstats', 'kableExtra'

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.
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'kableExtra', 'flashr'
Error(s) in re-building vignettes:
--- re-building 'eQTL_outline.Rmd' using rmarkdown
--- finished re-building 'eQTL_outline.Rmd'

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

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

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

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

--- re-building 'intro_mashbaselinemean.Rmd' using rmarkdown
Quitting from lines 19-21 (intro_mashbaselinemean.Rmd) 
Error: processing vignette 'intro_mashbaselinemean.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'intro_mashbaselinemean.Rmd'

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tidyverse'
Error(s) in re-building vignettes:
  ...
--- re-building 'rationale.Rmd' using rmarkdown
Quitting from lines 19-32 (rationale.Rmd) 
Error: processing vignette 'rationale.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'rationale.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Package required but not available: 'repmis'

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: 'httr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'js'
Packages required but not available: 'httr', 'texPreview', 'magick'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Found the following possibly unsafe calls:
File 'matlab/R/zzz.R':
  unlockBinding("savedTime", .MatlabNamespaceEnv)

colorbar : colorbar.EO: no visible global function definition for 'par'
colorbar : colorbar.EO: no visible global function definition for
  'axis'
colorbar : colorbar.EO: no visible global function definition for
  'axTicks'
colorbar : colorbar.EO: no visible global function definition for 'box'
colorbar : colorbar.NO: no visible global function definition for
  'axis'
colorbar : colorbar.NO: no visible global function definition for
  'axTicks'
colorbar : colorbar.NO: no visible global function definition for 'box'
imagesc : pretty.axp: no visible global function definition for 'par'
imagesc: no visible global function definition for 'axis'
imagesc: no visible global function definition for 'box'
jet.colors: no visible global function definition for 'rgb'
multiline.plot.colors : get.gca.colororder: no visible global function
  definition for 'rgb'
std: no visible global function definition for 'sd'
Undefined global functions or variables:
  axTicks axis box par rgb sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axTicks", "axis", "box", "par")
  importFrom("stats", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
Package required but not available: 'car'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'gputools'
'library' or 'require' call to 'bigmemory' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Description field: should contain one or more complete sentences.
MAT: no visible global function definition for 'dev.new'
MAT: no visible global function definition for 'points'
MAT: no visible global function definition for 'abline'
MAT: no visible global function definition for 'text'
MAT: no visible global function definition for 'legend'
MAT: no visible global function definition for 'lines'
MAT: no visible global function definition for 'par'
MAT: no visible global function definition for 'barplot'
MAT: no visible global function definition for 'cor'
print.MAT: no visible global function definition for 'sd'
print.MAT: no visible global function definition for 'cor'
simM3PL: no visible global function definition for 'rnorm'
simM3PL: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline barplot cor dev.new legend lines par points rnorm runif sd
  text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "lines", "par",
             "points", "text")
  importFrom("stats", "cor", "rnorm", "runif", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
'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: 'ASGSCA'
Package required but not available: 'TTR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'car'
Package unavailable to check Rd xrefs: 'car'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   4.     \-base:::withOneRestart(expr, restarts[[1L]])
   5.       \-base:::doWithOneRestart(return(expr), restart)
  -- Error (test-correct-levene.R:183:3): cases when some groups are constant after residuals give equal results --
  Error: there is no package called 'car'
  Backtrace:
      x
   1. +-matrixTests:::car_levene(x, g) test-correct-levene.R:183:2
   2. \-base::loadNamespace(x) test-correct-levene.R:19:4
   3.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     \-base:::withOneRestart(expr, restarts[[1L]])
   5.       \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 14 | WARN 10 | SKIP 0 | PASS 2147 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Packages required but not available: 'beastier', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
GSTplot : <anonymous>: no visible global function definition for
  't.test'
GSTplot: no visible global function definition for 'rt'
GSTplot: no visible global function definition for 'layout'
GSTplot: no visible global function definition for 'par'
GSTplot: no visible global function definition for 'text'
GSTplot: no visible global function definition for 'lines'
GSTplot: no visible global function definition for 'polygon'
GSTplot: no visible global function definition for 'abline'
GSTplot: no visible global function definition for 'ecdf'
GSTplot: no visible global function definition for 'knots'
GSTplot : <anonymous>: no visible global function definition for 'aov'
GSTplot: no visible global function definition for 'qf'
MAVTn : <anonymous>: no visible global function definition for 'aov'
MAVTn: no visible global function definition for 'p.adjust'
MAVTn: no visible global function definition for 'par'
MAVTn: no visible global function definition for 'abline'
MAVTn: no visible global function definition for 'legend'
MAVTn: no visible global function definition for 'locator'
Tols : olsf: no visible global function definition for 't.test'
Tols: no visible global function definition for 'cor'
Undefined global functions or variables:
  abline aov cor ecdf knots layout legend lines locator p.adjust par
  polygon qf rt t.test text
Consider adding
  importFrom("graphics", "abline", "layout", "legend", "lines",
             "locator", "par", "polygon", "text")
  importFrom("stats", "aov", "cor", "ecdf", "knots", "p.adjust", "qf",
             "rt", "t.test")
to your NAMESPACE file.
Package in Depends field not imported from: 'mnormt'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catt.test: no visible global function definition for 'pnorm'
fnorm2: no visible global function definition for 'sadmvn'
fnorm3: no visible global function definition for 'sadmvn'
Undefined global functions or variables:
  pnorm sadmvn
Consider adding
  importFrom("stats", "pnorm")
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
Package suggested but not available for checking: 'covr'
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
Packages required but not available: 'devtools', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'MazamaCoreUtils', 'MazamaSpatialUtils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MazamaCoreUtils', 'rmapshaper'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Note: found 66 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
MI.2: no visible global function definition for 'xtabs'
RNASeq.Data: no visible binding for global variable 'quantile'
loc.node: no visible global function definition for 'head'
loc.node: no visible global function definition for 'tail'
plotHybrid.Tree: no visible global function definition for 'par'
plotHybrid.Tree: no visible global function definition for 'text'
plotHybrid.Tree: no visible global function definition for 'image'
plotHybrid.Tree: no visible global function definition for 'grey'
plotHybrid.Tree: no visible global function definition for
  'heat.colors'
plotHybrid.Tree: no visible global function definition for 'head'
plotHybrid.Tree: no visible global function definition for 'segments'
plotbr: no visible global function definition for 'segments'
Undefined global functions or variables:
  grey head heat.colors image par quantile segments tail text xtabs
Consider adding
  importFrom("grDevices", "grey", "heat.colors")
  importFrom("graphics", "image", "par", "segments", "text")
  importFrom("stats", "quantile", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
cfull: no visible global function definition for 'combn'
cl: no visible global function definition for 'combn'
cn: no visible global function definition for 'combn'
crep: no visible global function definition for 'combn'
crich: no visible global function definition for 'combn'
ct: no visible global function definition for 'combn'
mjaccard: no visible global function definition for 'combn'
ml: no visible global function definition for 'combn'
mn: no visible global function definition for 'combn'
mrep: no visible global function definition for 'combn'
mrich: no visible global function definition for 'combn'
msorensen: no visible global function definition for 'combn'
mt: no visible global function definition for 'combn'
wnodf: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  'effsize' 'psych'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
Namespaces in Imports field not imported from:
  'formatR' 'utf8'
  All declared Imports should be used.
Note: found 6 marked Latin-1 strings
Package suggested but not available for checking: 'kangar00'
Package unavailable to check Rd xrefs: 'kangar00'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Unknown package 'orddom' in Rd xrefs
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
Malformed Title field: should not end in a period.
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:
  'babette', 'beastier', 'curl', 'devtools', 'mauricer'

Package suggested but not available for checking: 'lintr'

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:
  'curl', 'tidyverse', 'mlr3oml', 'covr'
Namespace in Imports field not imported from: 'lifecycle'
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building 'mcboost_basics_extensions.Rmd' using rmarkdown
Quitting from lines 73-81 (mcboost_basics_extensions.Rmd) 
Error: processing vignette 'mcboost_basics_extensions.Rmd' failed with diagnostics:
Input URL requires https:// connection for which fread() requires 'curl' package which cannot be found. Please install 'curl' using 'install.packages('curl')'.
--- failed re-building 'mcboost_basics_extensions.Rmd'

--- re-building 'mcboost_example.Rmd' using rmarkdown
Quitting from lines 19-27 (mcboost_example.Rmd) 
Error: processing vignette 'mcboost_example.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'mcboost_example.Rmd'

SUMMARY: processing the following files failed:
  'mcboost_basics_extensions.Rmd' 'mcboost_example.Rmd'

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  'MASS' 'lars' 'methods' 'parallel' 'smoothmest'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: 'lpSolve'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
laugreen: no visible global function definition for 'combn'
laugreen: no visible global function definition for 'lp'
maxpear: no visible global function definition for 'hclust'
maxpear: no visible global function definition for 'as.dist'
maxpear : <anonymous>: no visible global function definition for
  'cutree'
medv: no visible global function definition for 'cutree'
medv: no visible global function definition for 'hclust'
medv: no visible global function definition for 'as.dist'
minbinder: no visible global function definition for 'hclust'
minbinder: no visible global function definition for 'as.dist'
minbinder : <anonymous>: no visible global function definition for
  'cutree'
relabel : min.perm.labels: no visible global function definition for
  'lp.transport'
Undefined global functions or variables:
  as.dist combn cutree hclust lp lp.transport
Consider adding
  importFrom("stats", "as.dist", "cutree", "hclust")
  importFrom("utils", "combn")
to your NAMESPACE file.
getbetap.A: no visible global function definition for 'pbeta'
getbetap.A: no visible global function definition for 'cor.test'
Undefined global functions or variables:
  cor.test pbeta
Consider adding
  importFrom("stats", "cor.test", "pbeta")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'Rgraphviz', 'cplexAPI'
Running examples in 'MCDA-Ex.R' failed
The error most likely occurred in:

> ### Name: plotAlternativesValuesPreorder
> ### Title: Function to plot a preorder of alternatives, based on some score
> ###   or ranking.
> ### Aliases: plotAlternativesValuesPreorder
> ### Keywords: methods
> 
> ### ** Examples
> 
> library(MCDA)
> 
> alternativesValues <- c(10,1,8,3,8,3,4,4,8,5)
> 
> names(alternativesValues) <- c("x10","x1","x9","x2","x8",
+                                 "x3","x7","x4","x6","x5")
> 
> plotAlternativesValuesPreorder(alternativesValues, 
+                                 decreasing=TRUE, 
+                                 alternativesIDs=c("x10","x3","x7",
+                                                     "x4","x6","x5"))
Error in plotAlternativesValuesPreorder(alternativesValues, decreasing = TRUE,  : 
  Rgraphviz package could not be loaded
Execution halted
'LazyData' is specified without a 'data' directory
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.
mcgibbsit: no visible global function definition for 'is.mcmc.list'
mcgibbsit: no visible global function definition for 'start'
mcgibbsit: no visible global function definition for 'end'
mcgibbsit: no visible global function definition for 'thin'
mcgibbsit: no visible global function definition for 'nvar'
mcgibbsit: no visible global function definition for 'mcmc'
mcgibbsit: no visible global function definition for 'mcmc.list'
mcgibbsit: no visible global function definition for 'varnames'
mcgibbsit: no visible global function definition for 'qnorm'
mcgibbsit: no visible global function definition for 'niter'
mcgibbsit: no visible global function definition for 'quantile'
mcgibbsit : to.table: no visible global function definition for
  'window'
mcgibbsit: no visible global function definition for 'var'
read.mcmc: no visible global function definition for 'mcmc.list'
read.mcmc: no visible global function definition for 'mcmc'
Undefined global functions or variables:
  end is.mcmc.list mcmc mcmc.list niter nvar qnorm quantile start thin
  var varnames window
Consider adding
  importFrom("stats", "end", "qnorm", "quantile", "start", "var",
             "window")
to your NAMESPACE file.
call_localoptim: no visible global function definition for 'optim'
call_localoptim: no visible global function definition for 'nlminb'
call_localoptim: no visible global function definition for
  'txtProgressBar'
call_localoptim: no visible global function definition for
  'setTxtProgressBar'
call_localoptim : <anonymous>: no visible global function definition
  for 'optim'
call_localoptim : <anonymous>: no visible global function definition
  for 'nlminb'
multiStartoptim: no visible global function definition for 'median'
Undefined global functions or variables:
  median nlminb optim setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "median", "nlminb", "optim")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
mcheatmaps : coscolorFun: no visible global function definition for
  'rgb'
mcheatmaps : halfcmat: no visible global function definition for
  'order.dendrogram'
mcheatmaps : fullcmat: no visible global function definition for
  'order.dendrogram'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'hclust'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'as.dist'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'sd'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'cophenetic'
mcheatmaps : printDiag: no visible global function definition for
  'order.dendrogram'
mcheatmaps: no visible global function definition for 'strwidth'
mcheatmaps: no visible global function definition for 'pdf'
mcheatmaps: no visible global function definition for 'plot.new'
mcheatmaps: no visible global function definition for 'as.dendrogram'
mcheatmaps: no visible global function definition for 'reorder'
mcheatmaps: no visible global function definition for 'par'
mcheatmaps: no visible global function definition for
  'order.dendrogram'
mcheatmaps: no visible global function definition for 'heat.colors'
mcheatmaps: no visible global function definition for 'terrain.colors'
mcheatmaps: no visible global function definition for 'as.dist'
mcheatmaps: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  as.dendrogram as.dist cophenetic dev.off hclust heat.colors
  order.dendrogram par pdf plot.new reorder rgb sd strwidth
  terrain.colors
Consider adding
  importFrom("grDevices", "dev.off", "heat.colors", "pdf", "rgb",
             "terrain.colors")
  importFrom("graphics", "par", "plot.new", "strwidth")
  importFrom("stats", "as.dendrogram", "as.dist", "cophenetic", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'boot.heterogeneity'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 46 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
lik_locfit: no visible global function definition for 'predict'
mcll_coeff: no visible global function definition for 'optim'
mcll_est: no visible global function definition for 'cov'
mcll_est: no visible global function definition for 'optim'
mcll_se: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov optim predict
Consider adding
  importFrom("stats", "cov", "optim", "predict")
to your NAMESPACE file.
Packages required but not available: 'gRbase', 'abn', 'ggpubr'

Package suggested but not available for checking: 'ggdag'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'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: 'covr'
Namespace in Imports field not imported from: 'generics'
  All declared Imports should be used.
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ecr'

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.
do.linear.conjoint: no visible global function definition for
  'as.formula'
do.linear.conjoint: no visible global function definition for 'lm'
do.linear.conjoint: no visible global function definition for
  'coefficients'
is.close.to.orthogonal: no visible global function definition for 'cor'
mc.add.to.design: no visible global function definition for 'combn'
mc.good.designs: no visible global function definition for 'combn'
Undefined global functions or variables:
  as.formula coefficients combn cor lm
Consider adding
  importFrom("stats", "as.formula", "coefficients", "cor", "lm")
  importFrom("utils", "combn")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'coda'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'MASS' 'coda'
  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
Checking should be performed on sources prepared by 'R CMD build'.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'devtools', 'httr', 'covr', 'gh', 'curl', 'VIM', 'FactoMineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
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
Package suggested but not available for checking: 'covr'
'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: 'plotly'

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.
Namespace in Imports field not imported from: 'glmnet'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package required but not available: 'smacof'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'smacof', 'symbolicDA', 'animation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'MASS' 'datasets' 'dplyr' 'psych' 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'kableExtra'

Packages suggested but not available for checking: 'etl', 'macleish'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tvthemes'

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: 'httr'

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: 'dynlm'

Package suggested but not available for checking: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'meteoland'

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: 'httr', 'rvest'

Package suggested but not available for checking: 'covr'

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

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
  'LazyDataCompression' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'R6' 'ggplot2' 'lavaan'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
conf.interval: no visible global function definition for 'pbinom'
conf.statement: no visible global function definition for 'pbinom'
Undefined global functions or variables:
  pbinom
Consider adding
  importFrom("stats", "pbinom")
to your NAMESPACE file.
Packages required but not available: 'curl', 'httr', 'bib2df'

Packages suggested but not available for checking: 'covr', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.df: no visible global function definition for 'logLik'
coef_simple: no visible global function definition for 'coef'
fitall: no visible binding for global variable 'as.formula'
fitbest: no visible binding for global variable 'as.formula'
lmboot: no visible global function definition for 'lm'
residuals.ensemble : <anonymous>: no visible global function definition
  for 'resid'
residuals.ensemble : <anonymous>: no visible global function definition
  for 'rstudent'
residuals.ensemble : <anonymous>: no visible global function definition
  for 'fitted'
residuals.ensemble : <anonymous>: no visible global function definition
  for 'influence.measures'
stdcoef: no visible global function definition for 'coef'
stdcoef: no visible global function definition for 'update'
summary.ensemble : <anonymous>: no visible global function definition
  for 'logLik'
summary.ensemble : <anonymous>: no visible global function definition
  for 'AIC'
summary.ensemble : <anonymous>: no visible global function definition
  for 'fitted'
summary.resid_ensemble: no visible binding for global variable
  'rstudent'
summary.resid_ensemble: no visible global function definition for 'sd'
summary.variable_ensemble: no visible global function definition for
  'sd'
Undefined global functions or variables:
  AIC as.formula coef fitted influence.measures lm logLik resid
  rstudent sd update
Consider adding
  importFrom("stats", "AIC", "as.formula", "coef", "fitted",
             "influence.measures", "lm", "logLik", "resid", "rstudent",
             "sd", "update")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

Packages suggested but not available for checking: 'magick', 'animation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'magick'

Package suggested but not available for checking: 'ggimage'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'magick'
Namespaces in Imports field not imported from:
  'colourpicker' 'shinyBS' 'shinycssloaders'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  'adegenet' 'geosphere'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
codomToPropShared: no visible global function definition for
  'df2genind'
codomToPropShared: no visible global function definition for
  'propShared'
mgLandscape: no visible global function definition for 'SpatialPoints'
mgQuick: no visible global function definition for 'distm'
mgQuick: no visible binding for global variable 'distMeeus'
Undefined global functions or variables:
  SpatialPoints df2genind distMeeus distm propShared
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking: 'AER', 'car'
Package required but not available: 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'devtools', 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'usethis'

Package suggested but not available for checking: 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'aws.s3', 'covr', 'googleAuthR', 'googleCloudStorageR', 'httr'
Packages suggested but not available for checking: 'devtools', 'kableExtra'
Package suggested but not available for checking: 'kableExtra'
Package suggested but not available for checking: 'magick'
Package required but not available: '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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rstanarm'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'GenABEL'
Malformed Description field: should contain one or more complete sentences.
dometa: no visible global function definition for 'qchisq'
dometa: no visible global function definition for 'median'
dometa: no visible global function definition for 'pchisq'
forestplot: no visible global function definition for 'pchisq'
forestplot: no visible global function definition for 'qnorm'
forestplot: no visible global function definition for 'points'
forestplot: no visible global function definition for 'text'
metagwa.files: no visible global function definition for 'read.csv'
metagwa.files: no visible global function definition for 'write.csv'
metagwa.tables: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  median pchisq points qchisq qnorm read.csv text write.csv
Consider adding
  importFrom("graphics", "points", "text")
  importFrom("stats", "median", "pchisq", "qchisq", "qnorm")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'usethis', 'ggimage'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'survminer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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: 'xcms', 'Rgraphviz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'taxa', 'taxize', 'traits', 'biomformat'

Package suggested but not available for checking: 'phyloseq'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'rvest', 'WikidataQueryServiceR', 'webchem', 'KEGGREST', 'httr',
  'cmmr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'e1071' 'gbm' 'ggplot2' 'graphics' 'randomForest'
  All declared Imports should be used.
Package suggested but not available for checking: 'devtools'
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking: 'devtools', 'covr'
'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
Packages required but not available:
  'GEOquery', 'GEOmetadb', 'ggpubr', 'manhattanly', 'plotly'

Packages suggested but not available for checking: 'snplist', 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dataone', 'EML', 'emld'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
Package required but not available: 'DESeq2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'GEOquery', 'annaffy', 'hgu133plus2.db', 'hgu133a.db', 'hgu95av2.db'
Malformed Description field: should contain one or more complete sentences.
EScombination: no visible global function definition for 'model.matrix'
EScombination: no visible global function definition for 'p.adjust'
EScombination: no visible global function definition for 'pt'
EScombination.paired: no visible global function definition for
  'p.adjust'
EScombination.paired: no visible global function definition for 'pt'
calcfit2Diffrep: no visible global function definition for
  'model.matrix'
directEScombi: no visible global function definition for 'pnorm'
directEScombi: no visible global function definition for 'p.adjust'
directpvalcombi : fstatmeta: no visible global function definition for
  'qnorm'
directpvalcombi: no visible global function definition for 'pnorm'
directpvalcombi: no visible global function definition for 'p.adjust'
pvalcombination: no visible global function definition for
  'model.matrix'
pvalcombination: no visible global function definition for 'p.adjust'
pvalcombination: no visible global function definition for 'pt'
pvalcombination.paired: no visible global function definition for
  'p.adjust'
pvalcombination.paired: no visible global function definition for 'pt'
Undefined global functions or variables:
  model.matrix p.adjust pnorm pt qnorm
Consider adding
  importFrom("stats", "model.matrix", "p.adjust", "pnorm", "pt", "qnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'httr', 'repmis'
Namespace in Imports field not imported from: 'lmerTest'
  All declared Imports should be used.
Packages required but not available: 'GSEABase', 'genefilter'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Running 'mpost.R'
Running the tests in 'tests/mpost.R' failed.
Last 13 lines of output:
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  > 
  > library(grImport)
  Loading required package: XML
  > PostScriptTrace("fig.1")
  Error in system(command, as.integer(flag), f, stdout, stderr, timeout) : 
    character string expected as first argument
  Calls: PostScriptTrace -> system
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'DESeq2'
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'survival'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
fit.bivar: no visible binding for global variable 'binomial'
summary.fit.bivar: no visible global function definition for 'qt'
summary.fit.bivar: no visible global function definition for 'pt'
Undefined global functions or variables:
  binomial pt qt
Consider adding
  importFrom("stats", "binomial", "pt", "qt")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'nullabor', 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
crosssection: no visible global function definition for
  'colorRampPalette'
crosssection: no visible global function definition for
  'filled.contour'
crosssection: no visible global function definition for 'axis'
crosssection: no visible global function definition for 'par'
crosssection: no visible global function definition for 'contour'
temperatures: no visible binding for global variable 'time'
Undefined global functions or variables:
  axis colorRampPalette contour filled.contour par time
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "contour", "filled.contour", "par")
  importFrom("stats", "time")
to your NAMESPACE file.
Package required but not available: 'httr'

Package suggested but not available for checking: 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Malformed Description field: should contain one or more complete sentences.
getdata: no visible global function definition for 'read.csv'
plotdata: no visible global function definition for 'head'
Undefined global functions or variables:
  head read.csv
Consider adding
  importFrom("utils", "head", "read.csv")
to your NAMESPACE file.
RUVRand: no visible global function definition for 'barplot'
RUVRand: no visible global function definition for 'prcomp'
RuvRandIter: no visible global function definition for 'kmeans'
RuvRandIter: no visible global function definition for 'barplot'
RuvRandIter: no visible global function definition for 'prcomp'
opt: no visible global function definition for 'optim'
printdata: no visible global function definition for 'head'
Undefined global functions or variables:
  barplot head kmeans optim prcomp
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "kmeans", "optim", "prcomp")
  importFrom("utils", "head")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'pkgdown'
Namespace in Imports field not imported from: 'memoise'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'grDevices'
  All declared Imports should be used.
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
show,mewTyp: no visible global function definition for 'head'
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
Packages suggested but not available for checking: 'covr', 'alfred'
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building 'mfbvar_jss.Rnw' using knitr
kpsewhich: major issue: So far, you have not checked for updates as a MiKTeX user.

