Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpNJ6qs2/R.INSTALL26ff7bc6ab4f/fpc/man/regmix.Rd:112: file link ‘EMclust’ in package ‘mclust’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fpc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpFToklo/R.INSTALL120a349c00bf/fplot/man/fit.off.Rd:43: file link ‘jpeg_fit’ in package ‘fplot’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpFToklo/R.INSTALL120a349c00bf/fplot/man/png_fit.Rd:75: file link ‘bmp’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpFToklo/R.INSTALL120a349c00bf/fplot/man/png_fit.Rd:75: file link ‘jpeg’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpFToklo/R.INSTALL120a349c00bf/fplot/man/png_fit.Rd:75: file link ‘tiff’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fplot.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
'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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpdVxtZN/R.INSTALL77281e5f4d85/frair/man/fr_emdII.Rd:31: file link ‘lambertW0’ in package ‘lamW’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpdVxtZN/R.INSTALL77281e5f4d85/frair/man/fr_flexpnr.Rd:39: file link ‘lambertW0’ in package ‘lamW’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpdVxtZN/R.INSTALL77281e5f4d85/frair/man/fr_rogersII.Rd:33: file link ‘lambertW0’ in package ‘lamW’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/frair.Rcheck/00install.out’ for details.
'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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpXhCR2F/R.INSTALL788c139ec90a/freesurferformats/man/read.fs.volume.nii.Rd:49: file link ‘readNIfTI’ in package ‘oro.nifti’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/freesurferformats.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpLtQjUG/R.INSTALL1bc431802b4/freqdom/man/rar.Rd:38: file link ‘rmvnorm’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLtQjUG/R.INSTALL1bc431802b4/freqdom/man/rar.Rd:39: file link ‘rmvt’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLtQjUG/R.INSTALL1bc431802b4/freqdom/man/rma.Rd:39: file link ‘rmvnorm’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLtQjUG/R.INSTALL1bc431802b4/freqdom/man/rma.Rd:40: file link ‘rmvt’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/freqdom.Rcheck/00install.out’ for details.
PKG_CFLAGS set in ‘src/Makevars’ without any corresponding files
   PKG_CFLAGS set in ‘src/Makevars.win’ without any corresponding files
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_CFLAGS without any C files
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_CFLAGS without any C files
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpixlitE/R.INSTALL3df75f28ecac/fresh/man/bs_vars_wells.Rd:20: file link ‘sidebarPanel’ in package ‘shiny’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fresh.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpPOAxfy/R.INSTALL26de2c8e5cf2/FrF2.catlg128/man/Catalogues.Rd:37: file link ‘catlg’ in package ‘FrF2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPOAxfy/R.INSTALL26de2c8e5cf2/FrF2.catlg128/man/Catalogues.Rd:79: file link ‘catlg’ in package ‘FrF2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FrF2.catlg128.Rcheck/00install.out’ for details.
Non-standard file/directory found at top level:
  ‘FrF2.catlg128-Ex.R’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpfED0hF/R.INSTALL69d37a294387/FrF2/man/BsProb.design.Rd:102: file link ‘BsMD’ in package ‘BsMD’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfED0hF/R.INSTALL69d37a294387/FrF2/man/CIG.Rd:47: file link ‘layout’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfED0hF/R.INSTALL69d37a294387/FrF2/man/CIG.Rd:60: file link ‘independent.vertex.sets’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfED0hF/R.INSTALL69d37a294387/FrF2/man/godolphin.Rd:85: file link ‘rerandomize.design’ in package ‘DoE.base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfED0hF/R.INSTALL69d37a294387/FrF2/man/godolphin.Rd:146: file link ‘factor.names<-’ in package ‘DoE.base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FrF2.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'dggrids', 'INLA'
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Introduction.Rmd’
prepare_Rd: frt.Rd:21: Dropping empty section \note
prepare_Rd: frt.paired.Rd:23: Dropping empty section \note
prepare_Rd: shoes.Rd:19: Dropping empty section \details
prepare_Rd: shoes.Rd:21-22: Dropping empty section \references
prepare_Rd: tomatoes.Rd:16: Dropping empty section \details
prepare_Rd: tomatoes.Rd:18: Dropping empty section \references
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpJs96TS/R.INSTALLcd9119321b8/FSelectorRcpp/man/information_gain.Rd:48: file link ‘gain.ratio’ in package ‘FSelector’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJs96TS/R.INSTALLcd9119321b8/FSelectorRcpp/man/information_gain.Rd:48: file link ‘symmetrical.uncertainty’ in package ‘FSelector’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FSelectorRcpp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpeJXNEz/R.INSTALL48b42d6ac239/fs/man/path_file.Rd:55: file link ‘dirname’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fs.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpjZb1fs/R.INSTALLe7a7ed955e4/ftExtra/man/reexports.Rd:17: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ftExtra.Rcheck/00install.out’ for details.
'library' or 'require' calls to packages already attached by Depends:
  ‘Matrix’ ‘splines’
  Please remove these calls from your code.
prepare_Rd: baseline.Rd:123: Dropping empty section \examples
prepare_Rd: display.tests.Rd:43: Dropping empty section \references
prepare_Rd: display.tests.Rd:57: Dropping empty section \examples
prepare_Rd: extract.pars.Rd:114: Dropping empty section \examples
prepare_Rd: locate.peaks.Rd:72: Dropping empty section \examples
prepare_Rd: make.par.file.Rd:117: Dropping empty section \examples
prepare_Rd: run.all.Rd:76: Dropping empty section \examples
prepare_Rd: run.analysis.Rd:153: Dropping empty section \examples
prepare_Rd: run.baselines.Rd:91: Dropping empty section \examples
prepare_Rd: run.cluster.matrix.Rd:171: Dropping empty section \examples
prepare_Rd: run.lrg.peaks.Rd:95: Dropping empty section \examples
prepare_Rd: run.peaks.Rd:99: Dropping empty section \examples
prepare_Rd: run.strong.peaks.Rd:115: Dropping empty section \examples
Non-standard files/directories found at top level:
  ‘COPYRIGHT’ ‘pmden.R’
Copyright information should be in file inst/COPYRIGHTS
Rd file 'ftnonpar-internal.Rd':
  \usage lines wider than 90 characters:
     genmrcheck(y,yhat,thresh=-1,sigma=1,DYADIC=FALSE,beta=0.5,method=1,thr.const=2,schwelle = 1e+09)

Rd file 'genpmreg.Rd':
  \usage lines wider than 90 characters:
     genpmreg(y, beta = 0.5, squeezing.factor = 0.5, verbose = FALSE, localsqueezing = TRUE, DYADIC = TRUE, thr.const = 2, extrema.nr = -1,  ... [TRUNCATED]

Rd file 'l1pmreg.Rd':
  \usage lines wider than 90 characters:
     quantpmreg(y, beta = 0.5, squeezing.factor = 0.5, verbose = FALSE, localsqueezing = TRUE, DYADIC = TRUE, thr.const = 2, extrema.nr = -1 ... [TRUNCATED]
     l1pmreg(y, beta=0.5, squeezing.factor = 0.5, verbose = FALSE, localsqueezing = TRUE, DYADIC = TRUE, thr.const = 2, extrema.nr = -1, ban ... [TRUNCATED]

Rd file 'mintvmon.Rd':
  \usage lines wider than 90 characters:
     mintvmon(y, sigma = -1, DYADIC = TRUE, thresh = -1, method = 2, MONCONST = TRUE, CONVCONST = FALSE)

Rd file 'pmden.Rd':
  \usage lines wider than 90 characters:
     pmden(x, DISCR=FALSE,verbose = FALSE, bandwidth=-1, extrema.nr = -1, accuracy = mad(x)/1000,  extrema.mean = TRUE,maxkuipnr=19,asympbou ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpKgct8r/R.INSTALL440c3d553a1c/fulltext/man/cache_file_info.Rd:17: file link ‘pdf_info’ in package ‘pdftools’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpKgct8r/R.INSTALL440c3d553a1c/fulltext/man/ft_get.Rd:68: file link ‘setTxtProgressBar’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpKgct8r/R.INSTALL440c3d553a1c/fulltext/man/ft_serialize.Rd:24: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fulltext.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘names.txt’
Non-standard file/directory found at top level:
  ‘copying’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpPM4vmL/R.INSTALL79f740e89ad/FuncMap/man/FuncMap.Rd:15: file link ‘mvbutils’ in package ‘mvbutils’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPM4vmL/R.INSTALL79f740e89ad/FuncMap/man/FuncMap.Rd:53: file link ‘mvbutils’ in package ‘mvbutils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FuncMap.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpcBtbjx/R.INSTALL28c7639a1e94/functools/man/Mapply.Rd:16: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcBtbjx/R.INSTALL28c7639a1e94/functools/man/Reduce_Right.Rd:13: file link ‘Reduce’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcBtbjx/R.INSTALL28c7639a1e94/functools/man/Reduce_Right.Rd:10: file link ‘Reduce’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcBtbjx/R.INSTALL28c7639a1e94/functools/man/Reduce_Right.Rd:16: file link ‘Reduce’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcBtbjx/R.INSTALL28c7639a1e94/functools/man/Sapply.Rd:21: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcBtbjx/R.INSTALL28c7639a1e94/functools/man/Sapply.Rd:24: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcBtbjx/R.INSTALL28c7639a1e94/functools/man/Vapply.Rd:21: file link ‘vapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcBtbjx/R.INSTALL28c7639a1e94/functools/man/Vapply.Rd:24: file link ‘vapply’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/functools.Rcheck/00install.out’ for details.
.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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpzPUdT3/R.INSTALL29386f02aba/fungible/man/Ledermann.Rd:38: file link ‘ceiling’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzPUdT3/R.INSTALL29386f02aba/fungible/man/Ledermann.Rd:39: file link ‘floor’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzPUdT3/R.INSTALL29386f02aba/fungible/man/promaxQ.Rd:134: file link ‘promax’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fungible.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpkLR5xh/R.INSTALL27799dc7512/fun/man/sliding_puzzle.Rd:26: file link ‘X11’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fun.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpYpqIUu/R.INSTALL4e55278175a4/furrr/man/future_invoke_map.Rd:56: file link ‘invoke_map’ in package ‘purrr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/furrr.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘FusionLearn.Rmd’
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.
Found the following files/directories:
  ‘completeTrial_byArm_eventPriorRateC3=0.001_eventPriorRateT1=0_eventPriorRateT2=0_eventPriorWt=0.5.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.2.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.4.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.6.RData’
  ‘completeTrial_pooled_eventPriorRate=0.001_eventPriorWt=0.5.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.2.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.4.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.6.RData’
  ‘rcdf_byArm_arm=T1_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03.pdf’
  ‘rcdf_pooled_eventPriorRate=0.06.pdf’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmppiRmAT/R.INSTALL400b4458c3bb/future.BatchJobs/man/BatchJobsFuture.Rd:28: file link ‘ClusterFunctions’ in package ‘BatchJobs’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmppiRmAT/R.INSTALL400b4458c3bb/future.BatchJobs/man/BatchJobsFuture.Rd:40: file link ‘Future’ in package ‘future’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmppiRmAT/R.INSTALL400b4458c3bb/future.BatchJobs/man/BatchJobsFutureError.Rd:10: file link ‘FutureError’ in package ‘future’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmppiRmAT/R.INSTALL400b4458c3bb/future.BatchJobs/man/batchjobs_local.Rd:56: file link ‘transparent’ in package ‘future’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/future.BatchJobs.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpopXPgb/R.INSTALL7287424d70a5/future.batchtools/man/BatchtoolsFuture.Rd:61: file link ‘ClusterFunctions’ in package ‘batchtools’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpopXPgb/R.INSTALL7287424d70a5/future.batchtools/man/BatchtoolsFuture.Rd:66: file link ‘Future’ in package ‘future’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpopXPgb/R.INSTALL7287424d70a5/future.batchtools/man/BatchtoolsFutureError.Rd:10: file link ‘FutureError’ in package ‘future’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpopXPgb/R.INSTALL7287424d70a5/future.batchtools/man/batchtools_custom.Rd:57: file link ‘ClusterFunctions’ in package ‘batchtools’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpopXPgb/R.INSTALL7287424d70a5/future.batchtools/man/batchtools_local.Rd:77: file link ‘transparent’ in package ‘future’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/future.batchtools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpJpT2Fm/R.INSTALL7926757770fb/future.callr/man/CallrFuture.Rd:34: file link ‘MultiprocessFuture’ in package ‘future’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/future.callr.Rcheck/00install.out’ for details.
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
Found the following files/directories:
  ‘tmp-alloc.R’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpHz3Ngr/R.INSTALLf9048e518c7/fuzzyjoin/man/genome_join.Rd:38: file link ‘findOverlaps’ in package ‘IRanges’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHz3Ngr/R.INSTALLf9048e518c7/fuzzyjoin/man/genome_join.Rd:49: file link ‘findOverlaps’ in package ‘IRanges’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHz3Ngr/R.INSTALLf9048e518c7/fuzzyjoin/man/interval_join.Rd:45: file link ‘findOverlaps’ in package ‘IRanges’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHz3Ngr/R.INSTALLf9048e518c7/fuzzyjoin/man/interval_join.Rd:37: file link ‘findOverlaps’ in package ‘IRanges’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fuzzyjoin.Rcheck/00install.out’ for details.
NeedsCompilation field must take value ‘yes’ or ‘no’
'library' or 'require' call to ‘splines’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gensurf: no visible global function definition for ‘persp’
gensurf: no visible global function definition for ‘rainbow’
plotMF: no visible global function definition for ‘plot.new’
plotMF: no visible global function definition for ‘plot.window’
plotMF: no visible global function definition for ‘runif’
plotMF: no visible global function definition for ‘predict’
plotMF: no visible global function definition for ‘interpSpline’
plotMF: no visible global function definition for ‘lines’
plotMF: no visible global function definition for ‘text’
plotMF: no visible global function definition for ‘title’
plotMF: no visible global function definition for ‘axis’
plotMF: no visible global function definition for ‘box’
Undefined global functions or variables:
  axis box interpSpline lines persp plot.new plot.window predict
  rainbow runif text title
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "persp", "plot.new",
             "plot.window", "text", "title")
  importFrom("stats", "predict", "runif")
to your NAMESPACE file.
Rd file 'newFIS.Rd':
  \usage lines wider than 90 characters:
     newFIS(FISName, FISType = "mamdani", version = "1.0", andMethod = "min", orMethod = "max", impMethod = "min", aggMethod = "max", defuzz ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Unknown package ‘cffdrs’ in Rd xrefs
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.
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.
Found the following files/directories:
  ‘results_Wiener1.out’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpdiLSge/R.INSTALL79c31a16dcb3/gamboostLSS/man/cvrisk.Rd:60: file link ‘parLapply’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpdiLSge/R.INSTALL79c31a16dcb3/gamboostLSS/man/families.Rd:227: file link ‘mboost’ in package ‘mboost’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpdiLSge/R.INSTALL79c31a16dcb3/gamboostLSS/man/mboostLSS.Rd:100: file link ‘mboost’ in package ‘mboost’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpdiLSge/R.INSTALL79c31a16dcb3/gamboostLSS/man/methods.Rd:285: file link ‘mboost’ in package ‘mboost’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gamboostLSS.Rcheck/00install.out’ for details.
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.
Malformed Description field: should contain one or more complete sentences.
Non-standard files/directories found at top level:
  ‘changeLog’ ‘gnugpl2.txt’
'library' or 'require' calls in package code:
  ‘parallel’ ‘snowfall’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
GAMBoost: no visible global function definition for ‘binomial’
GAMBoost: no visible global function definition for ‘gaussian’
GAMBoost: no visible global function definition for ‘poisson’
GAMBoost: no visible binding for global variable ‘sd’
GAMBoost: no visible global function definition for ‘Matrix’
calc.confidence.bands: no visible global function definition for
  ‘predict’
cv.GAMBoost: no visible global function definition for ‘binomial’
cv.GAMBoost : eval.fold: no visible global function definition for
  ‘predict’
cv.GAMBoost: no visible global function definition for ‘mclapply’
cv.GAMBoost: no visible binding for global variable ‘var’
estimPVal: no visible global function definition for ‘mclapply’
plot.GAMBoost: no visible global function definition for ‘lines’
Undefined global functions or variables:
  Matrix binomial gaussian lines mclapply poisson predict sd var
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "binomial", "gaussian", "poisson", "predict", "sd",
             "var")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpa65qR4/R.INSTALL704079bd1316/gameofthrones/man/scale_got.Rd:97: file link ‘scale_fill_gradientn’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpa65qR4/R.INSTALL704079bd1316/gameofthrones/man/scale_got.Rd:97: file link ‘scale_color_gradientn’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gameofthrones.Rcheck/00install.out’ for details.
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').