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 569-576 (mfbvar_jss.Rnw) 
Error: processing vignette 'mfbvar_jss.Rnw' failed with diagnostics:
there is no package called 'alfred'
--- failed re-building 'mfbvar_jss.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'ECoL'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking:
  'tseries', 'tsDyn', 'forecast'
Package suggested but not available for checking: 'covr'
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.
Package required but not available: 'tseries'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'dataRetrieval'
Namespaces in Imports field not imported from:
  'boot' 'energy'
  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 Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'corpcor' 'evd' 'fields' 'numDeriv'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to 'RJSONIO' 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'
.onAttach: no visible binding for global variable '.MGRAST'
build.MGRAST: no visible binding for global variable '.MGRAST'
build.MGRAST: no visible global function definition for 'fromJSON'
call.MGRAST: no visible binding for global variable '.MGRAST'
call.MGRAST: no visible global function definition for 'download.file'
call.MGRAST: no visible global function definition for 'isValidJSON'
call.MGRAST: no visible global function definition for 'fromJSON'
doc.MGRAST: no visible binding for global variable '.MGRAST'
doc.MGRAST: no visible global function definition for 'str'
load.MGRAST: no visible binding for global variable '.MGRAST'
parse.MGRAST: no visible binding for global variable '.MGRAST'
this.package: no visible binding for global variable '.MGRAST'
Undefined global functions or variables:
  .MGRAST download.file fromJSON isValidJSON packageVersion str
Consider adding
  importFrom("utils", "download.file", "packageVersion", "str")
to your NAMESPACE file.
Packages suggested but not available for checking: 'covr', 'qdap'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'Safe-Censoring.Rmd' using rmarkdown
--- finished re-building 'Safe-Censoring.Rmd'

--- re-building 'Safe-Substitution.Rmd' using rmarkdown
Quitting from lines 93-94 (Safe-Substitution.Rmd) 
Error: processing vignette 'Safe-Substitution.Rmd' failed with diagnostics:
there is no package called 'qdap'
--- failed re-building 'Safe-Substitution.Rmd'

SUMMARY: processing the following file failed:
  'Safe-Substitution.Rmd'

Error: Vignette re-building failed.
Execution halted
calc_z_var: no visible binding for global variable 'median'
diffScore: no visible global function definition for 'new'
diffScore: no visible global function definition for 'model.matrix'
logNORMcdf: no visible global function definition for 'pnorm'
mGSZ.adj.mean.std: no visible binding for global variable 'sd'
pick.data.cols: no visible binding for global variable 'var'
plotProfile: no visible binding for global variable 'quantile'
plotProfile: no visible global function definition for 'lines'
plotProfile: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend lines median model.matrix new pnorm quantile sd var
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("methods", "new")
  importFrom("stats", "median", "model.matrix", "pnorm", "quantile",
             "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File
  LICENSE
is not mentioned in the DESCRIPTION file.
BCI: no visible global function definition for 'quantile'
Metro_Hastings: no visible global function definition for 'optim'
Metro_Hastings: no visible global function definition for 'runif'
Metro_Hastings: no visible global function definition for 'var'
plotMH: no visible global function definition for 'hist'
plotMH: no visible global function definition for 'frame'
plotMH: no visible global function definition for 'text'
Undefined global functions or variables:
  frame hist optim quantile runif text var
Consider adding
  importFrom("graphics", "frame", "hist", "text")
  importFrom("stats", "optim", "quantile", "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
Namespaces in Imports field not imported from:
  'MCMCpack' 'copula'
  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: 'structSSI'
'LazyData' is specified without a 'data' directory
Package required but not available: 'texreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'car'
Package unavailable to check Rd xrefs: 'car'
Running examples in 'miceadds-Ex.R' failed
The error most likely occurred in:

> ### Name: mi.anova
> ### Title: Analysis of Variance for Multiply Imputed Data Sets (Using the
> ###   D_2 Statistic)
> ### Aliases: mi.anova
> 
> ### ** Examples
> 
> #############################################################################
> # EXAMPLE 1: nhanes2 data | two-way ANOVA
> #############################################################################
> 
> library(mice)
> library(car)
Error in library(car) : there is no package called 'car'
Execution halted
Package required but not available: 'systemfit'

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

Package suggested but not available for checking: 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'systemfit'
Packages unavailable to check Rd xrefs: 'micEconAids', 'micEconSNQP'
Running 'cobbDouglasTest.R'
  Comparing 'cobbDouglasTest.Rout' to 'cobbDouglasTest.Rout.save' ... OK
  Running 'logDataSetTest.R'
  Comparing 'logDataSetTest.Rout' to 'logDataSetTest.Rout.save' ... OK
  Running 'quadFunc.R'
Running the tests in 'tests/quadFunc.R' failed.
Last 13 lines of output:
  19 0.6954 -1.4176 -0.2819    1.0042
  20 0.9640 -0.5104 -0.8462    0.3926
  > all.equal( estResultHom4ElaObs$qLabor + estResultHom4ElaObs$land +
  +    estResultHom4ElaObs$qVarInput, - estResultHom4ElaObs$time )
  [1] TRUE
  > max( abs( estResultHom4Ela - estResultHom4ElaObs ) )
  [1] 0.179
  > 
  > 
  > ################ panel data #####################
  > data( "GrunfeldGreene", package = "systemfit" )
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called 'systemfit'
  Calls: data -> find.package
  Execution halted
Package required but not available: 'systemfit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'car'
Error(s) in re-building vignettes:
  ...
--- re-building 'miceFast-intro.Rmd' using rmarkdown

Attaching package: 'mice'

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

    filter

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

    cbind, rbind

Quitting from lines 21-23 (miceFast-intro.Rmd) 
Error: processing vignette 'miceFast-intro.Rmd' failed with diagnostics:
there is no package called 'car'
--- failed re-building 'miceFast-intro.Rmd'

SUMMARY: processing the following file failed:
  'miceFast-intro.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'VIM'
Package unavailable to check Rd xrefs: 'VIM'
Package required but not available: 'sampleSelection'

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.
Note: found 9345 marked UTF-8 strings
Packages suggested but not available for checking: 'MVN', 'devtools'
Package unavailable to check Rd xrefs: 'MVN'
Running examples in 'micompr-Ex.R' failed
The error most likely occurred in:

> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
MANOVA assumptions require 'MVN' and 'biotools' packages.
Error in `*tmp*`[[i]] : subscript out of bounds
Calls: assumptions -> assumptions.cmpoutput
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   2. \-micompr:::assumptions.cmpoutput(cmp)
  -- Error (test_micomp.R:281:3): micomp assumptions have the correct properties --
  Error: subscript out of bounds
  Backtrace:
      x
   1. +-micompr::assumptions(mic1a) test_micomp.R:281:2
   2. \-micompr:::assumptions.micomp(mic1a)
   3.   \-base::lapply(obj, function(x) assumptions(x))
   4.     \-micompr:::FUN(X[[i]], ...)
   5.       +-micompr::assumptions(x)
   6.       \-micompr:::assumptions.cmpoutput(x)
  
  [ FAIL 2 | WARN 72 | SKIP 0 | PASS 291 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'paper.Rnw' using knitr
Quitting from lines 341-342 (paper.Rnw) 
Error: processing vignette 'paper.Rnw' failed with diagnostics:
subscript out of bounds
--- failed re-building 'paper.Rnw'

--- re-building 'tolatex-examples.Rnw' using knitr
Warning in wilcox.test.default(x = c(-2.17390550005803e-11, -2.17097451127302e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(2.13309370167281e-11, 2.12594386539422e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(1.99236183107132e-11, 1.97388771994156e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(1.00897068477934e-12, 1.02406971791424e-12,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(8.95727936267576e-13, 8.4909856923332e-13,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(9.80548975348938e-13, 8.81072992342524e-13,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(5.90887339058099e-11, 6.09077233093558e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(9.97119053991469e-15, 9.92695509127728e-15,  :
  cannot compute exact p-value with ties
--- finished re-building 'tolatex-examples.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'phyloseq', 'ggpubr', 'DESeq2', 'rstatix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'tibble'
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'microcontax.data'
Package unavailable to check Rd xrefs: 'microcontax.data'
'LazyData' is specified without a 'data' directory
Package required but not available: 'crul'

Package suggested but not available for checking: 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'ggpubr'
Namespaces in Imports field not imported from:
  'DT' 'ggiraph' 'ggplot2' 'grid' 'gtools' 'scales' 'shinyBS'
  'shinyWidgets' 'tidyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'devtools'

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
Namespaces in Imports field not imported from:
  'GenomicAlignments' 'R.utils' 'data.table' 'magrittr' 'tidyr'
  All declared Imports should be used.
Running examples in 'MicroSEC-Ex.R' failed
The error most likely occurred in:

> ### Name: fun_load_genome
> ### Title: Genome loading function.
> ### Aliases: fun_load_genome
> 
> ### ** Examples
> 
> fun_load_genome("Human")
Error: Install BSgenome.Hsapiens.UCSC.hg38 package.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'my-vignette.Rmd' using rmarkdown
Quitting from lines 118-178 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
Install BSgenome.Hsapiens.UCSC.hg38 package.
--- failed re-building 'my-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'usethis', 'httptest', 'plumber', 'httr'
Namespaces in Imports field not imported from:
  'config' 'desc' 'dplyr' 'glue' 'withr'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > test_check("microservices")
  == Failed tests ================================================================
  -- Error (test-endpoint-plumber-{route_name}.R:6:1): (code run outside of `test_that()`) --
  Error: there is no package called 'httr'
  Backtrace:
      x
   1. +-purrr::partial(...) test-endpoint-plumber-{route_name}.R:6:0
   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 12 ]
  Error: Test failures
  Execution halted
Packages required but not available:
  'AzureAuth', 'AzureGraph', 'curl', 'httr'

Packages suggested but not available for checking: 'blastula', 'emayili'

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

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

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: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
migration.cv.in : <anonymous>: no visible global function definition
  for 'sd'
migration.cv.out : <anonymous>: no visible global function definition
  for 'sd'
migration.field.diagram: no visible global function definition for
  'lines'
migration.field.diagram: no visible global function definition for
  'text'
migration.field.diagram: no visible global function definition for
  'polygon'
migration.field.diagram: no visible global function definition for 'lm'
migration.field.diagram: no visible global function definition for
  'predict'
migration.field.diagram: no visible global function definition for
  'points'
migration.field.diagram: no visible global function definition for
  'resid'
migration.field.diagram: no visible global function definition for
  'coef'
migration.field.diagram: no visible global function definition for
  'mtext'
migration.field.diagram: no visible global function definition for
  'density'
migration.field.diagram: no visible global function definition for
  'rug'
migration.gini.col : <anonymous>: no visible global function definition
  for 'dist'
migration.gini.in : <anonymous>: no visible global function definition
  for 'dist'
migration.gini.out : <anonymous>: no visible global function definition
  for 'dist'
migration.gini.row : <anonymous>: no visible global function definition
  for 'dist'
migration.gini.total: no visible global function definition for 'dist'
Undefined global functions or variables:
  coef density dist lines lm mtext points polygon predict resid rug sd
  text
Consider adding
  importFrom("graphics", "lines", "mtext", "points", "polygon", "rug",
             "text")
  importFrom("stats", "coef", "density", "dist", "lm", "predict",
             "resid", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
.default_model: no visible global function definition for 'is'
.guess_type: no visible global function definition for 'is.ts'
.parse_trans: no visible binding for global variable 'qnorm'
do_get_data_from_disk: no visible global function definition for
  'read.csv'
do_get_data_from_mi: no visible global function definition for 'data'
do_get_data_from_r : <anonymous>: no visible global function definition
  for 'is'
do_parametric_eval : <anonymous>: no visible global function definition
  for 'dev.off'
do_parametric_eval : <anonymous>: no visible global function definition
  for 'title'
do_var_options : varHandler2: no visible global function definition for
  'is'
do_var_options : varHandler3: no visible global function definition for
  'getClass'
do_var_options : varHandler3: no visible global function definition for
  'is'
do_var_options : changeHandler: no visible global function definition
  for 'is'
do_var_options : <anonymous>: no visible global function definition for
  'title'
do_var_options: no visible global function definition for 'getClass'
do_var_options: no visible global function definition for 'is'
helpHandler: no visible global function definition for 'browseURL'
is.method_in_mi: no visible global function definition for
  'selectMethod'
is.method_in_mi: no visible global function definition for 'signature'
Undefined global functions or variables:
  browseURL data dev.off getClass is is.ts qnorm read.csv selectMethod
  signature title
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "title")
  importFrom("methods", "getClass", "is", "selectMethod", "signature")
  importFrom("stats", "is.ts", "qnorm")
  importFrom("utils", "browseURL", "data", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
nat_hist: no visible global function definition for 'data'
nat_hist: no visible binding for global variable 'current.other'
t_mal: no visible global function definition for 'uniroot'
t_prog: no visible global function definition for 'rlnorm'
tdeath_lung: no visible global function definition for 'data'
tdeath_lung: no visible binding for global variable 'ci.lung'
tdeath_lung: no visible binding for global variable 'current.other'
tdeath_lung: no visible binding for global variable 'former.other'
tdeath_lung: no visible binding for global variable 'never.other'
tdeath_other: no visible global function definition for 'data'
tdeath_other: no visible binding for global variable 'ci.lung'
tdeath_other: no visible binding for global variable 'current.other'
tdeath_other: no visible binding for global variable 'former.other'
tdeath_other: no visible binding for global variable 'never.other'
Undefined global functions or variables:
  ci.lung current.other data former.other never.other rlnorm uniroot
Consider adding
  importFrom("stats", "rlnorm", "uniroot")
  importFrom("utils", "data")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'FactoMineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
MImix.default: no visible binding for global variable 'coef'
MImix.default: no visible binding for global variable 'vcov'
MImix.one: no visible global function definition for 'qnorm'
MImix.one: no visible global function definition for 'uniroot'
mixcdf.target: no visible global function definition for 'pnorm'
print.MImixresult: no visible global function definition for 'coef'
print.MImixresult: no visible global function definition for 'vcov'
summary.MImixresult: no visible global function definition for 'coef'
summary.MImixresult: no visible global function definition for 'vcov'
summary.MImixresult: no visible global function definition for 'qt'
Undefined global functions or variables:
  coef pnorm qnorm qt uniroot vcov
Consider adding
  importFrom("stats", "coef", "pnorm", "qnorm", "qt", "uniroot", "vcov")
to your NAMESPACE file.
Package suggested but not available for checking: 'pkgdown'
Package suggested but not available for checking: 'kableExtra'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'mimsy.Rmd' using rmarkdown
Quitting from lines 12-20 (mimsy.Rmd) 
Error: processing vignette 'mimsy.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'mimsy.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'ecospat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'qdap', 'JWileymisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
miney : plot.initial.matrix: no visible global function definition for
  'rect'
miney : plot.known.matrix: no visible global function definition for
  'rect'
miney : plot.known.matrix: no visible global function definition for
  'text'
miney: no visible global function definition for 'locator'
miney: no visible global function definition for 'rect'
miney: no visible global function definition for 'title'
Undefined global functions or variables:
  locator rect text title
Consider adding
  importFrom("graphics", "locator", "rect", "text", "title")
to your NAMESPACE file.
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'devtools', 'covr', 'testthis'

See section 'The DESCRIPTION file' 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
rminimax: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  'markdown' 'metafor'
  All declared Imports should be used.
Package required but not available: 'V8'

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
read_design: no visible global function definition for 'model.frame'
read_design: no visible global function definition for 'read.table'
read_design: no visible global function definition for 'model.matrix'
read_response: no visible global function definition for 'read.table'
update_beta: no visible global function definition for 'update'
update_beta: no visible global function definition for 'glm'
update_beta: no visible global function definition for 'poisson'
Undefined global functions or variables:
  glm model.frame model.matrix poisson read.table update
Consider adding
  importFrom("stats", "glm", "model.frame", "model.matrix", "poisson",
             "update")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
minxent.multiple: no visible global function definition for 'cov.wt'
minxent.single: no visible global function definition for 'optimize'
Undefined global functions or variables:
  cov.wt optimize
Consider adding
  importFrom("stats", "cov.wt", "optimize")
to your NAMESPACE file.
cdf.pval: no visible global function definition for 'median'
cdf.pval: no visible binding for global variable 'ecdf'
find_hits: no visible global function definition for 'na.omit'
mad.scores: no visible global function definition for 'as.formula'
mad.scores: no visible binding for global variable 'median'
mad.scores: no visible binding for global variable 'mad'
rm.outliers: no visible global function definition for 'as.formula'
rm.outliers: no visible binding for global variable 'median'
rm.outliers: no visible binding for global variable 'mad'
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.
Package suggested but not available for checking: 'tidyverse'
Error(s) in re-building vignettes:
  ...
--- re-building 'mipplot-first-steps.Rmd' using rmarkdown
Quitting from lines 35-37 (mipplot-first-steps.Rmd) 
Error: processing vignette 'mipplot-first-steps.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'mipplot-first-steps.Rmd'

SUMMARY: processing the following file failed:
  'mipplot-first-steps.Rmd'

Error: Vignette re-building failed.
Execution halted
.FCLoess: no visible global function definition for 'loess'
.FCLoessM: no visible global function definition for 'loess'
.FCLoessM: no visible global function definition for 'median'
.Import.Luminex: no visible global function definition for 'read.csv'
.Intra.Me: no visible global function definition for 'sd'
.Intra.Me: no visible global function definition for 'quantile'
.Intra.Me: no visible global function definition for 'qchisq'
.Intra.Median: no visible global function definition for 'median'
.boxplot.rtprofile: no visible global function definition for 'boxplot'
.denplot: no visible global function definition for 'density'
.denplot: no visible global function definition for 'abline'
.normalize.Luminex: no visible global function definition for 'sd'
.normalize.qrtpcr: no visible global function definition for 'density'
.validate.default: no visible global function definition for 't.test'
Undefined global functions or variables:
  abline boxplot density loess median qchisq quantile read.csv sd
  t.test
Consider adding
  importFrom("graphics", "abline", "boxplot")
  importFrom("stats", "density", "loess", "median", "qchisq", "quantile",
             "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tidyverse', 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'MiRKAT_Vignette.Rmd' using rmarkdown
This is vegan 2.5-7

Attaching package: 'propr'

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

    parallel

Quitting from lines 19-25 (MiRKAT_Vignette.Rmd) 
Error: processing vignette 'MiRKAT_Vignette.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'MiRKAT_Vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'SimDesign'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'globaltest', 'GlobalAncova'

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: 'BRugs'
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'devtools'

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

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
missForest: no visible global function definition for 'predict'
missForest: no visible global function definition for 'idiv'
missForest: no visible global function definition for 'var'
nrmse: no visible global function definition for 'var'
Undefined global functions or variables:
  idiv predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'FactoMineR'

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: 'covr'
Packages suggested but not available for checking: 'car', 'tseries'
Namespace in Imports field not imported from: 'grDevices'
  All declared Imports should be used.
'library' or 'require' call to 'CompQuadForm' which was already attached by Depends.
  Please remove these calls from your code.
linear.test: no visible global function definition for 'lm'
linear.test: no visible global function definition for 'pchisq'
linear.weight.test: no visible global function definition for 'lm'
linear.weight.test: no visible global function definition for 'dbeta'
linear.weight.test: no visible global function definition for 'pchisq'
logit.test: no visible global function definition for 'glm'
logit.test: no visible global function definition for 'binomial'
logit.test: no visible binding for global variable 'logit'
logit.test: no visible global function definition for 'pchisq'
logit.weight.test: no visible global function definition for 'glm'
logit.weight.test: no visible global function definition for 'binomial'
logit.weight.test: no visible binding for global variable 'logit'
logit.weight.test: no visible global function definition for 'dbeta'
logit.weight.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  binomial dbeta glm lm logit pchisq
Consider adding
  importFrom("stats", "binomial", "dbeta", "glm", "lm", "pchisq")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: 'quantmod'
Package suggested but not available for checking: 'animation'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'fma'
Running examples in 'mixAR-Ex.R' failed
The error most likely occurred in:

> ### Name: MixARGaussian-class
> ### Title: mixAR models with Gaussian noise components
> ### Aliases: MixARGaussian-class MixARGaussian
> ### Keywords: classes MixAR
> 
> ### ** Examples
> 
> showClass("MixARGaussian")
Class "MixARGaussian" [package "mixAR"]

Slots:
                                                             
Name:        prob      order      shift      scale     arcoef
Class:    numeric    numeric    numeric    numeric raggedCoef

Extends: "MixAR"
> 
> ## load ibm data from BJ
> ## data(ibmclose, package = "fma")
> 
> ## compute a predictive density, assuming exampleModels$WL_ibm model
> ## for the first date after the end of the data
> pdf1 <- mix_pdf(exampleModels$WL_ibm, xcond = as.numeric(fma::ibmclose))
Error in (function (cond)  : 
  error in evaluating the argument 'xcond' in selecting a method for function 'mix_pdf': there is no package called 'fma'
Calls: mix_pdf ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   4.     \-base:::withOneRestart(expr, restarts[[1L]])
   5.       \-base:::doWithOneRestart(return(expr), restart)
  -- Error (test-mix_se.R:24:5): mix_se works ------------------------------------
  Error: there is no package called 'fma'
  Backtrace:
      x
   1. +-base::diff(fma::ibmclose) test-mix_se.R:24:4
   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 3 | WARN 2 | SKIP 4 | PASS 318 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking: 'devtools', 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Package required but not available: 'phyloseq'

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 suggested but not available for checking: 'texreg'
Package unavailable to check Rd xrefs: 'texreg'
Package suggested but not available for checking: 'covr'
'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
Packages suggested but not available for checking: 'devtools', 'covr'
Packages in Depends field not imported from:
  'MASS' 'RODBC' 'tcltk' 'tcltk2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
fit.mixtNB: no visible global function definition for 'dnbinom'
fit.mixtNB: no visible global function definition for 'nlminb'
wald.test: no visible global function definition for 'pnorm'
wald.test: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  dnbinom nlminb p.adjust pnorm
Consider adding
  importFrom("stats", "dnbinom", "nlminb", "p.adjust", "pnorm")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  'ashr' 'fdrtool'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

Packages suggested but not available for checking: 'pkgdown', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
computeContourValues: no visible global function definition for
  'na.omit'
deselectNonMovementSteps : coOccurProb: no visible global function
  definition for 'dnorm'
deselectNonMovementSteps: no visible global function definition for
  'pnorm'
estVarMKDE: no visible global function definition for 'na.omit'
estVarMKDE: no visible global function definition for 'qnorm'
estVarMKDE: no visible global function definition for 'optimize'
plotMKDE: no visible global function definition for 'rainbow'
Undefined global functions or variables:
  dnorm na.omit optimize pnorm qnorm rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "dnorm", "na.omit", "optimize", "pnorm", "qnorm")
to your NAMESPACE file.
Packages suggested but not available for checking: 'covr', 'benchmarkme'
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
mkle: no visible global function definition for 'sd'
mkle: no visible global function definition for 'density'
mkle: no visible global function definition for 'optimize'
mkle.ci: no visible global function definition for 'sd'
mkle.ci: no visible binding for global variable 'var'
mkle.ci: no visible global function definition for 'quantile'
mkle.ci: no visible global function definition for 'qnorm'
opt.bw: no visible global function definition for 'sd'
opt.bw : mse: no visible global function definition for 'var'
opt.bw: no visible global function definition for 'optimize'
opt.bw: no visible global function definition for 'var'
Undefined global functions or variables:
  density optimize qnorm quantile sd var
Consider adding
  importFrom("stats", "density", "optimize", "qnorm", "quantile", "sd",
             "var")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: 'genefilter'
Package unavailable to check Rd xrefs: 'genefilter'
mkssd: no visible global function definition for 'txtProgressBar'
mkssd: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'reticulate'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'R6'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'rvest'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'DiscriMiner' 'MASS' 'caret' 'datasets' 'dplyr' 'e1071' 'klaR'
  'rhandsontable' 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'DiscriMiner' 'MASS' 'caret' 'datasets' 'dplyr' 'e1071' 'klaR'
  'rhandsontable' 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'sparklyr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Unexported objects imported by ':::' calls:
  'MASS:::lda.default' 'MASS:::qda.default'
  'e1071:::naiveBayes.default' 'e1071:::svm.default'
  'randomForest:::randomForest.default'
  See the note in ?`:::` about the use of this operator.
confusionBarplot: no visible global function definition for 'par'
confusionBarplot: no visible global function definition for 'barplot'
confusionBarplot: no visible global function definition for 'lines'
confusionBarplot: no visible global function definition for 'text'
confusionBarplot: no visible global function definition for 'legend'
confusionBarplot: no visible global function definition for 'axis'
confusionImage: no visible global function definition for 'par'
confusionImage: no visible global function definition for 'image'
confusionImage: no visible global function definition for 'text'
confusionImage: no visible global function definition for 'abline'
confusionImage: no visible global function definition for 'axis'
confusionImage: no visible global function definition for 'mtext'
confusionStars: no visible global function definition for 'par'
confusionStars: no visible global function definition for 'stars'
confusionStars: no visible global function definition for 'rect'
Undefined global functions or variables:
  abline axis barplot image legend lines mtext par rect stars text
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "image", "legend",
             "lines", "mtext", "par", "rect", "stars", "text")
to your NAMESPACE file.
plotCDF1: no visible global function definition for 'lines'
plotCDF2: no visible global function definition for 'gray'
plotCDF2: no visible global function definition for 'image'
plotCDF2: no visible global function definition for 'box'
plotCDF2: no visible global function definition for 'par'
plotCDF2: no visible global function definition for 'rect'
plotCDF2: no visible global function definition for 'text'
plotCM: no visible global function definition for 'image'
plotCM: no visible global function definition for 'axis'
plotCM: no visible global function definition for 'box'
plotDens1: no visible global function definition for 'lines'
plotDens2: no visible global function definition for 'gray'
plotDens2: no visible global function definition for 'rect'
plotDens2: no visible global function definition for 'axis'
plotDens2: no visible global function definition for 'text'
plotHM: no visible global function definition for 'terrain.colors'
plotHM: no visible global function definition for 'image'
plotHM: no visible global function definition for 'box'
plotHM: no visible global function definition for 'abline'
plotHM: no visible global function definition for 'text'
plotHM: no visible global function definition for 'par'
plotHM: no visible global function definition for 'rect'
plotRects: no visible global function definition for 'rainbow'
plotRects: no visible global function definition for 'abline'
plotRects: no visible global function definition for 'rect'
Undefined global functions or variables:
  abline axis box gray image lines par rainbow rect terrain.colors text
Consider adding
  importFrom("grDevices", "gray", "rainbow", "terrain.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "lines",
             "par", "rect", "text")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
dftest: no visible global function definition for 'slot'
mctest: no visible global function definition for 'rnorm'
mleurDiag: no visible global function definition for 'acf'
mleurDiag: no visible global function definition for 'pchisq'
mleurDiag: no visible global function definition for 'par'
mleurDiag: no visible global function definition for 'boxplot'
mleurDiag: no visible global function definition for 'shapiroTest'
mleurDiag: no visible global function definition for 'title'
mleurDiag: no visible global function definition for 'abline'
mleurDiag: no visible global function definition for 'lines'
simar1: no visible global function definition for 'rnorm'
simar1: no visible global function definition for 'rt'
simar1: no visible global function definition for 'convolve'
Undefined global functions or variables:
  abline acf boxplot convolve lines par pchisq rnorm rt shapiroTest
  slot title
Consider adding
  importFrom("graphics", "abline", "boxplot", "lines", "par", "title")
  importFrom("methods", "slot")
  importFrom("stats", "acf", "convolve", "pchisq", "rnorm", "rt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'covr', 'lintr', 'mleap', 'sparklyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages in Depends field not imported from:
  'methods' 'seqinr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CheckStability: no visible global function definition for 'cor'
CheckStability: no visible global function definition for 'var'
PriorNormPCA: no visible global function definition for 'barplot'
SortModes: no visible global function definition for 'rnorm'
mlicaMAIN: no visible global function definition for 'runif'
Undefined global functions or variables:
  barplot cor rnorm runif var
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "cor", "rnorm", "runif", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'nlme'
  All declared Imports should be used.
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'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
Packages suggested but not available for checking:
  'minfi', 'GEOquery', 'IlluminaHumanMethylation450kmanifest'
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  'BMA' 'abind' 'maxLik'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages suggested but not available for checking: 'car', 'AER', 'texreg'
Running examples in 'mlogit-Ex.R' failed
The error most likely occurred in:

> ### Name: hmftest
> ### Title: Hausman-McFadden Test
> ### Aliases: hmftest hmftest.formula hmftest.mlogit
> ### Keywords: htest
> 
> ### ** Examples
> 
> 
> ## from Greene's Econometric Analysis p. 731
> 
> data("TravelMode", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'AER'
Calls: data -> find.package
Execution halted
Running 'AER.R'
Running the tests in 'tests/AER.R' failed.
Last 13 lines of output:
  > 
  > library("lmtest")
  Loading required package: zoo
  
  Attaching package: 'zoo'
  
  The following objects are masked from 'package:base':
  
      as.Date, as.Date.numeric
  
  > data("BankWages", package = "AER")
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called 'AER'
  Calls: data -> find.package
  Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'caret' 'randomForest'
  All declared Imports should be used.
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'bestNormalize'
Package unavailable to check Rd xrefs: 'bestNormalize'
'LazyData' is specified without a 'data' directory
Running examples in 'mlr3pipelines-Ex.R' failed
The error most likely occurred in:

> ### Name: mlr_pipeops_boxcox
> ### Title: Box-Cox Transformation of Numeric Features
> ### Aliases: mlr_pipeops_boxcox PipeOpBoxCox
> 
> ### ** Examples
> 
> library("mlr3")
> 
> task = tsk("iris")
> pop = po("boxcox")
> 
> task$data()
       Species Petal.Length Petal.Width Sepal.Length Sepal.Width
  1:    setosa          1.4         0.2          5.1         3.5
  2:    setosa          1.4         0.2          4.9         3.0
  3:    setosa          1.3         0.2          4.7         3.2
  4:    setosa          1.5         0.2          4.6         3.1
  5:    setosa          1.4         0.2          5.0         3.6
 ---                                                            
146: virginica          5.2         2.3          6.7         3.0
147: virginica          5.0         1.9          6.3         2.5
148: virginica          5.2         2.0          6.5         3.0
149: virginica          5.4         2.3          6.2         3.4
150: virginica          5.1         1.8          5.9         3.0
> pop$train(list(task))[[1]]$data()
Error: The following packages could not be loaded: bestNormalize
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   2.   \-po$train(inputs) C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\mlr3pipelines\mlr3pipelines.Rcheck\tests\testthat\helper_functions.R:423:2
   3.     \-mlr3pipelines:::.__PipeOp__train(...)
   4.       \-mlr3misc::require_namespaces(self$packages)
  -- Error (test_pipeop_yeojohnson.R:17:3): PipeOpYeoJohnson - receive expected result --
  Error: The following packages could not be loaded: bestNormalize
  Backtrace:
      x
   1. \-mlr3pipelines:::train_pipeop(op, inputs = list(task))
   2.   \-po$train(inputs) C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\mlr3pipelines\mlr3pipelines.Rcheck\tests\testthat\helper_functions.R:423:2
   3.     \-mlr3pipelines:::.__PipeOp__train(...)
   4.       \-mlr3misc::require_namespaces(self$packages)
  
  [ FAIL 2 | WARN 43 | SKIP 78 | PASS 9843 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'mlr3extralearners'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'shinytest', 'devtools'
Namespaces in Imports field not imported from:
  'DT' 'data.table' 'e1071' 'mlr3' 'mlr3learners' 'mlr3measures' 'plyr'
  'purrr' 'ranger' 'readxl' 'shinyWidgets' 'shinyalert'
  'shinydashboard' 'shinyjs' 'shinythemes' 'stats' 'stringr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mlr3shiny)
  > library(shinytest)
  Error in library(shinytest) : there is no package called 'shinytest'
  Execution halted
Package suggested but not available for checking: 'plotly'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   7.       \-base:::doWithOneRestart(return(expr), restart)
  -- Error (test-1-autoplot.R:405:3): autoplot time + space ----------------------
  Error: there is no package called 'plotly'
  Backtrace:
      x
   1. +-ggplot2::autoplot(...)
   2. +-mlr3spatiotempcv:::autoplot.ResamplingSptCVCstf(...)
   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 3 | WARN 4 | SKIP 28 | PASS 227 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'factoextra'
Package unavailable to check Rd xrefs: 'factoextra'
'LazyData' is specified without a 'data' directory
Running examples in 'mlr3viz-Ex.R' failed
The error most likely occurred in:

> ### Name: autoplot.LearnerClustHierarchical
> ### Title: Plot for Hierarchical Clustering Learners
> ### Aliases: autoplot.LearnerClustHierarchical
> 
> ### ** Examples
> 
> library(mlr3)
> library(mlr3cluster)
> library(mlr3viz)
> 
> task = mlr_tasks$get("usarrests")
> 
> # agnes clustering
> learner = mlr_learners$get("clust.agnes")
> learner$train(task)
> autoplot(learner)
Error: The following packages could not be loaded: factoextra
Execution halted
Package suggested but not available for checking: 'lintr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'cmaesr', 'smoof', 'mlrMBO'
Package unavailable to check Rd xrefs: 'mlrMBO'
'LazyData' is specified without a 'data' directory
Running examples in 'mlrintermbo-Ex.R' failed
The error most likely occurred in:

> ### Name: OptimizerInterMBO
> ### Title: Tuner and Optimizer using mlrMBO
> ### Aliases: OptimizerInterMBO mlr_optimizers_intermbo mlr_tuners_intermbo
> ###   TunerInterMBO
> 
> ### ** Examples
> 
> library("paradox")
> library("bbotk")
> 
> # silly example function: minimize x^2 for -1 < x < 1
> domain <- ParamSet$new(list(ParamDbl$new("x", lower = -1, upper = 1)))
> codomain <- ParamSet$new(list(ParamDbl$new("y", tags = "minimize")))
> objective <- ObjectiveRFun$new(function(xs) list(y = xs$x^2), domain, codomain)
> 
> # initialize instance
> instance <- OptimInstanceSingleCrit$new(objective, domain, trm("evals", n_evals = 6))
> 
> # use intermbo optimizer
> optser <- opt("intermbo")
> 
> # optimizer has hyperparameters from mlrMBO
> optser$param_set$values$final.method <- "best.predicted"
> 
> # optimization happens here.
> optser$optimize(instance)
INFO  [10:08:38.851] [bbotk] Starting to optimize 1 parameter(s) with '<OptimizerInterMBO>' and '<TerminatorEvals> [n_evals=6]' 
INFO  [10:08:43.240] [bbotk] Evaluating 4 configuration(s) 
INFO  [10:08:43.283] [bbotk] Result of batch 1: 
INFO  [10:08:43.290] [bbotk]           x          y 
INFO  [10:08:43.290] [bbotk]   0.7410401 0.54914037 
INFO  [10:08:43.290] [bbotk]  -0.2002171 0.04008688 
INFO  [10:08:43.290] [bbotk]   0.2467707 0.06089576 
INFO  [10:08:43.290] [bbotk]  -0.9068912 0.82245165 
Error in encall(self$r.session, vals, n.objectives, still.needs.proposition,  : 
  callr subprocess failed: there is no package called 'mlrMBO'
Calls: <Anonymous> ... <Anonymous> -> .__OptimizerInterMBO__.optimize -> encall
Execution halted
Running 'run.R'
Running the tests in 'tests/run.R' failed.
Last 13 lines of output:
    1. \-mlrintermbo:::eval_mbo(list()) test_mbo.R:63:2
    2.   \-tuner$optimize(ti) test_mbo.R:59:4
    3.     \-bbotk:::.__Optimizer__optimize(...)
    4.       \-bbotk::optimize_default(inst, self, private)
    5.         +-base::tryCatch(...)
    6.         | \-base:::tryCatchList(expr, classes, parentenv, handlers)
    7.         |   \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
    8.         |     \-base:::doTryCatch(return(expr), name, parentenv, handler)
    9.         \-private$.optimize(inst)
   10.           \-mlrintermbo:::.__OptimizerInterMBO__.optimize(...)
   11.             \-mlrintermbo:::encall(...)
  
  [ FAIL 2 | WARN 0 | SKIP 5 | PASS 0 ]
  Error: Test failures
  Execution halted
Package required but not available: 'smoof'

Packages suggested but not available for checking: 'cmaesr', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'forecast', 'ggpubr', 'lintr', 'mlrMBO', 'rrlda', 'smoof',
  'tsfeatures'
Packages unavailable to check Rd xrefs: 'mlrMBO', 'tsfeatures'
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.
Package suggested but not available for checking: 'AER'
'LazyData' is specified without a 'data' directory
Package required but not available: 'MplusAutomation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Error(s) in re-building vignettes:
  ...
--- re-building 'MM2Sdata.Rnw' using knitr
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "MM2Sdata.tex" --max-iterations=20 -I "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/rinst/share/texmf/tex/latex" -I "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/rinst/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'MM2Sdata.Rnw' failed with diagnostics:
running 'texi2dvi' on 'MM2Sdata.tex' failed

LaTeX errors:
.Rcheck/vign_test/MM2Sdata/vignettes/MM2Sdata.tex:153: pdfTeX error (font expan
sion): auto expansion is only possible with scalable fonts.
<argument> ...shipout:D \box_use:N \l_shipout_box 
                                                  
l.153 ... 'citation("{}pkgname"{})'.}}\end{kframe}
.Rcheck/vign_test/MM2Sdata/vignettes/MM2Sdata.tex:153:  ==> Fatal error occurre
d, no output PDF file produced!

--- failed re-building 'MM2Sdata.Rnw'

SUMMARY: processing the following file failed:
  'MM2Sdata.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'GSVA'

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

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

Packages suggested but not available for checking:
  'devtools', 'usethis', 'shinytest'

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 suggested but not available for checking:
  'devtools', 'covr', 'ggpubr'
Namespaces in Imports field not imported from:
  'datasets' 'doParallel' 'parallel'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'Cluster-Analysis.rmd' using rmarkdown
Quitting from lines 26-95 (Cluster-Analysis.rmd) 
Error: processing vignette 'Cluster-Analysis.rmd' failed with diagnostics:
there is no package called 'ggpubr'
--- failed re-building 'Cluster-Analysis.rmd'

SUMMARY: processing the following file failed:
  'Cluster-Analysis.rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
mmm2: no visible global function definition for 'model.frame'
mmm2: no visible global function definition for 'model.matrix'
mmm2: no visible global function definition for 'model.response'
mmm2: no visible global function definition for 'as.formula'
Undefined global functions or variables:
  as.formula model.frame model.matrix model.response
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
get.score: no visible global function definition for 'sd'
get.score: no visible global function definition for 'coef'
get.score: no visible global function definition for 'as'
get.score.main: no visible global function definition for 'sd'
get.score.main: no visible global function definition for 'coef'
get.subgroup: no visible global function definition for 'sd'
sample.tte: no visible global function definition for 'runif'
Undefined global functions or variables:
  as coef runif sd
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "coef", "runif", "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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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: 'aMNLFA'
Namespaces in Imports field not imported from:
  'caret' 'datasets' 'e1071' 'nnet' 'shiny' 'stats'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Flury'
'LazyData' is specified without a 'data' directory
Package required but not available: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'sads'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'curl'
Running examples in 'mockthat-Ex.R' failed
The error most likely occurred in:

> ### Name: mock
> ### Title: Mocking helper functions
> ### Aliases: mock mock_call mock_args mock_arg mock_n_called
> 
> ### ** Examples
> 
> url <- "https://eu.httpbin.org/get?foo=123"
> 
> mk <- mock("mocked request")
> dl <- function(x) curl::curl(x)
> 
> with_mock(`curl::curl` = mk, dl(url))
Error in loadNamespace(name) : there is no package called 'curl'
Calls: with_mock ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    3. \-mockthat::with_mock(...)
    4.   \-mockthat:::extract_mocks(mfuns, env = mock_env)
    5.     \-base::Map(extract_mock, names(funs), funs, MoreArgs = list(env = env))
    6.       \-base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
    7.         \-(function (fun_name, new_val, env) ...
    8.           \-base::asNamespace(pkg_name)
    9.             \-base::getNamespace(ns)
   10.               \-base::loadNamespace(name)
   11.                 \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   12.                   \-base:::withOneRestart(expr, restarts[[1L]])
   13.                     \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 11 | WARN 1 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'highcharter', '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
Packages suggested but not available for checking: 'brms', 'rstanarm'
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
Package required but not available: '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: 'covr'
Note: found 12 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
Packages required but not available: 'kableExtra', 'archivist', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'SparseM' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'glmnet' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  'ggplot2' 'lattice'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
Note: found 18 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'modelplotr.Rmd' using rmarkdown
Quitting from lines 13-19 (modelplotr.Rmd) 
Error: processing vignette 'modelplotr.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'modelplotr.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
Package unavailable to check Rd xrefs: 'rstanarm'
Package required but not available: 'kableExtra'

Packages suggested but not available for checking: 'AER', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Packages required but not available:
  'modeltime', 'modeltime.resample', 'timetk'

Packages suggested but not available for checking:
  'tidyverse', 'covr', 'qpdf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'modeltime', 'timetk'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'modeltime', 'timetk'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'timetk', 'plotly', 'forecast', 'prophet'

Packages suggested but not available for checking:
  'rstan', 'tidyverse', 'tidyquant', 'qpdf', 'covr'

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

Packages suggested but not available for checking:
  'tidyverse', 'tidyquant', 'covr'

See section 'The DESCRIPTION file' 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
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'library' or 'require' calls to packages already attached by Depends:
  'date' 'raster' 'rgdal' 'sfsmisc'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'date' 'raster' 'rgdal' 'sfsmisc' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages required but not available: 'curl', 'devtools'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'geojsonio', 'httr'

Packages suggested but not available for checking:
  'geojsonlint', 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'AER'
Package unavailable to check Rd xrefs: 'AER'
Running examples in 'modmarg-Ex.R' failed
The error most likely occurred in:

> ### Name: marg.ivreg
> ### Title: Predicted Margins for 'ivreg' objects from the 'AER' package
> ### Aliases: marg.ivreg
> 
> ### ** Examples
> 
> # From ?AER::ivreg
> 
> # data
> data("CigarettesSW", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'AER'
Calls: data -> find.package
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   2.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     \-base:::withOneRestart(expr, restarts[[1L]])
   4.       \-base:::doWithOneRestart(return(expr), restart)
  -- Error (test_ivreg.R:416:3): P values are calculated correctly ---------------
  Error: there is no package called 'AER'
  Backtrace:
      x
   1. \-base::loadNamespace(x) test_ivreg.R:416:2
   2.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     \-base:::withOneRestart(expr, restarts[[1L]])
   4.       \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 8 | WARN 26 | SKIP 0 | PASS 195 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
       x
    1. +-testthat::expect_s3_class(mod::as_module("covr"), "module") test-utils.R:2:8
    2. | \-testthat::quasi_label(enquo(object), arg = "object")
    3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
    4. \-mod::as_module("covr")
    5.   \-base::asNamespace(package, base.OK = FALSE)
    6.     \-base::getNamespace(ns)
    7.       \-base::loadNamespace(name)
    8.         \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
    9.           \-base:::withOneRestart(expr, restarts[[1L]])
   10.             \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 25 ]
  Error: Test failures
  Execution halted
Note: found 20506 marked Latin-1 strings
  Note: found 72 marked UTF-8 strings
.clustOrder: no visible global function definition for 'hclust'
.clustOrder: no visible global function definition for 'as.dist'
consensusMEDissimilarity: no visible global function definition for
  'cor'
mergeCloseModules: no visible global function definition for 'cor'
mergeCloseModules: no visible global function definition for 'hclust'
mergeCloseModules: no visible global function definition for 'as.dist'
moduleEigengenes: no visible global function definition for 'cor'
moduleEigengenes: no visible global function definition for 'cov'
moduleNumber: no visible global function definition for 'cutree'
orderMEs: no visible global function definition for 'cor'
orderMEs: no visible global function definition for 'as.dist'
plotHclustColors: no visible global function definition for 'barplot'
plotHclustColors: no visible global function definition for 'strwidth'
plotHclustColors: no visible global function definition for 'rect'
plotHclustColors: no visible global function definition for 'text'
plotHclustColors: no visible global function definition for 'lines'
Undefined global functions or variables:
  as.dist barplot cor cov cutree hclust lines rect strwidth text
Consider adding
  importFrom("graphics", "barplot", "lines", "rect", "strwidth", "text")
  importFrom("stats", "as.dist", "cor", "cov", "cutree", "hclust")
to your NAMESPACE file.
Packages suggested but not available for checking: 'devtools', 'lintr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'smoof', 'pkgdown'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'Basic_Usage.Rmd' using rmarkdown
Quitting from lines 106-114 (Basic_Usage.Rmd) 
Error: processing vignette 'Basic_Usage.Rmd' failed with diagnostics:
there is no package called 'smoof'
--- failed re-building 'Basic_Usage.Rmd'

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

--- re-building 'Modification_Usage.Rmd' using rmarkdown
Quitting from lines 70-94 (Modification_Usage.Rmd) 
Error: processing vignette 'Modification_Usage.Rmd' failed with diagnostics:
there is no package called 'smoof'
--- failed re-building 'Modification_Usage.Rmd'

--- re-building 'problem-definition.Rmd' using rmarkdown
--- finished re-building 'problem-definition.Rmd'

--- re-building 'writing-functions-for-moeadr.Rmd' using rmarkdown
--- finished re-building 'writing-functions-for-moeadr.Rmd'

SUMMARY: processing the following files failed:
  'Basic_Usage.Rmd' 'Modification_Usage.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'httr', 'aws.iam', 'aws.s3', 'MolgenisAuth', 'arrow'

Package suggested but not available for checking: 'DSMolgenisArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

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: 'texreg'
agostino.test: no visible global function definition for
  'complete.cases'
agostino.test: no visible global function definition for 'pnorm'
anscombe.test: no visible global function definition for
  'complete.cases'
anscombe.test: no visible global function definition for 'pnorm'
bonett.test: no visible global function definition for 'complete.cases'
bonett.test: no visible global function definition for 'pnorm'
jarque.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  complete.cases pchisq pnorm
Consider adding
  importFrom("stats", "complete.cases", "pchisq", "pnorm")
to your NAMESPACE file.
Packages required but not available: 'crawl', 'car'

Packages suggested but not available for checking: 'ggmap', 'moveHMM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'devtools', 'covr'
Note: found 16 marked UTF-8 strings
'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
Package suggested but not available for checking: 'covr'
Package required but not available: 'taxize'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'here'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ztable'
  All declared Imports should be used.
Note: found 13 marked UTF-8 strings
mopsocd : initialize_pop: no visible global function definition for
  'runif'
mopsocd : compute_velocity: no visible global function definition for
  'runif'
mopsocd : mutate: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
checkTH: no visible global function definition for 'pchisq'
getOrderPval: 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
ametrine : <anonymous>: no visible global function definition for
  'approx'
ametrine: no visible global function definition for 'rgb'
isolum : <anonymous>: no visible global function definition for
  'approx'
isolum: no visible global function definition for 'rgb'
morgenstemning : <anonymous>: no visible global function definition for
  'approx'
morgenstemning: 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
Package suggested but not available for checking: 'devtools'
Package suggested but not available for checking: 'car'
Malformed Title field: should not end in a period.
cor.gen: no visible global function definition for 'rnorm'
cor.gen: no visible global function definition for 'resid'
cor.gen: no visible global function definition for 'lm'
cor.gen: no visible binding for global variable 'sd'
cor.gen: no visible global function definition for 'cor'
cor.gen: no visible global function definition for 'write.table'
stat.gen: no visible global function definition for 'rexp'
stat.gen: no visible global function definition for 'rnorm'
stat.gen: no visible binding for global variable 'sd'
stat.gen: no visible global function definition for 'write.table'
Undefined global functions or variables:
  cor lm resid rexp rnorm sd write.table
Consider adding
  importFrom("stats", "cor", "lm", "resid", "rexp", "rnorm", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package required but not available: 'forecast'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyverse'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'ggformula' 'magrittr' 'rlang'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'ggridges' 'ggstance'
  All declared Imports should be used.
Packages required but not available: 'ecr', 'smoof'

Package suggested but not available for checking: 'mlrMBO'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'NlcOptim'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'annotate'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'ez'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'pkgdown'
getmouseDV: no visible global function definition for 'tail'
interpltraj: no visible global function definition for 'approx'
trim1: no visible global function definition for 'tail'
Undefined global functions or variables:
  approx tail
Consider adding
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
Package required but not available: 'elevatr'

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.
Package required but not available: 'httr'

Package suggested but not available for checking: 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'move', 'curl', 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'move'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'corpus.useR.2008.abstracts'
Package suggested but not available for checking: 'CGHcall'
Malformed Description field: should contain one or more complete sentences.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'mpa/R/zzz.R':
  .First.lib calls:
    cat("\n mpa: CoWords Method")
    cat("\n ")
    cat("\n Universidad Nacional de Colombia")
    cat("\n ")
    cat("\n Elaborado por: Daniel Rodriguez <dhrodriguezt@unal.edu.co>")
    cat("\n                Campo Elias Pardo <cepardot@unal.edu.co>")
    cat("\n For help: ?mpa   \n\n")

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

diagram.mpa: no visible global function definition for 'abline'
diagram.mpa: no visible global function definition for 'text'
Undefined global functions or variables:
  abline text
Consider adding
  importFrom("graphics", "abline", "text")
to your NAMESPACE file.
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required but not available: 'ggpubr'

Packages suggested but not available for checking:
  'covr', 'tidyverse', 'modelsummary'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
mpcv: no visible binding for global variable 'median'
mpcv: no visible global function definition for 'cov'
mpcv: no visible global function definition for 'dist'
plot.mpcv: no visible binding for global variable 'median'
plot.mpcv: no visible global function definition for 'par'
plot.mpcv: no visible global function definition for 'rect'
plot.mpcv: no visible global function definition for 'lines'
plot.mpcv: no visible global function definition for 'points'
plot.mpcv: no visible global function definition for 'legend'
Undefined global functions or variables:
  cov dist legend lines median par points rect
Consider adding
  importFrom("graphics", "legend", "lines", "par", "points", "rect")
  importFrom("stats", "cov", "dist", "median")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
GetExampleData: no visible binding for global variable 'MPINetData'
Getenvir: no visible binding for global variable 'MPINetData'
getPSS: no visible global function definition for 'lines'
performpcls: no visible global function definition for 'binomial'
Undefined global functions or variables:
  MPINetData binomial lines
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "binomial")
to your NAMESPACE file.
Package suggested but not available for checking: 'matlib'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'mvoutlier'
Package required but not available: 'texreg'

Package suggested but not available for checking: 'rhdf5'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'MplusAutomation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'KernSmooth' 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of 'imag' to
  'imaginary'
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of 'imag' to
  'imaginary'
.onAttach: no visible global function definition for
  'packageDescription'
export.summary.mpm: no visible global function definition for
  'write.table'
mpm: no visible binding for global variable 'median'
plot.mpm: no visible global function definition for 'rainbow'
plot.mpm: no visible global function definition for 'quantile'
plot.mpm: no visible global function definition for 'par'
plot.mpm: no visible global function definition for 'points'
plot.mpm: no visible global function definition for 'smoothScatter'
plot.mpm: no visible global function definition for 'colorRampPalette'
plot.mpm: no visible global function definition for 'symbols'
plot.mpm: no visible global function definition for 'text'
plot.mpm: no visible global function definition for 'lines'
plot.mpm: no visible global function definition for 'box'
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
place: no visible global function definition for 'points'
plot,mproc: no visible binding for global variable 'rainbow'
plot,mproc: no visible global function definition for 'plot.default'
plot,mproc: no visible global function definition for 'axis'
plot,mproc: no visible global function definition for 'points'
Undefined global functions or variables:
  axis plot.default points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "plot.default", "points")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'animation'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ppersp: no visible global function definition for 'colorRampPalette'
Undefined global functions or variables:
  colorRampPalette
Consider adding
  importFrom("grDevices", "colorRampPalette")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: 'rstan'

Packages suggested but not available for checking:
  'tidyverse', 'kableExtra', 'MendelianRandomization'

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: 'covr'
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'geojsonio', 'rmapshaper'

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.
densityfn: no visible global function definition for 'dnbinom'
densityfn: no visible global function definition for 'dpois'
densityfn: no visible global function definition for 'dgeom'
form.add: no visible global function definition for 'formula'
mreg: no visible global function definition for 'model.frame'
mreg: no visible global function definition for 'model.response'
mreg: no visible global function definition for 'model.matrix'
mreg: no visible global function definition for 'model.offset'
mreg: no visible global function definition for 'nlm'
paper: no visible global function definition for 'model.matrix'
randfn: no visible global function definition for 'rnbinom'
randfn: no visible global function definition for 'rpois'
randfn: no visible global function definition for 'rgeom'
randfn: no visible global function definition for 'rbinom'
summary.mreg: no visible global function definition for 'pnorm'
summary.mreg: no visible global function definition for 'printCoefmat'
Undefined global functions or variables:
  dgeom dnbinom dpois formula model.frame model.matrix model.offset
  model.response nlm pnorm printCoefmat rbinom rgeom rnbinom rpois
Consider adding
  importFrom("stats", "dgeom", "dnbinom", "dpois", "formula",
             "model.frame", "model.matrix", "model.offset",
             "model.response", "nlm", "pnorm", "printCoefmat", "rbinom",
             "rgeom", "rnbinom", "rpois")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
'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: 'Rgraphviz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'rstan'
Package unavailable to check Rd xrefs: 'rstan'
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  'mvtnorm' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MRsurvival: no visible global function definition for 'rmvnorm'
MRsurvival: no visible global function definition for 'optim'
MRsurvival : <anonymous>: no visible global function definition for
  'quantile'
Undefined global functions or variables:
  optim quantile rmvnorm
Consider adding
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
msap: no visible global function definition for 'packageVersion'
msap: no visible global function definition for 'read.csv'
msap: no visible global function definition for 'write.csv'
msap: no visible global function definition for 'sd'
msap: no visible global function definition for 'wilcox.test'
msap: no visible global function definition for 'dist'
msap: no visible global function definition for 'rainbow'
msap: no visible global function definition for 'png'
msap: no visible global function definition for 'legend'
msap: no visible global function definition for 'dev.off'
pcoa: no visible global function definition for 'cmdscale'
pcoa: no visible global function definition for 'png'
pcoa: no visible global function definition for 'par'
pcoa: no visible global function definition for 'rainbow'
pcoa: no visible global function definition for 'points'
pcoa: no visible global function definition for 'dev.off'
pcoa: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  cmdscale dev.off dist legend packageVersion par png points rainbow
  read.csv sd wilcox.test write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow")
  importFrom("graphics", "legend", "par", "points")
  importFrom("stats", "cmdscale", "dist", "sd", "wilcox.test")
  importFrom("utils", "packageVersion", "read.csv", "write.csv")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: '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
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'mscsweblm4r'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking: 'covr', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Package suggested but not available for checking: 'mscstexta4r'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
cv.msda: no visible global function definition for 'predict'
formatoutput: no visible global function definition for 'new'
msda.prep: no visible global function definition for 'cov'
plot.msda: no visible global function definition for 'par'
plot.msda: no visible global function definition for 'matplot'
plot.msda: no visible global function definition for 'rainbow'
plot.msda: no visible global function definition for 'approx'
plot.msda: no visible global function definition for 'axis'
predict.msda: no visible binding for global variable 'sd'
predict.msda: no visible global function definition for 'predict'
zeromat: no visible global function definition for 'new'
Undefined global functions or variables:
  approx axis cov matplot new par predict rainbow sd
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "matplot", "par")
  importFrom("methods", "new")
  importFrom("stats", "approx", "cov", "predict", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Namespaces in Imports field not imported from:
  'MASS' 'moments' 'mvtnorm'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'covr', 'devtools', 'kableExtra', 'r4ss', 'rfishbase'
Package unavailable to check Rd xrefs: 'r4ss'
Running examples in 'MSEtool-Ex.R' failed
The error most likely occurred in:

> ### Name: LH2OM
> ### Title: Predict missing life-history parameters
> ### Aliases: LH2OM predictLH
> 
> ### ** Examples
> 
> myOM<-LH2OM(MSEtool::testOM)
Predicting L50 from Linf 

Predicting K from M 

Error: Package "rfishbase" needed for this function to work. Please install it.
Execution halted
Packages required but not available: 'nnfor', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'animation'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'tidyselect'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ranger'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'forecast', 'Rssa', 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'usethis'
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyverse'
Namespace in Imports field not imported from: '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
Package suggested but not available for checking: 'Rgraphviz'
BS.var: no visible binding for global variable 'var'
BS.var: no visible global function definition for 'cov'
Dist.CIs: no visible global function definition for 'qnorm'
MSM.CIs: no visible global function definition for 'qnorm'
plot,msSurv-missing: no visible global function definition for 'update'
summary,msSurv: no visible global function definition for 'quantile'
Undefined global functions or variables:
  cov qnorm quantile update var
Consider adding
  importFrom("stats", "cov", "qnorm", "quantile", "update", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'crul'

Package suggested but not available for checking: 'httptest'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'car'
'LazyData' is specified without a 'data' directory
Running examples in 'mthapower-Ex.R' failed
The error most likely occurred in:

> ### Name: mthapower
> ### Title: Power calculations - mtDNA haplogroups
> ### Aliases: mthapower
> 
> ### ** Examples
> 
> # Example 1:
> pow <- mthapower(n.cases=203, p0=0.443, Nh=13, OR.cas.ctrl=2.33, sig.level=0.05)
> 
> # Example 2:
> # Create data frames
> pow.H150 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.5, sig.level=0.05)
> pow.H175 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.75, sig.level=0.05)
> pow.H200 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2, sig.level=0.05)
> pow.H250 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2.5, sig.level=0.05)
> 
> # Bind the three data frames:
> bindata <- rbind(pow.H150,pow.H175,pow.H200,pow.H250)
> # Adds column OR to binded data frame:
> bindata$OR <- rep(factor(c(1.50,1.75,2,2.5)),
+               times = c(nrow(pow.H150),
+                         nrow(pow.H175),
+                         nrow(pow.H200),
+                         nrow(pow.H250)))
> # Create plot:
> # install.packages("car")
> library(car)
Error in library(car) : there is no package called 'car'
Execution halted
'library' or 'require' call to 'MASS' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Designer.sobol: no visible global function definition for 'runif'
basicMonteCarlo: no visible global function definition for 'runif'
lhs003: no visible global function definition for 'runif'
plmm.mtk : GenereXplmm: no visible binding for global variable 'poly'
plmm.mtk : calc.plm: no visible global function definition for 'lm.fit'
plmm.mtk: no visible global function definition for 'var'
plmm.mtk: no visible global function definition for 'lm'
plmm.mtk: no visible global function definition for 'formula'
plmm.mtk: no visible global function definition for 'update'
plmm.mtk: no visible global function definition for 'stepAIC'
plot.plmm: no visible global function definition for 'par'
plot.plmm: no visible global function definition for 'barplot'
plot.plmm: no visible global function definition for 'segments'
plot.plmm: no visible global function definition for 'abline'
plot.plmm: no visible global function definition for 'title'
plot.plmm: no visible global function definition for 'legend'
plot.regressionSI: no visible global function definition for 'par'
plot.regressionSI: no visible global function definition for 'title'
plot.regressionSI: no visible global function definition for 'abline'
plot,mtkProcess: no visible global function definition for 'dev.new'
Undefined global functions or variables:
  abline barplot dev.new formula legend lm lm.fit par poly runif
  segments stepAIC title update var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "par",
             "segments", "title")
  importFrom("stats", "formula", "lm", "lm.fit", "poly", "runif",
             "update", "var")
to your NAMESPACE file.
Note: found 2 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'magick'

Package suggested but not available for checking: 'shinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'Matrix' 'capushe' 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2632 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'ggplot2'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  'DiceKriging' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CrossValidationMuFicokm: no visible global function definition for
  'covMatrix'
CrossValidationMuFicokmAll: no visible global function definition for
  'covMatrix'
MuFicokm: no visible global function definition for 'km'
compute.beta.hat: no visible global function definition for 'lm'
computeAuxVariables: no visible global function definition for
  'covMatrix'
kmCok: no visible global function definition for 'new'
kmCok: no visible global function definition for 'drop.response'
kmCok: no visible global function definition for 'model.matrix'
kmCok: no visible global function definition for 'covStruct.create'
kmCok: no visible global function definition for 'validObject'
kmCok: no visible global function definition for 'covParametersBounds'
kmCok: no visible binding for global variable 'kmEstimate'
kmCok : cv: no visible global function definition for 'leaveOneOut.km'
predict.kmCok: no visible global function definition for 'model.matrix'
predict.kmCok: no visible global function definition for 'covMat1Mat2'
predict.kmCok: no visible global function definition for 'qnorm'
predict.kmCok: no visible global function definition for 'qt'
predict.kmCok: no visible global function definition for 'covMatrix'
summary.MuFicokm: no visible global function definition for
  'covparam2vect'
Undefined global functions or variables:
  covMat1Mat2 covMatrix covParametersBounds covStruct.create
  covparam2vect drop.response km kmEstimate leaveOneOut.km lm
  model.matrix new qnorm qt validObject
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "lm", "model.matrix", "qnorm", "qt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages suggested but not available for checking: 'plotly', 'kableExtra'
Namespace in Imports field not imported from: 'gtools'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'muHVT.Rmd' using rmarkdown
Quitting from lines 18-120 (muHVT.Rmd) 
Error: processing vignette 'muHVT.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building 'muHVT.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: 'randomcoloR'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
multeq.diff: no visible global function definition for 'cov'
multeq.diff: no visible global function definition for 'pt'
multeq.diff: no visible global function definition for 'qt'
multeq.rat: no visible global function definition for 'cov'
multeq.rat: no visible global function definition for 'pt'
multeq.rat: no visible global function definition for 'qt'
Undefined global functions or variables:
  cov pt qt
Consider adding
  importFrom("stats", "cov", "pt", "qt")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
synthetic_multiband: no visible global function definition for 'runif'
synthetic_multiband: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'switchBox', 'leukemiasEset', 'qpdf'
Error(s) in re-building vignettes:
  ...
--- re-building 'Tutorial.Rmd' using rmarkdown
Quitting from lines 50-78 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
Bioconductor does not yet build and check packages for R version 4.2; see
  https://bioconductor.org/install
--- failed re-building 'Tutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
calculate_direction: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'cowsay'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'Matrix'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == Skipped tests ===============================================================
  * On CRAN (4)
  
  == Failed tests ================================================================
  -- Error (test-cluster-utils.R:45:3): can load package -------------------------
  Error: there is no package called 'covr'
  Backtrace:
      x
   1. \-multidplyr::cluster_library(cl, "covr") test-cluster-utils.R:45:2
   2.   \-base::lapply(packages, library, character.only = TRUE)
   3.     \-base:::FUN(X[[i]], ...)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 48 ]
  Error: Test failures
  Execution halted
Package required but not available: 'ez'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
Package required but not available: 'JWileymisc'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'usethis', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
multinb.fit: no visible global function definition for 'nlminb'
multinbmod: no visible global function definition for 'is.empty.model'
multinbmod: no visible global function definition for 'model.matrix'
multinbmod: no visible binding for global variable 'contrasts'
multinbmod: no visible global function definition for 'model.response'
multinbmod: no visible global function definition for 'model.offset'
Undefined global functions or variables:
  contrasts is.empty.model model.matrix model.offset model.response
  nlminb
Consider adding
  importFrom("stats", "contrasts", "is.empty.model", "model.matrix",
             "model.offset", "model.response", "nlminb")
to your NAMESPACE file.
Package suggested but not available for checking: 'statnet'
Package required but not available: 'rstan'

Package suggested but not available for checking: 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'rPorta', 'covr'
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'rgenoud'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.onAttach: no visible global function definition for
  'packageDescription'
genoudRob: no visible global function definition for 'genoud'
get.XYdata: no visible global function definition for 'terms'
get.xdata: no visible global function definition for 'terms'
get.xdata: no visible global function definition for 'model.matrix'
get.xy: no visible global function definition for 'terms'
get.xynames: no visible global function definition for 'terms'
get.ydata: no visible global function definition for 'terms'
get.ydata: no visible global function definition for 'model.response'
get.ydata: no visible global function definition for 'model.frame'
mt.dev: no visible global function definition for 'pt'
mt.dev.grad: no visible global function definition for 'pt'
mt.dev.grad: no visible global function definition for 'dt'
mt.mle: no visible global function definition for 'optim'
multinomRob: no visible global function definition for 'var'
plot.multinomRob: no visible global function definition for 'par'
plot.multinomRob: no visible global function definition for 'title'
rdirich: no visible global function definition for 'rgamma'
residual.generator: no visible global function definition for 'median'
rmultinomial: no visible global function definition for 'runif'
rmultinomial: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  dt genoud median model.frame model.matrix model.response optim
  packageDescription par pt rbinom rgamma runif terms title var
Consider adding
  importFrom("graphics", "par", "title")
  importFrom("stats", "dt", "median", "model.frame", "model.matrix",
             "model.response", "optim", "pt", "rbinom", "rgamma",
             "runif", "terms", "var")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Package required but not available: 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
multiPIM : expand.factors: no visible global function definition for
  'formula'
multiPIM : expand.factors: no visible global function definition for
  'model.matrix'
multiPIM : <anonymous>: no visible global function definition for 'glm'
multiPIM : <anonymous>: no visible binding for global variable
  'binomial'
multiPIM : <anonymous>: no visible global function definition for
  'qlogis'
multiPIM : <anonymous>: no visible global function definition for
  'as.formula'
multiPIM : <anonymous>: no visible global function definition for 'lm'
multiPIM: no visible global function definition for 'glm'
multiPIM: no visible global function definition for 'qlogis'
multiPIM: no visible binding for global variable 'binomial'
multiPIM: no visible global function definition for 'plogis'
multiPIM: no visible global function definition for 'sd'
multiPIM: no visible global function definition for 'lm'
summary.multiPIM: no visible binding for global variable 'sd'
summary.multiPIM: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  as.formula binomial formula glm lm model.matrix plogis pnorm qlogis
  sd
Consider adding
  importFrom("stats", "as.formula", "binomial", "formula", "glm", "lm",
             "model.matrix", "plogis", "pnorm", "qlogis", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: 'Rgraphviz'
Error(s) in re-building vignettes:
  ...
--- re-building 'TwoModeNetworks.Rnw' using knitr
Quitting from lines 128-132 (TwoModeNetworks.Rnw) 
Error: processing vignette 'TwoModeNetworks.Rnw' failed with diagnostics:
there is no package called 'Rgraphviz'
--- failed re-building 'TwoModeNetworks.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'qpdf'
'LazyData' is specified without a 'data' directory
CCM_boot : <anonymous>: no visible global function definition for 'sd'
SSR_check_signal: no visible global function definition for 'cor'
SSR_check_signal: no visible global function definition for 'cor.test'
SSR_check_signal: no visible global function definition for 'lm'
SSR_pred_boot: no visible global function definition for 'cor'
make_ccm_data: no visible global function definition for 'rnorm'
make_ccm_data: no visible global function definition for 'runif'
make_ccm_data: no visible global function definition for 'rlnorm'
Undefined global functions or variables:
  cor cor.test lm rlnorm rnorm runif sd
Consider adding
  importFrom("stats", "cor", "cor.test", "lm", "rlnorm", "rnorm",
             "runif", "sd")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  'poweRlaw' 'rmutil'
  All declared Imports should be used.
PrbMlt.default: no visible binding for global variable 'na.omit'
PrbMlt.default: no visible global function definition for 'anova'
Undefined global functions or variables:
  anova na.omit
Consider adding
  importFrom("stats", "anova", "na.omit")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  'stats' 'utils'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 6 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

Depends: includes the non-default packages:
  'car', 'pdist', 'pls', 'gplots', 'mvtnorm', 'robustbase', 'gtools',
  'bitops', 'caTools', 'pcaPP', 'rrcov'
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
plotFID: no visible global function definition for 'points'
Undefined global functions or variables:
  points
Consider adding
  importFrom("graphics", "points")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
prentice.test: 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').
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'get_sarted_with_mutSignatures.Rmd' using rmarkdown
Quitting from lines 15-34 (get_sarted_with_mutSignatures.Rmd) 
Error: processing vignette 'get_sarted_with_mutSignatures.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'get_sarted_with_mutSignatures.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
mvb.simu: no visible global function definition for 'runif'
plot.lps: no visible global function definition for 'matplot'
unifit: no visible global function definition for 'model.frame'
unifit: no visible global function definition for 'model.matrix'
unifit: no visible global function definition for 'model.response'
unilps: no visible global function definition for 'model.frame'
unilps: no visible global function definition for 'model.matrix'
unilps: no visible global function definition for 'model.response'
Undefined global functions or variables:
  matplot model.frame model.matrix model.response runif
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "runif")
to your NAMESPACE file.
Checking should be performed on sources prepared by 'R CMD build'.
conceptIndicesSkm: no visible global function definition for
  'txtProgressBar'
conceptIndicesSkm: no visible global function definition for
  'setTxtProgressBar'
conceptVectorsSkm: no visible global function definition for
  'txtProgressBar'
conceptVectorsSkm: no visible global function definition for
  'setTxtProgressBar'
mvcmb: no visible global function definition for 'runif'
mvcmb: no visible global function definition for 'str'
mvcsph: no visible global function definition for 'pdf'
mvcsph: no visible global function definition for 'heatmap'
mvcsph: no visible global function definition for 'dev.off'
mvcsph: no visible global function definition for 'hclust'
mvcsph: no visible global function definition for 'dist'
mvcsph: no visible global function definition for 'str'
Undefined global functions or variables:
  dev.off dist hclust heatmap pdf runif setTxtProgressBar str
  txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "dist", "hclust", "heatmap", "runif")
  importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
to your NAMESPACE file.
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'dagitty', 'ggdag'
Error(s) in re-building vignettes:
  ...
--- re-building 'mvGPS-intro.Rmd' using rmarkdown
Quitting from lines 33-51 (mvGPS-intro.Rmd) 
Error: processing vignette 'mvGPS-intro.Rmd' failed with diagnostics:
could not find function "dagify"
--- failed re-building 'mvGPS-intro.Rmd'

SUMMARY: processing the following file failed:
  'mvGPS-intro.Rmd'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'car'
mvnpermute: no visible global function definition for 'lm'
mvnpermute: no visible global function definition for 'coef'
mvnpermute: no visible global function definition for 'resid'
Undefined global functions or variables:
  coef lm resid
Consider adding
  importFrom("stats", "coef", "lm", "resid")
to your NAMESPACE file.
Packages required but not available: 'mvoutlier', 'kableExtra', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'ggplot2' 'grDevices' 'knitr' 'utils'
  All declared Imports should be used.
Package required but not available: 'robCompositions'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'sampleSelection'
mvorpb: no visible global function definition for 'pnorm'
mvorpb: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
rtn: no visible global function definition for 'runif'
rtn: no visible global function definition for 'qnorm'
rtn: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm runif
Consider adding
  importFrom("stats", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: 'rdryad'
Namespace in Imports field not imported from: 'matrixcalc'
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building 'mvSLOUCH_Carnivorans.Rmd' using rmarkdown
Failed with error:  'there is no package called 'rdryad''
Quitting from lines 43-75 (mvSLOUCH_Carnivorans.Rmd) 
Error: processing vignette 'mvSLOUCH_Carnivorans.Rmd' failed with diagnostics:
argument is not interpretable as logical
--- failed re-building 'mvSLOUCH_Carnivorans.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'RColorBrewer' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'RColorBrewer'
  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
mxkssd: no visible global function definition for 'txtProgressBar'
mxkssd: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package suggested but not available for checking: 'tidyverse'
Error(s) in re-building vignettes:
  ...
--- re-building 'mmod_tutorial.Rmd' using rmarkdown
Quitting from lines 42-45 (mmod_tutorial.Rmd) 
Error: processing vignette 'mmod_tutorial.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'mmod_tutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
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.
abcpred_nmer: no visible global function definition for 'write.table'
algpred: no visible global function definition for 'read.table'
algpred: no visible global function definition for 'write.table'
allermatch: no visible global function definition for 'read.table'
allermatch: no visible global function definition for 'write.table'
bcepred_nmer: no visible global function definition for 'write.table'
bimas_nmer: no visible global function definition for 'write.table'
filter.firstlayer: no visible global function definition for
  'read.table'
filter.firstlayer: no visible global function definition for
  'write.table'
iedb_arb_mhci_nmer: no visible global function definition for
  'write.table'
iedb_arb_mhcii_nmer: no visible global function definition for
  'write.table'
iedb_consensus_mhci_nmer: no visible global function definition for
  'write.table'
iedb_consensus_mhcii_nmer: no visible global function definition for
  'write.table'
netmhcNN_nmer: no visible global function definition for 'write.table'
netmhcWT_nmer: no visible global function definition for 'write.table'
propred_nmer: no visible global function definition for 'write.table'
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
update_episode: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'taxize'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
abs_dif: no visible global function definition for 'as.formula'
env_dif: no visible global function definition for 'lm'
env_dif: no visible global function definition for 'as.formula'
env_dif_logistic: no visible global function definition for
  'as.formula'
fam_env: no visible global function definition for 'as.formula'
log_dif: no visible global function definition for 'as.formula'
Undefined global functions or variables:
  as.formula lm
Consider adding
  importFrom("stats", "as.formula", "lm")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rvest', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'devtools', 'httr', 'rvest'
Note: found 50 marked UTF-8 strings
Packages suggested but not available for checking: 'covr', 'GEOquery'
Package required but not available: 'survminer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'missMDA', 'VIM'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'usethis'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 're2r'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Note: found 47936 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking: 'covr', 'imputeTS'
Package required but not available: 'vsn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Packages required but not available: 'tseries', 'car'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
Packages required but not available: 'httr', 'rvest'

Packages suggested but not available for checking: 'covr', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gh', 'usethis', 'curl'

Package suggested but not available for checking: 'covr'

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: 'httr'
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  Loading required package: rgl
  Registered S3 method overwritten by 'nat':
    method             from
    as.mesh3d.ashape3d rgl 
  Some nat functions depend on a CMTK installation. See ?cmtk and README.md for details.
  
  Attaching package: 'nat'
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, union
  
  > library(httr)
  Error in library(httr) : there is no package called 'httr'
  Execution halted
Package required but not available: 'crul'

Package suggested but not available for checking: 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'gurobi'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'tuneR'
  All declared Imports should be used.
Package suggested but not available for checking: 'rvest'
Note: found 140 marked UTF-8 strings
Package suggested but not available for checking: 'DEXSeq'
Package unavailable to check Rd xrefs: 'DEXSeq'
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: 'sSeq'
NB.estimator: no visible global function definition for 'optimize'
NB.estimator: no visible global function definition for 'uniroot'
NB.example.dataset: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  optimize uniroot write.table
Consider adding
  importFrom("stats", "optimize", "uniroot")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  'caret' 'datasets' 'dplyr' 'e1071' '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' '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' 'rhandsontable' 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'drc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'bookdown'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
ncbit : FUN: no visible global function definition for 'read.table'
ncbit : FUN: no visible global function definition for 'head'
Undefined global functions or variables:
  head read.table
Consider adding
  importFrom("utils", "head", "read.table")
to your NAMESPACE file.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  [1] 329 - 233 ==   96.2
  [2] 197 - 293 ==  -96.2
  [3] 208 - 336 == -128.2
  [4] 318 - 190 ==  128.2
  -- Failure (test-file-functions.R:62:2): grid mappings are read and applied ----
  latlon.data$y not equal to lat.dat[indices].
  4/4 mismatches (average diff: 28)
  [1] 49.5 - 12.4 ==  37.1
  [2] 49.5 - 12.4 ==  37.1
  [3] 40.4 - 59.1 == -18.8
  [4] 40.4 - 59.1 == -18.8
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 45 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking: 'pkgdown', 'geoknife'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  == Failed tests ================================================================
  -- Error (test_read-write_timeseries_dsg.R:18:3): Create basic DSG file --------
  Error: there is no package called 'geoknife'
  Backtrace:
      x
   1. +-ncdfgeom:::get_sample_timeseries_data() test_read-write_timeseries_dsg.R:18:2
   2. \-base::loadNamespace(x) C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\ncdfgeom\ncdfgeom.Rcheck\tests\testthat\helper-functions.R:77:2
   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 2 | PASS 688 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'geometry.Rmd' using rmarkdown
--- finished re-building 'geometry.Rmd'

--- re-building 'ncdfgeom.Rmd' using rmarkdown
Linking to GEOS 3.6.2, GDAL 3.0.4, PROJ 7.0.0

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

****Support Package****
This package is a USGS-R Support package. 
see: https://owi.usgs.gov/R/packages.html#support
--- finished re-building 'ncdfgeom.Rmd'

--- re-building 'timeseries.Rmd' using rmarkdown
Quitting from lines 34-46 (timeseries.Rmd) 
Error: processing vignette 'timeseries.Rmd' failed with diagnostics:
there is no package called 'geoknife'
--- failed re-building 'timeseries.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
d0: no visible global function definition for 'qnorm'
dncgamma: no visible global function definition for 'dpois'
indncgamma: no visible global function definition for 'pgamma'
indncgamma: no visible global function definition for 'dpois'
inxncgamma: no visible global function definition for 'qnorm'
inxncgamma: no visible global function definition for 'pgamma'
inxncgamma: no visible global function definition for 'dpois'
pncgamma: no visible global function definition for 'pgamma'
pncgamma: no visible global function definition for 'dpois'
Undefined global functions or variables:
  dpois pgamma qnorm
Consider adding
  importFrom("stats", "dpois", "pgamma", "qnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'Deriv' 'compiler' 'stringi'
  All declared Imports should be used.
Packages suggested but not available for checking: 'magick', 'plotly'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 're2r'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'MASS' 'fields' 'mvtnorm'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Note: found 7332 marked UTF-8 strings
Namespace in Imports field not imported from: 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'animation'

Package suggested but not available for checking: 'tergm'

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 required but not available: 'heatmaply'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rtweet'

See section 'The DESCRIPTION file' 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
population: no visible global function definition for 'weighted.mean'
population: no visible global function definition for 'rpois'
population: no visible global function definition for 'lm'
population: no visible global function definition for 'coefficients'
population: no visible global function definition for 'sd'
population: no visible global function definition for 'par'
population: no visible global function definition for 'lines'
Undefined global functions or variables:
  coefficients lines lm par rpois sd weighted.mean
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "coefficients", "lm", "rpois", "sd",
             "weighted.mean")
to your NAMESPACE file.
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
Package required but not available: 'ssh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'neonUtilities', 'rhdf5'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'covr', 'neonUtilities', 'rhdf5', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'curl'

Package suggested but not available for checking: 'rhdf5'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'Matrix' 'igraph'
  All declared Imports should be used.
netVal: no visible global function definition for 'cutree'
netVal: no visible global function definition for 'hclust'
netVal: no visible global function definition for 'as.dist'
Undefined global functions or variables:
  as.dist cutree hclust
Consider adding
  importFrom("stats", "as.dist", "cutree", "hclust")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'genefilter', 'graphite', 'httr', 'ndexr', 'RCy3'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
EnvInd: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
Package suggested but not available for checking: 'hasseDiagram'
Package unavailable to check Rd xrefs: 'hasseDiagram'
Note: found 1 marked UTF-8 string
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'knitcitations'
Namespace in Imports field not imported from: 'CoDiNA'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'DiagrammeRsvg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'usethis', 'httr', 'rvest'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'sna'
  All declared Imports should be used.
Package suggested but not available for checking: 'networktools'
Package suggested but not available for checking: 'pkgdown'
Namespaces in Imports field not imported from:
  'mgcv' 'stats'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
simulate.sisnetwork: no visible global function definition for 'var'
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
Package suggested but not available for checking: 'googledrive'
Package required but not available: 'smacof'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'fxregime'
Note: found 2 marked Latin-1 strings
Malformed Description field: should contain one or more complete sentences.
mlptrain : rect: no visible global function definition for 'polygon'
mlptrain : drawnet: no visible global function definition for 'title'
mlptrain : drawnet: no visible global function definition for 'polygon'
mlptrain : drawnet: no visible global function definition for 'text'
mlptrain : drawnet: no visible global function definition for 'lines'
mlptrain: no visible global function definition for 'runif'
mlptrain: no visible global function definition for 'locator'
mlptrain: no visible global function definition for 'polygon'
mlptrain: no visible global function definition for 'text'
rbftrain : rect: no visible global function definition for 'polygon'
rbftrain : drawnet: no visible global function definition for 'title'
rbftrain : drawnet: no visible global function definition for 'polygon'
rbftrain : drawnet: no visible global function definition for 'text'
rbftrain : drawnet: no visible global function definition for 'lines'
rbftrain : graph: no visible global function definition for 'title'
rbftrain : graph: no visible global function definition for 'polygon'
rbftrain : graph: no visible global function definition for 'text'
rbftrain : graph: no visible global function definition for 'lines'
rbftrain : graph: no visible global function definition for 'points'
rbftrain: no visible global function definition for 'runif'
rbftrain: no visible global function definition for 'locator'
rbftrain: no visible global function definition for 'polygon'
rbftrain: no visible global function definition for 'text'
rbftrain: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  kmeans lines locator points polygon runif text title
Consider adding
  importFrom("graphics", "lines", "locator", "points", "polygon", "text",
             "title")
  importFrom("stats", "kmeans", "runif")
to your NAMESPACE file.
Packages suggested but not available for checking: 'httr', 'covr'
Error(s) in re-building vignettes:
  ...
--- re-building 'neurobase.Rmd' using rmarkdown
--- finished re-building 'neurobase.Rmd'