Found the following calls to attach():
File ‘gamlss.nl/R/nlgamlss.R’:
  attach(data)
See section ‘Good practice’ in ‘?attach’.
Found the following significant warnings:
  Rd warning: /private/var/folders/94/71j6vmsn3zvf95p0_hlnxcfr0000gn/T/RtmpdYWAMS/Rbuild7d476ce42a7d/gamlss/man/gamlss-package.Rd:44: file link ‘gamlss.dist’ in package ‘gamlss.dist’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gamlss.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpwnL6dM/R.INSTALL339611eaaf2/gamlss.tr/man/fitTail.Rd:63: file link ‘logSurv’ in package ‘gamlss’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gamlss.tr.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Introduction.Rmd’
Non-standard file/directory found at top level:
  ‘Read-and-delete-me’
Package in Depends field not imported from: ‘GANPAdata’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
prepare_Rd: GANPA-package.Rd:30: Dropping empty section \seealso
prepare_Rd: GANPA-package.Rd:31: Dropping empty section \examples
prepare_Rd: GSE.Test.Main.Rd:24: Dropping empty section \details
prepare_Rd: GSE.Test.Main.Rd:32: Dropping empty section \note
prepare_Rd: GSE.Test.Main.Rd:33: Dropping empty section \seealso
prepare_Rd: weight.gsets.test.Rd:14: Dropping empty section \details
prepare_Rd: weight.gsets.test.Rd:25: Dropping empty section \note
prepare_Rd: weight.gsets.with.msprot.Rd:17: Dropping empty section \details
prepare_Rd: weight.gsets.with.msprot.Rd:27: Dropping empty section \note
prepare_Rd: weight.gsets.with.msprot.Rd:31: Dropping empty section \examples
Rd file 'GSE.Test.Main.Rd':
  \usage lines wider than 90 characters:
     GSE.Test.Main(gExprs.obj, gsets, gNET, check.exprs = TRUE, msp.groups, size.min = 15, size.max = 500, permN = 1000, randN = 30, permFDR ... [TRUNCATED]
  \examples lines wider than 100 characters:
     # GSE.Test.Main(gExprs.obj=gExprs.p53, gsets=gsets.msigdb.pnas, gNET=gNET, check.exprs=TRUE, msp.groups=msp.groups, size.min=15, size.m ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmphZUilQ/R.INSTALL14f54247841b/gapfill/man/Image.Rd:95: file link ‘ggplot2’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gapfill.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘regress’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpXHu6uH/R.INSTALL282a4410964e/GA/man/ga.Rd:116: file link ‘stopCluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXHu6uH/R.INSTALL282a4410964e/GA/man/gaisl.Rd:123: file link ‘stopCluster’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GA.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpI0WN60/R.INSTALL7e171cb055cd/gaston/man/write.bed.matrix.Rd:37: file link ‘saveRDS’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gaston.Rcheck/00install.out’ for details.
'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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpxV591m/R.INSTALL42ce16c368cf/GB2group/man/fitgroup.gb2.Rd:124: file link ‘gini.gb2’ in package ‘GB2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GB2group.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpTv54tN/R.INSTALL3178107291ef/GB2/man/Thomae.Rd:49: file link ‘genhypergeo_series’ in package ‘hypergeo’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GB2.Rcheck/00install.out’ for details.
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.
Found the following files/directories:
  ‘checkdata.csv’ ‘gbmforest.sas’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpLeYQAG/R.INSTALL1b5a9e5a41e/gbm/man/calibrate.plot.Rd:47: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLeYQAG/R.INSTALL1b5a9e5a41e/gbm/man/grid.arrange.Rd:10: file link ‘grid.arrange’ in package ‘gridExtra’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLeYQAG/R.INSTALL1b5a9e5a41e/gbm/man/plot.gbm.Rd:44: file link ‘co.intervals’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLeYQAG/R.INSTALL1b5a9e5a41e/gbm/man/plot.gbm.Rd:45: file link ‘equal.count’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLeYQAG/R.INSTALL1b5a9e5a41e/gbm/man/plot.gbm.Rd:48: file link ‘co.intervals’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLeYQAG/R.INSTALL1b5a9e5a41e/gbm/man/plot.gbm.Rd:48: file link ‘equal.count’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLeYQAG/R.INSTALL1b5a9e5a41e/gbm/man/plot.gbm.Rd:57: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLeYQAG/R.INSTALL1b5a9e5a41e/gbm/man/plot.gbm.Rd:74: file link ‘lattice’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLeYQAG/R.INSTALL1b5a9e5a41e/gbm/man/quantile.rug.Rd:30: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gbm.Rcheck/00install.out’ for details.
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.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpM74Njm/R.INSTALL161e555d5a52/GCalignR/man/plot.GCalign.Rd:16: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GCalignR.Rcheck/00install.out’ for details.
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.
Package suggested but not available for checking: ‘gputools’
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpV1b3f3/R.INSTALL3d6a3f120a9f/gdalcubes/man/animate.Rd:53: file link ‘image_animate’ in package ‘magick’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gdalcubes.Rcheck/00install.out’ for details.
Found the following calls to attach():
File ‘g.data/R/g.data.attach.R’:
  attach(NULL, pos, basename(dir))
See section ‘Good practice’ in ‘?attach’.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp2EK5RG/R.INSTALL66775fb46d60/gdata/man/ans.Rd:14: file link ‘.Last.value’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp2EK5RG/R.INSTALL66775fb46d60/gdata/man/ans.Rd:20: file link ‘.Last.value’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp2EK5RG/R.INSTALL66775fb46d60/gdata/man/first.Rd:34: file link ‘tail’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp2EK5RG/R.INSTALL66775fb46d60/gdata/man/left.Rd:27: file link ‘tail’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp2EK5RG/R.INSTALL66775fb46d60/gdata/man/read.xls.Rd:66: file link ‘read.csv’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp2EK5RG/R.INSTALL66775fb46d60/gdata/man/reorder.Rd:56: file link ‘reorder’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp2EK5RG/R.INSTALL66775fb46d60/gdata/man/trim.Rd:37: file link ‘sub’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp2EK5RG/R.INSTALL66775fb46d60/gdata/man/trim.Rd:37: file link ‘gsub’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp2EK5RG/R.INSTALL66775fb46d60/gdata/man/unmatrix.Rd:23: file link ‘as.vector’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp2EK5RG/R.INSTALL66775fb46d60/gdata/man/upperTriangle.Rd:47: file link ‘upper.tri’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gdata.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpT5Nofm/R.INSTALL5954134665c3/gdistance/man/accCost.Rd:63: file link ‘shortest_paths’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpT5Nofm/R.INSTALL5954134665c3/gdistance/man/passage.Rd:102: file link ‘commuteDistance’ in package ‘gdistance’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gdistance.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gdns)
  > 
  > test_check("gdns")
  ── 1. Failure: we can do something (@test-gdns.R#4)  ───────────────────────────
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 11 - 10 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: we can do something (@test-gdns.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp5tA3Qs/R.INSTALL403a71e91a2c/gdtools/man/version_cairo.Rd:15: file link ‘packageVersion’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gdtools.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘gdxrrw’
Non-standard files/directories found at top level:
  ‘README.too’ ‘blurb’
Package vignette with placeholder title ‘Vignette Title’:
  ‘GEint_example.Rmd’
Running examples in ‘gemtc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: atrialFibrillation
> ### Title: Prevention of stroke in atrial fibrillation patients
> ### Aliases: atrialFibrillation
> 
> ### ** Examples
> 
> # Build a model similar to Model 4(b) from Cooper et al. (2009):
> classes <- list("control"=c("01"),
+                 "anti-coagulant"=c("02","03","04","09"),
+                 "anti-platelet"=c("05","06","07","08","10","11","12","16","17"),
+                 "mixed"=c("13","14","15"))
> 
> regressor <- list(coefficient='shared',
+                   variable='stroke',
+                   classes=classes)
> 
> model <- mtc.model(atrialFibrillation,
+                    type="regression",
+                    regressor=regressor,
+                    om.scale=10)
Error in x[...] <- m : NAs are not allowed in subscripted assignments
Calls: mtc.model ... %in% -> mtc.network.graph -> comp -> [<- -> [<-.factor
Execution halted
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp8oAB44/R.INSTALL1b87239ad47b/GenAlgo/man/maha.Rd:23: file link ‘cov.mve’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8oAB44/R.INSTALL1b87239ad47b/GenAlgo/man/maha.Rd:45: file link ‘cov.mve’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8oAB44/R.INSTALL1b87239ad47b/GenAlgo/man/maha.Rd:46: file link ‘var’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GenAlgo.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpMp54GU/R.INSTALL1bba37c76451/genBart/man/genModelResults.Rd:20: file link ‘eBayes’ in package ‘limma’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMp54GU/R.INSTALL1bba37c76451/genBart/man/genModelResults.Rd:22: file link ‘glmLRT’ in package ‘edgeR’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMp54GU/R.INSTALL1bba37c76451/genBart/man/genModelResults.Rd:78: file link ‘eBayes’ in package ‘limma’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMp54GU/R.INSTALL1bba37c76451/genBart/man/genModelResults.Rd:81: file link ‘glmLRT’ in package ‘edgeR’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/genBart.Rcheck/00install.out’ for details.
clopper.pearson.ci: no visible global function definition for ‘qbeta’
cm.clopper.pearson.ci: no visible global function definition for
  ‘uniroot’
cm.clopper.pearson.ci : <anonymous>: no visible global function
  definition for ‘pbeta’
cm.n.clopper.pearson: no visible global function definition for
  ‘uniroot’
cm.n.clopper.pearson : <anonymous>: no visible global function
  definition for ‘pbeta’
n.clopper.pearson: no visible global function definition for ‘uniroot’
n.clopper.pearson : <anonymous>: no visible global function definition
  for ‘pbeta’
rgbinom: no visible global function definition for ‘runif’
Undefined global functions or variables:
  pbeta qbeta runif uniroot
Consider adding
  importFrom("stats", "pbeta", "qbeta", "runif", "uniroot")
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 suggested but not available for checking: ‘genderdata’
t1p1: no visible global function definition for ‘var’
t1p1: no visible global function definition for ‘pt’
t1p2: no visible global function definition for ‘pt’
Undefined global functions or variables:
  pt var
Consider adding
  importFrom("stats", "pt", "var")
to your NAMESPACE file.
Rd file 'flexorhtest.Rd':
  \examples lines wider than 100 characters:
          plot(x,y, main="Location and Strong Order Restrictions",cex.axis=1.5, cex.lab=1.5, cex.main=1.5, cex=1.5)

These lines will be truncated in the PDF manual.
load.genelist: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
Rd file 'geneListPie-package.Rd':
  \examples lines wider than 100 characters:
     glist<-c("ABCB7","ABCF1","ABHD2","ACAD9","ACIN1","AMOTL1","ANLN","ANXA4","APBA2","APBA3","BAI3","BCLAF1","BEST1")

Rd file 'geneListProfile.Rd':
  \examples lines wider than 100 characters:
     glist<-c("ABCB7","ABCF1","ABHD2","ACAD9","ACIN1","AMOTL1","ANLN","ANXA4","APBA2","APBA3","BAI3","BCLAF1","BEST1")

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘RHugin’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp83sJ6m/R.INSTALL43944c8d5310/geneNetBP/man/fit-methods.Rd:60: file link ‘tabu’ in package ‘bnlearn’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp83sJ6m/R.INSTALL43944c8d5310/geneNetBP/man/fit-methods.Rd:61: file link ‘gs’ in package ‘bnlearn’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp83sJ6m/R.INSTALL43944c8d5310/geneNetBP/man/fit-methods.Rd:61: file link ‘iamb’ in package ‘bnlearn’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp83sJ6m/R.INSTALL43944c8d5310/geneNetBP/man/fit-methods.Rd:61: file link ‘fast.iamb’ in package ‘bnlearn’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp83sJ6m/R.INSTALL43944c8d5310/geneNetBP/man/fit-methods.Rd:61: file link ‘inter.iamb’ in package ‘bnlearn’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp83sJ6m/R.INSTALL43944c8d5310/geneNetBP/man/fit-methods.Rd:62: file link ‘mmhc’ in package ‘bnlearn’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp83sJ6m/R.INSTALL43944c8d5310/geneNetBP/man/fit-methods.Rd:77: file link ‘bn-class’ in package ‘bnlearn’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geneNetBP.Rcheck/00install.out’ for details.
fit.dbn: no visible global function definition for ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpcqilnh/R.INSTALL1e6e35b666f/GeneNet/man/cor0.test.Rd:22: file link ‘pcor0’ in package ‘fdrtool’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpcqilnh/R.INSTALL1e6e35b666f/GeneNet/man/ggm.estimate.pcor.Rd:26: file link ‘dyn.pcor’ in package ‘longitudinal’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpcqilnh/R.INSTALL1e6e35b666f/GeneNet/man/ggm.estimate.pcor.Rd:16: file link ‘dyn.pcor’ in package ‘longitudinal’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpcqilnh/R.INSTALL1e6e35b666f/GeneNet/man/ggm.estimate.pcor.Rd:35: file link ‘dyn.pcor’ in package ‘longitudinal’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpcqilnh/R.INSTALL1e6e35b666f/GeneNet/man/ggm.estimate.pcor.Rd:68: file link ‘dyn.pcor’ in package ‘longitudinal’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GeneNet.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package unavailable to check Rd xrefs: ‘GeneticsDesign’
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.
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘genotypeR.Rmd’
Found the following files/directories:
  ‘test.csv’ ‘test_temp_cross.csv’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpQrrAH1/R.INSTALL1fb6635d0e19/genridge/man/contourf.Rd:64: file link ‘contour.default’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQrrAH1/R.INSTALL1fb6635d0e19/genridge/man/contourf.Rd:66: file link ‘contour.default’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQrrAH1/R.INSTALL1fb6635d0e19/genridge/man/contourf.Rd:96: file link ‘contourplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQrrAH1/R.INSTALL1fb6635d0e19/genridge/man/plot3d.ridge.Rd:87: file link ‘shade3d’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQrrAH1/R.INSTALL1fb6635d0e19/genridge/man/plot3d.ridge.Rd:93: file link ‘wire3d’ in package ‘rgl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/genridge.Rcheck/00install.out’ for details.
Rd file 'AbstractModel-class.Rd':
  \examples lines wider than 100 characters:
     abm <- ab.create(model.call="ksvm", model.args=ksvm_model_args, predict.args=list(type="probabilities"), xtrans=as.matrix)
     abm <- ab.create(model.call="rpart", model.args=list(control=rpart.control(minsplit=0)), predict.args=list(type='prob'))
     abm <- ab.create(model.call="nnet", model.args=list(size=3, linout=TRUE, maxit=400, rang=0.001, decay=0.0001), xtrans=as.matrix)
     abm <- ab.create(model.call="rpart", model.args=list(method='anova', control=rpart.control(minsplit=2, cp=1e-03)))

Rd file 'predict.gensemble.Rd':
  \usage lines wider than 90 characters:
     predict(object, X, type = c("prob", "class"), method = c("prob", "vote"), return.all = F, ...)

These lines will be truncated in the PDF manual.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmprkImKB/R.INSTALL7ed4d9aaa59/geoBayes/man/alik_cutoff.Rd:41: file link ‘approx’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprkImKB/R.INSTALL7ed4d9aaa59/geoBayes/man/alik_inla.Rd:82: file link ‘spDists’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprkImKB/R.INSTALL7ed4d9aaa59/geoBayes/man/alik_optim.Rd:79: file link ‘spDists’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprkImKB/R.INSTALL7ed4d9aaa59/geoBayes/man/mcsglmm.Rd:124: file link ‘spDists’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprkImKB/R.INSTALL7ed4d9aaa59/geoBayes/man/mcsglmm_mala.Rd:127: file link ‘spDists’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprkImKB/R.INSTALL7ed4d9aaa59/geoBayes/man/mcstrga.Rd:123: file link ‘spDists’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprkImKB/R.INSTALL7ed4d9aaa59/geoBayes/man/mcstrga_mala.Rd:126: file link ‘spDists’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprkImKB/R.INSTALL7ed4d9aaa59/geoBayes/man/rsglmm.Rd:104: file link ‘spDists’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprkImKB/R.INSTALL7ed4d9aaa59/geoBayes/man/spcovariance.Rd:53: file link ‘spDists’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geoBayes.Rcheck/00install.out’ for details.
PAEA : <anonymous>: no visible global function definition for
  ‘integrate’
PAEAAnalysis: no visible global function definition for
  ‘txtProgressBar’
PAEAAnalysis : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
PAEAAnalysis: no visible global function definition for ‘par’
PAEAAnalysis: no visible global function definition for ‘barplot’
chdirSig: no visible global function definition for ‘prcomp’
chdirSig: no visible global function definition for ‘rchisq’
chdirSig: no visible global function definition for ‘txtProgressBar’
chdirSig : <anonymous> : <anonymous>: no visible global function
  definition for ‘setTxtProgressBar’
chdirplots : <anonymous>: no visible global function definition for
  ‘par’
chdirplots : <anonymous>: no visible global function definition for
  ‘arrows’
chdirplots : <anonymous>: no visible global function definition for
  ‘barplot’
multigmtPAEAAnalysis: no visible global function definition for
  ‘txtProgressBar’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘setTxtProgressBar’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘data’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘write.table’
Undefined global functions or variables:
  arrows barplot data integrate par prcomp rchisq setTxtProgressBar
  txtProgressBar write.table
Consider adding
  importFrom("graphics", "arrows", "barplot", "par")
  importFrom("stats", "integrate", "prcomp", "rchisq")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘PAEA_p_values-Cancer_Cell_Line_Encyclopedia.gmt.txt’
  ‘PAEA_p_values-ChEA.gmt.txt’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmphLY9IK/R.INSTALL68cb26375893/geojsonio/man/as.json.Rd:12: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphLY9IK/R.INSTALL68cb26375893/geojsonio/man/geojson_json.Rd:60: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphLY9IK/R.INSTALL68cb26375893/geojsonio/man/geojson_write.Rd:68: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphLY9IK/R.INSTALL68cb26375893/geojsonio/man/topojson_write.Rd:79: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geojsonio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpvyscia/R.INSTALL2c456f186889/geojson/man/geo_write.Rd:18: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpvyscia/R.INSTALL2c456f186889/geojson/man/geobuf.Rd:33: file link ‘geobuf2json’ in package ‘protolite’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpvyscia/R.INSTALL2c456f186889/geojson/man/geobuf.Rd:34: file link ‘json2geobuf’ in package ‘protolite’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geojson.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpPinsWm/R.INSTALL373c2f7d5050/geoknife/man/webprocess-class.Rd:17: file link ‘algorithm’ in package ‘geoknife’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPinsWm/R.INSTALL373c2f7d5050/geoknife/man/webprocess-class.Rd:53: file link ‘algorithm’ in package ‘geoknife’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geoknife.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Rd file 'fujitopo.Rd':
  \examples lines wider than 100 characters:
     PLOC=list(LON=range(fujitopo$lon), x=range(fujitopo$lon), LAT=range(fujitopo$lat), y=range(fujitopo$lat))