--- re-building 'nifti_basics.Rmd' using rmarkdown
Quitting from lines 11-19 (nifti_basics.Rmd) 
Error: processing vignette 'nifti_basics.Rmd' failed with diagnostics:
there is no package called 'httr'
--- failed re-building 'nifti_basics.Rmd'

--- re-building 'simple_io.Rmd' using rmarkdown
trying URL 'https://johnmuschelli.com/open_ms_data/cross_sectional/raw/patient01/T1W.nii.gz'
 length 21807043 bytes (20.8 MB)
==================================================
downloaded 20.8 MB

--- finished re-building 'simple_io.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'devtools'

Package suggested but not available for checking: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'aws.s3'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
balloon: no visible global function definition for 'convolve'
physnoise: no visible global function definition for 'sd'
physnoise: no visible global function definition for 'rnorm'
rrice: no visible global function definition for 'rnorm'
simTSrestingstate: no visible global function definition for 'runif'
simTSrestingstate: no visible global function definition for 'fft'
spatialnoise: no visible global function definition for 'rnorm'
spatialnoise: no visible global function definition for 'qgamma'
spatialnoise: no visible global function definition for 'pnorm'
specifydesign: no visible global function definition for 'convolve'
systemnoise: no visible global function definition for 'rnorm'
tasknoise: no visible global function definition for 'rnorm'
tasknoise: no visible global function definition for 'sd'
temporalnoise: no visible global function definition for 'arima.sim'
Undefined global functions or variables:
  arima.sim convolve fft pnorm qgamma rnorm runif sd
Consider adding
  importFrom("stats", "arima.sim", "convolve", "fft", "pnorm", "qgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
Packages required but not available: 'devtools', 'httr'

Packages suggested but not available for checking: 'robotstxt', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyRSS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'stringi'
  All declared Imports should be used.
Note: found 4485 marked UTF-8 strings
Package suggested but not available for checking: 'lintr'
'LazyData' is specified without a 'data' directory
nfca : nFCAmain: no visible global function definition for 'hist'
nfca : nFCAmain: no visible global function definition for
  'flush.console'
nfca : nFCAmain: no visible global function definition for 'qnorm'
nfca : nFCAmain: no visible global function definition for 'read.csv'
nfca : nFCAmain: no visible global function definition for 'cor'
nfca : nFCAmain: no visible global function definition for 'as.dist'
nfca : nFCAmain: no visible global function definition for 'cophenetic'
nfca : nFCAmain: no visible global function definition for 'hclust'
nfca : thresholdTEST: no visible global function definition for
  'read.csv'
nfca : gScript: no visible global function definition for 'read.csv'
nfca : gScript0: no visible global function definition for 'read.csv'
nfca : gMatrix: no visible global function definition for 'read.csv'
nfca: no visible global function definition for 'cor'
Undefined global functions or variables:
  as.dist cophenetic cor flush.console hclust hist qnorm read.csv
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cophenetic", "cor", "hclust", "qnorm")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Running examples in 'nFCA-Ex.R' failed
The error most likely occurred in:

> ### Name: nfca
> ### Title: Numerical Formal Concept Analysis for Systematic Clustering
> ### Aliases: nfca
> 
> ### ** Examples
> 
> # View a build-in correlation matrix: nfca_example
> data("nfca_example", package = "nFCA")
> nfca_example
      H    W    S    D   HF   HM   WF   WM   H1   W1    O
1  1.00 0.95 0.90 0.90 0.85 0.85 0.80 0.80 0.40 0.30 0.10
2  0.95 1.00 0.88 0.88 0.70 0.70 0.87 0.87 0.20 0.45 0.15
3  0.90 0.88 1.00 0.82 0.80 0.80 0.76 0.76 0.10 0.10 0.02
4  0.90 0.88 0.82 1.00 0.82 0.82 0.81 0.81 0.10 0.10 0.05
5  0.85 0.70 0.80 0.82 1.00 0.95 0.65 0.65 0.08 0.06 0.01
6  0.85 0.70 0.80 0.82 0.95 1.00 0.60 0.60 0.06 0.07 0.01
7  0.80 0.87 0.76 0.81 0.65 0.60 1.00 0.95 0.03 0.05 0.01
8  0.80 0.87 0.76 0.81 0.65 0.60 0.95 1.00 0.01 0.02 0.01
9  0.40 0.20 0.10 0.10 0.08 0.06 0.03 0.01 1.00 0.02 0.01
10 0.30 0.45 0.10 0.10 0.06 0.07 0.05 0.02 0.02 1.00 0.02
11 0.10 0.15 0.02 0.05 0.01 0.01 0.01 0.01 0.01 0.02 1.00
>      
> # 1. using the default 'histogram' method and choosing threshold
> # automatically   
> nfca(data = nfca_example)
Warning in system("ruby multistagefca.rb") : 'ruby' not found
Warning in file.rename("example.dot", "example.txt") :
  cannot rename file 'example.dot' to 'example.txt', reason 'The system cannot find the file specified'
Warning in file(file, "rt") :
  cannot open file 'example.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: nfca ... thresholdTEST -> as.matrix -> read.csv -> read.table -> file
Execution halted
Packages required but not available: 'FKF.SP', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'nflfastR'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'usethis'

Package suggested but not available for checking: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

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
Packages suggested but not available for checking: 'graphite', 'NFPdata'
Error(s) in re-building vignettes:
--- re-building 'NFP.Rmd' using rmarkdown
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: graphite
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'graphite'
Quitting from lines 135-143 (NFP.Rmd) 
Error: processing vignette 'NFP.Rmd' failed with diagnostics:
could not find function "pathways"
--- failed re-building 'NFP.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'rvest', 'curl'

Packages suggested but not available for checking:
  'wikilake', 'covr', 'crul'

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

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: 'rvest', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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
Package required but not available: 'concaveman'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'rgdal' 'sp'
  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: 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'bbw'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages which this enhances but not available for checking:
  'estatapi', 'jpndistrict'
Package unavailable to check Rd xrefs: 'cshapes'
Malformed Description field: should contain one or more complete sentences.
Note: found 170 marked UTF-8 strings
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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 required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'curl'

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: 'MLInterfaces'

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: 'covr'
'LazyData' is specified without a 'data' directory
nlmeODE: no visible global function definition for 'deriv'
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Pwr.lme: no visible global function definition for 'anova'
Pwr.lme: no visible global function definition for 'qf'
Pwr.lme: no visible global function definition for 'pf'
logLik1.lme: no visible global function definition for 'coef'
logLik1.lme: no visible global function definition for 'model.matrix'
logLik1.lme: no visible global function definition for 'predict'
logLik1.lme: no visible global function definition for 'formula'
runScript: no visible binding for global variable 'example'
sigmaTolme: no visible global function definition for 'vcov'
simulateY.lme: no visible global function definition for 'runif'
simulateY.lme: no visible global function definition for 'fitted'
simulateY.lme: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  anova coef example fitted formula model.matrix pf predict qf rnorm
  runif vcov
Consider adding
  importFrom("stats", "anova", "coef", "fitted", "formula",
             "model.matrix", "pf", "predict", "qf", "rnorm", "runif",
             "vcov")
  importFrom("utils", "example")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'devtools', 'pkgdown', 'covr', 'forecast'
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'qdap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'car'
Package unavailable to check Rd xrefs: 'car'
Error(s) in re-building vignettes:
  ...
--- re-building 'Bootstrapping.Rmd' using rmarkdown
Quitting from lines 21-25 (Bootstrapping.Rmd) 
Error: processing vignette 'Bootstrapping.Rmd' failed with diagnostics:
there is no package called 'car'
--- failed re-building 'Bootstrapping.Rmd'

--- re-building 'Models-and-Functions.Rmd' using rmarkdown
--- finished re-building 'Models-and-Functions.Rmd'

--- re-building 'nlraa-AgronJ-paper.Rmd' using rmarkdown
--- finished re-building 'nlraa-AgronJ-paper.Rmd'

--- re-building 'nlraa-Oddi-LFMC.Rmd' using rmarkdown
--- finished re-building 'nlraa-Oddi-LFMC.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Package in Depends field not imported from: 'proto'
  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:
  'stats:::nlsModel' 'stats:::nlsModel.plinear'
  See the note in ?`:::` about the use of this operator.
nls2: no visible global function definition for 'nls.control'
nls2: no visible global function definition for 'as.formula'
nls2: no visible global function definition for 'coef'
nls2: no visible global function definition for 'runif'
nls2 : <anonymous>: no visible global function definition for
  'deviance'
Undefined global functions or variables:
  as.formula coef deviance nls.control runif
Consider adding
  importFrom("stats", "as.formula", "coef", "deviance", "nls.control",
             "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'deSolve'
  All declared Imports should be used.
Package required but not available: 'devtools'

Package suggested but not available for checking: 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'imguR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'INLA'
Malformed Description field: should contain one or more complete sentences.
nnmf_als: no visible global function definition for 'rnorm'
nnmf_mm: no visible global function definition for 'rnorm'
nnmf_prob: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'devtools'
Namespace in Imports field not imported from: 'BiocManager'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Packages required but not available: 'systemfit', 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'forecast', 'tsutils'

Package suggested but not available for checking: 'thief'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'multicool'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'lwgeom' 's2'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
Packages required but not available: 'dynlm', 'meboot'

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

Packages suggested but not available for checking: 'covr', 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'choroplethr', 'hurricaneexposure'

Package suggested but not available for checking: 'hurricaneexposuredata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'R6' 'crayon' 'digest' 'hash'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'paws'

Packages suggested but not available for checking: 'arrow', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'sofa', 'elastic'
Packages unavailable to check Rd xrefs: 'sofa', 'elastic'
makeRules: no visible global function definition for 'sd'
makeRules: no visible global function definition for 'rnorm'
nodeHarvest: no visible global function definition for 'capture.output'
nodeHarvest: no visible global function definition for 'lm'
nodeHarvest: no visible global function definition for 'coef'
plot.nodeHarvest: no visible global function definition for 'rgb'
Undefined global functions or variables:
  capture.output coef lm rgb rnorm sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "coef", "lm", "rnorm", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'rJava'
  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: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'rsdmx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'V8', 'shinytest', 'covr'
'LazyData' is specified without a 'data' directory
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > test_check("nomnoml")
  == Skipped tests ===============================================================
  * On CRAN (2)
  
  == Failed tests ================================================================
  -- Error (test-shiny.R:3:1): (code run outside of `test_that()`) ---------------
  Error: there is no package called 'shinytest'
  Backtrace:
      x
   1. \-base::library(shinytest) test-shiny.R:3:0
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 2 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: 'do'

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

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

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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'AER'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'lpSolve', 'gdata', 'Hmisc', 'rms', 'geometry', 'psych', 'pwt'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  'Hmisc' 'gdata' 'geometry' 'lpSolve' 'psych' 'rms'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Hmisc' 'gdata' 'geometry' 'lpSolve' 'psych' 'pwt' 'rms'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
additive: no visible global function definition for 'lp'
ar.dual.dea: no visible global function definition for 'lp'
cost.dea: no visible global function definition for 'lp'
ddf: no visible global function definition for 'lp'
dea: no visible global function definition for 'lp'
direc.dea: no visible global function definition for 'lp'
dual.dea: no visible global function definition for 'lp'
effdea.b.f: no visible global function definition for 'convhulln'
effdea.b.f: no visible global function definition for 'lp'
faremalm2: no visible binding for global variable 'Lag'
faremalm2: no visible global function definition for 'na.omit'
int.dea: no visible global function definition for 'lp'
lp2: no visible global function definition for 'lp'
revenue.dea: no visible global function definition for 'lp'
sbm.tone: no visible global function definition for 'lp'
sbm.vrs: no visible global function definition for 'lp'
Undefined global functions or variables:
  Lag convhulln lp na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'Matrix' 'e1071' 'glmnet'
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  'histogram' 'optimx'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dnormgam: no visible global function definition for 'qgamma'
dnormgam: no visible global function definition for 'fft'
dnormgam: no visible global function definition for 'dgamma'
dnormgam: no visible global function definition for 'approx'
normgam.fit : mkdfftNormalGammaOptim : <anonymous>: no visible global
  function definition for 'dnorm'
normgam.fit : estimation_param_normexp_RMA : max.density: no visible
  global function definition for 'density'
normgam.fit: no visible global function definition for 'sd'
normgam.fit: no visible global function definition for 'median'
normgam.fit: no visible global function definition for 'IQR'
normgam.fit: no visible global function definition for 'optimx'
normgam.fit: no visible global function definition for 'coef'
normgam.signal: no visible global function definition for 'approx'
normgam.signal: no visible global function definition for 'hist'
Undefined global functions or variables:
  IQR approx coef density dgamma dnorm fft hist median optimx qgamma sd
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "IQR", "approx", "coef", "density", "dgamma",
             "dnorm", "fft", "median", "qgamma", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
Malformed Description field: should contain one or more complete sentences.
ajb.norm.test: no visible global function definition for 'rnorm'
frosini.norm.test: no visible global function definition for 'var'
frosini.norm.test: no visible global function definition for 'pnorm'
frosini.norm.test: no visible global function definition for 'rnorm'
geary.norm.test: no visible global function definition for 'rnorm'
hegazy1.norm.test: no visible global function definition for 'var'
hegazy1.norm.test: no visible global function definition for 'qnorm'
hegazy1.norm.test: no visible global function definition for 'rnorm'
hegazy2.norm.test: no visible global function definition for 'var'
hegazy2.norm.test: no visible global function definition for 'qnorm'
hegazy2.norm.test: no visible global function definition for 'rnorm'
jb.norm.test: no visible global function definition for 'rnorm'
kurtosis.norm.test: no visible global function definition for 'rnorm'
skewness.norm.test: no visible global function definition for 'rnorm'
spiegelhalter.norm.test: no visible global function definition for
  'rnorm'
wb.norm.test: no visible global function definition for 'qnorm'
wb.norm.test: no visible global function definition for 'var'
wb.norm.test: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  pnorm qnorm rnorm var
Consider adding
  importFrom("stats", "pnorm", "qnorm", "rnorm", "var")
to your NAMESPACE file.
normality.test1: no visible global function definition for 'cov.wt'
normality.test1: no visible global function definition for 'cor'
normality.test1: no visible global function definition for 'pnorm'
normality.test1: no visible global function definition for 'pchisq'
normality.test2: no visible global function definition for 'cov.wt'
normality.test2: no visible global function definition for 'cor'
normality.test2: no visible global function definition for 'acf'
normality.test2: no visible global function definition for 'pnorm'
normality.test2: no visible global function definition for 'pchisq'
whitenoise.test: no visible global function definition for 'acf'
whitenoise.test: no visible global function definition for 'spec.pgram'
whitenoise.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  acf cor cov.wt pchisq pnorm spec.pgram
Consider adding
  importFrom("stats", "acf", "cor", "cov.wt", "pchisq", "pnorm",
             "spec.pgram")
to your NAMESPACE file.
Packages required but not available: 'forecast', 'tseries'

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
Package required but not available: 'httr'

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

> ### Name: download_model
> ### Title: Download Model Fitted to the 'novelforest' Data
> ### Aliases: download_model
> 
> ### ** Examples
> 
> novelforest_model <- download_model()
To save the model locally, use argument save_to = 'path/filename.rds'
Downloading model (size: 16.5 Mb)
> 
> # library(brms)  # recommended
> summary(novelforest_model)
Loading required package: rstan
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'rstan'
Error in .requirePackage(package) : 
  unable to find required package 'rstan'
Calls: summary ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
Execution halted
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.newReportId : <anonymous>: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
'LazyData' is specified without a 'data' directory
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'car'
'LazyData' is specified without a 'data' directory
Running examples in 'NPC-Ex.R' failed
The error most likely occurred in:

> ### Name: NPC
> ### Title: Nonparametric Combination of Dependent Hypothesis Tests
> ### Aliases: NPC
> 
> ### ** Examples
> 
> 
> library(NPC)
> ## Required for this example
> library(mvtnorm)
> library(car)
Error in library(car) : there is no package called 'car'
Execution halted
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'smcure' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NPHMC: no visible global function definition for 'integrate'
NPHMC: no visible global function definition for 'qnorm'
NPHMC: no visible global function definition for 'pnorm'
NPHMC: no visible global function definition for 'lines'
NPHMC: no visible global function definition for 'smcure'
NPHMC: no visible global function definition for 'coxph'
Undefined global functions or variables:
  coxph integrate lines pnorm qnorm smcure
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "integrate", "pnorm", "qnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: 'ez'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'CAMAN' 'Hmisc' 'latexpdf' 'spatstat'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: 'rts'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'Rlabkey'

Packages suggested but not available for checking:
  'covr', 'kableExtra', 'pkgdown'

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
nps.test: no visible global function definition for 'qnorm'
nps.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
npst: no visible global function definition for 'mclapply'
Undefined global functions or variables:
  mclapply
Package suggested but not available for checking: 'tidyverse'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'basic_functionalities.Rmd' using rmarkdown
--- finished re-building 'basic_functionalities.Rmd'

--- re-building 'example1.Rmd' using rmarkdown
Quitting from lines 22-25 (example1.Rmd) 
Error: processing vignette 'example1.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'example1.Rmd'

--- re-building 'example2.Rmd' using rmarkdown
Quitting from lines 22-25 (example2.Rmd) 
Error: processing vignette 'example2.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'example2.Rmd'

SUMMARY: processing the following files failed:
  'example1.Rmd' 'example2.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: 'crul'

Package suggested but not available for checking: 'covr'

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

Packages suggested but not available for checking: 'covr', 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package in Depends field not imported from: 'mco'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boundedPolyMutation: no visible global function definition for 'runif'
boundedSBXover: no visible global function definition for 'runif'
nsga2R : <anonymous>: 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: 'xgboost'
  All declared Imports should be used.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking: 'covr', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.mcmc.bar: no visible global function definition for 'rnorm'
.mcmc.bar: no visible global function definition for 'runif'
.mcmc.comb: no visible global function definition for 'rnorm'
.mcmc.comb: no visible global function definition for 'runif'
.mcmc.rd: no visible global function definition for 'rnorm'
.mcmc.rd: no visible global function definition for 'runif'
.mcmc.trans: no visible global function definition for 'rnorm'
.mcmc.trans: no visible global function definition for 'runif'
.simulate.bar: no visible global function definition for 'rlnorm'
.simulate.bar: no visible global function definition for 'rbeta'
.simulate.bar: no visible global function definition for 'rbinom'
.simulate.comb: no visible global function definition for 'rlnorm'
.simulate.comb: no visible global function definition for 'rbeta'
.simulate.comb: no visible global function definition for 'rbinom'
.simulate.rd: no visible global function definition for 'rlnorm'
.simulate.rd: no visible global function definition for 'rbinom'
.simulate.trans: no visible global function definition for 'rlnorm'
.simulate.trans: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  rbeta rbinom rlnorm rnorm runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rlnorm", "rnorm", "runif")
to your NAMESPACE file.
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  'MASS' 'Rdpack' 'base' 'graphics' 'parallel'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'bioimagetools'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Note: found 6409 marked UTF-8 strings
Packages required but not available: 'curl', 'httr'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 7284 marked UTF-8 strings
Packages suggested but not available for checking: 'tigris', 'socialmixr'
Error(s) in re-building vignettes:
  ...
--- re-building 'o2geosocial.Rmd' using rmarkdown
Registered S3 methods overwritten by 'o2geosocial':
  method                    from       
  plot.outbreaker_chains    outbreaker2
  print.custom_likelihoods  outbreaker2
  print.custom_priors       outbreaker2
  print.outbreaker_chains   outbreaker2
  summary.outbreaker_chains outbreaker2
Quitting from lines 152-165 (o2geosocial.Rmd) 
Error: processing vignette 'o2geosocial.Rmd' failed with diagnostics:
there is no package called 'socialmixr'
--- failed re-building 'o2geosocial.Rmd'

SUMMARY: processing the following file failed:
  'o2geosocial.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

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 hidden files and directories:
  .gitignore
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'objectSignals'
A package should be listed in only one of these fields.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
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.
Color: no visible global function definition for 'new'
NegativeInteger: no visible global function definition for 'new'
NonnegativeInteger: no visible global function definition for 'new'
NonpositiveInteger: no visible global function definition for 'new'
PositiveInteger: no visible global function definition for 'new'
setMultipleEnum: no visible global function definition for 'setClass'
setMultipleEnum: no visible global function definition for 'prototype'
setNumericWithRange: no visible global function definition for
  'setClass'
setNumericWithRange: no visible global function definition for
  'prototype'
setPropertySet: no visible binding for global variable 'extends'
setPropertySet: no visible global function definition for 'setRefClass'
setSingleEnum: no visible global function definition for 'setClass'
setSingleEnum: no visible global function definition for 'prototype'
as.list,PropertySet: no visible global function definition for 'as'
initialize,SingleEnum: no visible global function definition for
  'callNextMethod'
initialize,SingleEnum: no visible global function definition for 'head'
Undefined global functions or variables:
  as callNextMethod extends head new prototype setClass setRefClass
Consider adding
  importFrom("methods", "as", "callNextMethod", "extends", "new",
             "prototype", "setClass", "setRefClass")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
A package should be listed in only one of these fields.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
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.
Signal.gen: 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').
Packages in Depends field not imported from:
  'ROCR' 'e1071' 'mda' 'pls'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
log_wrapper: no visible global function definition for 'glm'
log_wrapper: no visible global function definition for 'binomial'
log_wrapper: no visible global function definition for 'coef'
log_wrapper: no visible global function definition for 'anova'
obliqueRF.default: no visible binding for global variable 'predict'
obliqueRF.default: no visible global function definition for
  'prediction'
obliqueRF.default: no visible global function definition for
  'performance'
pls_wrapper: no visible global function definition for 'kernelpls.fit'
pls_wrapper: no visible global function definition for 'coef'
ridge_slow_wrapper: no visible global function definition for
  'gen.ridge'
ridge_slow_wrapper: no visible global function definition for 'predict'
ridge_svd_wrapper: no visible global function definition for
  'gen.ridge'
rnd_wrapper: no visible global function definition for 'rnorm'
svm_wrapper: no visible global function definition for 'svm'
svm_wrapper: no visible global function definition for 'predict'
Undefined global functions or variables:
  anova binomial coef gen.ridge glm kernelpls.fit performance predict
  prediction rnorm svm
Consider adding
  importFrom("stats", "anova", "binomial", "coef", "glm", "predict",
             "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.
IBMD: no visible global function definition for 'runif'
IBMD: no visible global function definition for 'quantile'
RAI: no visible global function definition for 'runif'
RAI: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile runif
Consider adding
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
obsSensCCC: no visible global function definition for 'coef'
obsSensCCC: no visible global function definition for 'confint'
obsSensCCN: no visible global function definition for 'coef'
obsSensCCN: no visible global function definition for 'confint'
obsSensCNN: no visible global function definition for 'coef'
obsSensCNN: no visible global function definition for 'confint'
obsSensCNN: no visible global function definition for 'sd'
obsSensCNN: no visible global function definition for 'model.matrix'
obsSensNNN: no visible global function definition for 'coef'
obsSensNNN: no visible global function definition for 'confint'
obsSensNNN: no visible global function definition for 'sd'
obsSensNNN: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  coef confint model.matrix sd
Consider adding
  importFrom("stats", "coef", "confint", "model.matrix", "sd")
to your NAMESPACE file.
Packages required but not available: 'bib2df', 'rgbif', 'taxize'

Packages suggested but not available for checking: 'RefManageR', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rio'
Namespace in Imports field not imported from: 'units'
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building 'integration_shiny.Rmd' using rmarkdown
--- finished re-building 'integration_shiny.Rmd'

--- re-building 'oceanis.Rmd' using rmarkdown
Quitting from lines 48-50 (oceanis.Rmd) 
Error: processing vignette 'oceanis.Rmd' failed with diagnostics:
there is no package called 'rio'
--- failed re-building 'oceanis.Rmd'

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

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

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: 'covr'
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tidyverse'
Namespaces in Imports field not imported from:
  'RColorBrewer' 'graphics'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'jsonvalidate'
'LazyData' is specified without a 'data' directory
Package required but not available: 'gsheet'

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 suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'rsdmx'