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpVISdFJ/R.INSTALL4b81d0d0f1a/GeomComb/man/comb_WA.Rd:74: file link ‘winsor.mean’ in package ‘psych’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GeomComb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpAgVtM9/R.INSTALL38ab4fecbb1d/geonetwork/man/geonetwork.Rd:18: file link ‘CRS’ in package ‘rgdal’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geonetwork.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpJJye6R/R.INSTALLe30299b523b/geoR/man/as.geodata.Rd:48: file link ‘SpatialPointsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJJye6R/R.INSTALLe30299b523b/geoR/man/cov.spatial.Rd:166: file link ‘CovarianceFct’ in package ‘RandomFields’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJJye6R/R.INSTALLe30299b523b/geoR/man/grf.Rd:90: file link ‘GaussRF’ in package ‘RandomFields’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJJye6R/R.INSTALLe30299b523b/geoR/man/grf.Rd:113: file link ‘GaussRF’ in package ‘RandomFields’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJJye6R/R.INSTALLe30299b523b/geoR/man/grf.Rd:183: file link ‘GaussRF’ in package ‘RandomFields’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geoR.Rcheck/00install.out’ for details.
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.
Package which this enhances but not available for checking: ‘INLA’
Malformed Description field: should contain one or more complete sentences.
Found the following calls to data() loading into the global environment:
File ‘geotools/R/zzz.R’:
  data(fr_geo_rad)
See section ‘Good practice’ in ‘?data’.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp4POK2k/R.INSTALLc2648bc7ff4/geoTS/man/split_replace.Rd:70: file link ‘doParallel’ in package ‘doParallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geoTS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpl20DtT/R.INSTALL228b3fc0c934/geoviz/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geoviz.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpZpBna0/R.INSTALL48434cc189bd/GerminaR/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GerminaR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpNzVzys/R.INSTALLcb95f543ed6/gert/man/fetch.Rd:34: file link ‘ssh_key_info’ in package ‘credentials’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gert.Rcheck/00install.out’ for details.
GESTr: no visible global function definition for ‘rnorm’
GESTr: no visible global function definition for ‘sd’
GESTr : <anonymous>: no visible global function definition for ‘pnorm’
TranSAM : magChange: no visible global function definition for ‘median’
TranSAM : dstat: no visible global function definition for ‘sd’
TranSAM: no visible binding for global variable ‘sd’
TranSAM: no visible global function definition for ‘quantile’
findReplicateGroups: no visible global function definition for ‘qnorm’
findReplicateGroups: no visible global function definition for ‘sd’
fitGMM : simulateData: no visible global function definition for
  ‘rnorm’
fitGMM : simulateData: no visible global function definition for ‘sd’
fitGMM: no visible global function definition for ‘median’
fitGMM: no visible global function definition for ‘ks.test’
fitRockeDurbin: no visible global function definition for ‘dist’
fitRockeDurbin : findLowGenes: no visible global function definition
  for ‘median’
fitRockeDurbin : findLowGenes: no visible global function definition
  for ‘mad’
fitRockeDurbin: no visible binding for global variable ‘sd’
getMonotonicConfidences_multiclass: no visible global function
  definition for ‘pnorm’
getMonotonicConfidences_multiclass: no visible global function
  definition for ‘sd’
Undefined global functions or variables:
  dist ks.test mad median pnorm qnorm quantile rnorm sd
Consider adding
  importFrom("stats", "dist", "ks.test", "mad", "median", "pnorm",
             "qnorm", "quantile", "rnorm", "sd")
to your NAMESPACE file.
Rd file 'TranSAM.Rd':
  \usage lines wider than 90 characters:
     TranSAM(x,samples1,samples2,minChange=0.2,var_filter=0.01,maxFDR=1,changeStep=0.1,scoreFun="magChange")
  \examples lines wider than 100 characters:
     selected.columns <- sort(c(sample(1:ncol(ABIdata),30),which(colnames(ABIdata) %in% c("GSM194513","GSM194514","GSM194515","GSM194516","G ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘gbcbd_cache’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp53E2IW/R.INSTALL1a6351615509/getlandsat/man/lsat_scenes.Rd:10: file link ‘read_csv’ in package ‘readr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp53E2IW/R.INSTALL1a6351615509/getlandsat/man/lsat_scenes.Rd:16: file link ‘read_csv’ in package ‘readr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp53E2IW/R.INSTALL1a6351615509/getlandsat/man/lsat_scenes.Rd:18: file link ‘read_csv’ in package ‘readr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/getlandsat.Rcheck/00install.out’ for details.
'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.
Missing or unexported object: ‘stable::dstable.quick’
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘multtest’ which was already attached by Depends.
  Please remove these calls from your code.
Rd file 'gexmap.Rd':
  \usage lines wider than 90 characters:
     gexmap(genome = "homosapiens", scale = "", source = "", res = "", isGO = FALSE, isMAP = TRUE, lim_chi = 5, global_test_choice = 4, pcor ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp1mkBNf/R.INSTALL49c64f9c96e2/gfoRmula/man/gformula.Rd:148: file link ‘setDTthreads’ in package ‘data.table’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp1mkBNf/R.INSTALL49c64f9c96e2/gfoRmula/man/gformula_binary_eof.Rd:127: file link ‘setDTthreads’ in package ‘data.table’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp1mkBNf/R.INSTALL49c64f9c96e2/gfoRmula/man/gformula_continuous_eof.Rd:127: file link ‘setDTthreads’ in package ‘data.table’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp1mkBNf/R.INSTALL49c64f9c96e2/gfoRmula/man/gformula_survival.Rd:146: file link ‘setDTthreads’ in package ‘data.table’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gfoRmula.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp8jH27t/R.INSTALL4fd42ecd9852/ggalluvial/man/alluvial-data.Rd:54: file link ‘enquo’ in package ‘rlang’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggalluvial.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpNjJjh3/R.INSTALL6ddf57f512f4/ggalt/man/geom_xspline.Rd:187: file link ‘geom_line’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggalt.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpyvyscJ/R.INSTALL25a3342e4889/gganimate/man/gif_file.Rd:26: file link ‘as.factor’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gganimate.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpuXjS9s/R.INSTALL2834400b126a/ggChernoff/man/chernoffGrob.Rd:30: file link ‘grobTree’ in package ‘grid’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggChernoff.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpAJeZtM/R.INSTALL4a291a9c3a85/ggdag/man/as.tbl.tidy_daggity.Rd:23: file link ‘as_tibble’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpAJeZtM/R.INSTALL4a291a9c3a85/ggdag/man/as_tbl_graph.Rd:27: file link ‘as_tbl_graph’ in package ‘tidygraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpAJeZtM/R.INSTALL4a291a9c3a85/ggdag/man/d_relationship.Rd:151: file link ‘dseparated’ in package ‘dagitty’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpAJeZtM/R.INSTALL4a291a9c3a85/ggdag/man/equivalent.Rd:103: file link ‘equivalentDAGs’ in package ‘dagitty’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpAJeZtM/R.INSTALL4a291a9c3a85/ggdag/man/equivalent.Rd:51: file link ‘create_layout’ in package ‘ggraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpAJeZtM/R.INSTALL4a291a9c3a85/ggdag/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpAJeZtM/R.INSTALL4a291a9c3a85/ggdag/man/tidy_dagitty.Rd:14: file link ‘create_layout’ in package ‘ggraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpAJeZtM/R.INSTALL4a291a9c3a85/ggdag/man/variable_family.Rd:171: file link ‘children’ in package ‘dagitty’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggdag.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpiNSXtm/R.INSTALL5194791b8662/ggdemetra/man/geom_arima.Rd:26: file link ‘geom_label’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpiNSXtm/R.INSTALL5194791b8662/ggdemetra/man/geom_diagnostics.Rd:50: file link ‘ttheme_default’ in package ‘gridExtra’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpiNSXtm/R.INSTALL5194791b8662/ggdemetra/man/geom_outlier.Rd:27: file link ‘geom_label’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpiNSXtm/R.INSTALL5194791b8662/ggdemetra/man/geom_outlier.Rd:29: file link ‘geom_label_repel’ in package ‘ggrepel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpiNSXtm/R.INSTALL5194791b8662/ggdemetra/man/geom_outlier.Rd:36: file link ‘geom_label’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpiNSXtm/R.INSTALL5194791b8662/ggdemetra/man/geom_outlier.Rd:38: file link ‘geom_label_repel’ in package ‘ggrepel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpiNSXtm/R.INSTALL5194791b8662/ggdemetra/man/geom_outlier.Rd:76: file link ‘geom_label_repel’ in package ‘ggrepel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggdemetra.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpG1cAly/R.INSTALL2a1f609deb04/ggdistribute/man/annotate_corner.Rd:17: file link ‘geom_label’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpG1cAly/R.INSTALL2a1f609deb04/ggdistribute/man/theme_mejr.Rd:48: file link ‘theme_update’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpG1cAly/R.INSTALL2a1f609deb04/ggdistribute/man/theme_mejr.Rd:48: file link ‘theme_set’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggdistribute.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp6zJP5q/R.INSTALL2d7938d2352a/ggetho/man/stat_pop_etho.Rd:45: file link ‘mean_cl_boot’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6zJP5q/R.INSTALL2d7938d2352a/ggetho/man/stat_pop_etho.Rd:103: file link ‘stat_smooth’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6zJP5q/R.INSTALL2d7938d2352a/ggetho/man/time_scales.Rd:147: file link ‘scale_x_continuous’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggetho.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpKxWSnr/R.INSTALL2dc842ee084e/ggfocus/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggfocus.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpE1wBdi/R.INSTALL30ed32072254/gghalves/man/geom_half_violin.Rd:84: file link ‘bw.nrd’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gghalves.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpsNF8gI/R.INSTALL53f935890e95/gghighlight/man/gghighlight.Rd:36: file link ‘geom_label_repel’ in package ‘ggrepel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gghighlight.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpI5fvHb/R.INSTALL54ed76cddc5b/ggimage/man/reexports.Rd:15: file link ‘as.grob’ in package ‘ggplotify’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggimage.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘intro.Rmd’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp4nhQ51/R.INSTALL5f687f72a12c/ggmap/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggmap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpp96eAU/R.INSTALL354c1e4c4854/ggnormalviolin/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggnormalviolin.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpLNEzsz/R.INSTALL35cc7a5cc396/ggpage/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggpage.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmphAFpLt/R.INSTALL36fb15d6e7b4/ggparty/man/geom_node_label.Rd:101: file link ‘geom_label’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggparty.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpZx3wMF/R.INSTALL38061e36c8b4/ggplot.multistats/man/draw_key_hexagon.Rd:18: file link ‘polygonGrob’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZx3wMF/R.INSTALL38061e36c8b4/ggplot.multistats/man/stat_summaries_hex.Rd:77: file link ‘stat_summary_hex’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggplot.multistats.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpfcdYyT/R.INSTALL92e4eb156b9/ggpmisc/man/geom_grob.Rd:62: file link ‘geom_label’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfcdYyT/R.INSTALL92e4eb156b9/ggpmisc/man/geom_plot.Rd:62: file link ‘geom_label’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfcdYyT/R.INSTALL92e4eb156b9/ggpmisc/man/geom_table.Rd:67: file link ‘geom_label’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggpmisc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpvrdVbU/R.INSTALL56765a4441b9/ggPMX/man/facet_wrap_paginate.Rd:50: file link ‘label_parsed’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpvrdVbU/R.INSTALL56765a4441b9/ggPMX/man/facet_wrap_paginate.Rd:51: file link ‘label_value’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpvrdVbU/R.INSTALL56765a4441b9/ggPMX/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggPMX.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpev4BWY/R.INSTALL3881267011ad/ggpol/man/facet_share.Rd:47: file link ‘label_parsed’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpev4BWY/R.INSTALL3881267011ad/ggpol/man/facet_share.Rd:48: file link ‘label_value’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggpol.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpxV5BnH/R.INSTALL38e715fa3f5e/ggpolypath/man/geom_polypath.Rd:118: file link ‘polygonGrob’ in package ‘grid’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggpolypath.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpEeieRh/R.INSTALL3a964be791f6/ggquiver/man/reexports.Rd:14: file link ‘%>%’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggquiver.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpS9yRYM/R.INSTALL2a994ddca53b/ggrepel/man/geom_text_repel.Rd:111: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpS9yRYM/R.INSTALL2a994ddca53b/ggrepel/man/geom_text_repel.Rd:127: file link ‘geom_label’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggrepel.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ggplot2’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ggroc: no visible global function definition for ‘ggplot’
ggroc: no visible global function definition for ‘aes’
ggroc: no visible global function definition for ‘geom_point’
ggroc: no visible global function definition for ‘geom_line’
ggroc: no visible global function definition for ‘theme’
ggroc: no visible global function definition for ‘element_text’
ggroc: no visible global function definition for ‘labs’
ggroc: no visible global function definition for ‘ggsave’
Undefined global functions or variables:
  aes element_text geom_line geom_point ggplot ggsave labs theme
Found the following files/directories:
  ‘roc.pdf’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpN2XB2j/R.INSTALL28aa73b23634/ggstance/man/geom_linerangeh.Rd:109: file link ‘geom_pointrange’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpN2XB2j/R.INSTALL28aa73b23634/ggstance/man/geom_linerangeh.Rd:110: file link ‘geom_errorbar’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpN2XB2j/R.INSTALL28aa73b23634/ggstance/man/geom_linerangeh.Rd:111: file link ‘geom_crossbar’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpN2XB2j/R.INSTALL28aa73b23634/ggstance/man/position-vertical.Rd:72: file link ‘position_fill’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpN2XB2j/R.INSTALL28aa73b23634/ggstance/man/stat_binh.Rd:112: file link ‘stat_bin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpN2XB2j/R.INSTALL28aa73b23634/ggstance/man/stat_boxploth.Rd:68: file link ‘stat_boxplot’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpN2XB2j/R.INSTALL28aa73b23634/ggstance/man/stat_counth.Rd:68: file link ‘stat_count’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpN2XB2j/R.INSTALL28aa73b23634/ggstance/man/stat_xdensity.Rd:88: file link ‘stat_ydensity’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpN2XB2j/R.INSTALL28aa73b23634/ggstance/man/stat_xdensity.Rd:58: file link ‘bw.nrd’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggstance.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpIRXypt/R.INSTALL1ab9b618099/ggstatsplot/man/reexports.Rd:28: file link ‘%$%’ in package ‘ipmisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpIRXypt/R.INSTALL1ab9b618099/ggstatsplot/man/reexports.Rd:28: file link ‘%<-%’ in package ‘ipmisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpIRXypt/R.INSTALL1ab9b618099/ggstatsplot/man/reexports.Rd:28: file link ‘%<>%’ in package ‘ipmisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpIRXypt/R.INSTALL1ab9b618099/ggstatsplot/man/reexports.Rd:28: file link ‘%>%’ in package ‘ipmisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpIRXypt/R.INSTALL1ab9b618099/ggstatsplot/man/reexports.Rd:28: file link ‘%|%’ in package ‘ipmisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpIRXypt/R.INSTALL1ab9b618099/ggstatsplot/man/reexports.Rd:28: file link ‘%||%’ in package ‘ipmisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpIRXypt/R.INSTALL1ab9b618099/ggstatsplot/man/reexports.Rd:28: file link ‘as_tibble’ in package ‘ipmisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpIRXypt/R.INSTALL1ab9b618099/ggstatsplot/man/reexports.Rd:28: file link ‘tibble’ in package ‘ipmisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpIRXypt/R.INSTALL1ab9b618099/ggstatsplot/man/reexports.Rd:30: file link ‘pairwise_p’ in package ‘pairwiseComparisons’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggstatsplot.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /private/var/folders/67/ys78wlfd43zc4rzmvbtfthqh0000gn/T/RtmpjkG5XC/Rbuildbdf33a3b0c12/ggtern/man/geom_errorbarX.Rd:78: file link ‘geom_errorbar’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /private/var/folders/67/ys78wlfd43zc4rzmvbtfthqh0000gn/T/RtmpjkG5XC/Rbuildbdf33a3b0c12/ggtern/man/geom_label_viewport.Rd:106: file link ‘geom_label’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8HyGfC/R.INSTALL7e6f6ff9eb34/ggtern/man/scale_X_continuous.Rd:44: file link ‘extended_breaks’ in package ‘scales’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggtern.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpWcHuJE/R.INSTALL40715f474bb9/ggTimeSeries/man/stat_calendar_heatmap.Rd:34: file link ‘strftime’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggTimeSeries.Rcheck/00install.out’ for details.
Running examples in ‘GGUM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GUM
> ### Title: Fit the graded unfolding model (GUM)
> ### Aliases: GUM
> 
> ### ** Examples
> 
> # Generate data:
> gen <- GenData.GGUM(400, 5, 3, "GUM", seed = 139)
> # Fit the GUM:
> fit <- GUM(gen$data, 3)

|-                                                           |Error in colSums(D1$taus) : 'x' must be numeric
Calls: GUM -> colSums
Execution halted
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpN3OjEn/R.INSTALL50997c0dfec2/ggvis/man/ggvisControlOutput.Rd:16: file link ‘uiOutput’ in package ‘shiny’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggvis.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp5IdfyG/R.INSTALL41a2754dee9c/ggvoronoi/man/fortify_voronoi.Rd:10: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp5IdfyG/R.INSTALL41a2754dee9c/ggvoronoi/man/ggvoronoi-package.Rd:9: file link ‘ggplot2’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp5IdfyG/R.INSTALL41a2754dee9c/ggvoronoi/man/ggvoronoi-package.Rd:9: file link ‘sp’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp5IdfyG/R.INSTALL41a2754dee9c/ggvoronoi/man/ggvoronoi-package.Rd:9: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp5IdfyG/R.INSTALL41a2754dee9c/ggvoronoi/man/ggvoronoi-package.Rd:9: file link ‘gArea’ in package ‘rgeos’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp5IdfyG/R.INSTALL41a2754dee9c/ggvoronoi/man/voronoi_polygon.Rd:19: file link ‘StatVoronoi’ in package ‘ggvoronoi’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggvoronoi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpG6r5Xb/R.INSTALL66c05655f5d2/ghibli/man/ghibli_palettes.Rd:20: file link ‘colour’ in package ‘prismatic’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ghibli.Rcheck/00install.out’ for details.
Namespace with empty importFrom: ‘statmod’
Malformed Title field: should not end in a period.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp6DO9sm/R.INSTALL1ac524f7780c/gh/man/gh_token.Rd:49: file link ‘default_backend’ in package ‘keyring’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6DO9sm/R.INSTALL1ac524f7780c/gh/man/gh_token.Rd:85: file link ‘default_backend’ in package ‘keyring’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gh.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpxGtnvu/R.INSTALL6aa46fb669a3/GiANT/man/plot.Rd:32: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpxGtnvu/R.INSTALL6aa46fb669a3/GiANT/man/plotOverrepresentation.Rd:36: file link ‘vennDiagram’ in package ‘limma’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GiANT.Rcheck/00install.out’ for details.
acovamcmc: no visible global function definition for ‘rnorm’
acovamcmc: no visible global function definition for ‘rgamma’
acovamcmc: no visible binding for global variable ‘quantile’
acovamcmc: no visible global function definition for ‘quantile’
acovamcmc: no visible global function definition for ‘var’
plot.acovamcmc: no visible global function definition for ‘dev.new’
plot.acovamcmc: no visible global function definition for ‘par’
plot.acovamcmc: no visible global function definition for ‘density’
plot.acovamcmc: no visible global function definition for ‘acf’
plot.acovamcmc: no visible global function definition for ‘contour’
plot.acovamcmc: no visible global function definition for ‘image’
plot.acovamcmc: no visible global function definition for ‘persp’
Undefined global functions or variables:
  acf contour density dev.new image par persp quantile rgamma rnorm var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "contour", "image", "par", "persp")
  importFrom("stats", "acf", "density", "quantile", "rgamma", "rnorm",
             "var")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘gibbs.met/R/firstlib.R’:
  .First.lib calls:
    cat("Naive Gibbs Sampling with Metropolis steps(gibbs.met) loaded\n",     "COPYRIGHT 2008 (c) Longhai Li (http://math.usask.ca/~longhai)\n",     "Type ?begin.gibbs.met for help to this package\n", sep = "")

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

met_gaussian : one_transition: no visible global function definition
  for ‘rnorm’
met_gaussian : one_transition: no visible global function definition
  for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘mc_mvn_closemix.eps’ ‘mc_mvn_farmix_met.eps’ ‘mc_mvn_lowcor.eps’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmptIyZmb/R.INSTALL6d502b565d1/Gifi/man/plot.homals.Rd:35: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmptIyZmb/R.INSTALL6d502b565d1/Gifi/man/plot.morals.Rd:25: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmptIyZmb/R.INSTALL6d502b565d1/Gifi/man/plot.princals.Rd:34: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Gifi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpRC8hZW/R.INSTALL71e55dd3ae03/gim/man/gim.Rd:70: file link ‘coefficients’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gim.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Found the following sources/headers not terminated with a newline:
  inst/include/GiRaF.hpp
  inst/include/lattice.hpp
  inst/include/sampler.hpp
Some compilers warn on such files.
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').
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpu3wsSS/R.INSTALL49725d4c8c19/git2r/man/git_time.Rd:23: file link ‘time zones’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpu3wsSS/R.INSTALL49725d4c8c19/git2r/man/when.Rd:13: file link ‘time zones’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/git2r.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp5qHWbP/R.INSTALL2a575ad00e5b/githubinstall/man/reexports.Rd:14: file link ‘github_pull’ in package ‘devtools’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/githubinstall.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘.gitlab-ci.yml’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp8JhrS5/R.INSTALL58bf9953ea9/glancedata/man/plot_numerical_vars.Rd:33: file link ‘stat_qq_line’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8JhrS5/R.INSTALL58bf9953ea9/glancedata/man/plot_numerical_vars.Rd:34: file link ‘stat_qq’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/glancedata.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpwHzeCQ/R.INSTALL1f252615caf/gld/man/fit.fkml.Rd:99: file link ‘summary.starship’ in package ‘gld’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpwHzeCQ/R.INSTALL1f252615caf/gld/man/fit.fkml.moments.val.Rd:53: file link ‘gld’ in package ‘gld’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpwHzeCQ/R.INSTALL1f252615caf/gld/man/starship.Rd:91: file link ‘summary.starship’ in package ‘gld’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpwHzeCQ/R.INSTALL1f252615caf/gld/man/starship.Rd:104: file link ‘gld’ in package ‘gld’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gld.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘glmaag.Rmd’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpNdPRb5/R.INSTALL3d178c170b3/glmbb/man/glmbb.Rd:60: file link ‘binomial’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNdPRb5/R.INSTALL3d178c170b3/glmbb/man/glmbb.Rd:60: file link ‘quasibinomial’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/glmbb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpRSQomf/R.INSTALL58c15009df2a/glmdisc/man/contr.ltfr.Rd:5: file link ‘contr.ltfr’ in package ‘caret’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpRSQomf/R.INSTALL58c15009df2a/glmdisc/man/contr.ltfr.Rd:13: file link ‘contr.ltfr’ in package ‘caret’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpRSQomf/R.INSTALL58c15009df2a/glmdisc/man/contr.ltfr.Rd:10: file link ‘contr.ltfr’ in package ‘caret’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/glmdisc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpjZTZ6y/R.INSTALL4f9378e1691a/glmmfields/man/glmmfields.Rd:98: file link ‘vb’ in package ‘rstan’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpjZTZ6y/R.INSTALL4f9378e1691a/glmmfields/man/glmmfields.Rd:114: file link ‘sampling’ in package ‘rstan’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpjZTZ6y/R.INSTALL4f9378e1691a/glmmfields/man/glmmfields.Rd:131: file link ‘sampling’ in package ‘rstan’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpjZTZ6y/R.INSTALL4f9378e1691a/glmmfields/man/loo.Rd:14: file link ‘loo.array’ in package ‘loo’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/glmmfields.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp13wSQ7/R.INSTALL65c414ae8ecc/glmmTMB/man/bootmer_methods.Rd:20: file link ‘isLMM’ in package ‘lme4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp13wSQ7/R.INSTALL65c414ae8ecc/glmmTMB/man/weights.glmmTMB.Rd:29: file link ‘weights.glm’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/glmmTMB.Rcheck/00install.out’ for details.
Running examples in ‘glmnetcr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coef.glmnetcr
> ### Title: Extract All Model Coefficients
> ### Aliases: coef.glmnetcr
> ### Keywords: methods
> 
> ### ** Examples
> 
> data(diabetes)
> x <- diabetes[, 2:dim(diabetes)[2]]
> y <- diabetes$y
> glmnet.fit <- glmnetcr(x, y)
Error in glmnet(glmnet.data$x, glmnet.data$y, family = "binomial", weights = glmnet.data$weights,  : 
  argument "exclude" is missing, with no default
Calls: glmnetcr -> glmnet
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘glmnetcr.Rnw’ using Sweave
Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 4.0

Error: processing vignette 'glmnetcr.Rnw' failed with diagnostics:
 chunk 2 
Error in glmnet(glmnet.data$x, glmnet.data$y, family = "binomial", weights = glmnet.data$weights,  : 
  argument "exclude" is missing, with no default

--- failed re-building 'glmnetcr.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpwFWS3C/R.INSTALL148869858224/glmnetUtils/man/cv.glmnet.Rd:104: file link ‘coef.cv.glmnet’ in package ‘glmnet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpwFWS3C/R.INSTALL148869858224/glmnetUtils/man/cva.glmnet.Rd:155: file link ‘coef.cv.glmnet’ in package ‘glmnet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpwFWS3C/R.INSTALL148869858224/glmnetUtils/man/glmnet.Rd:110: file link ‘coef.glmnet’ in package ‘glmnet’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/glmnetUtils.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpsJZnF7/R.INSTALL43002119beb2/GlmSimulatoR/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GlmSimulatoR.Rcheck/00install.out’ for details.
Found an obsolete/platform-specific call in the following function:
  ‘plot.glmulti’
Found the platform-specific device:
  ‘windows’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
consensus,list: no visible global function definition for ‘.readRDS’
glmulti,character-character-ANY-ANY: no visible global function
  definition for ‘regsubsets’
Undefined global functions or variables:
  .readRDS regsubsets
Rd file 'glmulti.Rd':
  \usage lines wider than 90 characters:
     glmulti(y, xr, data, exclude = c(), name = "glmulti.analysis", intercept = TRUE, marginality = FALSE, bunch=30, chunk = 1, chunks = 1,
                     level = 2, minsize = 0, maxsize = -1, minK = 0, maxK = -1, method = "h", crit = "aic", confsetsize = 100, popsize = 100 ... [TRUNCATED]
  \examples lines wider than 100 characters:
     # It explains the general approach and shows how to use glmulti with mixed models from the lme4 package.
     # this procedure allows support of arbitrarily any fitting function, or the use of sophisticated constraints on the model structure

Rd file 'write.Rd':
  \usage lines wider than 90 characters:
     write(x, file = "data", ncolumns = if (is.character(x)) 1 else 5, append = FALSE, sep = " ")

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpcGxLrT/R.INSTALLb3221298fc5/glmx/man/glmx.control.Rd:47: file link ‘glm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/glmx.Rcheck/00install.out’ for details.
globalboosttest: no visible global function definition for ‘predict’
globalboosttest: no visible global function definition for ‘lm’
globalboosttest: no visible global function definition for ‘glm’
globalboosttest: no visible binding for global variable ‘binomial’
globalboosttest: no visible global function definition for ‘points’
globalboosttest: no visible global function definition for ‘AIC’
Undefined global functions or variables:
  AIC binomial glm lm points predict
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "AIC", "binomial", "glm", "lm", "predict")
to your NAMESPACE file.
prepare_Rd: globalboosttest.Rd:56: Dropping empty section \seealso
Rd file 'globalboosttest.Rd':
  \usage lines wider than 90 characters:
     globalboosttest(X,Y,Z=NULL,nperm=1000,mstop=1000,mstopAIC=FALSE,pvalueonly=TRUE,plot=FALSE,...)

These lines will be truncated in the PDF manual.
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.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpY5SO1o/R.INSTALL10485e27ab02/glogis/man/glogisfit.Rd:63: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpY5SO1o/R.INSTALL10485e27ab02/glogis/man/glogisfit.Rd:91: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/glogis.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpb5gK28/R.INSTALL24c74a215932/glue/man/glue_collapse.Rd:13: file link ‘NA_character_’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/glue.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp7i01C6/R.INSTALL48ae6b086022/gmailr/man/gm_auth.Rd:24: file link ‘gargle_oauth_email’ in package ‘gargle’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp7i01C6/R.INSTALL48ae6b086022/gmailr/man/gm_auth.Rd:38: file link ‘gargle_oauth_cache’ in package ‘gargle’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp7i01C6/R.INSTALL48ae6b086022/gmailr/man/gm_auth.Rd:42: file link ‘gargle_oob_default’ in package ‘gargle’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp7i01C6/R.INSTALL48ae6b086022/gmailr/man/gm_auth_configure.Rd:33: file link ‘AuthState’ in package ‘gargle’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp7i01C6/R.INSTALL48ae6b086022/gmailr/man/gm_token.Rd:10: file link ‘httr’ in package ‘httr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gmailr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpDnjCWN/R.INSTALL4fbe6b6037ff/GmAMisc/man/pointsInPolygons.Rd:90: file link ‘dbinom’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpDnjCWN/R.INSTALL4fbe6b6037ff/GmAMisc/man/pointsInPolygons.Rd:90: file link ‘pbinom’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GmAMisc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpcMfpg2/R.INSTALL43751a411513/gmat/man/cor_ug.Rd:54: file link ‘triangulate’ in package ‘gRbase’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gmat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp5HbwNH/R.INSTALL43b3380e0c11/gMCP/man/entangled.Rd:43: file link ‘graphMCP-class’ in package ‘gMCP’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gMCP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpYrj3Hx/R.INSTALL47b97f4916cb/Gmedian/man/GmedianCov.Rd:22: file link ‘eigs_sym’ in package ‘RSpectra’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Gmedian.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘gmediate.Rmd’
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpODfjwB/R.INSTALL185a32d6dcf0/gmnl/man/AIC.gmnl.Rd:28: file link ‘BIC’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gmnl.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpsygXbo/R.INSTALL5a845c490e79/gMOIP/man/plotCones3D.Rd:39: file link ‘points3d’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpsygXbo/R.INSTALL5a845c490e79/gMOIP/man/plotHull2D.Rd:45: file link ‘geom_label’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpsygXbo/R.INSTALL5a845c490e79/gMOIP/man/plotHull3D.Rd:46: file link ‘points3d’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpsygXbo/R.INSTALL5a845c490e79/gMOIP/man/plotHull3D.Rd:49: file link ‘text3d’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpsygXbo/R.INSTALL5a845c490e79/gMOIP/man/plotPlane3D.Rd:19: file link ‘planes3d’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpsygXbo/R.INSTALL5a845c490e79/gMOIP/man/plotPoints3D.Rd:20: file link ‘text3d’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpsygXbo/R.INSTALL5a845c490e79/gMOIP/man/plotRectangle3D.Rd:18: file link ‘points3d’ in package ‘rgl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gMOIP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpw3ZpKK/R.INSTALL143a41efa09d/gmp/man/extreme.Rd:66: file link ‘max’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gmp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpI31YHA/R.INSTALL18a94abc7921/GNAR/man/GNAR.Rd:5: file link ‘fiveNet’ in package ‘GNAR’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpI31YHA/R.INSTALL18a94abc7921/GNAR/man/GNAR.Rd:5: file link ‘fiveVTS’ in package ‘GNAR’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpI31YHA/R.INSTALL18a94abc7921/GNAR/man/GNARtoigraph.Rd:8: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpI31YHA/R.INSTALL18a94abc7921/GNAR/man/is.GNARnet.Rd:25: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GNAR.Rcheck/00install.out’ for details.
File ‘gnmf/libs/gnmf.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpzEZh6q/R.INSTALL19883b8f8d7b/goffda/man/fda.usc_efic.Rd:43: file link ‘func.mean’ in package ‘fda.usc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzEZh6q/R.INSTALL19883b8f8d7b/goffda/man/sim-frmfr.Rd:71: file link ‘r_cm2013_flmfr’ in package ‘goffda’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzEZh6q/R.INSTALL19883b8f8d7b/goffda/man/sim-frmfr.Rd:71: file link ‘r_gof2019_flmfr’ in package ‘goffda’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzEZh6q/R.INSTALL19883b8f8d7b/goffda/man/sim-frmfr.Rd:72: file link ‘r_ik2018_flmfr’ in package ‘goffda’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/goffda.Rcheck/00install.out’ for details.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GANPA’ ‘WGCNA’
A package should be listed in only one of these fields.
'library' or 'require' calls to packages already attached by Depends:
  ‘GANPA’ ‘WGCNA’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘GANPA’ ‘WGCNA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GOGANPA: no visible global function definition for ‘GSE.Test.Main’
selectRho: no visible global function definition for
  ‘scaleFreeFitIndex’
Undefined global functions or variables:
  GSE.Test.Main scaleFreeFitIndex
Found the following files/directories:
  ‘GOGANPAResult.MeanAbs.MultiW.csv’ ‘GOGANPAResult.MeanAbs.NoW.csv’
  ‘GOGANPAResult.MeanAbs.OrigW.csv’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp6gyY35/R.INSTALL1a7f12c81adb/gogarch/man/unvech.Rd:39: file link ‘vec’ in package ‘fBasics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gogarch.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmprCIKaY/R.INSTALL223043c21cb/googleCloudRunner/man/cr_plumber_pubsub.Rd:18: file link ‘plumb’ in package ‘plumber’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/googleCloudRunner.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpKZKvqh/R.INSTALL74ce65a59550/googleCloudStorageR/man/gcs_save_all.Rd:35: file link ‘zipr’ in package ‘zip’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpKZKvqh/R.INSTALL74ce65a59550/googleCloudStorageR/man/gcs_upload.Rd:52: file link ‘write.csv’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpKZKvqh/R.INSTALL74ce65a59550/googleCloudStorageR/man/gcs_upload.Rd:53: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/googleCloudStorageR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmps12IFF/R.INSTALL454029c9d7e/googledrive/man/drive_auth.Rd:26: file link ‘gargle_oauth_email’ in package ‘gargle’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmps12IFF/R.INSTALL454029c9d7e/googledrive/man/drive_auth.Rd:43: file link ‘gargle_oauth_cache’ in package ‘gargle’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmps12IFF/R.INSTALL454029c9d7e/googledrive/man/drive_auth.Rd:47: file link ‘gargle_oob_default’ in package ‘gargle’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmps12IFF/R.INSTALL454029c9d7e/googledrive/man/drive_auth_configure.Rd:27: file link ‘AuthState’ in package ‘gargle’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmps12IFF/R.INSTALL454029c9d7e/googledrive/man/drive_token.Rd:10: file link ‘httr’ in package ‘httr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmps12IFF/R.INSTALL454029c9d7e/googledrive/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmps12IFF/R.INSTALL454029c9d7e/googledrive/man/request_generate.Rd:66: file link ‘request_build’ in package ‘gargle’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/googledrive.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpAJVzP5/R.INSTALL6c112174d8df/googleLanguageR/man/gl_speech.Rd:37: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/googleLanguageR.Rcheck/00install.out’ for details.
Found the following sources/headers not terminated with a newline:
  inst/include/googlePolylines.h
  inst/include/variants.h
Some compilers warn on such files.
Package vignette with placeholder title ‘Vignette Title’:
  ‘sfencode.Rmd’
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp0g79sQ/R.INSTALL458443c103d5/GPareto/man/GPareto-package.Rd:180: file link ‘DiceKriging’ in package ‘DiceKriging’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp0g79sQ/R.INSTALL458443c103d5/GPareto/man/ParetoSetDensity.Rd:49: file link ‘ks’ in package ‘ks’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp0g79sQ/R.INSTALL458443c103d5/GPareto/man/crit_optimizer.Rd:71: file link ‘pso’ in package ‘pso’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp0g79sQ/R.INSTALL458443c103d5/GPareto/man/fastfun-class.Rd:48: file link ‘simulate’ in package ‘DiceKriging’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp0g79sQ/R.INSTALL458443c103d5/GPareto/man/integration_design_optim.Rd:43: file link ‘KrigInv’ in package ‘KrigInv’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp0g79sQ/R.INSTALL458443c103d5/GPareto/man/plotGPareto.Rd:59: file link ‘simulate’ in package ‘DiceKriging’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp0g79sQ/R.INSTALL458443c103d5/GPareto/man/plotSymDifRNP.Rd:18: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp0g79sQ/R.INSTALL458443c103d5/GPareto/man/plot_uncertainty.Rd:40: file link ‘KrigInv’ in package ‘KrigInv’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GPareto.Rcheck/00install.out’ for details.
Unknown package ‘DiceOptim’ in Rd xrefs
Random.Start: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
CumulativeVarPlot: no visible global function definition for ‘axis’
PCplot: no visible global function definition for ‘par’
PCplot: no visible global function definition for ‘rainbow’
PCplot: no visible global function definition for ‘density’
gDist: no visible global function definition for ‘density’
gDist: no visible global function definition for ‘abline’
gPCA.batchdetect: no visible global function definition for ‘var’
Undefined global functions or variables:
  abline axis density par rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "par")
  importFrom("stats", "density", "var")
to your NAMESPACE file.
The following files are already in R: ‘Sweave.sty’
Please remove them from your package.
Namespaces with empty importFrom:
  ‘scatterplot3d’ ‘sqldf’
Resdata : prepdata: no visible global function definition for ‘sqldf’
gpca : Build3d: no visible global function definition for ‘dev.new’
gpca : Build3d: no visible global function definition for
  ‘scatterplot3d’
gpca : Build3d: no visible global function definition for ‘text’
gpca : Build3d: no visible global function definition for ‘abline’
gpca : Build3d: no visible global function definition for ‘rect’
gpca: no visible global function definition for ‘cor’
gpca: no visible global function definition for ‘dev.new’
gpca: no visible global function definition for ‘text’
gpca: no visible global function definition for ‘abline’
gpca: no visible global function definition for ‘rect’
gpca: no visible global function definition for ‘scatterplot3d’
gpca: no visible global function definition for ‘segments’
gpca: no visible global function definition for ‘points’
gpca: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline cor dev.new points rect scatterplot3d segments sqldf text
  write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "points", "rect", "segments", "text")
  importFrom("stats", "cor")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘.txt’ ‘.txt.1’ ‘.txt.2’ ‘.txt.3’ ‘CorrelInter.txt’
.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.
gpfr: no visible global function definition for ‘rnorm’
gpfr: no visible global function definition for ‘runif’
gpfrpred : <anonymous>: no visible global function definition for
  ‘predict’
gpfrtrain: no visible global function definition for ‘nlminb’
gppredict: no visible global function definition for ‘predict’
gpr: no visible global function definition for ‘rnorm’
gpr: no visible global function definition for ‘runif’
gpr: no visible global function definition for ‘lm’
gpr: no visible global function definition for ‘resid’
gpr: no visible global function definition for ‘nlminb’
main1: no visible global function definition for ‘lm’
main1: no visible global function definition for ‘resid’
main2 : <anonymous>: no visible global function definition for
  ‘predict’
main2: no visible global function definition for ‘predict’
main3: no visible global function definition for ‘lm’
main3: no visible global function definition for ‘resid’
plot.gpfr: no visible global function definition for ‘polygon’
plot.gpfr: no visible global function definition for ‘rgb’
plot.gpfr: no visible global function definition for ‘matpoints’
plot.gpfr: no visible global function definition for ‘matlines’
plot.gpfr: no visible global function definition for ‘lines’
plot.gpr: no visible global function definition for ‘polygon’
plot.gpr: no visible global function definition for ‘rgb’
plot.gpr: no visible global function definition for ‘points’
plot.gpr: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines lm matlines matpoints nlminb points polygon predict resid rgb
  rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "matlines", "matpoints", "points",
             "polygon")
  importFrom("stats", "lm", "nlminb", "predict", "resid", "rnorm",
             "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘DiceOptim’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmplVBLSa/R.INSTALL5c3647ec9d48/GPGame/man/GPGame.Rd:86: file link ‘DiceKriging’ in package ‘DiceKriging’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplVBLSa/R.INSTALL5c3647ec9d48/GPGame/man/GPGame.Rd:86: file link ‘KrigInv’ in package ‘KrigInv’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplVBLSa/R.INSTALL5c3647ec9d48/GPGame/man/GPGame.Rd:86: file link ‘GPareto’ in package ‘GPareto’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GPGame.Rcheck/00install.out’ for details.
Unknown package ‘DiceOptim’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
Checking should be performed on sources prepared by ‘R CMD build’.
Packages in Depends field not imported from:
  ‘foreach’ ‘ggplot2’ ‘isotone’ ‘plyr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  ‘geneA_GPprofile.pdf’ ‘geneA_abstr.png’ ‘geneA_gene.png’
  ‘geneA_reltr.png’ ‘geneB_abstr.png’ ‘geneB_gene.png’
  ‘geneB_reltr.png’ ‘geneC_abstr.png’ ‘geneC_gene.png’
  ‘geneC_reltr.png’ ‘testdb.sqlite’
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmplGqIuB/R.INSTALL4eda3ca7ba3d/gpuR/man/pmax.Rd:21: file link ‘pmax’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplGqIuB/R.INSTALL4eda3ca7ba3d/gpuR/man/pmax.Rd:21: file link ‘pmin’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplGqIuB/R.INSTALL4eda3ca7ba3d/gpuR/man/qr.R-methods.Rd:26: file link ‘qr.R’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplGqIuB/R.INSTALL4eda3ca7ba3d/gpuR/man/qr.R-methods.Rd:26: file link ‘qr.Q’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gpuR.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Found the following files/directories:
  ‘Data_Kendall's tau-distance’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpSdYEGX/R.INSTALL23ff56a5b721/GRANBase/man/deltaDF.Rd:24: file link ‘anti_join’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GRANBase.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘mgcv’ ‘rgl’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpDFFBLm/R.INSTALL242c4cb81e4d/graphTweets/man/gt_collect.Rd:13: file link ‘tibble’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpDFFBLm/R.INSTALL242c4cb81e4d/graphTweets/man/reexports.Rd:15: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpDFFBLm/R.INSTALL242c4cb81e4d/graphTweets/man/reexports.Rd:17: file link ‘%<-%’ in package ‘zeallot’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/graphTweets.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpMlRbxt/R.INSTALL5f0445696ed9/gratia/man/basis.Rd:29: file link ‘ti’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMlRbxt/R.INSTALL5f0445696ed9/gratia/man/basis.Rd:11: file link ‘ti’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMlRbxt/R.INSTALL5f0445696ed9/gratia/man/draw.mgcv_smooth.Rd:31: file link ‘label_both’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMlRbxt/R.INSTALL5f0445696ed9/gratia/man/draw.smooth_samples.Rd:55: file link ‘geom_line’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gratia.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp9wJp49/R.INSTALL5fd455a9bfd3/gravitas/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gravitas.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpQBy5hN/R.INSTALL53ab23e4c4d4/greport/man/survReport.Rd:44: file link ‘survplot.npsurv’ in package ‘rms’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQBy5hN/R.INSTALL53ab23e4c4d4/greport/man/survReport.Rd:48: file link ‘survplot.npsurv’ in package ‘rms’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/greport.Rcheck/00install.out’ for details.
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
bestcut2: no visible global function definition for ‘pchisq’
cov.func: no visible global function definition for ‘rbinom’
cov.func: no visible global function definition for ‘cov’
cov.func: no visible global function definition for ‘pnorm’
cox.summary: no visible global function definition for ‘predict’
em.func: no visible global function definition for ‘quantile’
genSurvData: no visible global function definition for ‘rweibull’
greyzone.func: no visible global function definition for ‘points’
greyzone.func: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cov pchisq pnorm points predict quantile rbinom rweibull
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("stats", "cov", "pchisq", "pnorm", "predict", "quantile",
             "rbinom", "rweibull")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
grid.graph: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpctv3Xm/R.INSTALL36b3c4ec749/gridSVG/man/gridsvg.Rd:55: file link ‘dev.off’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gridSVG.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpTJWVJS/R.INSTALL24ec5b9c0dc1/gridtext/man/richtext_grob.Rd:81: file link ‘textGrob’ in package ‘grid’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gridtext.Rcheck/00install.out’ for details.
Non-standard file/directory found at top level:
  ‘R.css’
Package in Depends field not imported from: ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GriegSmith: no visible global function definition for ‘is.ppp’
envelopes: no visible binding for global variable ‘quantile’
plot.GriegSmith: no visible global function definition for ‘lines’
plot.GriegSmith: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis is.ppp lines quantile
Consider adding
  importFrom("graphics", "axis", "lines")
  importFrom("stats", "quantile")
to your NAMESPACE file.
Rd file 'GriegSmith.Rd':
  \examples lines wider than 100 characters:
                     if (max(datapoints[,1]) != max(datapoints[,2])) stop("Your count data must have equal dimensions")