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
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'Deducer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rvest'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
avgokmts: no visible global function definition for 'aggregate'
downloadstn: no visible global function definition for 'read.csv'
nearstn: no visible binding for global variable 'okstations'
nearstn: no visible binding for global variable 'Commissioned'
nearstn: no visible binding for global variable 'Decommissioned'
okcurobs: no visible global function definition for 'read.csv'
okmts: no visible binding for global variable 'okstations'
okmts: no visible binding for global variable 'TIME'
retrievemts: no visible global function definition for 'read.csv'
totalprecip: no visible binding for global variable 'TIME'
totalprecip: no visible global function definition for 'aggregate'
vincenty: no visible global function definition for 'runif'
Undefined global functions or variables:
  Commissioned Decommissioned TIME aggregate okstations read.csv runif
Consider adding
  importFrom("stats", "aggregate", "runif")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
OLScurve: no visible global function definition for 'as.formula'
OLScurve: no visible global function definition for 'na.omit'
OLScurve: no visible global function definition for 'lm'
OLScurve: no visible global function definition for 'predict'
OLScurve: no visible global function definition for 'residuals'
OLScurve: no visible global function definition for 'model.frame'
OLScurve: no visible global function definition for 'model.matrix'
plot.OLScurve : plotOLScurve: no visible global function definition for
  'reshape'
print.OLScurve: no visible global function definition for 'na.omit'
print.OLScurve: no visible global function definition for 'model.frame'
print.OLScurve: no visible global function definition for
  'model.matrix'
print.OLScurve: no visible global function definition for 'cov'
print.OLScurve: no visible global function definition for 'cor'
print.OLScurve: no visible global function definition for 'sd'
subjplot.OLScurve : plotOLScurve: no visible global function definition
  for 'devAskNewPage'
subjplot.OLScurve : plotOLScurve: no visible global function definition
  for 'reshape'
subjplot.OLScurve : plotOLScurve : mypanel: no visible global function
  definition for 'gray'
subjplot.OLScurve: no visible global function definition for
  'devAskNewPage'
Undefined global functions or variables:
  as.formula cor cov devAskNewPage gray lm model.frame model.matrix
  na.omit predict reshape residuals sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "gray")
  importFrom("stats", "as.formula", "cor", "cov", "lm", "model.frame",
             "model.matrix", "na.omit", "predict", "reshape",
             "residuals", "sd")
to your NAMESPACE file.
Package required but not available: 'car'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
fhcor: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor
Consider adding
  importFrom("stats", "cor")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'base'
  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
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'gt'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'KEGGREST'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 842 marked UTF-8 strings
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
MLparameters: no visible global function definition for 'optim'
comp.freq: no visible global function definition for 'x11'
comp.freq: no visible global function definition for 'par'
Undefined global functions or variables:
  optim par x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par")
  importFrom("stats", "optim")
to your NAMESPACE file.
Packages required but not available:
  'car', 'sva', 'GenomicFeatures', 'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'genefilter', 'tidyverse', 'TCGAbiolinks'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
generate.data: no visible global function definition for 'rbinom'
least.common.ancestor: no visible global function definition for
  'na.omit'
oncotree.fit : estimate.error.rates: no visible global function
  definition for 'optim'
plot.boottree: no visible global function definition for 'par'
plot.boottree: no visible global function definition for
  'dev.interactive'
plot.boottree: no visible global function definition for 'mtext'
plot.oncotree: no visible global function definition for 'par'
plot.oncotree: no visible global function definition for 'xinch'
plot.oncotree: no visible global function definition for 'yinch'
plot.oncotree: no visible global function definition for 'lines'
plot.oncotree: no visible global function definition for 'rect'
plot.oncotree: no visible global function definition for 'strwidth'
plot.oncotree: no visible global function definition for 'strheight'
plot.oncotree: no visible global function definition for 'text'
Undefined global functions or variables:
  dev.interactive lines mtext na.omit optim par rbinom rect strheight
  strwidth text xinch yinch
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "lines", "mtext", "par", "rect", "strheight",
             "strwidth", "text", "xinch", "yinch")
  importFrom("stats", "na.omit", "optim", "rbinom")
to your NAMESPACE file.
Package suggested but not available for checking: 'devtools'
Namespaces in Imports field not imported from:
  'e1071' 'fs' 'pdp'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rhdf5', 'Rhdf5lib'

Package suggested but not available for checking: 'covr'

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
Namespaces in Imports field not imported from:
  'R6' 'safer'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plotly', 'MDSMap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'AID'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'VIM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'plotly'
Note: found 32 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rgraphviz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'randomForest' 'ranger'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'shinytest'
Namespaces in Imports field not imported from:
  'R6' 'dplyr' 'miniUI' 'text2vec'
  All declared Imports should be used.
ci.prop: no visible global function definition for 'qf'
ci.prop: no visible global function definition for 'qnorm'
ePCP: no visible global function definition for 'qnorm'
sevennum: no visible global function definition for 'na.omit'
sevennum: no visible global function definition for 'quantile'
Undefined global functions or variables:
  na.omit qf qnorm quantile
Consider adding
  importFrom("stats", "na.omit", "qf", "qnorm", "quantile")
to your NAMESPACE file.
Packages required but not available: 'forecast', 'imputeTS'

Package suggested but not available for checking: 'quantmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'crul'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'crul'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/OpenCL/OpenCL.Rcheck/00install.out' for details.
Packages required but not available: 'webutils', 'curl'

Package suggested but not available for checking: 'unix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Packages required but not available: 'ckanr', 'curl'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Note: found 2518 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking: 'httr', 'plumber'
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'curl'

Package suggested but not available for checking: 'lintr'

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: 'covr', 'umx'
Package unavailable to check Rd xrefs: 'umx'
Package suggested but not available for checking: 'openNLPmodels.en'
Package required but not available: 'tidyverse'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'ssh', 'ggmap', 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'osfr'

Packages suggested but not available for checking:
  'plotly', 'curl', 'rdrop2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Df2SpLinesDf: no visible global function definition for 'slot'
PlotTraj: no visible global function definition for 'par'
PlotTraj: no visible global function definition for 'grid'
PlotTraj: no visible global function definition for 'box'
PlotTrajFreq: no visible global function definition for 'par'
PlotTrajFreq: no visible global function definition for 'grid'
PlotTrajFreq: no visible global function definition for
  'colorRampPalette'
PlotTrajFreq: no visible global function definition for 'legend'
PlotTrajFreq: no visible binding for global variable 'title'
PlotTrajFreq: no visible global function definition for 'dev.off'
ReadFiles: no visible global function definition for 'read.table'
Undefined global functions or variables:
  box colorRampPalette dev.off grid legend par read.table slot title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off")
  importFrom("graphics", "box", "grid", "legend", "par", "title")
  importFrom("methods", "slot")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package required but not available: 'curl'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'InterVA5', 'InSilicoVA'

Package suggested but not available for checking: 'nbc4va'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
nlsolve: no visible global function definition for 'optim'
nlsolve: no visible global function definition for 'runif'
optAUC: no visible global function definition for 'var'
Undefined global functions or variables:
  optim runif var
Consider adding
  importFrom("stats", "optim", "runif", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'org.At.tair.db', 'annotate'
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'geometry'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'tidyverse', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'Matrix'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'boot' 'splines'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
getMinimumArborescence: no visible global function definition for
  'capture.output'
getMinimumCutTree: no visible global function definition for
  'capture.output'
getMinimumCutTree: no visible global function definition for 'par'
getMinimumSpanningTree: no visible global function definition for
  'capture.output'
getShortestPathTree: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output par
Consider adding
  importFrom("graphics", "par")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Agrestiind.CI: no visible global function definition for 'qnorm'
BPexact.CI: no visible global function definition for 'uniroot'
BPmidp.CI: no visible global function definition for 'uniroot'
Cornfieldexact.CI: no visible global function definition for 'uniroot'
Cornfieldmidp.CI: no visible global function definition for 'uniroot'
Gart.CI: no visible global function definition for 'qnorm'
Invsinh.CI: no visible global function definition for 'qnorm'
Woolf.CI: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm uniroot
Consider adding
  importFrom("stats", "qnorm", "uniroot")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'library' or 'require' calls to packages already attached by Depends:
  'Matrix' 'splines'
  Please remove these calls from your code.
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nr' to 'nrow'
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nc' to 'ncol'
bgmm: no visible global function definition for 'ecdf'
bgmm : SplineGMM: no visible global function definition for
  'constrOptim'
blr: no visible global function definition for 'ecdf'
blr: no visible global function definition for 'constrOptim'
blr: no visible global function definition for 'lm'
parentcdf : combinations: no visible global function definition for
  'combn'
parentcdf : solver: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
'library' or 'require' call to 'methods' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'grid' 'lattice' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: 'gert'

Packages suggested but not available for checking: 'httr', 'vaultr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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
Package suggested but not available for checking: 'IsoGene'
genRidge: no visible global function definition for 'plogis'
ordGene: no visible global function definition for 'anova'
ordGene: no visible global function definition for 'lm'
ordSelect: no visible binding for global variable 'sd'
ordSmooth: no visible binding for global variable 'sd'
plot.ordPen: no visible global function definition for 'grey'
plot.ordPen: no visible global function definition for 'devAskNewPage'
plot.ordPen: no visible global function definition for 'lines'
predict.ordPen: no visible global function definition for 'plogis'
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines")
  importFrom("stats", "anova", "lm", "plogis", "sd")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  'ggplot2' 'gridExtra' 'scales' 'tools'
  All declared Imports should be used.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
ORICC1: no visible binding for global variable 'sd'
ORICC1: no visible global function definition for 'write.table'
ORICC1: no visible global function definition for 'postscript'
ORICC1: no visible global function definition for 'jpeg'
ORICC1: no visible global function definition for 'points'
ORICC1: no visible global function definition for 'dev.off'
ORICC1: no visible global function definition for 'par'
ORICC2: no visible binding for global variable 'sd'
ORICC2: no visible global function definition for 'write.table'
ORICC2: no visible global function definition for 'postscript'
ORICC2: no visible global function definition for 'jpeg'
ORICC2: no visible global function definition for 'points'
ORICC2: no visible global function definition for 'dev.off'
ORICC2: no visible global function definition for 'par'
Undefined global functions or variables:
  dev.off jpeg par points postscript sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "postscript")
  importFrom("graphics", "par", "points")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package suggested but not available for checking: 'forecast'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'generalizedCV.Rmd' using rmarkdown
Quitting from lines 282-317 (generalizedCV.Rmd) 
Error: processing vignette 'generalizedCV.Rmd' failed with diagnostics:
there is no package called 'forecast'
--- failed re-building 'generalizedCV.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown'
  All declared Imports should be used.
Package required but not available: 'benchmarkme'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
mdr.c: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
  'LazyDataCompression' is specified without a 'data' directory
Namespace in Imports field not imported from: 'grDevices'
  All declared Imports should be used.
Package required but not available: 'genefilter'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
plot.SplineBasis: no visible global function definition for 'matplot'
plot,SplineBasis-matrix: no visible global function definition for
  'matplot'
plot,SplineBasis-missing: no visible global function definition for
  'matplot'
Undefined global functions or variables:
  matplot
Consider adding
  importFrom("graphics", "matplot")
to your NAMESPACE file.
'library' or 'require' call to 'polynom' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'polynom'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
chebyshev.c.polynomials: no visible global function definition for
  'polynomial'
chebyshev.s.polynomials: no visible global function definition for
  'polynomial'
chebyshev.t.polynomials: no visible global function definition for
  'polynomial'
chebyshev.u.polynomials: no visible global function definition for
  'polynomial'
gegenbauer.polynomials: no visible global function definition for
  'polynomial'
ghermite.h.polynomials: no visible global function definition for
  'polynomial'
glaguerre.polynomials: no visible global function definition for
  'polynomial'
hermite.h.polynomials: no visible global function definition for
  'polynomial'
hermite.he.polynomials: no visible global function definition for
  'polynomial'
jacobi.g.polynomials: no visible global function definition for
  'polynomial'
jacobi.p.polynomials: no visible global function definition for
  'polynomial'
legendre.polynomials: no visible global function definition for
  'polynomial'
monic.polynomials: no visible global function definition for
  'polynomial'
orthogonal.polynomials: no visible global function definition for
  'polynomial'
orthonormal.polynomials: no visible global function definition for
  'polynomial'
polynomial.derivatives: no visible global function definition for
  'deriv'
polynomial.integrals: no visible global function definition for
  'integral'
polynomial.values: no visible global function definition for 'predict'
schebyshev.t.polynomials: no visible global function definition for
  'polynomial'
schebyshev.u.polynomials: no visible global function definition for
  'polynomial'
slegendre.polynomials: no visible global function definition for
  'polynomial'
Undefined global functions or variables:
  deriv integral polynomial predict
Consider adding
  importFrom("stats", "deriv", "predict")
to your NAMESPACE file.
Packages required but not available: 'googleAuthR', 'googleCloudVisionR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'qpdf'
Namespaces in Imports field not imported from:
  'knitr' '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
Packages required but not available: 'crul', 'httr'

Packages suggested but not available for checking: 'lintr', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  'igraph' 'sp'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
as_igraph : <anonymous>: no visible global function definition for
  'distHaversine'
as_igraph: no visible global function definition for 'graph.edgelist'
as_igraph: no visible global function definition for 'E'
as_igraph: no visible global function definition for 'E<-'
as_sp_lines: no visible global function definition for 'Lines'
as_sp_points: no visible global function definition for
  'SpatialPointsDataFrame'
as_sp_polygons: no visible global function definition for 'Polygons'
as_sp_polygons: no visible global function definition for
  'SpatialPolygons'
as_sp_polygons: no visible global function definition for
  'SpatialPolygonsDataFrame'
make_SLDF: no visible global function definition for 'SpatialLines'
make_SLDF: no visible global function definition for
  'SpatialLinesDataFrame'
osm_crs: no visible global function definition for 'CRS'
plot.osmar: no visible global function definition for 'gray'
plot_nodes: no visible global function definition for 'points'
plot_ways: no visible global function definition for 'lines'
ways_nodes2Line: no visible global function definition for 'Line'
ways_nodes2Polygon: no visible global function definition for 'Polygon'
Undefined global functions or variables:
  CRS E E<- Line Lines Polygon Polygons SpatialLines
  SpatialLinesDataFrame SpatialPointsDataFrame SpatialPolygons
  SpatialPolygonsDataFrame distHaversine graph.edgelist gray lines
  points
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "points")
to your NAMESPACE file.
Note: found 80 marked UTF-8 strings
Packages required but not available: 'curl', 'httr', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Note: found 263 marked UTF-8 strings
Packages required but not available: 'osmdata', 'qpdf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'osmdata'

Package suggested but not available for checking: 'curl'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'Rcplex'
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'R6' 'openssl'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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

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.
Namespace in Imports field not imported from: 'quantreg'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
odm: no visible binding for global variable 'sd'
odm : <anonymous>: no visible global function definition for 'sd'
odm : <anonymous>: no visible global function definition for 'quantile'
odm: no visible global function definition for 'prcomp'
quant.const: no visible global function definition for 'quantile'
quant.const.D: no visible global function definition for 'reshape'
quant.const.D: no visible global function definition for 'quantile'
quant.linear.D: no visible global function definition for 'reshape'
quant.nonlin : FrankModel: no visible global function definition for
  'qt'
quant.nonlin : FrankModel: no visible global function definition for
  'pt'
quant.nonlin: no visible global function definition for 'predict'
quant.nonlin.D: no visible global function definition for 'reshape'
quant.nonlin.D: no visible global function definition for 'predict'
quant.nonpar.D: no visible global function definition for 'reshape'
rgrubbs.test: no visible global function definition for 'sd'
plot,OutlierDM-missing: no visible binding for global variable 'pch'
summary,OutlierDM: no visible global function definition for 'head'
Undefined global functions or variables:
  head pch prcomp predict pt qt quantile reshape sd
Consider adding
  importFrom("stats", "prcomp", "predict", "pt", "qt", "quantile",
             "reshape", "sd")
  importFrom("utils", "head")
to your NAMESPACE file.
Package required but not available: 'HDoutliers'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'AER'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(testthat)
  > library(outreg)
  > 
  > test_check("outreg")
  == Failed tests ================================================================
  -- Error (test_validfits.R:48:3): supported objects ----------------------------
  Error: there is no package called 'AER'
  Backtrace:
      x
   1. \-base::library(AER) test_validfits.R:48:2
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
  Error: Test failures
  Execution halted
Package required but not available: 'devtools'

Package suggested but not available for checking: 'ssh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'outsider.base', 'curl'

Package suggested but not available for checking: 'ssh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'adephylo'

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: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'covr', 'devtools', 'pkgdown'
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

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: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'geometa', 'httr'

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: 'curl', 'covr', 'rvest'
Running examples in 'oxcgrt-Ex.R' failed
The error most likely occurred in:

> ### Name: calculate_index
> ### Title: Calculate an OxCGRT index or indices
> ### Aliases: calculate_index calculate_gov_response
> ###   calculate_containment_health calculate_stringency
> ###   calculate_economic_support calculate_indices
> 
> ### ** Examples
> 
> ## Get policy actions data for Afghanistan on 1 September 2020
> x <- get_data(json = get_json_actions(ccode = "AFG",
+                                       from = NULL,
+                                       to = "2020-09-01"))
Error: Required package curl not found. Please run: install.packages('curl')
Execution halted
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Backtrace:
      x
   1. +-json_time %>% get_data() test-get_data.R:7:0
   2. \-oxcgrt::get_data(.)
   3.   \-jsonlite::fromJSON(txt = json, flatten = TRUE)
   4.     \-jsonlite:::loadpkg("curl")
   5.       \-base::tryCatch(...)
   6.         \-base:::tryCatchList(expr, classes, parentenv, handlers)
   7.           \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   8.             \-value[[3L]](cond)
   9.               \-jsonlite:::stop(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 19 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'calculate.Rmd' using rmarkdown
Quitting from lines 37-60 (calculate.Rmd) 
Error: processing vignette 'calculate.Rmd' failed with diagnostics:
there is no package called 'rvest'
--- failed re-building 'calculate.Rmd'

--- re-building 'retrieve.Rmd' using rmarkdown
Quitting from lines 45-46 (retrieve.Rmd) 
Error: processing vignette 'retrieve.Rmd' failed with diagnostics:
Required package curl not found. Please run: install.packages('curl')
--- failed re-building 'retrieve.Rmd'

SUMMARY: processing the following files failed:
  'calculate.Rmd' 'retrieve.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'httr'

Packages suggested but not available for checking: 'covr', 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
loadCSVtoP2distance: no visible global function definition for
  'read.table'
p2distance : calcularDistancia: no visible binding for global variable
  'sd'
p2distance : ordenarVariables: no visible global function definition
  for 'cor'
p2distance : calculoFactoresPonderacion: no visible global function
  definition for 'lm'
p2distance: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor lm read.table sd
Consider adding
  importFrom("stats", "cor", "lm", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'survival' which was already attached by Depends.
  Please remove these calls from your code.
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.
p3state: no visible global function definition for 'survfit'
p3state: no visible global function definition for 'terms'
p3state: no visible global function definition for 'as.formula'
p3state: no visible global function definition for 'coxph'
p3state: no visible binding for global variable 'na.exclude'
plot.p3state: no visible global function definition for 'matplot'
plot.p3state: no visible global function definition for 'devAskNewPage'
plot.p3state: no visible global function definition for 'persp'
plot.p3state: no visible global function definition for 'colours'
plot.p3state: no visible global function definition for
  'filled.contour'
Undefined global functions or variables:
  as.formula colours coxph devAskNewPage filled.contour matplot
  na.exclude persp survfit terms
Consider adding
  importFrom("grDevices", "colours", "devAskNewPage")
  importFrom("graphics", "filled.contour", "matplot", "persp")
  importFrom("stats", "as.formula", "na.exclude", "terms")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
pacbpred : thetaFunc: no visible global function definition for 'lsfit'
pacbpred : thetaFunc: no visible global function definition for 'rnorm'
pacbpred: no visible global function definition for 'var'
pacbpred: no visible global function definition for 'runif'
pacbpred: no visible global function definition for 'rnorm'
pacbpred: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  lsfit rbinom rnorm runif var
Consider adding
  importFrom("stats", "lsfit", "rbinom", "rnorm", "runif", "var")
to your NAMESPACE file.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cranlogs', 'pkgsearch', 'rversions'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gert', 'httr', 'rhub', 'whoami'

Packages suggested but not available for checking:
  'covr', 'devtools', 'lintr', 'rasciidoc', 'usethis'

VignetteBuilder package required for checking but not installed: 'rasciidoc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

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:
  'survminer', 'systemfit', 'IPDFileCheck', 'car', 'tidyverse'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'usethis'

Packages suggested but not available for checking: 'covr', 'golem'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'FactoMineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'devtools', 'httr'
[,ClassW: warning in switch(EXP = i, u1 = {: partial argument match of
  'EXP' to 'EXPR'
[,ClassW: warning in return(x@u1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@u2): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@w1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
[<-,ClassW: warning in switch(EXP = i, u1 = {: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW: warning in x@u1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@u2 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@w1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: 'devtools'
Namespace in Imports field not imported from: 'ape'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'e1071'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'genbankr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
paf: no visible global function definition for 'as.formula'
paf: no visible global function definition for 'model.response'
paf: no visible global function definition for 'model.frame'
paf: no visible global function definition for 'model.matrix'
plot.paf: no visible global function definition for 'lines'
Undefined global functions or variables:
  as.formula lines model.frame model.matrix model.response
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
Packages suggested but not available for checking: 'covr', 'ggpubr'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'Introduction_to_pafr.Rmd' using rmarkdown
Quitting from lines 83-91 (Introduction_to_pafr.Rmd) 
Error: processing vignette 'Introduction_to_pafr.Rmd' failed with diagnostics:
there is no package called 'ggpubr'
--- failed re-building 'Introduction_to_pafr.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'pdftools'
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'pagemap.Rmd' using rmarkdown
Quitting from lines 20-29 (pagemap.Rmd) 
Error: processing vignette 'pagemap.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'pagemap.Rmd'

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

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

Packages suggested but not available for checking: 'WikipediR', 'WikidataR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
CalGIF: no visible binding for global variable 'PAGIData'
CalGIF2: no visible binding for global variable 'PAGIData'
PAGI.Main: no visible binding for global variable 'PAGIData'
PAGI.Main: no visible global function definition for 'p.adjust'
PAGI.Main: no visible global function definition for 'pt'
getclass.labels: no visible binding for global variable 'ExampleData'
getdataset: no visible binding for global variable 'ExampleData'
Undefined global functions or variables:
  ExampleData PAGIData p.adjust pt
Consider adding
  importFrom("stats", "p.adjust", "pt")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'org.Dr.eg.db', 'org.Mm.eg.db', 'p2data', 'scde'
Packages required but not available: 'plotly', 'heatmaply'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
paired.Loc: no visible global function definition for 'qt'
paired.Loc: no visible global function definition for 'median'
paired.Loc: no visible global function definition for 'qsignrank'
paired.Loc: no visible global function definition for 'qnorm'
paired.Scale: no visible global function definition for 'var'
paired.Scale: no visible global function definition for 'cor'
paired.Scale: no visible global function definition for 'qt'
paired.Scale: no visible global function definition for 'median'
paired.Scale: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  cor median qnorm qsignrank qt var
Consider adding
  importFrom("stats", "cor", "median", "qnorm", "qsignrank", "qt", "var")
to your NAMESPACE file.
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.
'LazyData' is specified without a 'data' directory
pairsD3: no visible global function definition for 'gray.colors'
Undefined global functions or variables:
  gray.colors
Consider adding
  importFrom("grDevices", "gray.colors")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'alr4'
Error(s) in re-building vignettes:
  ...
--- re-building 'MultipleComparisons.Rmd' using rmarkdown
--- finished re-building 'MultipleComparisons.Rmd'

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

--- re-building 'pcp.Rmd' using rmarkdown
Quitting from lines 131-152 (pcp.Rmd) 
Error: processing vignette 'pcp.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building 'pcp.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Packages required but not available: 'curl', 'pkgcache'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyverse'
Error(s) in re-building vignettes:
  ...
--- re-building 'h-block-crossvalidation.Rmd' using rmarkdown
This is rioja 0.9-26
Quitting from lines 29-39 (h-block-crossvalidation.Rmd) 
Error: processing vignette 'h-block-crossvalidation.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'h-block-crossvalidation.Rmd'

SUMMARY: processing the following file failed:
  'h-block-crossvalidation.Rmd'

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: 'CorShrink'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'lattice' 'vegan'
  Please remove these calls from your code.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'trend'
  All declared Imports should be used.
Note: found 9 marked UTF-8 strings
Namespace in Imports field not imported from: 'iterators'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'Rcpp'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 34 marked UTF-8 strings
Packages required but not available: 'rerddap', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'PAMmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'smoothmest'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GOpredict: no visible global function definition for 'fisher.test'
KEGGpredict: no visible global function definition for 'fisher.test'
ProteinCluster: no visible global function definition for 'ecdf'
ProteinCluster: no visible global function definition for 'as.hclust'
ProteinCluster: no visible global function definition for
  'as.dendrogram'
ProteinCluster : addE: no visible global function definition for
  'is.leaf'
SignificantSubcluster: no visible global function definition for
  'order.dendrogram'
SignificantSubcluster: no visible global function definition for
  'fisher.test'
Undefined global functions or variables:
  as.dendrogram as.hclust ecdf fisher.test is.leaf order.dendrogram
Consider adding
  importFrom("stats", "as.dendrogram", "as.hclust", "ecdf",
             "fisher.test", "is.leaf", "order.dendrogram")
to your NAMESPACE file.
Packages required but not available: 'rstan', 'plotly', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'tseries', 'forecast'
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Paneldata.formula: no visible global function definition for
  'model.frame'
Paneldata.formula: no visible global function definition for
  'model.matrix'
Paneldata.formula: no visible global function definition for
  'model.response'
summary.Paneldata: no visible global function definition for 'coef'
summary.Paneldata: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.frame model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pt")
to your NAMESPACE file.
Packages suggested but not available for checking: 'brms', 'car', 'covr'
Packages unavailable to check Rd xrefs: 'AER', 'brms'
Running examples in 'panelr-Ex.R' failed
The error most likely occurred in:

> ### Name: asym_gee
> ### Title: Asymmetric effects models fit with GEE
> ### Aliases: asym_gee
> 
> ### ** Examples
> 
> data("WageData")
> wages <- panel_data(WageData, id = id, wave = t)
> model <- asym_gee(lwage ~ lag(union) + wks, data = wages)
Loading required namespace: geepack
Loading required namespace: car
Failed with error:  'there is no package called 'car''
Error: You must have 'car' installed to use this function.
Backtrace:
 1. panelr::asym_gee(lwage ~ lag(union) + wks, data = wages)
 2. panelr:::need_package("car")
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- Error (test_asym_gee.R:12:1): (code run outside of `test_that()`) -----------
  Error: You must have 'car' installed to use this function.
  Backtrace:
      x
   1. \-panelr::asym_gee(wks ~ union + lwage, data = wages) test_asym_gee.R:12:0
   2.   \-panelr:::need_package("car")
  -- Error (test_wbm.R:283:1): (code run outside of `test_that()`) ---------------
  Error: You must have the brms package installed to use wbm_stan.
  Backtrace:
      x
   1. \-panelr::wbm_stan(...) test_wbm.R:283:0
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 210 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'reshape.Rmd' using rmarkdown
Loading required package: lme4
Loading required package: Matrix

Attaching package: 'panelr'

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

    filter

--- finished re-building 'reshape.Rmd'

--- re-building 'wbm.Rmd' using rmarkdown
Failed with error:  'there is no package called 'car''
Quitting from lines 445-447 (wbm.Rmd) 
Error: processing vignette 'wbm.Rmd' failed with diagnostics:
You must have 'car' installed to use this function.
--- failed re-building 'wbm.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'texreg'

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

Package suggested but not available for checking: 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'caret' 'geoR' 'gstat' 'pryr'
  All declared Imports should be used.
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rgraphviz'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'AER', 'afex', 'brms', 'car', 'FactoMineR', 'metaBMA', 'projpred',
  'rstanarm'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'ggpubr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'magrittr' 'tibble'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
.formula.make: no visible global function definition for 'formula'
regress: no visible global function definition for 'lm'
regress: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  formula lm model.matrix
Consider adding
  importFrom("stats", "formula", "lm", "model.matrix")
to your NAMESPACE file.
'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: 'mnis'

Packages suggested but not available for checking: 'covr', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'flexsurv'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'parallel'
  All declared Imports should be used.
Packages suggested but not available for checking: 'covr', 'sparklyr'
Package suggested but not available for checking: 'AER'
Running examples in 'PartCensReg-Ex.R' failed
The error most likely occurred in:

> ### Name: Cens.SMN.PCR
> ### Title: Estimation and diagnostics for partially linear censored
> ###   regression models
> ### Aliases: Cens.SMN.PCR
> ### Keywords: package censored censoring diagnostic partial partially
> 
> ### ** Examples
> 
> dtawage = get(data(PSID1976,package = "AER"))
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'AER'
Calls: get -> data -> find.package
Execution halted
Package required but not available: 'tseries'

Packages suggested but not available for checking: 'egcm', 'TTR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'partialAR', 'TTR'

Package suggested but not available for checking: 'egcm'

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.
Package in Depends field not imported from: 'nnet'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fitOR: no visible global function definition for 'multinom'
fitOR: no visible global function definition for 'formula'
fitOR: no visible global function definition for 'coef'
fitOR: no visible global function definition for 'optim'
reportOR: no visible global function definition for 'qnorm'
reportOR: no visible global function definition for 'pchisq'
reportOR: no visible global function definition for 'coef'
simData: no visible global function definition for 'rnorm'
simData: no visible global function definition for 'runif'
Undefined global functions or variables:
  coef formula multinom optim pchisq qnorm rnorm runif
Consider adding
  importFrom("stats", "coef", "formula", "optim", "pchisq", "qnorm",
             "rnorm", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'dplyr'
  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: 'stats'
  All declared Imports should be used.
partitionMap: no visible global function definition for 'predict'
partitionMap: no visible global function definition for 'rnorm'
partitionMap: no visible binding for global variable 'sd'
partitionMap: no visible global function definition for 'sd'
partitionMap: no visible global function definition for 'quantile'
Undefined global functions or variables:
  predict quantile rnorm sd
Consider adding
  importFrom("stats", "predict", "quantile", "rnorm", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package suggested but not available for checking: 'AER'
Errors in running code in vignettes:
when running code in 'mob.Rnw'
  ...

> predict(pid_tree2, newdata = pid, type = "link")
      1       2       3       4       5       6 
 0.7123 -0.7704  0.7920 -2.5371  0.4535 -3.1414 

> data("Journals", package = "AER")

  When sourcing 'mob.R':
Error: there is no package called 'AER'
Execution halted

  'constparty.Rnw'... OK
  'ctree.Rnw' using 'UTF-8'... OK
  'mob.Rnw'... failed
  'partykit.Rnw'... OK
Malformed Description field: should contain one or more complete sentences.
parviol: no visible global function definition for 'plot.new'
parviol: no visible global function definition for 'plot.window'
parviol: no visible global function definition for 'title'
parviol: no visible global function definition for 'lines'
parviol: no visible global function definition for 'text'
parviol: no visible global function definition for 'rgb'
selecto: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot.new plot.window rgb text title
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot.new", "plot.window", "text",
             "title")
to your NAMESPACE file.
Package required but not available: 'plotly'

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: 'covr'
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Packages in Depends field not imported from:
  'ape' 'caper'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
conch: no visible global function definition for 'read.tree'
conch: no visible global function definition for 'reorder'
conch: no visible global function definition for 'read.nexus'
conch: no visible global function definition for '.compressTipLabel'
conch: no visible global function definition for 'drop.tip'
conch: no visible global function definition for 'extract.clade'
conch: no visible global function definition for 'which.edge'
conch: no visible global function definition for 'write.tree'
pastis_main: no visible global function definition for 'combn'
read_input: no visible global function definition for 'read.tree'
read_input: no visible global function definition for 'reorder'
read_input: no visible global function definition for 'read.csv'
read_input: no visible global function definition for 'read.dna'
Undefined global functions or variables:
  .compressTipLabel combn drop.tip extract.clade read.csv read.dna
  read.nexus read.tree reorder which.edge write.tree
Consider adding
  importFrom("stats", "reorder")
  importFrom("utils", "combn", "read.csv")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'e1071'
  Please remove these calls from your code.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'logger'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: 'pathfindR'
Note: found 1 marked UTF-8 string
Packages required but not available: 'magick', 'KEGGREST'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'R6' 'glue' 'logging' 'purrr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'MplusAutomation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'pdftools'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(testthat)
  > library(patientProfilesVis)
  > 
  > test_check("patientProfilesVis")
  Fontconfig error: Cannot load default config file
  == Failed tests ================================================================
  -- Error (test_createSubjectProfileReport.R:3:1): (code run outside of `test_that()`) --
  Error: there is no package called 'pdftools'
  Backtrace:
      x
   1. \-base::library(pdftools) test_createSubjectProfileReport.R:3:0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 365 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'patientProfiles-template-SDTM.Rmd' using rmarkdown
--- finished re-building 'patientProfiles-template-SDTM.Rmd'

--- re-building 'patientProfilesVis-introduction.Rmd' using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open file 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/patientProfilesVis/patientProfilesVis.Rcheck/vign_test/patientProfilesVis/vignettes/patientProfilesVis-introduction_files/figure-html/exampleIntervalModule-ae-customMissingPartialDates-include-1.png' for writing
Warning in png(..., res = dpi, units = "in") : opening device failed
Quitting from lines 591-594 (patientProfilesVis-introduction.Rmd) 
Error: processing vignette 'patientProfilesVis-introduction.Rmd' failed with diagnostics:
unable to start png() device
--- failed re-building 'patientProfilesVis-introduction.Rmd'

SUMMARY: processing the following file failed:
  'patientProfilesVis-introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
Checking should be performed on sources prepared by 'R CMD build'.
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package required but not available: 'SelectBoost'

Packages suggested but not available for checking:
  'animation', 'biomaRt', 'repmis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
add_noise: no visible global function definition for 'rnorm'
estimate_risk_dream6 : <anonymous>: no visible global function
  definition for 'var'
generate_sample: no visible global function definition for 'rnorm'
generate_sample: no visible global function definition for 'runif'
sample_function: no visible global function definition for 'runif'
sample_function : <anonymous>: no visible global function definition
  for 'var'
sample_function_multi_mod_weight: no visible global function definition
  for 'runif'
sample_function_multi_mod_weight : <anonymous>: no visible global
  function definition for 'var'
sample_function_single_mod: no visible global function definition for
  'runif'
Undefined global functions or variables:
  rnorm runif var
Consider adding
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
Package required but not available: 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'paws.compute', 'paws.storage', 'paws.database', 'paws.networking',
  'paws.management', 'paws.machine.learning', 'paws.analytics',
  'paws.security.identity', 'paws.application.integration',
  'paws.cost.management', 'paws.customer.engagement'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

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
Namespace in Imports field not imported from: 'ade4'
  All declared Imports should be used.
Found the following significant warnings:
  putty/windows/winstore.c:665:38: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
  putty/windows/winstore.c:673:42: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/pbdRPC/pbdRPC.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
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
'library' or 'require' call to 'foreach' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dotplot.pbo: no visible global function definition for 'reorder'
pbo: no visible global function definition for '%dopar%'
pbo: no visible global function definition for 'foreach'
pbo: no visible global function definition for 'lm'
xyplot.pbo: no visible global function definition for 'ecdf'
xyplot.pbo: no visible global function definition for 'doubleYScale'
xyplot.pbo: no visible global function definition for 'reorder'
Undefined global functions or variables:
  %dopar% doubleYScale ecdf foreach lm reorder
Consider adding
  importFrom("stats", "ecdf", "lm", "reorder")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'FactoMineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'plotly'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'Matrix' 'pander'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'Rgraphviz', 'dagitty'
Package unavailable to check Rd xrefs: 'Rgraphviz'
Running examples in 'pcalg-Ex.R' failed
The error most likely occurred in:

> ### Name: ages
> ### Title: Estimate an APDAG within the Markov equivalence class of a DAG
> ###   using AGES
> ### Aliases: ages
> ### Keywords: models graphs
> 
> ### ** Examples
> 
> 
> ## Example 1: ages adds correct orientations: Bar --> V6 and Bar --> V8
> 
> set.seed(77)
> 
> p <- 8
> n <- 5000
> ## true DAG:
> vars <- c("Author", "Bar", "Ctrl", "Goal", paste0("V",5:8))
> gGtrue <- randomDAG(p, prob = 0.3, V = vars)
> data = rmvDAG(n, gGtrue)
> 
> 
> ## Estimate the aggregated PDAG with ages
> ages.fit <- ages(data = data)
> 
> 
> ## Estimate the essential graph with ges
> ## We specify the phases in order to have a fair comparison of the algorithms
> ## Without the phases specified it would be easy to find examples
> ## where each algorithm outperforms the other
> score <- new("GaussL0penObsScore", data)
> ges.fit <- ges(score, phase = c("forward","backward"), iterate = FALSE)
> 
> ## Plots
> par(mfrow=c(1,3))
> plot(ges.fit$essgraph, main="Estimated CPDAG with GES")
Error: package required but not installed: 'Rgraphviz'
Execution halted
Running 'test_LINGAM.R'
  Running 'test_addBgKnowledge.R'
Running the tests in 'tests/test_addBgKnowledge.R' failed.
Complete output:
  > library(pcalg)
  > 
  > res <- rep(FALSE, 10)
  > set.seed(123)
  > g <- pcalg::randomDAG(n = 7, prob = 0.3)
  > plot(g)
  Error: package required but not installed: 'Rgraphviz'
  Execution halted
Errors in running code in vignettes:
when running code in 'pcalgDoc.Rnw'
  ...
+     alpha = 0.01)

> stopifnot(require(Rgraphviz))
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'Rgraphviz'

  When sourcing 'pcalgDoc.R':
Error: require(Rgraphviz) is not TRUE
Execution halted
when running code in 'vignette2018.Rnw'
  ...
> library(pcalg)

> stopifnot(require(Rgraphviz))
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'Rgraphviz'

  When sourcing 'vignette2018.R':
Error: require(Rgraphviz) is not TRUE
Execution halted

  'pcalgDoc.Rnw' using 'UTF-8'... failed
  'vignette2018.Rnw' using 'UTF-8'... failed
Error(s) in re-building vignettes:
--- re-building 'pcalgDoc.Rnw' using Sweave
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'Rgraphviz'

Error: processing vignette 'pcalgDoc.Rnw' failed with diagnostics:
 chunk 6 (label = exIntroPlot) 
Error : require(Rgraphviz) is not TRUE

--- failed re-building 'pcalgDoc.Rnw'

--- re-building 'vignette2018.Rnw' using Sweave
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'Rgraphviz'

Error: processing vignette 'vignette2018.Rnw' failed with diagnostics:
 chunk 2 (label = loadPackage) 
Error : require(Rgraphviz) is not TRUE

--- failed re-building 'vignette2018.Rnw'

SUMMARY: processing the following files failed:
  'pcalgDoc.Rnw' 'vignette2018.Rnw'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'fda'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'rstan'

Package suggested but not available for checking: 'covr'

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: 'covr'
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'base'
  All declared Imports should be used.
Package required but not available: 'phylobase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
PdofCSGt.bootstrap5: no visible global function definition for 'rnorm'
PdofCSGt.bootstrap5: no visible global function definition for 'rt'
PdofCSt.T1or2: no visible global function definition for 'combn'
PofCSGt: no visible global function definition for 'combn'
PofCSLt.bootstrap5: no visible global function definition for 'rnorm'
PofCSLt.bootstrap5: no visible global function definition for 'rt'
PofCSt: no visible global function definition for 'pnorm'
tindep: no visible binding for global variable 'var'
tindep: no visible global function definition for 'pt'
Undefined global functions or variables:
  combn pnorm pt rnorm rt var
Consider adding
  importFrom("stats", "pnorm", "pt", "rnorm", "rt", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package required but not available: 'stplanr'

Packages suggested but not available for checking: 'covr', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'car', 'texreg'
Packages required but not available: 'httr', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'PythonInR'
Package required but not available: 'pdftools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'qpdf'

Package suggested but not available for checking: 'tesseract'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'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.
pdist: no visible global function definition for 'dist'
pdist: no visible global function definition for 'new'
Undefined global functions or variables:
  dist new
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'glmnet'
  All declared Imports should be used.
Package required but not available: 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'car', 'coefplot', 'papeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'lintr', 'curl'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'pds3.Rmd' using rmarkdown
Quitting from lines 59-62 (pds3.Rmd) 
Error: processing vignette 'pds3.Rmd' failed with diagnostics:
there is no package called 'curl'
--- failed re-building 'pds3.Rmd'

SUMMARY: processing the following file failed:
  'pds3.Rmd'

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
band.chol.cv: no visible global function definition for 'cov'
pdsoft.cv: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
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 120 marked UTF-8 strings
Running 'script.R'
Running the tests in 'tests/script.R' failed.
Last 13 lines of output:
  > overlapping.bed <- file.path(exampleData, "overlapping_peaks.bed")
  > 
  > ##test_that("PeakError_compute.R correct", {
  > out.file <- tempfile()
  > cmd <- paste(Rscript, PeakError_compute.R, peaks.bed, labels.bed, ">", out.file)
  > status <- system(cmd)
  Error: Usage: compute_error.R peaks.bed labels.bed > errors.bed
  Execution halted
  > errors <- read.table(out.file, sep="\t", header=TRUE)
  Error in file(file, "rt") : cannot open the connection
  Calls: read.table -> file
  In addition: Warning message:
  In file(file, "rt") :
    cannot open file 'C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\PeakError\tmp\Rtmp2rRjID\file2beb811d02473': No such file or directory
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
PearsonICA: no visible global function definition for 'rnorm'
PearsonICAdemo: no visible global function definition for 'rnorm'
PearsonICAdemo: no visible global function definition for 'dev.new'
PearsonICAdemo: no visible global function definition for 'par'
PearsonICAdemo: no visible global function definition for 'axis'
PearsonICAdemo: no visible global function definition for 'title'
PearsonICAdemo: no visible global function definition for 'lines'
Undefined global functions or variables:
  axis dev.new lines par rnorm title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "axis", "lines", "par", "title")
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  'Rcpp' 'RcppArmadillo' 'ggplot2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
AssoTestProc: no visible global function definition for 'rbinom'
AssoTestProc: no visible global function definition for 'princomp'
AssoTestProc: no visible global function definition for 'loadings'
AssoTestProc: no visible global function definition for 'lm'
CNVtypeAnay: no visible global function definition for 'cov'
ClusProc: no visible global function definition for 'princomp'
ClusProc: no visible global function definition for 'prcomp'
ClusProc0: no visible global function definition for 'kmeans'
ClusProc0: no visible global function definition for 'cov'
Inde: no visible global function definition for 'lm'
Inde: no visible global function definition for 'var'
STE: no visible global function definition for 'pchisq'
STIM: no visible global function definition for 'cor'
STIM: no visible global function definition for 'pchisq'
plot.clust: no visible global function definition for 'princomp'
plot.clust: no visible global function definition for 'loadings'
plot.clust: no visible global function definition for 'qplot'
plot.clust: no visible global function definition for 'geom_histogram'
plot.clust: no visible global function definition for 'aes_string'
plot.clust: no visible global function definition for 'barplot'
plot.clust: no visible global function definition for 'title'
plot.clust: no visible global function definition for 'mtext'
plot.clust: no visible global function definition for 'text'
Undefined global functions or variables:
  aes_string barplot cor cov geom_histogram kmeans lm loadings mtext
  pchisq prcomp princomp qplot rbinom text title var
Consider adding
  importFrom("graphics", "barplot", "mtext", "text", "title")
  importFrom("stats", "cor", "cov", "kmeans", "lm", "loadings", "pchisq",
             "prcomp", "princomp", "rbinom", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
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.
blup: no visible global function definition for 'model.matrix'
blup: no visible global function definition for 'model.frame'
blup: no visible global function definition for 'read.table'
calcG: no visible global function definition for 'as'
gblup: no visible global function definition for 'model.matrix'
gblup: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  as model.frame model.matrix read.table
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "model.frame", "model.matrix")
  importFrom("utils", "read.table")
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
Package suggested but not available for checking: 'car'
Package unavailable to check Rd xrefs: 'car'
Running examples in 'pedometrics-Ex.R' failed
The error most likely occurred in:

> ### Name: plotHD
> ### Title: Histogram and density plot
> ### Aliases: plotHD
> ### Keywords: dplot
> 
> ### ** Examples
> 
> x <- rnorm(100, 10, 2)
> plotHD(x, HD = "stack")
Error: Package 'car' needed for this function to work. Please install it.
Execution halted
Packages required but not available:
  'TTR', 'curl', 'httr', 'rvest', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'dvir' 'ibdsim2' 'paramlink2' 'pedbuildr' 'segregatr'
  All declared Imports should be used.
Package suggested but not available for checking: 'kableExtra'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'pedtools.Rmd' using rmarkdown
Quitting from lines 17-23 (pedtools.Rmd) 
Error: processing vignette 'pedtools.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'pedtools.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
PEMM_fun : find.lambda: no visible global function definition for
  'optimize'
PEMM_fun: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov optimize
Consider adding
  importFrom("stats", "cov", "optimize")
to your NAMESPACE file.
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'globaltest'
Namespace in Imports field not imported from: 'lhs'
  All declared Imports should be used.
Package suggested but not available for checking: 'survminer'
Error(s) in re-building vignettes:
  ...
--- re-building 'pencal-vignette.Rmd' using rmarkdown
Quitting from lines 149-161 (pencal-vignette.Rmd) 
Error: processing vignette 'pencal-vignette.Rmd' failed with diagnostics:
there is no package called 'survminer'
--- failed re-building 'pencal-vignette.Rmd'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'devtools'
performance.curves.plot: no visible global function definition for
  'postscript'
performance.curves.plot: no visible global function definition for
  'axis'
performance.curves.plot: no visible global function definition for
  'lines'
performance.curves.plot: no visible global function definition for
  'legend'
performance.curves.plot: no visible global function definition for
  'grid'
performance.curves.plot: no visible global function definition for
  'dev.off'
precision.recall.curves.plot: no visible global function definition for
  'postscript'
precision.recall.curves.plot: no visible global function definition for
  'axis'
precision.recall.curves.plot: no visible global function definition for
  'lines'
precision.recall.curves.plot: no visible global function definition for
  'legend'
precision.recall.curves.plot: no visible global function definition for
  'grid'
precision.recall.curves.plot: no visible global function definition for
  'dev.off'
Undefined global functions or variables:
  axis dev.off grid legend lines postscript
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "axis", "grid", "legend", "lines")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'quantmod', 'plotly', 'ggpubr'
Packages unavailable to check Rd xrefs: 'quantmod', 'tseries', 'car'
Packages suggested but not available for checking:
  'devtools', 'DMwR', 'quantmod'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'AER', 'afex', 'brms', 'car', 'forecast', 'rstanarm'
Package suggested but not available for checking: 'dendextendRcpp'
Namespace in Imports field not imported from: 'rms'
  All declared Imports should be used.
Package suggested but not available for checking: 'canvasXpress'
permalgorithm: 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').
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
ksample.pclt: no visible global function definition for 'pchisq'
pCI: no visible global function definition for 'qbeta'
permKS.formula: no visible global function definition for 'terms'
permTREND.default: no visible global function definition for 'cor'
permTREND.formula: no visible global function definition for 'terms'
permTS.formula: no visible global function definition for 'terms'
trend.pclt: no visible global function definition for 'pnorm'
twosample.pclt: no visible global function definition for 'pnorm'
twosample.pclt: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cor pchisq pnorm qbeta terms
Consider adding
  importFrom("stats", "cor", "pchisq", "pnorm", "qbeta", "terms")
to your NAMESPACE file.
Package suggested but not available for checking: 'car'
Running examples in 'permutes-Ex.R' failed
The error most likely occurred in:

> ### Name: clusterperm.glmer
> ### Title: Cluster-based permutation tests for time series data, based on
> ###   generalized linear mixed-effects models or other 'buildmer' models.
> ###   This is an alias for 'clusterperm.lmer' provided for discoverability.
> ### Aliases: clusterperm.glmer
> 
> ### ** Examples
> 
> ## Don't show: 
> perms <- perm.glmer(Fz ~ Deviant*Session + (1|Subject),data=MMN[MMN$Time > 200 & MMN$Time < 205,],nperm=2,type='anova')
Loading required namespace: car
Failed with error:  'there is no package called 'car''
Error in pkgcheck(c("buildmer", "car")) : 
  Please install the following missing package: car
Calls: perm.glmer -> perm.lmer -> pkgcheck
Execution halted
hasMethod: no visible global function definition for 'getS3method'
Undefined global functions or variables:
  getS3method
Consider adding
  importFrom("utils", "getS3method")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Note: found 63777 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Package required but not available: 'personalized'

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 required but not available: 'devtools', 'usethis'

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: 'httr'

Packages suggested but not available for checking: 'covr', 'badger'

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: 'curl', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'httr'
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
Packages required but not available: 'RSelenium', 'rio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'animation'

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: 'car'
'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: 'httr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'animation'

Package suggested but not available for checking: 'gsDesign'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'gsDesign'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'magick', 'seqLogo'
Packages suggested but not available for checking:
  'kableExtra', 'tidyverse'
Error(s) in re-building vignettes:
--- re-building 'advanced_usage.Rmd' using rmarkdown
Quitting from lines 13-20 (advanced_usage.Rmd) 
Error: processing vignette 'advanced_usage.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'advanced_usage.Rmd'

--- re-building 'huxtable_tips.Rmd' using rmarkdown
Quitting from lines 13-20 (huxtable_tips.Rmd) 
Error: processing vignette 'huxtable_tips.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'huxtable_tips.Rmd'

--- re-building 'pharmaRTF.Rmd' using rmarkdown
Quitting from lines 13-20 (pharmaRTF.Rmd) 
Error: processing vignette 'pharmaRTF.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'pharmaRTF.Rmd'

--- re-building 'tf_from_file.Rmd' using rmarkdown
Quitting from lines 13-21 (tf_from_file.Rmd) 
Error: processing vignette 'tf_from_file.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'tf_from_file.Rmd'

SUMMARY: processing the following files failed:
  'advanced_usage.Rmd' 'huxtable_tips.Rmd' 'pharmaRTF.Rmd'
  'tf_from_file.Rmd'

Error: Vignette re-building failed.
Execution halted
PharmPow_crossover: no visible global function definition for
  'read.table'
PharmPow_crossover: no visible global function definition for
  'write.csv'
PharmPow_crossover: no visible global function definition for 'pdf'
PharmPow_crossover: no visible global function definition for 'dev.off'
PharmPow_parallel: no visible global function definition for
  'read.table'
PharmPow_parallel: no visible global function definition for
  'write.csv'
PharmPow_parallel: no visible global function definition for 'pdf'
PharmPow_parallel: no visible global function definition for 'dev.off'
fig_PharmPow_crossover: no visible global function definition for
  'read.csv'
fig_PharmPow_parallel: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  dev.off pdf read.csv read.table write.csv
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "read.csv", "read.table", "write.csv")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: 'kableExtra'

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
fox: no visible binding for global variable 'sd'
fox: no visible global function definition for 'cor'
fox: no visible global function definition for 'interaction.plot'
fox: no visible global function definition for 'reorder'
kang: no visible global function definition for 'var'
kang: no visible binding for global variable 'sd'
kang: no visible global function definition for 'cor'
kang: no visible global function definition for 'interaction.plot'
kang: no visible global function definition for 'reorder'
nahu: no visible global function definition for 'interaction.plot'
nahu: no visible global function definition for 'reorder'
thsu: no visible global function definition for 'median'
thsu: no visible binding for global variable 'sd'
thsu: no visible global function definition for 'cor'
thsu: no visible global function definition for 'interaction.plot'
thsu: no visible global function definition for 'reorder'
Undefined global functions or variables:
  cor interaction.plot median reorder sd var
Consider adding
  importFrom("stats", "cor", "interaction.plot", "median", "reorder",
             "sd", "var")
to your NAMESPACE file.
Packages required but not available: 'httr', 'daymetr', 'MODISTools'

Packages suggested but not available for checking: 'covr', '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: 'car'
pheno.ddm: no visible global function definition for 'new'
pheno.flm.fit: no visible binding for global variable 'na.exclude'
pheno.flm.fit: no visible global function definition for 'terms'
pheno.flm.fit: no visible global function definition for 'residuals'
pheno.flm.fit: no visible global function definition for 'qt'
pheno.lad.fit: no visible binding for global variable 'na.exclude'
pheno.mlm.fit: no visible binding for global variable 'na.exclude'
pheno.mlm.fit: no visible global function definition for 'residuals'
Undefined global functions or variables:
  na.exclude new qt residuals terms
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "na.exclude", "qt", "residuals", "terms")
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: 'car'

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: 'tidyverse'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'pavo'
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
Package required but not available: 'pkgnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'phylobase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'RNeXML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'phylobase'

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
Namespace in Imports field not imported from: 'rgdal'
  All declared Imports should be used.
Package required but not available: 'phyloseq'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'adephylo', 'phylobase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'NHPoisson', 'phylobase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'pez', 'covr', 'INLA'
Package suggested but not available for checking: 'lintr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'animation'
incident: no visible global function definition for 'splinefun'
incident: no visible global function definition for 'integrate'
phytoprod: no visible global function definition for 'approx'
phytoprod: no visible global function definition for 'splinefun'
phytoprod: no visible global function definition for 'integrate'
reflectance: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx integrate splinefun
Consider adding
  importFrom("stats", "approx", "integrate", "splinefun")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'FrF2.catlg128'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'magick'
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gh', 'httr', 'usethis'

Package suggested but not available for checking: 'covr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tidyverse', 'pinnacle.API'
Running examples in 'pinnacle.data-Ex.R' failed
The error most likely occurred in:

> ### Name: USA_Election_2016
> ### Title: USA_Election_2016
> ### Aliases: USA_Election_2016
> ### Keywords: datasets
> 
> ### ** Examples
> 
> if (require("odds.converter")) {
+ library(tidyverse)
+ # What is Hilary Clinton's the highest implied winning probability at Pinnacle?
+ 
+ USA_Election_2016[which.min(USA_Election_2016$MoneyUS1),"EnteredDateTime"]
+ odds.converter::odds.us2prob(min(USA_Election_2016$MoneyUS1))
+ }
Loading required package: odds.converter
Error in library(tidyverse) : there is no package called 'tidyverse'
Execution halted
Packages suggested but not available for checking:
  'devtools', 'kableExtra', 'tidyverse'
Note: found 2048 marked UTF-8 strings
Error(s) in re-building vignettes:
  ...
--- re-building 'pinochet.Rmd' using rmarkdown
Quitting from lines 52-58 (pinochet.Rmd) 
Error: processing vignette 'pinochet.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'pinochet.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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: 'tidyverse'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'Introduction.Rmd' using rmarkdown
Quitting from lines 119-141 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'Introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
plot.pred.int: no visible global function definition for 'plot.default'
plot.pred.int: no visible global function definition for 'axis'
plot.pred.int: no visible global function definition for 'box'
plot.pred.int : cidist: no visible global function definition for
  'ecdf'
plot.pred.int : negcidist: no visible global function definition for
  'ecdf'
plot.pred.int : pi.col.fun: no visible global function definition for
  'gray'
plot.pred.int: no visible global function definition for 'segments'
plot.pred.int: no visible global function definition for 'points'
plot.pred.int: no visible global function definition for 'abline'
pred.int: no visible binding for global variable 'sd'
prop.test.mult: no visible global function definition for 'qnorm'
sim.basic: no visible global function definition for 'rbinom'
sim.basic: no visible global function definition for 'rnorm'
t.test.mult: no visible global function definition for 'qt'
Undefined global functions or variables:
  abline axis box ecdf gray plot.default points qnorm qt rbinom rnorm
  sd segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "box", "plot.default",
             "points", "segments")
  importFrom("stats", "ecdf", "qnorm", "qt", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'ggplot2'
  All declared Imports should be used.
Package suggested but not available for checking: 'devtools'
Packages suggested but not available for checking: 'animation', 'ggsubplot'
'LazyData' is specified without a 'data' directory
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'httr'

Package suggested but not available for checking: 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

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: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'curl'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'curl', 'pkgcache'

Package suggested but not available for checking: 'asciicast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking: 'covr', 'rsconnect'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'whoami'
Package unavailable to check Rd xrefs: 'whoami'
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("pkgload")
  == Failed tests ================================================================
  -- Error (test-depend.r:53:3): Declared dependencies are added to .Depends object --
  Error: Dependency package(s) 'httr' not available.
  Backtrace:
      x
   1. \-pkgload::load_all("testDependsExists") test-depend.r:53:2
   2.   \-pkgload:::load_depends(path)
   3.     \-pkgload:::abort_for_missing_packages(res, depends$package)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 316 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'devtools'
Package unavailable to check Rd xrefs: 'devtools'
Package required but not available: 'covr'

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: 'httr', 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'curl'

Packages suggested but not available for checking: 'covr', 'whoami'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'devtools', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
PKmod: no visible global function definition for 'deriv'
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
PKadjust: no visible binding for global variable 'jpeg'
PKadjust: no visible binding for global variable 'bmp'
PKadjust: no visible binding for global variable 'png'
PKadjust: no visible binding for global variable 'tiff'
PKadjust: no visible binding for global variable 'dev.new'
PKadjust: no visible global function definition for 'dev.off'
PKfigure: no visible global function definition for 'dev.cur'
PKfigure: no visible global function definition for 'dev.off'
PKoutput: no visible global function definition for 'heatmap'
PKoutput: no visible global function definition for
  'packageDescription'
PKshow: no visible global function definition for 'browseURL'
addList1: no visible global function definition for 'formula'
addList1.old: no visible global function definition for 'formula'
addList2: no visible global function definition for 'formula'
generate.plot: no visible global function definition for 'dev.off'
writeHTML: no visible global function definition for
  'packageDescription'
writeLst: no visible global function definition for
  'packageDescription'
writeLst.tab: no visible global function definition for
  'packageDescription'
writeTable: no visible global function definition for
  'packageDescription'
writeTable: no visible global function definition for 'quantile'
initialize,nonmem: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  bmp browseURL dev.cur dev.new dev.off formula heatmap jpeg
  packageDescription png quantile read.table tiff
Consider adding
  importFrom("grDevices", "bmp", "dev.cur", "dev.new", "dev.off", "jpeg",
             "png", "tiff")
  importFrom("stats", "formula", "heatmap", "quantile")
  importFrom("utils", "browseURL", "packageDescription", "read.table")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
           F     KA     KE      V
  0.5 0.1485 0.1083 0.0673 0.0290
  1   0.1483 0.0554 0.0815 0.0282
  
  == Failed tests ================================================================
  -- Error (test-models.R:20:3): models pbtk1cpt_model ---------------------------
  Error: The mcsim.pbtk1cpt.exe doesn't exist.
  Backtrace:
      x
   1. \-pksensi::solve_mcsim(...) test-models.R:20:2
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 20 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'tigris', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'kableExtra'
Package required but not available: 'googleway'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'kableExtra'
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
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 150 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required but not available: 'VariantAnnotation'

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

Package suggested but not available for checking: 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'MASS' 'Matrix' 'RColorBrewer' 'arm' 'epiDisplay' 'foreign' 'gbm'
  'grid' 'lattice' 'latticeExtra' 'lme4' 'nnet' 'parallel' 'splines'
  'survey' 'twang' 'xtable'
  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
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
bwfw.hmm: no visible global function definition for 'dnorm'
bwfw1.hmm: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  'PlackettLuce' 'StatRank' 'pmr' 'prefmod' 'rankdist'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'Formula' 'sm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages suggested but not available for checking:
  'AER', 'car', 'clusterSEs', 'texreg'
Packages unavailable to check Rd xrefs: 'AER', 'car'
Error(s) in re-building vignettes:
  ...
--- re-building 'A_plmPackage.Rmd' using rmarkdown
Quitting from lines 1895-1897 (A_plmPackage.Rmd) 
Error: processing vignette 'A_plmPackage.Rmd' failed with diagnostics:
there is no package called 'car'
--- failed re-building 'A_plmPackage.Rmd'

--- re-building 'B_plmFunction.Rmd' using rmarkdown
Quitting from lines 20-75 (B_plmFunction.Rmd) 
Error: processing vignette 'B_plmFunction.Rmd' failed with diagnostics:
there is no package called 'texreg'
--- failed re-building 'B_plmFunction.Rmd'

--- re-building 'C_plmModelComponents.Rmd' using rmarkdown
Quitting from lines 164-165 (C_plmModelComponents.Rmd) 
Error: processing vignette 'C_plmModelComponents.Rmd' failed with diagnostics:
there is no package called 'AER'
--- failed re-building 'C_plmModelComponents.Rmd'

SUMMARY: processing the following files failed:
  'A_plmPackage.Rmd' 'B_plmFunction.Rmd' 'C_plmModelComponents.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'covr', 'pkgdown', 'biomformat', 'phyloseq', 'factoextra'
Packages unavailable to check Rd xrefs: 'factoextra', 'DESeq2'
'LazyData' is specified without a 'data' directory
Package required but not available: 'ggtern'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'animation', 'rgbif'
Namespaces in Imports field not imported from:
  'hexbin' 'quantreg'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'plotly'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'devtools', 'shinytest', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'dplyr' 'patchwork'
  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.
generateEnvelope: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  'dplyr' 'stats'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'MplusAutomation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
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.
llla.bi: no visible global function definition for 'as.formula'
llla.bi: no visible global function definition for 'glm'
llla.bi: no visible global function definition for 'binomial'
llla.bi: no visible binding for global variable 'logit'
llla.bi: no visible global function definition for 'vcov'
llla.bi: no visible global function definition for 'coef'
llla.mc: no visible global function definition for 'model.matrix'
llla.mc: no visible global function definition for 'as.formula'
llla.mc: no visible global function definition for 'coxph'
llla.mc: no visible global function definition for 'vcov'
llla.mc: no visible global function definition for 'coef'
llla.mle: no visible global function definition for 'as.formula'
llla.mle: no visible global function definition for 'glm'
llla.mle: no visible global function definition for 'poisson'
llla.mle: no visible global function definition for 'coef'
llla.mle: no visible global function definition for 'vcov'
mclgen: no visible global function definition for 'reshape'
simRasch.1D: no visible global function definition for 'rnorm'
simRasch.1D: no visible global function definition for 'runif'
vcov.sandwich.glm: no visible global function definition for
  'model.matrix'
vcov.sandwich.glm: no visible global function definition for 'weights'
vcov.sandwich.glm: no visible global function definition for
  'residuals'
vcov.sandwich.glm: no visible global function definition for 'vcov'
Undefined global functions or variables:
  as.formula binomial coef coxph glm logit model.matrix poisson reshape
  residuals rnorm runif vcov weights
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "glm",
             "model.matrix", "poisson", "reshape", "residuals", "rnorm",
             "runif", "vcov", "weights")
to your NAMESPACE file.
Package suggested but not available for checking: 'SensoMineR'
Packages suggested but not available for checking: 'FactoMineR', 'plspm'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'plsmselect.Rmd' using rmarkdown
Quitting from lines 137-140 (plsmselect.Rmd) 
Error: processing vignette 'plsmselect.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'plsmselect.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'plsRglm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plsRglm'

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 suggested but not available for checking: 'covr'
print.densityEHpi: no visible global function definition for 'str'
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Packages required but not available: 'analogsea', 'ssh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'webutils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package required but not available: 'httr'

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: 'covr'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
.MCM: no visible global function definition for 'runif'
.MCM: no visible global function definition for 'rmultinom'
.MCM: no visible global function definition for 'mahalanobis'
.MCM: no visible global function definition for 'optimize'
.MCM : f: no visible global function definition for 'mahalanobis'
.MCM: no visible global function definition for 'alarm'
.igpark: no visible global function definition for 'kmeans'
.loglik: no visible global function definition for 'mahalanobis'
.plot.gpcm: no visible global function definition for 'lines'
.plot.gpcm: no visible global function definition for 'legend'
.rwgpar: no visible global function definition for 'rexp'
.weights: no visible global function definition for 'mahalanobis'
Undefined global functions or variables:
  alarm kmeans legend lines mahalanobis optimize rexp rmultinom runif
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "kmeans", "mahalanobis", "optimize", "rexp",
             "rmultinom", "runif")
  importFrom("utils", "alarm")
to your NAMESPACE file.
Package suggested but not available for checking: 'car'
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Package required but not available: 'enviGCMS'

Package suggested but not available for checking: 'MSnbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Quandl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'forecast', 'covr'
Running examples in 'pmml-Ex.R' failed
The error most likely occurred in:

> ### Name: pmml.ARIMA
> ### Title: Generate PMML for an ARIMA object the *forecast* package.
> ### Aliases: pmml.ARIMA
> 
> ### ** Examples
> 
> library(forecast)
Error in library(forecast) : there is no package called 'forecast'
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  [11:27:35] WARNING: amalgamation/../src/learner.cc:1095: Starting in XGBoost 1.4.0, the default evaluation metric used with the objective 'binary:logitraw' was changed from 'auc' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
  == Skipped tests ===============================================================
  * On CRAN (5)
  * forecast cannot be loaded (21)
  
  == Failed tests ================================================================
  -- Error (test_schema_validation.R:15:1): (code run outside of `test_that()`) --
  Error: there is no package called 'forecast'
  Backtrace:
      x
   1. \-base::library(forecast) test_schema_validation.R:15:0
  
  [ FAIL 1 | WARN 2 | SKIP 26 | PASS 195 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'lintr'
'LazyData' is specified without a 'data' directory
dbm: no visible global function definition for 'optim'
dbm: no visible global function definition for 'new'
destat: no visible global function definition for 'weighted.mean'
local.knn: no visible global function definition for 'sd'
local.knn: no visible global function definition for 'optim'
mdpref: no visible global function definition for 'sd'
mdpref: no visible global function definition for 'text'
mdpref: no visible global function definition for 'lines'
phicom: no visible global function definition for 'optim'
phicom: no visible global function definition for 'new'
pl: no visible global function definition for 'optim'
pl: no visible global function definition for 'new'
rol: no visible global function definition for 'nlm'
rol: no visible global function definition for 'new'
wdbm: no visible global function definition for 'optim'
wdbm: no visible global function definition for 'new'
Undefined global functions or variables:
  lines new nlm optim sd text weighted.mean
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("methods", "new")
  importFrom("stats", "nlm", "optim", "sd", "weighted.mean")
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
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'ggrepel' 'gridExtra'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'projmgr', 'httr'

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.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pnmtrem1: no visible global function definition for 'pnorm'
pnmtrem1: no visible global function definition for 'dnorm'
pnmtrem1: no visible global function definition for 'ginv'
pnmtrem1 : fun: no visible global function definition for 'pnorm'
pnmtrem1 : derf: no visible global function definition for 'dnorm'
pnmtrem1 : derf: no visible global function definition for 'pnorm'
pnmtrem1 : fun: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm ginv pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
'library' or 'require' call to 'rgenoud' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
smooth: no visible global function definition for 'genoud'
Undefined global functions or variables:
  genoud
Packages required but not available: 'projmgr', 'httr'

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
Packages required but not available: 'httr', 'usethis'

Packages suggested but not available for checking: 'covr', 'httptest'

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:
  'kableExtra', 'tidyverse'
Namespace in Imports field not imported from: 'plogr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'abc' 'doParallel' 'gdistance' 'geosphere' 'lhs' 'metRology' 'raster'
  'trend'
  All declared Imports should be used.
Packages required but not available: 'projmgr', 'httr'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'SmarterPoland'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
bipoilogMLE: no visible global function definition for 'optim'
bipoilogMLE: no visible global function definition for 'write.table'
poilogMLE: no visible global function definition for 'optim'
rbipoilog : sim: no visible global function definition for 'rnorm'
rbipoilog : sim: no visible global function definition for 'rpois'
rpoilog : sim: no visible global function definition for 'rnorm'
rpoilog : sim: no visible global function definition for 'rpois'
Undefined global functions or variables:
  optim rnorm rpois write.table
Consider adding
  importFrom("stats", "optim", "rnorm", "rpois")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package required but not available: 'blastula'

Packages suggested but not available for checking:
  'arrow', 'covr', 'sparklyr'

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'devtools', 'whoami'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
approxMargMLE: no visible global function definition for 'optim'
approxMargMLECI : ciFunction: no visible global function definition for
  'qchisq'
approxMargMLECI: no visible global function definition for 'uniroot'
margMLE: no visible global function definition for 'optim'
margMLECI: no visible global function definition for 'optim'
margMLECI : unNormLikeMinusVal: no visible global function definition
  for 'qchisq'
margMLECI: no visible global function definition for 'uniroot'
profMLECI : ciFunction: no visible global function definition for
  'qchisq'
profMLECI: no visible global function definition for 'uniroot'
rtbinom: no visible global function definition for 'rbinom'
rtpois: no visible global function definition for 'rpois'
waldCI: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  optim qchisq qnorm rbinom rpois uniroot
Consider adding
  importFrom("stats", "optim", "qchisq", "qnorm", "rbinom", "rpois",
             "uniroot")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Packages in Depends field not imported from:
  'combinat' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.Depth: no visible global function definition for 'quantile'
PS.FDR: no visible global function definition for 'quantile'
Permu.Ind: no visible global function definition for 'permn'
Permu.Ind: no visible global function definition for 'hcube'
Trans.Data: no visible global function definition for 'write.table'
Trans.Data: no visible global function definition for 'predict'
Trans.Data: no visible global function definition for 'lm'
Undefined global functions or variables:
  hcube lm permn predict quantile write.table
Consider adding
  importFrom("stats", "lm", "predict", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: 'hexSticker'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages in Depends field not imported from:
  'MASS' 'scatterplot3d'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.poLCA: no visible global function definition for 'layout'
plot.poLCA: no visible global function definition for 'par'
poLCA: no visible global function definition for 'model.frame'
poLCA: no visible global function definition for 'model.response'
poLCA: no visible global function definition for 'model.matrix'
poLCA: no visible global function definition for 'runif'
poLCA: no visible global function definition for 'ginv'
poLCA: no visible global function definition for 'flush.console'
poLCA.makeplot.dich: no visible global function definition for
  'scatterplot3d'
poLCA.makeplot.poly: no visible global function definition for
  'scatterplot3d'
poLCA.se: no visible global function definition for 'ginv'
poLCA.simdata: no visible global function definition for 'runif'
poLCA.simdata: no visible global function definition for 'rnorm'
poLCA.table: no visible global function definition for 'model.frame'
print.poLCA: no visible global function definition for 'pt'
print.poLCA: no visible global function definition for 'flush.console'
rmulti: no visible global function definition for 'runif'
Undefined global functions or variables:
  flush.console ginv layout model.frame model.matrix model.response par
  pt rnorm runif scatterplot3d
Consider adding
  importFrom("graphics", "layout", "par")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "pt", "rnorm", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Package suggested but not available for checking: 'devtools'
Note: found 21 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 9 marked Latin-1 strings
Packages required but not available:
  'httr', 'robotstxt', 'rvest', 'usethis'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Packages required but not available: 'brms', 'repmis'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'RcppCWB'

Packages suggested but not available for checking: 'covr', 'httr', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
qPolyaAeppliSingle: no visible global function definition for 'qgamma'
rPolyaAeppli: no visible global function definition for 'rpois'
rPolyaAeppli: no visible global function definition for 'rgeom'
Undefined global functions or variables:
  qgamma rgeom rpois
Consider adding
  importFrom("stats", "qgamma", "rgeom", "rpois")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'magick', 'pins'

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

Package suggested but not available for checking: 'mappoly'

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: 'mappoly', 'polymapR'
Running examples in 'polyqtlR-Ex.R' failed
The error most likely occurred in:

> ### Name: convert_mappoly_to_phased.maplist
> ### Title: Function to extract the phased map from a mappoly.map object
> ### Aliases: convert_mappoly_to_phased.maplist
> 
> ### ** Examples
> 
> data(maps.hexafake, package = "mappoly")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'mappoly'
Calls: data -> find.package
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'polyqtlR_vignette.rmd' using rmarkdown
Quitting from lines 172-174 (polyqtlR_vignette.rmd) 
Error: processing vignette 'polyqtlR_vignette.rmd' failed with diagnostics:
there is no package called 'polymapR'
--- failed re-building 'polyqtlR_vignette.rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'VariantAnnotation', 'GenomicFeatures'
Packages unavailable to check Rd xrefs: 'GenomicFeatures', 'VariantAnnotation'
Namespace in Imports field not imported from: 'regtools'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: 'Rcmdr'
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'matrixcalc' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'matrixcalc'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
print.mixed.pom: no visible global function definition for 'pnorm'
print.pom: no visible global function definition for 'pnorm'
siteocc : get.mod.matrix: no visible binding for global variable
  'na.pass'
siteocc : get.mod.matrix: no visible global function definition for
  'formula'
siteocc : get.mod.matrix: no visible global function definition for
  'model.matrix'
siteocc: no visible global function definition for 'nlminb'
siteocc: no visible global function definition for
  'is.positive.definite'
Undefined global functions or variables:
  formula is.positive.definite model.matrix na.pass nlminb pnorm
Consider adding
  importFrom("stats", "formula", "model.matrix", "na.pass", "nlminb",
             "pnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'RcppProgress'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rstan', 'brms'

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: 'pkgdown'
Package suggested but not available for checking: 'magick'
Error(s) in re-building vignettes:
  ...
--- re-building 'popdemo.Rmd' using rmarkdown
Quitting from lines 94-99 (popdemo.Rmd) 
Error: processing vignette 'popdemo.Rmd' failed with diagnostics:
there is no package called 'magick'
--- failed re-building 'popdemo.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'covr', 'devtools'
Package suggested but not available for checking: 'covr'
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'WhopGenome'
'LazyData' is specified without a 'data' directory
asymmetricIntervals: no visible global function definition for 'stack'
bonferroniIntervals: no visible global function definition for 'stack'
bonferroniIntervals: no visible global function definition for 'lm'
bonferroniIntervals: no visible global function definition for
  'predict'
bootstrapIntervals: no visible global function definition for 'stack'
component1a: no visible global function definition for 'pnorm'
component1b: no visible global function definition for 'pnorm'
component2: no visible global function definition for 'dgamma'
eqnForMin: no visible global function definition for 'pnorm'
eqnForMin: no visible global function definition for 'integrate'
integrand : <anonymous>: no visible global function definition for
  'pnorm'
integrand: no visible global function definition for 'dnorm'
integrate2: no visible global function definition for 'integrate'
integrate2a: no visible global function definition for 'integrate'
integrate2b: no visible global function definition for 'integrate'
integrate4a: no visible global function definition for 'integrate'
integrate4b: no visible global function definition for 'integrate'
optimalCScalar2: no visible global function definition for 'uniroot'
optimalLambda: no visible global function definition for 'optimise'
optimalLambdaC: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dgamma dnorm integrate lm optimise pnorm predict stack uniroot
Consider adding
  importFrom("stats", "dgamma", "dnorm", "integrate", "lm", "optimise",
             "pnorm", "predict", "uniroot")
  importFrom("utils", "stack")
to your NAMESPACE file.
'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 unavailable to check Rd xrefs: 'rags2ridges', 'ragt2ridges'
Packages required but not available: 'forecast', 'timetk', 'httr', 'curl'

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

Packages suggested but not available for checking:
  'covr', 'httptest', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'forecast'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'quantmod'
Package required but not available: 'quantmod'

Package suggested but not available for checking: 'readtext'

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: 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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: 'rstan'

Packages suggested but not available for checking: 'covr', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'kableExtra'

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: 'crul', 'rvest'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: 'rstan'
Packages suggested but not available for checking: 'covr', 'cartography'
Error(s) in re-building vignettes:
  ...
--- re-building 'potential.Rmd' using rmarkdown
Linking to GEOS 3.6.2, GDAL 3.0.4, PROJ 7.0.0
Quitting from lines 70-88 (potential.Rmd) 
Error: processing vignette 'potential.Rmd' failed with diagnostics:
there is no package called 'cartography'
--- failed re-building 'potential.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'BIGDAWG'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'usethis'
Packages required but not available: 'httr', 'js'

Package suggested but not available for checking: 'httptest'

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

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: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'library' or 'require' call to 'tcltk' which was already attached by Depends.
  Please remove these calls from your code.
fnfam: no visible global function definition for 'qnorm'
fx: no visible global function definition for 'qnorm'
normplot : <local> : replot: no visible global function definition for
  'qnorm'
normplot : <local> : replot: no visible global function definition for
  'pnorm'
normplot : <local> : replot: no visible global function definition for
  'dnorm'
normplot : <local> : replot: no visible global function definition for
  'points'
normplot : <local> : replot: no visible global function definition for
  'lines'
normplot : <local> : regen: no visible global function definition for
  'rnorm'
normplot : <local> : regen: no visible global function definition for
  'rexp'
nsibs: no visible global function definition for 'qnorm'
ntdt: no visible global function definition for 'uniroot'
plotNtdt: no visible global function definition for 'lines'
plotNtdt: no visible global function definition for 'legend'
ptdt: no visible global function definition for 'optimize'
ptdt: no visible global function definition for 'uniroot'
ptdt: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm legend lines optimize pnorm points qnorm rexp rnorm uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
Package suggested but not available for checking: 'devtools'
Error(s) in re-building vignettes:
--- re-building 'ABE.Rmd' using rmarkdown
--- finished re-building 'ABE.Rmd'

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

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

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

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

--- re-building 'vignette.Rmd' using rmarkdown
Quitting from lines 275-277 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'factoextra'
Error(s) in re-building vignettes:
  ...
--- re-building 'fcm.Rmd' using rmarkdown
Quitting from lines 45-48 (fcm.Rmd) 
Error: processing vignette 'fcm.Rmd' failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building 'fcm.Rmd'

--- re-building 'upfc.Rmd' using rmarkdown
Quitting from lines 46-49 (upfc.Rmd) 
Error: processing vignette 'upfc.Rmd' failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building 'upfc.Rmd'

SUMMARY: processing the following files failed:
  'fcm.Rmd' 'upfc.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'curl'

Package suggested but not available for checking: 'covr'

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: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
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
Namespaces in Imports field not imported from:
  'rpart' 'withr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'lmtest' 'sandwich'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
TT.test : <anonymous>: no visible global function definition for
  't.test'
TT.test: no visible binding for global variable 'sd'
TT.test: no visible global function definition for 'setNames'
kirjelda : combo: no visible binding for global variable 'sd'
kor.tabel: no visible binding for global variable 'cor.test'
Undefined global functions or variables:
  cor.test sd setNames t.test
Consider adding
  importFrom("stats", "cor.test", "sd", "setNames", "t.test")
to your NAMESPACE file.
Package suggested but not available for checking: 'devtools'
Namespaces in Imports field not imported from:
  'class' 'forcats' 'irr' 'lpSolve' 'purrr'
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building 'introduction_to_prcr.Rmd' using rmarkdown
Quitting from lines 19-20 (introduction_to_prcr.Rmd) 
Error: processing vignette 'introduction_to_prcr.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'introduction_to_prcr.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'covr', 'devtools', 'tidyverse'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'PRDA.Rmd' using rmarkdown
--- finished re-building 'PRDA.Rmd'

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

--- re-building 'retrospective.Rmd' using rmarkdown
Quitting from lines 21-24 (retrospective.Rmd) 
Error: processing vignette 'retrospective.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'retrospective.Rmd'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'shinycssloaders' 'shinythemes'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'usethis'

Package suggested but not available for checking: 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'TH.data' 'moonBook'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'lazyeval'
  All declared Imports should be used.
Packages which this enhances but not available for checking:
  'AER', 'sampleSelection'
Packages unavailable to check Rd xrefs: 'AER', 'sampleSelection'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
gausspred: no visible global function definition for 'qt'
mvapred: no visible global function definition for 'qt'
Undefined global functions or variables:
  qt
Consider adding
  importFrom("stats", "qt")
to your NAMESPACE file.