Rd file 'belongtoint.Rd':
  \examples lines wider than 100 characters:
             sum(vect[,1] >= xval & vect[,1] < (xval+int.x) & vect[,2] >= yval & vect[,2] < (yval+int.y));

Rd file 'envelopes.Rd':
  \examples lines wider than 100 characters:
                     perm<-matrix(sample(as.vector(countdata),size=2^(dimention*2),replace=FALSE),nrow=2^dimention,byrow=TRUE);
             ret.val<-cbind(apply(GSpermprev[,-1],1,quantile,probs=c(.05)),apply(GSpermprev[,-1],1,quantile,probs=c(.95)))

Rd file 'sumofsquares.Rd':
  \examples lines wider than 100 characters:
             squaredsums<-sum(apply(submatricies,1,addem,data=singlecounts,xmatlen=xsublength,ymatlen=ysublength));

Rd file 'sums.Rd':
  \usage lines wider than 90 characters:
     sums(coords, dim, xmin = min(coords[, 1]), xmax = max(coords[, 1]), ymin = min(coords[, 2]), ymax = max(coords[, 2]))
  \examples lines wider than 100 characters:
     function (coords,dim,xmin=min(coords[,1]),xmax=max(coords[,1]),ymin=min(coords[,2]),ymax=max(coords[,2])){
             cnts<-matrix(apply(bins,1,belongtoint,vect=coords,int.x=xints,int.y=yints),nrow=dim,byrow=TRUE);

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpNKIhMR/R.INSTALL4915206cc1e5/GROAN/man/phenoRegressor.SVR.Rd:68: file link ‘best.svm’ in package ‘e1071’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNKIhMR/R.INSTALL4915206cc1e5/GROAN/man/phenoRegressor.SVR.Rd:172: file link ‘tune.svm’ in package ‘e1071’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNKIhMR/R.INSTALL4915206cc1e5/GROAN/man/phenoRegressor.SVR.Rd:172: file link ‘best.svm’ in package ‘e1071’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GROAN.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ppls’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpHzuuy4/R.INSTALL21fc562601e7/groc/man/covRob-robust.Rd:42: file link ‘covMest’ in package ‘rrcov’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/groc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp6MNUjy/R.INSTALL22521c77c252/gromovlab/man/gromovdist.Rd:76: file link ‘igraph-package’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gromovlab.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpVQrrr4/R.INSTALL26111d256584/groupdata2/man/group.Rd:141: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/groupdata2.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpHsZFLo/R.INSTALL2ea979fa330b/growth/man/elliptic.Rd:58: file link ‘dskewlaplace’ in package ‘rmutil’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHsZFLo/R.INSTALL2ea979fa330b/growth/man/elliptic.Rd:464: file link ‘dpowexp’ in package ‘rmutil’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHsZFLo/R.INSTALL2ea979fa330b/growth/man/elliptic.Rd:465: file link ‘dskewlaplace’ in package ‘rmutil’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/growth.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘grpregOverlap’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpfazsep/R.INSTALL29643302e7f8/grpreg/man/auc.Rd:29: file link ‘survConcordance’ in package ‘survival’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/grpreg.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘p1_20up-vs-p2_25up_in_str1.txt’ ‘p1_20up-vs-p2_25up_in_str2.txt’
  ‘p2_25up-vs-p1_20up_in_str1.txt’ ‘p2_25up-vs-p1_20up_in_str2.txt’
  ‘s0_20up.txt’ ‘s0_30up.txt’ ‘s0_f2up.txt’ ‘strs.vec_01mx.txt’
  ‘strs.vec_02mx.txt’ ‘strs.vec_03mx.txt’ ‘strs.vec_04mx.txt’
  ‘strs.vec_05mx.txt’ ‘strs.vec_06mx.txt’ ‘strs.vec_30up.txt’
  ‘strs.vec_50up.txt’ ‘strs.vec_f2up.txt’ ‘uni_p1_20up-p2_25up.txt’
Found the following files/directories:
  ‘FMD mag discontinuities_disc.png’ ‘FMD mag
  discontinuities_disc1.res’ ‘FMD mag discontinuities_disc2.res’
  ‘IDYLLWILD_bvmed.png’ ‘IDYLLWILD_fig.png’ ‘Schuster's
  diagram_schu.png’ ‘hour.res’
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
Rd file 'GSA.Rd':
  \usage lines wider than 90 characters:
     method=c("maxmean","mean","absmean"), resp.type=c("Quantitative","Two class unpaired","Survival","Multiclass", "Two class paired", "tCo ... [TRUNCATED]
  \examples lines wider than 100 characters:
     GSA.obj<-GSA(x,y, genenames=genenames, genesets=genesets,  resp.type="Two class unpaired", nperms=100)
     #   GSA.obj<-GSA(x,y, genenames=genenames, genesets=geneset.obj$genesets,  resp.type="Two class unpaired", nperms=100)

Rd file 'GSA.func.Rd':
  \usage lines wider than 90 characters:
     s0 = NULL, s0.perc = NULL, minsize = 15, maxsize= 500, restand = TRUE, restand.basis=c("catalog","data")) 
  \examples lines wider than 100 characters:
     #   GSA.func.obj<-GSA.func(x,y, genenames=genenames, genesets=geneset.obj$genesets,  resp.type="Two class unpaired")

Rd file 'GSA.genescores.Rd':
  \examples lines wider than 100 characters:
     GSA.obj<-GSA(x,y, genenames=genenames, genesets=genesets,  resp.type="Two class unpaired", nperms=100)

Rd file 'GSA.listsets.Rd':
  \examples lines wider than 100 characters:
     GSA.obj<-GSA(x,y, genenames=genenames, genesets=genesets,  resp.type="Two class unpaired", nperms=100)

Rd file 'GSA.plot.Rd':
  \examples lines wider than 100 characters:
     GSA.obj<-GSA(x,y, genenames=genenames, genesets=genesets,  resp.type="Two class unpaired", nperms=100)

These lines will be truncated in the PDF manual.
garsim: no visible global function definition for ‘rnorm’
garsim: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  rnorm rpois
Consider adding
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
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 suggested but not available for checking: ‘SDMTools’
Found the following files/directories:
  ‘ORCDRC.txt’
Namespaces with empty importFrom:
  ‘gee’ ‘geepack’
Malformed Description field: should contain one or more complete sentences.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Introduction.Rmd’
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpaW4bfd/R.INSTALL44d017b49bdb/gsubfn/man/transform2.Rd:30: file link ‘within’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gsubfn.Rcheck/00install.out’ for details.
Rd file 'gtcorr.matrix.Rd':
  \usage lines wider than 90 characters:
     gtcorr.matrix(r, c, m = 1, p, sigma = 0, se = 1, sp = 1, r.prime, c.prime, arrangement = c("rectangular", "diagonal", "random"), model  ... [TRUNCATED]

Rd file 'gtcorr.matrix.user.Rd':
  \usage lines wider than 90 characters:
     gtcorr.matrix.user(clusters, p, sigma=0, se=1, sp=1, model = c("beta-binomial", "Madsen", "Morel-Neerchal"))

These lines will be truncated in the PDF manual.
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.
Found the following possibly unsafe calls:
File ‘gtools/R/unByteCode.R’:
  unlockBinding(name, env = env)
Running ‘testthat.R’ [129s/183s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(checkmate)
  > library(gt)
  
  Attaching package: 'gt'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("gt")
  ── 1. Failure: the correct color values are obtained when defining a palette (@t
  ``%>%`(...)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 2167 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: the correct color values are obtained when defining a palette (@test-data_color.R#630) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpasQ5MC/R.INSTALL4d4e16dba24f/Guerry/man/gfrance.Rd:20: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpasQ5MC/R.INSTALL4d4e16dba24f/Guerry/man/gfrance85.Rd:21: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Guerry.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘GuessCompx.Rmd’
Package vignette with placeholder title ‘Vignette Title’:
  ‘GUILDS.Rmd’
Found the following files/directories:
  ‘RRprof.out’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp2sRFcK/R.INSTALL4c12233c4b6/gunit/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gunit.Rcheck/00install.out’ for details.
simCCCent : <anonymous>: no visible global function definition for
  ‘simulate.formula’
Undefined global functions or variables:
  simulate.formula
Non-standard file/directory found at top level:
  ‘TITEL’
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.
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.

Found the following calls to data() loading into the global environment:
File ‘GWG/R/obese.R’:
  data(OB_above)
  data(OB_below)
File ‘GWG/R/overweight.R’:
  data(OW_above)
  data(OW_below)
See section ‘Good practice’ in ‘?data’.
Package which this enhances but not available for checking: ‘RGtk2Extras’
browseDataAsCSV: no visible global function definition for ‘write.csv’
browseDataAsCSV: no visible global function definition for ‘browseURL’
tcltkDialog: no visible global function definition for ‘runif’
tl_get_column_name: no visible global function definition for ‘tail’
.add,gTexttcltk-guiWidgetsToolkittcltk-character: no visible global
  function definition for ‘rnorm’
.font<-,gTexttcltk-guiWidgetsToolkittcltk: no visible global function
  definition for ‘rnorm’
.font<-,tcltkObject-guiWidgetsToolkittcltk: no visible global function
  definition for ‘rnorm’
.gdf,guiWidgetsToolkittcltk: no visible global function definition for
  ‘head’
.visible<-,gGraphicstcltk-guiWidgetsToolkittcltk-ANY: no visible global
  function definition for ‘dev.set’
Undefined global functions or variables:
  browseURL dev.set head rnorm runif tail write.csv
Consider adding
  importFrom("grDevices", "dev.set")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "browseURL", "head", "tail", "write.csv")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpLJ7kRl/R.INSTALL651b4c578ce2/gWQS/man/gwqs.Rd:144: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gWQS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpvdA09F/R.INSTALL56666b808fbf/gWQSRS/man/gwqsrs.Rd:139: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gWQSRS.Rcheck/00install.out’ for details.
'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.
Found the following files/directories:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmprHXs94/R.INSTALL2a4e285b9afa/h2o4gpu/man/reexports.Rd:22: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprHXs94/R.INSTALL2a4e285b9afa/h2o4gpu/man/reexports.Rd:24: file link ‘use_condaenv’ in package ‘reticulate’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprHXs94/R.INSTALL2a4e285b9afa/h2o4gpu/man/reexports.Rd:24: file link ‘use_virtualenv’ in package ‘reticulate’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/h2o4gpu.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp3snuEb/R.INSTALL4da55b3b9e80/hackeRnews/man/to_datetime_origin.Rd:25: file link ‘as.POSIXct’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hackeRnews.Rcheck/00install.out’ for details.
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.
Rd file 'hsKeyValReader.Rd':
  \usage lines wider than 90 characters:
     hsKeyValReader(file = "", chunkSize = -1, skip = 0, sep = "\t",FUN = function(k, v) cat(paste(k, v, sep = ": "), sep = "\n"))

Rd file 'hsLineReader.Rd':
  \examples lines wider than 100 characters:
       str <- "Hello here are some\nlines of text\nto read in, chunkSize\nlines at a time.\nHow interesting.\nhuh?"

Rd file 'hsTableReader.Rd':
  \examples lines wider than 100 characters:
       str <- "key1\t3.9\nkey1\t8.9\nkey1\t1.2\nkey1\t3.9\nkey1\t8.9\nkey1\t1.2\nkey2\t9.9\nkey2\t10.1\nkey3\t1.0\nkey3\t3.4\nkey4\t9.4\n"
       hsTableReader(con,cols,chunkSize=5,FUN=reducerFullKeys,ignoreKey=FALSE,singleKey=FALSE,PFUN=reducerPartialKey)
       hsTableReader(con,cols,chunkSize=6,FUN=reducerKeyAtOnce,ignoreKey=FALSE,singleKey=TRUE,PFUN=reducerPartialKey)
       hsTableReader(con,cols,chunkSize=6,FUN=reducerManyCompleteKeys,ignoreKey=FALSE,singleKey=FALSE,PFUN=reducerPartialKey)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘datafile.txt’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp4snhHs/R.INSTALL54bc265fdda2/hagis/man/autoplot.hagis.complexities.Rd:26: file link ‘ggplot2’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4snhHs/R.INSTALL54bc265fdda2/hagis/man/autoplot.hagis.gene.summary.Rd:26: file link ‘ggplot2’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hagis.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpDQQExn/R.INSTALL54e33b3362ae/haldensify/man/format_long_hazards.Rd:32: file link ‘cut_number’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpDQQExn/R.INSTALL54e33b3362ae/haldensify/man/format_long_hazards.Rd:40: file link ‘cut.default’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpDQQExn/R.INSTALL54e33b3362ae/haldensify/man/format_long_hazards.Rd:41: file link ‘cut_number’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpDQQExn/R.INSTALL54e33b3362ae/haldensify/man/haldensify.Rd:34: file link ‘cut_number’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/haldensify.Rcheck/00install.out’ for details.
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.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpBop1qc/R.INSTALL45123f24b226/hardhat/man/get_levels.Rd:54: file link ‘.getXlevels’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBop1qc/R.INSTALL45123f24b226/hardhat/man/model_offset.Rd:20: file link ‘model.offset’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBop1qc/R.INSTALL45123f24b226/hardhat/man/model_offset.Rd:27: file link ‘model.offset’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hardhat.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [15s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hardhat)
  > 
  > test_check("hardhat")
  ── 1. Error: missing ordered factor levels are handled correctly (@test-forge-fo
  Can't convert `f` <ordered<c05d9>> to match type of `f` <ordered<10564>>.
  Backtrace:
    1. testthat::expect_warning(xx <- forge(new, x$blueprint), NA)
   11. vctrs::stop_incompatible_type(...)
   12. vctrs:::stop_incompatible(...)
   13. vctrs:::stop_vctrs(...)
  
  ── 2. Failure: ignoring novel levels still passes through incompatible classes (
  `scream(new, ptype, allow_novel_levels = TRUE)` threw an error with unexpected class.
  Expected class: vctrs_error_incompatible_cast
  Actual class:   vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition
  Message:        Can't convert `f` <integer> to match type of `f` <factor<10564>>.
  Backtrace:
    1. testthat::expect_error(...)
    8. vctrs::vec_default_cast(...)
    9. vctrs::stop_incompatible_cast(...)
   10. vctrs::stop_incompatible_type(...)
   11. vctrs:::stop_incompatible(...)
   12. vctrs:::stop_vctrs(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 402 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: missing ordered factor levels are handled correctly (@test-forge-formula.R#510) 
  2. Failure: ignoring novel levels still passes through incompatible classes (@test-scream.R#50) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp4fFHWV/R.INSTALL70dd4778233e/harrypotter/man/scale_hp.Rd:97: file link ‘scale_fill_gradientn’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4fFHWV/R.INSTALL70dd4778233e/harrypotter/man/scale_hp.Rd:97: file link ‘scale_color_gradientn’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/harrypotter.Rcheck/00install.out’ for details.
Namespace with empty importFrom: ‘utils’
Non-standard file/directory found at top level:
  ‘test’
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘dev’
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 8 bytes from a string of length 299 [-Wstringop-truncation]
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 40 bytes from a string of length 1023 [-Wstringop-truncation]
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 8 bytes from a string of length 23 [-Wstringop-truncation]
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 32 bytes from a string of length 299 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/haven.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
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.
GNU make is a SystemRequirements.
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.
Non-standard file/directory found at top level:
  ‘examples’
Rd file 'fSAE.Rd':
  \examples lines wider than 100 characters:
     est.global <- fSAE(y0 ~ x + area2, data=d$sam, area=NULL, popdata=colSums(d$Xpop), method="synthetic")

Rd file 'plot.sae.Rd':
  \usage lines wider than 90 characters:
         main = switch(type, coef = "coefficients", raneff = "random effects", "SAE estimates"),

Rd file 'uweights.Rd':
  \examples lines wider than 100 characters:
     sae <- fSAE(y0 ~ x + area2, data=d$sam, area="area", popdata=d$Xpop, method="hybrid", keep.data=TRUE)

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmphz8FtW/R.INSTALL53d4441194e1/HDclassif/man/hdda.Rd:28: file link ‘getHDclassif.show’ in package ‘HDclassif’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmphz8FtW/R.INSTALL53d4441194e1/HDclassif/man/hddc.Rd:40: file link ‘getHDclassif.show’ in package ‘HDclassif’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmphz8FtW/R.INSTALL53d4441194e1/HDclassif/man/hddc.Rd:50: file link ‘parLapply’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HDclassif.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpqHSFQt/R.INSTALL546078c3ae2a/hdd/man/cash-.hdd.Rd:21: file link ‘getHdd_extract.cap’ in package ‘hdd’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpqHSFQt/R.INSTALL546078c3ae2a/hdd/man/readfst.Rd:21: file link ‘read_fst’ in package ‘fst’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpqHSFQt/R.INSTALL546078c3ae2a/hdd/man/txt2hdd.Rd:41: file link ‘cols_only’ in package ‘readr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hdd.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpwqU7Hi/R.INSTALL554c19583cc7/HDMD/man/HDMD-package.Rd:44: file link ‘psych-package’ in package ‘psych’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HDMD.Rcheck/00install.out’ for details.
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.
Rd file 'AminoAcids.Rd':
  \examples lines wider than 100 characters:
     Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
       Factor3d =scatterplot3d(Factor54$scores[,1:3], pch = AminoAcids, main="Factor Scores", box = FALSE, grid=FALSE, xlab="pah", ylab="pss ... [TRUNCATED]
       legend(x=5, y=4.5, legend=c("hydrophobic", "polar", "small"), col=c("blue", "green", "orange"), pch=21, box.lty =0)

Rd file 'FactorTransform.Rd':
  \usage lines wider than 90 characters:
     FactorTransform(Source, Search = AminoAcids, Replace = AAMetric.Atchley, Factor = 1, bycol = TRUE, SeqName = NULL,  alignment=FALSE, fi ... [TRUNCATED]

Rd file 'HDMD-package.Rd':
  \examples lines wider than 100 characters:
     Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
     plot(-1*AA54_lda_RawMetric1Centered[,1], -1*AA54_lda_RawMetric1Centered[,2], pch = grouping, xlab="Canonical Variate 1", ylab="Canonica ... [TRUNCATED]

Rd file 'NMI.Rd':
  \usage lines wider than 90 characters:
     NMI(Hx, Hy, Hxy, type = c("NULL", "marginal", "joint", "min.marginal", "max.marginal", "min.conditional", "max.conditional"))

Rd file 'factor.pa.ginv.Rd':
  \usage lines wider than 90 characters:
     factor.pa.ginv(r, nfactors = 1, residuals = FALSE, prerotate = FALSE, rotate = "varimax", m = 4, n.obs = NA, scores = c("none", "regres ... [TRUNCATED]
  \examples lines wider than 100 characters:
     Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
       Factor3d =scatterplot3d(Factor54$scores[,1:3], pch = AminoAcids, main="Factor Scores", box = FALSE, grid=FALSE, xlab="pah", ylab="pss ... [TRUNCATED]
       legend(x=5, y=4.5, legend=c("hydrophobic", "polar", "small"), col=c("blue", "green", "orange"), pch=21, box.lty =0)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpcQlbke/R.INSTALL56881ae833ce/hdnom/man/fit_mcp.Rd:18: file link ‘cv.ncvsurv’ in package ‘ncvreg’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcQlbke/R.INSTALL56881ae833ce/hdnom/man/fit_mnet.Rd:18: file link ‘cv.ncvsurv’ in package ‘ncvreg’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcQlbke/R.INSTALL56881ae833ce/hdnom/man/fit_mnet.Rd:20: file link ‘cv.ncvsurv’ in package ‘ncvreg’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcQlbke/R.INSTALL56881ae833ce/hdnom/man/fit_scad.Rd:18: file link ‘cv.ncvsurv’ in package ‘ncvreg’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcQlbke/R.INSTALL56881ae833ce/hdnom/man/fit_snet.Rd:18: file link ‘cv.ncvsurv’ in package ‘ncvreg’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcQlbke/R.INSTALL56881ae833ce/hdnom/man/fit_snet.Rd:20: file link ‘cv.ncvsurv’ in package ‘ncvreg’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hdnom.Rcheck/00install.out’ for details.
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').
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpNECQaE/R.INSTALL67726a74ce39/healthcareai/man/reexports.Rd:15: file link ‘%>%’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNECQaE/R.INSTALL67726a74ce39/healthcareai/man/step_dummy_hcai.Rd:50: file link ‘bake.recipe’ in package ‘recipes’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNECQaE/R.INSTALL67726a74ce39/healthcareai/man/step_dummy_hcai.Rd:51: file link ‘prep.recipe’ in package ‘recipes’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/healthcareai.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpAxRazc/R.INSTALL500554157906/healthforum/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/healthforum.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp9ha3JW/R.INSTALL5b6d304538a3/heatmaply/man/heatmaply.Rd:185: file link ‘viridis’ in package ‘viridis’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9ha3JW/R.INSTALL5b6d304538a3/heatmaply/man/heatmaply.Rd:186: file link ‘scale_fill_gradientn’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9ha3JW/R.INSTALL5b6d304538a3/heatmaply/man/heatmaply.Rd:318: file link ‘scale_fill_gradientn’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9ha3JW/R.INSTALL5b6d304538a3/heatmaply/man/heatmaply.Rd:385: file link ‘has_edgePar’ in package ‘dendextend’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heatmaply.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
heatmap.plus: no visible binding for global variable ‘dist’
heatmap.plus: no visible binding for global variable ‘hclust’
heatmap.plus : <anonymous>: no visible global function definition for
  ‘reorder’
heatmap.plus: no visible global function definition for ‘as.dendrogram’
heatmap.plus: no visible global function definition for
  ‘order.dendrogram’
heatmap.plus: no visible binding for global variable ‘sd’
heatmap.plus: no visible global function definition for ‘par’
heatmap.plus: no visible global function definition for ‘layout’
heatmap.plus: no visible global function definition for ‘image’
heatmap.plus: no visible global function definition for ‘axis’
heatmap.plus: no visible global function definition for ‘mtext’
heatmap.plus: no visible global function definition for ‘frame’
heatmap.plus: no visible global function definition for ‘title’
Undefined global functions or variables:
  as.dendrogram axis dist frame hclust image layout mtext
  order.dendrogram par reorder sd title
Consider adding
  importFrom("graphics", "axis", "frame", "image", "layout", "mtext",
             "par", "title")
  importFrom("stats", "as.dendrogram", "dist", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
prepare_Rd: heatmap.plus.package.Rd:69: Dropping empty section \details
prepare_Rd: heatmap.plus.package.Rd:70: Dropping empty section \value
prepare_Rd: heatmap.plus.package.Rd:73: Dropping empty section \note
prepare_Rd: heatmap.plus.package.Rd:71: Dropping empty section \references
Rd file 'heatmap.plus.package.Rd':
  \usage lines wider than 90 characters:
     heatmap.plus(x, Rowv = NULL, Colv = if (symm) "Rowv" else NULL, distfun = dist, hclustfun = hclust, reorderfun = function(d, w) reorder ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpsea1qK/R.INSTALL5f086d8c08dc/heddlr/man/export_template.Rd:19: file link ‘stdout’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heddlr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpBiVS0I/R.INSTALL56d147195c2c/heemod/man/calibrate_model.Rd:65: file link ‘optimise’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBiVS0I/R.INSTALL56d147195c2c/heemod/man/calibrate_model.Rd:66: file link ‘optimise’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBiVS0I/R.INSTALL56d147195c2c/heemod/man/cluster.Rd:47: file link ‘parLapply’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBiVS0I/R.INSTALL56d147195c2c/heemod/man/define_parameters.Rd:42: file link ‘row_number’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBiVS0I/R.INSTALL56d147195c2c/heemod/man/reexports.Rd:14: file link ‘%>%’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/00install.out’ for details.
Running examples in ‘HEMDAG-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Do.HTD.holdout
> ### Title: HTD-DAG holdout
> ### Aliases: Do.HTD.holdout
> 
> ### ** Examples
> 
> data(graph);
> data(scores);
> data(labels);
> data(test.index);
> tmpdir <- paste0(tempdir(),"/");
> save(g, file=paste0(tmpdir,"graph.rda"));
> save(L, file=paste0(tmpdir,"labels.rda"));
> save(S, file=paste0(tmpdir,"scores.rda"));
> save(test.index, file=paste0(tmpdir,"test.index.rda"));
> ind.dir <- dag.dir <- flat.dir <- ann.dir <- tmpdir;
> hierScore.dir <- perf.dir <- tmpdir;
> recall.levels <- seq(from=0.2, to=1, by=0.4);
> ind.test.set <- "test.index";
> dag.file <- "graph";
> flat.file <- "scores";
> ann.file <- "labels";
> Do.HTD.holdout(norm=FALSE, norm.type="MaxNorm", n.round=3, f.criterion ="F", folds=5, seed=23,
+ recall.levels=recall.levels, compute.performance=TRUE, flat.file=flat.file, ann.file=ann.file, 
+ dag.file=dag.file, ind.test.set=ind.test.set, ind.dir=ind.dir, flat.dir=flat.dir, ann.dir=ann.dir,
+ dag.dir=dag.dir, hierScore.dir=hierScore.dir, perf.dir=perf.dir);
MaxNorm NORMALIZATION: DONE 
Error: assert_that: missing values present in assertion
Execution halted
Package suggested but not available for checking: ‘FRB’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpkJ85hJ/R.INSTALL534d35f9fa6d/here/man/here.Rd:45: file link ‘has_file’ in package ‘rprojroot’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/here.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘synbreed’
Package suggested but not available for checking: ‘glmmADMB’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp8CeNZ3/R.INSTALL337253a91c81/hero/man/adjacent.Rd:35: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8CeNZ3/R.INSTALL337253a91c81/hero/man/adjacent.Rd:19: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8CeNZ3/R.INSTALL337253a91c81/hero/man/adjacent.Rd:43: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8CeNZ3/R.INSTALL337253a91c81/hero/man/assemble.Rd:48: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8CeNZ3/R.INSTALL337253a91c81/hero/man/enlarge.Rd:34: file link ‘gBuffer’ in package ‘rgeos’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8CeNZ3/R.INSTALL337253a91c81/hero/man/enlarge.Rd:18: file link ‘gBuffer’ in package ‘rgeos’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8CeNZ3/R.INSTALL337253a91c81/hero/man/plot.hero.Rd:33: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8CeNZ3/R.INSTALL337253a91c81/hero/man/plot.hero_bspline.Rd:16: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8CeNZ3/R.INSTALL337253a91c81/hero/man/prepare.matrix.Rd:40: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8CeNZ3/R.INSTALL337253a91c81/hero/man/spdiffpen.Rd:25: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hero.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpvX3QMU/R.INSTALL2a9b202b15c/hesim/man/IndivCtstmTrans.Rd:22: file link ‘mstate’ in package ‘mstate’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpvX3QMU/R.INSTALL2a9b202b15c/hesim/man/absorbing.Rd:10: file link ‘mstate’ in package ‘mstate’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpvX3QMU/R.INSTALL2a9b202b15c/hesim/man/create_IndivCtstmTrans.Rd:50: file link ‘mstate’ in package ‘mstate’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpvX3QMU/R.INSTALL2a9b202b15c/hesim/man/create_trans_dt.Rd:10: file link ‘mstate’ in package ‘mstate’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hesim.Rcheck/00install.out’ for details.
Warning: no function found corresponding to methods exports from ‘het.test’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Packages in Depends field not imported from:
  ‘methods’ ‘vars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
whites.htest: no visible global function definition for ‘residuals’
whites.htest: no visible global function definition for ‘lm’
whites.htest: no visible global function definition for ‘pchisq’
whites.htest: no visible global function definition for ‘new’
Undefined global functions or variables:
  lm new pchisq residuals
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "lm", "pchisq", "residuals")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running ‘testthat.R’ [37s/54s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hettx)
  > 
  > test_check("hettx")
  ── 1. Error: Main complier methods work (@test_estimate_systematic.R#99)  ──────
  min(n11, n10, n01, n00) > 1 is not TRUE
  Backtrace:
   1. hettx::estimate_systematic(...)
   2. hettx:::est.beta.LATE(...)
   3. base::stopifnot(min(n11, n10, n01, n00) > 1)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 29 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Main complier methods work (@test_estimate_systematic.R#99) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpabvXFe/R.INSTALL5a0b3e0ac89d/heuristicsmineR/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heuristicsmineR.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘hexSticker.png’
Package vignette with placeholder title ‘Vignette Title’:
  ‘hexbin-classes.Rmd’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpLDGSjw/R.INSTALL2b34420ab0df/hgutils/man/compound-pipe.Rd:10: file link ‘%<>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLDGSjw/R.INSTALL2b34420ab0df/hgutils/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hgutils.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘HHG.Rmd’
Found the following significant warnings:
  Rd warning: /tmp/Rtmp5OlAXT/Rbuild3dc162c6a94b/hhh4contacts/man/noroBE.Rd:37: file link ‘gUnaryUnion’ in package ‘rgeos’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hhh4contacts.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpVa3Iqa/R.INSTALL6c472917e77c/hierarchicalSets/man/plot.HierarchicalSet.Rd:21: file link ‘trans’ in package ‘scales’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hierarchicalSets.Rcheck/00install.out’ for details.
':::' 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.
booties: no visible binding for global variable ‘sd’
booties: no visible binding for global variable ‘quantile’
hierDiversity: no visible global function definition for
  ‘txtProgressBar’
hierDiversity: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  quantile sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp7Xbcrq/R.INSTALL7a8c6436c95c/hierfstat/man/gstat.randtest.Rd:83: file link ‘as.randtest’ in package ‘ade4’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hierfstat.Rcheck/00install.out’ for details.
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.
'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.
Rd file 'HItest3.Rd':
  \examples lines wider than 100 characters:
                                                     # individuals will have nonzero contributions from each of the

Rd file 'spatial.AD.Rd':
  \examples lines wider than 100 characters:
     # simulate secondary contact by sorting aling the x dimension and assigning parental genotypes on each side of the centerline:
     # selection, inlcuding heterozygote disadvantage at locus 2 and a DM incompatibility between 3 and 4:
     G10 <- spatial.AD(minX,minY,maxX,maxY,XY,Genotypes,beta,sel,mid,h,DM,sigmac,R,M,gens=10,immigrants=TRUE)

Rd file 'spatial.HZ.Rd':
  \examples lines wider than 100 characters:
     # simulate secondary contact by sorting aling the x dimension and assigning parental genotypes on each side of the centerline:
     # selection, inlcuding heterozygote disadvantage at locus 2 and a DM incompatibility between 3 and 4:
     G10 <- spatial.HZ(minX,minY,maxX,maxY,XY,Genotypes,beta,sel,mid,h,DM,sigmad,sigmac,sigmam,R,M,gens=10,immigrants=TRUE)

Rd file 'thirdclass.Rd':
  \examples lines wider than 100 characters:
                                                     # individuals will have nonzero contributions from each of the 

These lines will be truncated in the PDF 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.
Func.ABOD: no visible global function definition for ‘combn’
Func.ABOD: no visible global function definition for ‘var’
Func.SOD: no visible global function definition for ‘var’
Func.trans : erf: no visible global function definition for ‘pnorm’
Func.trans: no visible global function definition for ‘sd’
Undefined global functions or variables:
  combn pnorm sd var
Consider adding
  importFrom("stats", "pnorm", "sd", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package suggested but not available for checking: ‘INLA’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpwriBHn/R.INSTALL513867d1f672/highriskzone/man/plot.bootcorr.Rd:12: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpwriBHn/R.INSTALL513867d1f672/highriskzone/man/plot.bootcorr.Rd:22: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpwriBHn/R.INSTALL513867d1f672/highriskzone/man/plot.highriskzone.Rd:14: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpwriBHn/R.INSTALL513867d1f672/highriskzone/man/plot.highriskzone.Rd:39: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpwriBHn/R.INSTALL513867d1f672/highriskzone/man/plot.hrzeval.Rd:15: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpwriBHn/R.INSTALL513867d1f672/highriskzone/man/plot.hrzeval.Rd:52: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpwriBHn/R.INSTALL513867d1f672/highriskzone/man/thin.Rd:27: file link ‘rbinom’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/highriskzone.Rcheck/00install.out’ for details.
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.
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.
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.
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.

Found the following calls to data() loading into the global environment:
File ‘hiPOD/R/predictPoolNCP.R’:
  data(ncp.pool.pred)
See section ‘Good practice’ in ‘?data’.
Found the following files/directories:
  ‘hiPOD_examples’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpgL0JyO/R.INSTALL52ca52a91dbd/hipread/man/callback.Rd:102: file link ‘ChunkCallback’ in package ‘hipread’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpgL0JyO/R.INSTALL52ca52a91dbd/hipread/man/callback.Rd:140: file link ‘ChunkCallback’ in package ‘hipread’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpgL0JyO/R.INSTALL52ca52a91dbd/hipread/man/callback.Rd:140: file link ‘HipChunkCallback’ in package ‘hipread’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpgL0JyO/R.INSTALL52ca52a91dbd/hipread/man/callback.Rd:205: file link ‘ChunkCallback’ in package ‘hipread’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpgL0JyO/R.INSTALL52ca52a91dbd/hipread/man/callback.Rd:205: file link ‘HipChunkCallback’ in package ‘hipread’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpgL0JyO/R.INSTALL52ca52a91dbd/hipread/man/callback.Rd:279: file link ‘ChunkCallback’ in package ‘hipread’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpgL0JyO/R.INSTALL52ca52a91dbd/hipread/man/callback.Rd:279: file link ‘HipChunkCallback’ in package ‘hipread’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpgL0JyO/R.INSTALL52ca52a91dbd/hipread/man/hipread_long_yield.Rd:164: file link ‘HipYield’ in package ‘hipread’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpgL0JyO/R.INSTALL52ca52a91dbd/hipread/man/hipread_long_yield.Rd:208: file link ‘HipYield’ in package ‘hipread’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hipread.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpAsdA3k/R.INSTALL5cd7255b7921/HistData/man/SnowMap.Rd:153: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpAsdA3k/R.INSTALL5cd7255b7921/HistData/man/SnowMap.Rd:156: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpAsdA3k/R.INSTALL5cd7255b7921/HistData/man/SnowMap.Rd:190: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HistData.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp81euTj/R.INSTALL5b2f30d0fde8/HistogramTools/man/histogram-message.Rd:33: file link ‘RProtoBuf’ in package ‘RProtoBuf’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp81euTj/R.INSTALL5b2f30d0fde8/HistogramTools/man/informationloss.Rd:43: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp81euTj/R.INSTALL5b2f30d0fde8/HistogramTools/man/message-histogram.Rd:30: file link ‘RProtoBuf’ in package ‘RProtoBuf’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp81euTj/R.INSTALL5b2f30d0fde8/HistogramTools/man/plot.Rd:49: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp81euTj/R.INSTALL5b2f30d0fde8/HistogramTools/man/plothist.Rd:31: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp81euTj/R.INSTALL5b2f30d0fde8/HistogramTools/man/plothist.Rd:34: file link ‘plot.histogram’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp81euTj/R.INSTALL5b2f30d0fde8/HistogramTools/man/plothist.Rd:42: file link ‘plot.histogram’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp81euTj/R.INSTALL5b2f30d0fde8/HistogramTools/man/quantiles.Rd:34: file link ‘wtd.quantile’ in package ‘Hmisc’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HistogramTools.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘FGN’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpUkQzvm/R.INSTALL327b4e8771e9/Hmisc/man/ffCompress.Rd:52: file link ‘cleanup.import’ in package ‘Hmisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpUkQzvm/R.INSTALL327b4e8771e9/Hmisc/man/rcspline.plot.Rd:131: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpUkQzvm/R.INSTALL327b4e8771e9/Hmisc/man/summaryS.Rd:24: file link ‘dotplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpUkQzvm/R.INSTALL327b4e8771e9/Hmisc/man/transcan.Rd:261: file link ‘lm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Hmisc.Rcheck/00install.out’ for details.
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.
Found the following files/directories:
  ‘HMM2est.image’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmptL5Peo/R.INSTALL49d51acf91f3/hms/man/vec_ptype2.hms.Rd:18: file link ‘stop_incompatible_type’ in package ‘vctrs’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmptL5Peo/R.INSTALL49d51acf91f3/hms/man/vec_ptype2.hms.Rd:22: file link ‘stop_incompatible_type’ in package ‘vctrs’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hms.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘glmmADMB’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpnlBp6j/R.INSTALL769142c2d298/Holidays/man/Holidays-package.Rd:12: file link ‘registerHolidays’ in package ‘TimeWarp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpnlBp6j/R.INSTALL769142c2d298/Holidays/man/Holidays-package.Rd:29: file link ‘registerHolidays’ in package ‘TimeWarp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpnlBp6j/R.INSTALL769142c2d298/Holidays/man/Holidays-package.Rd:29: file link ‘allHolidays’ in package ‘TimeWarp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Holidays.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpnSQCOA/R.INSTALLa0b430ba4ba/homals/man/plot.homals.Rd:46: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/homals.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpNoZfIp/R.INSTALL2d446d7193a7/homologene/man/reexports.Rd:16: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNoZfIp/R.INSTALL2d446d7193a7/homologene/man/reexports.Rd:16: file link ‘%<>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNoZfIp/R.INSTALL2d446d7193a7/homologene/man/reexports.Rd:16: file link ‘%$%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/homologene.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpZuTqNi/Rbuild181a4751942f/hopit/man/hopit.Rd:40: file link ‘na.omit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZuTqNi/Rbuild181a4751942f/hopit/man/hopit.Rd:41: file link ‘na.exclude’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpZuTqNi/Rbuild181a4751942f/hopit/man/hopit.Rd:42: file link ‘na.pass’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hopit.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘ALB_msk_alt.grd’ ‘ALB_msk_alt.gri’ ‘ALB_msk_alt.vrt’
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.
Found the following files/directories:
  ‘NUL’
File ‘hpa/libs/hpa.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
    Objects: ‘hpaBinary.o’, ‘hpaML.o’, ‘hpaSelection.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following files/directories:
  ‘output.swf’
bracket: no visible global function definition for ‘segments’
Undefined global functions or variables:
  segments
Consider adding
  importFrom("graphics", "segments")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpbcpsbL/R.INSTALL5c351437e6d/hrbrthemes/man/gg_check.Rd:12: file link ‘dictionary’ in package ‘hunspell’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbcpsbL/R.INSTALL5c351437e6d/hrbrthemes/man/theme_ipsum_es.Rd:60: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbcpsbL/R.INSTALL5c351437e6d/hrbrthemes/man/theme_ipsum_ps.Rd:59: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbcpsbL/R.INSTALL5c351437e6d/hrbrthemes/man/theme_ipsum_pub.Rd:60: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbcpsbL/R.INSTALL5c351437e6d/hrbrthemes/man/theme_ipsum_rc.Rd:124: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbcpsbL/R.INSTALL5c351437e6d/hrbrthemes/man/theme_ipsum_tw.Rd:60: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbcpsbL/R.INSTALL5c351437e6d/hrbrthemes/man/theme_tinyhand.Rd:57: file link ‘margin’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hrbrthemes.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hsdar.Rcheck/00install.out’ for details.
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.
Rd file 'hsicCCA.Rd':
  \usage lines wider than 90 characters:
     hsicCCA(x, y, M, sigmax = NULL, sigmay = NULL, numrepeat = 5, numiter = 100, reltolstop = 1e-04)

Rd file 'ktaCCA.Rd':
  \usage lines wider than 90 characters:
     ktaCCA(x, y, M, sigmax = NULL, sigmay = NULL, numrepeat = 5, numiter = 100, reltolstop = 1e-04)

These lines will be truncated in the PDF manual.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpuOwKlR/R.INSTALL5de61ad95f07/hsstan/man/hsstan.Rd:89: file link ‘sampling’ in package ‘rstan’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuOwKlR/R.INSTALL5de61ad95f07/hsstan/man/kfold.hsstan.Rd:34: file link ‘sampling’ in package ‘rstan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hsstan.Rcheck/00install.out’ for details.
Huber: no visible global function definition for ‘quantile’
SSVD.iter.thresh: no visible global function definition for ‘mad’
error.est.full: no visible global function definition for ‘mad’
error.est.full : <anonymous>: no visible global function definition for
  ‘median’
low_rank: no visible global function definition for ‘median’
low_rank: no visible global function definition for ‘mad’
low_rank: no visible global function definition for ‘sd’
select.indices: no visible global function definition for ‘mad’
select.indices: no visible global function definition for ‘median’
select.indices: no visible global function definition for ‘pnorm’
select.indices: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  mad median p.adjust pnorm quantile sd
Consider adding
  importFrom("stats", "mad", "median", "p.adjust", "pnorm", "quantile",
             "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp672pT7/R.INSTALL3b33a1e613e/HTLR/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HTLR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp0862Xm/R.INSTALL2e3e62c7c586/htmltools/man/as.tags.Rd:17: file link ‘as.character’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/htmltools.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpZX35qw/R.INSTALL3dcd1d37f4ec/htmlwidgets/man/createWidget.Rd:17: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZX35qw/R.INSTALL3dcd1d37f4ec/htmlwidgets/man/onStaticRenderComplete.Rd:15: file link ‘tags’ in package ‘htmltools’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZX35qw/R.INSTALL3dcd1d37f4ec/htmlwidgets/man/prependContent.Rd:15: file link ‘tags’ in package ‘htmltools’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/htmlwidgets.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpG0XdO8/R.INSTALL56ae2a694b7/httpcache/man/cachedPOST.Rd:24: file link ‘POST’ in package ‘httpcache’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpG0XdO8/R.INSTALL56ae2a694b7/httpcache/man/loadLogfile.Rd:11: file link ‘read.delim’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/httpcache.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpUIZ1Jh/R.INSTALL2e58c1bfdff/httptest/man/expect_header.Rd:23: file link ‘expect_warning’ in package ‘testthat’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpUIZ1Jh/R.INSTALL2e58c1bfdff/httptest/man/expect_json_equivalent.Rd:38: file link ‘expect_equivalent’ in package ‘testthat’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpUIZ1Jh/R.INSTALL2e58c1bfdff/httptest/man/expect_verb.Rd:35: file link ‘grepl’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpUIZ1Jh/R.INSTALL2e58c1bfdff/httptest/man/gsub_response.Rd:34: file link ‘gsub’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpUIZ1Jh/R.INSTALL2e58c1bfdff/httptest/man/gsub_response.Rd:15: file link ‘gsub’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpUIZ1Jh/R.INSTALL2e58c1bfdff/httptest/man/mockPaths.Rd:24: file link ‘.libPaths’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/httptest.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpufVwzF/R.INSTALL380632a6f71b/httpuv/man/encodeURI.Rd:37: file link ‘URLdecode’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/httpuv.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpijw6bs/R.INSTALL399049cf2b4b/httr/man/content.Rd:49: file link ‘read_html’ in package ‘xml2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/httr.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp3st7Xn/R.INSTALL55510124809/humanize/man/reexports.Rd:22: file link ‘is.date’ in package ‘assertthat’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp3st7Xn/R.INSTALL55510124809/humanize/man/reexports.Rd:22: file link ‘is.count’ in package ‘assertthat’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp3st7Xn/R.INSTALL55510124809/humanize/man/reexports.Rd:24: file link ‘today’ in package ‘lubridate’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/humanize.Rcheck/00install.out’ for details.
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: ‘hurricaneexposuredata’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpk27Khi/R.INSTALL30d361bece4d/hutils/man/replace_pattern_in.Rd:15: file link ‘gsub’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpk27Khi/R.INSTALL30d361bece4d/hutils/man/replace_pattern_in.Rd:17: file link ‘gsub’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hutils.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp4QIvIp/R.INSTALL1ecf9ca3aa/huxtable/man/report_latex_dependencies.Rd:37: file link ‘tlmgr_install’ in package ‘tinytex’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4QIvIp/R.INSTALL1ecf9ca3aa/huxtable/man/rowspecs.Rd:27: file link ‘select_helpers’ in package ‘tidyselect’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4QIvIp/R.INSTALL1ecf9ca3aa/huxtable/man/rowspecs.Rd:43: file link ‘with_vars’ in package ‘tidyselect’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/huxtable.Rcheck/00install.out’ for details.
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.
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.
Running examples in ‘HybridFS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HybridFS
> ### Title: A Hybrid Feature Selection Function
> ### Aliases: HybridFS
> 
> ### ** Examples
> 
> FS=HybridFS(input.df=validation,target.var.name="Survived")
Error: 'predictions' contains NA.
Execution halted
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.
Rd file 'hybridMC.Rd':
  \usage lines wider than 90 characters:
     hybridMC(y.start, n.samp=1, logDens, dLogDens, epsilon, LFsteps, compWeights=NULL, MPwidth=1, MPweights=NULL, progress=0 ,...)

These lines will be truncated in the PDF manual.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpRJkSuA/R.INSTALL594a2fe6b482/hydroGOF/man/ggof.Rd:103: file link ‘drawTimeAxis’ in package ‘hydroTSM’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpRJkSuA/R.INSTALL594a2fe6b482/hydroGOF/man/plot2.Rd:53: file link ‘drawTimeAxis’ in package ‘hydroTSM’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpRJkSuA/R.INSTALL594a2fe6b482/hydroGOF/man/plotbands.Rd:83: file link ‘drawTimeAxis’ in package ‘hydroTSM’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hydroGOF.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘minpack.lm’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Dstart: no visible global function definition for ‘coef’
Dstart: no visible global function definition for ‘lm’
SSkosugi: no visible global function definition for ‘pnorm’
SSkosugi: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  coef dnorm lm pnorm
Consider adding
  importFrom("stats", "coef", "dnorm", "lm", "pnorm")
to your NAMESPACE file.
Rd file 'Brook.Rd':
  \examples lines wider than 100 characters:
     brook.ns=nlsLM(y~Brook(x,thr,ths,alp,nscal),data=pf, control=nls.lm.control(maxiter=200),start=c(thr=Dstart(pf)[1],ths=Dstart(pf)[2], a ... [TRUNCATED]

Rd file 'Expo.Rd':
  \examples lines wider than 100 characters:
     expo.ns=nlsLM(y~Expo(x,thr,ths,alp),data=pf, control=nls.lm.control(maxiter=200),start=c(thr=Dstart(pf)[1],ths=Dstart(pf)[2], alp=Dstar ... [TRUNCATED]

Rd file 'Ruso.Rd':
  \examples lines wider than 100 characters:
     ruso.ns=nlsLM(y~Ruso(x,thr,ths,alp,nscal),data=pf, control=nls.lm.control(maxiter=200),start=c(thr=Dstart(pf)[1],ths=Dstart(pf)[2], alp ... [TRUNCATED]

Rd file 'SSfredlund.Rd':
  \examples lines wider than 100 characters:
     fredlund.ns=nlsLM(y~SSfredlund(x,thr,ths,alp,nscal,mscal),data=pf,control=nls.lm.control(maxiter=200,options(warn=-1)))

Rd file 'SSkosugi.Rd':
  \examples lines wider than 100 characters:
     kosugi.ns=nlsLM(y~SSkosugi(x,thr,ths,alp,nscal),data=subset(isric, Sample=="Benin2"),control=nls.lm.control(maxiter=200,options(warn=-1 ... [TRUNCATED]

Rd file 'SSvgm.Rd':
  \examples lines wider than 100 characters:
     vn.ns=nlsLM(y~SSvgm(x,thr,ths,alp,nscal,mscal),data=subset(isric, Sample=="Benin2"),control=nls.lm.control(maxiter=200,options(warn=-1) ... [TRUNCATED]

Rd file 'Tani.Rd':
  \examples lines wider than 100 characters:
     tani.ns=nlsLM(y~Tani(x,thr,ths,alp),data=pf, control=nls.lm.control(maxiter=200),start=c(thr=Dstart(pf)[1],ths=Dstart(pf)[2], alp=Dstar ... [TRUNCATED]

These lines will be truncated in the PDF manual.
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_CFLAGS but not in PKG_LIBS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hyperSpec.Rcheck/00install.out’ for details.
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.
Rd file 'requiprobable.Rd':
  \examples lines wider than 100 characters:
     for (i in 1:10) unlabeled[[i]]$tip.label<-sample(c("A1","A2","B1","B2","B3","C1","C2","C3","C4","C5"))

Rd file 'rgenetree.Rd':
  \examples lines wider than 100 characters:
     ##Now lets start with 3 genes, set the number of genes at each tip of spec and vary mu between the branches of spec 

These lines will be truncated in the PDF manual.
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.
Rd file 'conint.Rd':
  \usage lines wider than 90 characters:
     conint(TrnX = NULL, TrnY = NULL, m, n1, n2, s1, s2, side = "both", alpha = 0.95, method = "n")

Rd file 'hypothesis-package.Rd':
  \examples lines wider than 100 characters:
     hypothesis(TrnX=c(3,4,5),TrnY=c(4,5,6),m,u0=4,3,3,s1=NULL,s2=NULL,sigma1=NULL,sigma2=NULL,alpha=0.05,method="n",H0="u=u0",p)

Rd file 'hypothesis.Rd':
  \usage lines wider than 90 characters:
     hypothesis(TrnX = NULL, TrnY = NULL, m, u0, n1, n2, s1 = NULL, s2 = NULL, sigma1 = NULL, sigma2 = NULL, alpha = 0.05, method = "n", H0  ... [TRUNCATED]
  \examples lines wider than 100 characters:
      hypothesis(TrnX=c(3,4,5),TrnY=c(4,5,6),m,u0=4,3,3,s1=NULL,s2=NULL,sigma1=NULL,sigma2=NULL,alpha=0.05,method="n",H0="u=u0",p)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmppjitya/R.INSTALLefb8bf84e3/hypr/man/cmat.Rd:27: file link ‘as.fractions’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmppjitya/R.INSTALLefb8bf84e3/hypr/man/cmat.Rd:40: file link ‘C’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmppjitya/R.INSTALLefb8bf84e3/hypr/man/conversions.Rd:37: file link ‘as.fractions’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmppjitya/R.INSTALLefb8bf84e3/hypr/man/hmat.Rd:21: file link ‘as.fractions’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmppjitya/R.INSTALLefb8bf84e3/hypr/man/hypr.Rd:25: file link ‘C’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmppjitya/R.INSTALLefb8bf84e3/hypr/man/hypr.Rd:71: file link ‘C’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmppjitya/R.INSTALLefb8bf84e3/hypr/man/hypr.Rd:71: file link ‘contr.hypothesis’ in package ‘hypr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hypr.Rcheck/00install.out’ for details.
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 vignette with placeholder title ‘Vignette Title’:
  ‘vignette-IAbin.Rmd’
Found the following files/directories:
  ‘AIC.txt’ ‘AICc.txt’ ‘IAS.pdf’ ‘IAS2.pdf’ ‘IAS3.pdf’
  ‘P.microlepis-AIC.txt’ ‘P.microlepis-AICc.txt’ ‘P.microlepis-IAS.pdf’
  ‘P.microlepis-IAS2.pdf’ ‘P.microlepis-IAS3.pdf’
Found the following sources/headers with CR or CRLF line endings:
  inst/include/MHRProbit.h
  inst/include/MHRmixture.h
  inst/include/MHXIProbit.h
  inst/include/MHXImixture.h
  inst/include/MixtureMain.h
  inst/include/ProbitMain.h
  inst/include/pRMHProbit.h
  inst/include/pRMHXIProbit.h
  inst/include/pRMHXImixture.h
  inst/include/pRMHmixture.h
  inst/include/prMixture.h
Some Unix compilers require LF line endings.
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.
Non-standard file/directory found at top level:
  ‘perl’
create.ibd.dat: no visible global function definition for ‘read.table’
create.pairs.frame: no visible global function definition for ‘terms’
ibd.moments: no visible global function definition for ‘var’
ibdreg: no visible global function definition for ‘terms’
ibdreg: no visible global function definition for ‘as.formula’
linkage.tests: no visible global function definition for ‘pchisq’
pchibar: no visible global function definition for ‘pchisq’
plot.linkage.all: no visible global function definition for ‘title’
plotpval: no visible global function definition for ‘lines’
sim.ibd.var: no visible global function definition for ‘read.table’
sim.mark.prop: no visible global function definition for ‘runif’
Undefined global functions or variables:
  as.formula lines pchisq read.table runif terms title var
Consider adding
  importFrom("graphics", "lines", "title")
  importFrom("stats", "as.formula", "pchisq", "runif", "terms", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘ped7.pre’
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').
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpxbWkVa/R.INSTALL6b5937a4c34c/ibmdbR/man/idadf.Rd:55: file link ‘sqlUpdate’ in package ‘RODBC’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpxbWkVa/R.INSTALL6b5937a4c34c/ibmdbR/man/idadf.Rd:62: file link ‘sqlUpdate’ in package ‘RODBC’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ibmdbR.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘ibmsunburst.Rmd’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpoOOlbP/R.INSTALL15ad27132fcb/Iboot/man/Iboot-package.Rd:37: file link ‘stats’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Iboot.Rcheck/00install.out’ for details.
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.
..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.
Rd file 'curveConcent.Rd':
  \examples lines wider than 100 characters:
     curveConcent(x=hhbudgets[, "transporte"], y=hhbudgets[,"ingreso"], w=hhbudgets[,"factor"], col="red", xlab="Ranking by income")
     curveConcent(x=hhbudgets[, "mantenimiento"], y=hhbudgets[,"ingreso"], w=hhbudgets[,"factor"], col="blue", add=TRUE)
     curveConcent(x=hhbudgets[, "publico"], y=hhbudgets[,"ingreso"], w=hhbudgets[,"factor"], col="green", add=TRUE)
     legend("topleft", legend = c("All transport", "Private: Maintenance and repair", "Public transport"), col=c("red", "blue", "green"), lt ... [TRUNCATED]

Rd file 'decompAtkinson.Rd':
  \examples lines wider than 100 characters:
     summary(decompAtkinson(x=hhbudgets[,"transporte"], z=hhbudgets[,"tenencia"], w=hhbudgets[,"factor"], decomp="DP", ELMO=FALSE))
     summary(decompAtkinson(x=hhbudgets[,"transporte"], z=hhbudgets[,"tenencia"], w=hhbudgets[,"factor"], decomp="DP", epsilon=0.25))

Rd file 'decompGEI.Rd':
  \examples lines wider than 100 characters:
     summary(decompGEI(x=hhbudgets[,"transporte"], z=hhbudgets[,"tenencia"], w=hhbudgets[,"factor"], alpha=1.5))

Rd file 'decompSGini.Rd':
  \examples lines wider than 100 characters:
     decompSGini(x=hhbudgets[,"transporte"], z=hhbudgets[,"estructura"], w=hhbudgets[,"factor"], decomp="YL", ELMO=FALSE)
     summary(decompSGini(x=hhbudgets[,"transporte"], z=hhbudgets[,"tenencia"], w=hhbudgets[,"factor"], param=1.5))

These lines will be truncated in the PDF manual.
'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.
Rd file 'hts.Rd':
  \examples lines wider than 100 characters:
                   measure="mpi384_measure.txt",control="mpi384_control.txt",dilution="mpi384_dilution.txt",

Rd file 'ic50.Rd':
  \examples lines wider than 100 characters:
                    measure="mpi384_measure.txt",control="mpi384_control.txt",dilution="mpi384_dilution.txt",

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘.last384_control.txt’ ‘.last384_dilution.txt’ ‘.last384_measure.txt’
  ‘.last96_control.txt’ ‘.last96_dilution.txt’ ‘.last96_measure.txt’
  ‘HCC2429_1.txt’ ‘HCC2429_2.txt’ ‘HCC2429_results’ ‘NSCLC_results’
  ‘NSCLC_screen’ ‘mpi384_control.txt’ ‘mpi384_dilution.txt’
  ‘mpi384_measure.txt’
ICA: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpVxO40t/R.INSTALL74ec34c18b5/ICAMS/man/CheckAndFixChrNames.Rd:15: file link ‘BSgenome’ in package ‘BSgenome’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpVxO40t/R.INSTALL74ec34c18b5/ICAMS/man/MutectVCFFilesToZipFile.Rd:85: file link ‘zipr’ in package ‘zip’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpVxO40t/R.INSTALL74ec34c18b5/ICAMS/man/StrelkaIDVCFFilesToZipFile.Rd:62: file link ‘zipr’ in package ‘zip’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpVxO40t/R.INSTALL74ec34c18b5/ICAMS/man/StrelkaSBSVCFFilesToZipFile.Rd:71: file link ‘zipr’ in package ‘zip’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ICAMS.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
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: ‘icd’
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.
Rd file 'ickde.Rd':
  \usage lines wider than 90 characters:
     ickde(I, h, f, m, n.iterations = 10, x1, xm, right.limit = 10000,kernel="gaussian", old=TRUE)

These lines will be truncated in the PDF manual.
INCAncinner : dian: no visible global function definition for ‘cutree’
INCAncinner : bestela: no visible global function definition for
  ‘cutree’
center: no visible global function definition for ‘var’
dbhatta: no visible global function definition for ‘as.dist’
dcor: no visible global function definition for ‘cor’
dcor: no visible global function definition for ‘as.dist’
dgower: no visible global function definition for ‘as.dist’
dmahal: no visible global function definition for ‘as.dist’
dproc2: no visible global function definition for ‘as.dist’
plot.incaix: no visible global function definition for ‘barplot’
plot.incanc: no visible global function definition for ‘lines’
plot.incanc: no visible global function definition for ‘legend’
selectioncluster : dian: no visible global function definition for
  ‘cutree’
selectioncluster : bestela: no visible global function definition for
  ‘cutree’
Undefined global functions or variables:
  as.dist barplot cor cutree legend lines var
Consider adding
  importFrom("graphics", "barplot", "legend", "lines")
  importFrom("stats", "as.dist", "cor", "cutree", "var")
to your NAMESPACE file.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpUmY95U/R.INSTALL447c4cfcfd13/icosa/man/heatMapLegend.Rd:54: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpUmY95U/R.INSTALL447c4cfcfd13/icosa/man/heatMapLegend.Rd:48: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/icosa.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpwdkDKH/R.INSTALL5c7f66990ae9/ICSOutlier/man/comp.simu.test.Rd:24: file link ‘clusterSetRNGStream’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpwdkDKH/R.INSTALL5c7f66990ae9/ICSOutlier/man/dist.simu.test.Rd:24: file link ‘clusterSetRNGStream’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpwdkDKH/R.INSTALL5c7f66990ae9/ICSOutlier/man/ics.outlier.Rd:37: file link ‘clusterSetRNGStream’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ICSOutlier.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpWHmE5H/R.INSTALL599b7ffc06b4/ICSShiny/man/ICSShiny.Rd:30: file link ‘clusterSetRNGStream’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ICSShiny.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpUCV4Dh/R.INSTALL5cae77ab7132/idar/man/SF.Rd:25: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpUCV4Dh/R.INSTALL5cae77ab7132/idar/man/fdis.Rd:16: file link ‘as.matrix’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpUCV4Dh/R.INSTALL5cae77ab7132/idar/man/midar.Rd:34: file link ‘multifocalsimulator’ in package ‘idar’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpUCV4Dh/R.INSTALL5cae77ab7132/idar/man/pisar.Rd:71: file link ‘multifocalsimulator’ in package ‘idar’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/idar.Rcheck/00install.out’ for details.
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.
GNU make is a SystemRequirements.
Non-standard file/directory found at top level:
  ‘README.Idcoefs2b1.txt’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpGPAgHR/R.INSTALL767d427d5fb4/idmodelr/man/scenario_analysis.Rd:45: file link ‘unnest’ in package ‘tidyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/idmodelr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpZswkzh/R.INSTALL40e31ed22453/IDPmisc/man/longtsPlot.Rd:95: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IDPmisc.Rcheck/00install.out’ for details.
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 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.
Packages suggested but not available for checking: 'ie2misc', 'ie2miscdata'
Package suggested but not available for checking: ‘ie2misc’
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.
Found the following files/directories:
  ‘Demo_Gibbs_result.RData’ ‘Demo_traceplot.pdf’ ‘RMSE_demo.RData’
  ‘RMSE_plot.pdf’ ‘ROC_plot.pdf’ ‘ROC_result.RData’ ‘demo_data.RData’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpQkyBA1/R.INSTALL325c132fc9ce/ifultools/man/ACVStoPACS.Rd:44: file link ‘ar.yw’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQkyBA1/R.INSTALL325c132fc9ce/ifultools/man/scaleData.Rd:28: file link ‘exp’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQkyBA1/R.INSTALL325c132fc9ce/ifultools/man/variance.Rd:33: file link ‘var’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ifultools.Rcheck/00install.out’ for details.
Found the following assignments to the global environment:
File ‘IgorR/R/ReadIgorBinary.R’:
  assign(WaveName, rval, envir = .GlobalEnv)
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpiKoFaH/R.INSTALL3fb95eaa0778/igraph/man/cluster_leading_eigen.Rd:120: file link ‘as.dendrogram’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpiKoFaH/R.INSTALL3fb95eaa0778/igraph/man/plot.common.Rd:13: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpiKoFaH/R.INSTALL3fb95eaa0778/igraph/man/plot.common.Rd:184: file link ‘tkfont.create’ in package ‘tcltk’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpiKoFaH/R.INSTALL3fb95eaa0778/igraph/man/plot.common.Rd:186: file link ‘tkfont.create’ in package ‘tcltk’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpiKoFaH/R.INSTALL3fb95eaa0778/igraph/man/plot.common.Rd:217: file link ‘tkfont.create’ in package ‘tcltk’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/igraph.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpEdape5/R.INSTALL77892bb19677/iheatmapr/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/iheatmapr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpnnHTuQ/R.INSTALL353e4777ba36/ihpdr/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ihpdr.Rcheck/00install.out’ for details.
ihs.mle: no visible global function definition for ‘as.formula’
pihs: no visible global function definition for ‘pnorm’
qihs: no visible global function definition for ‘qnorm’
rihs: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  as.formula pnorm qnorm rnorm
Consider adding
  importFrom("stats", "as.formula", "pnorm", "qnorm", "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp6vLDzE/R.INSTALL5ce818bf2835/ilc/man/plot_dd.Rd:31: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ilc.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘fit.mod6.ps’ ‘res.mod6d.ps’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpChYpDO/R.INSTALL4abb4de08dc0/imager/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/imager.Rcheck/00install.out’ for details.
IMIS: no visible global function definition for ‘sample.prior’
IMIS: no visible global function definition for ‘var’
IMIS: no visible global function definition for ‘cov’
IMIS: no visible global function definition for ‘prior’
IMIS: no visible global function definition for ‘likelihood’
IMIS : posterior: no visible global function definition for ‘prior’
IMIS : posterior: no visible global function definition for
  ‘likelihood’
IMIS: no visible global function definition for ‘optim’
IMIS: no visible global function definition for ‘rnorm’
IMIS: no visible global function definition for ‘mahalanobis’
IMIS: no visible global function definition for ‘cov.wt’
IMIS: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  cov cov.wt dnorm likelihood mahalanobis optim prior rnorm
  sample.prior var
Consider adding
  importFrom("stats", "cov", "cov.wt", "dnorm", "mahalanobis", "optim",
             "rnorm", "var")
to your NAMESPACE file.
prepare_Rd: IMIS.Rd:26: Dropping empty section \keyword
Found the following significant warnings:
  Rd warning: C:/Users/sunpn563/AppData/Local/Temp/RtmpGkWkg1/Rbuild26fc48a06982/immer/man/immer-package.Rd:100: file link ‘tam.mml.mfr’ in package ‘TAM’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/immer.Rcheck/00install.out’ for details.
heter_IV2: no visible global function definition for ‘poly’
heter_IV2: no visible global function definition for ‘lm’
heter_IV2: no visible global function definition for ‘step’
heter_IV2: no visible global function definition for ‘pnorm’
heter_IV2: no visible global function definition for ‘qnorm’
homo_IV1: no visible global function definition for ‘coef’
homo_IV1: no visible global function definition for ‘pnorm’
homo_IV1: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  coef lm pnorm poly qnorm step
Consider adding
  importFrom("stats", "coef", "lm", "pnorm", "poly", "qnorm", "step")
to your NAMESPACE file.
prepare_Rd: heter_IV2.Rd:82-84: Dropping empty section \note
prepare_Rd: heter_IV2.Rd:88-90: Dropping empty section \seealso
prepare_Rd: homo_IV1.Rd:65-67: Dropping empty section \note
prepare_Rd: homo_IV1.Rd:71-73: Dropping empty section \seealso
prepare_Rd: impact.Rd:31-33: Dropping empty section \source
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpd0olil/R.INSTALL34db5f01888e/impimp/man/impimp.Rd:41: file link ‘print.data.frame’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/impimp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpzcbnSR/R.INSTALL378423d998b1/implyr/man/src_impala.Rd:16: file link ‘dbConnect,OdbcDriver-method’ in package ‘odbc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzcbnSR/R.INSTALL378423d998b1/implyr/man/src_impala.Rd:17: file link ‘dbConnect,JDBCDriver-method’ in package ‘RJDBC’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/implyr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpuoX1Ln/R.INSTALL64cc427cc500/ImportExport/man/spss_import.Rd:24: file link ‘read_sav’ in package ‘haven’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuoX1Ln/R.INSTALL64cc427cc500/ImportExport/man/spss_import.Rd:35: file link ‘read_sav’ in package ‘haven’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuoX1Ln/R.INSTALL64cc427cc500/ImportExport/man/spss_import.Rd:41: file link ‘read_sav’ in package ‘haven’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ImportExport.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpVh4oRl/R.INSTALL3714182d0e36/imptree/man/node_imptree.Rd:19: file link ‘as.integer’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpVh4oRl/R.INSTALL3714182d0e36/imptree/man/print.imptree.Rd:15: file link ‘getOption’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/imptree.Rcheck/00install.out’ for details.
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.
Rd file 'impute.mdr.Rd':
  \usage lines wider than 90 characters:
     impute.mdr(dataset, colresp, cs, combi, cv.fold = 10, na.method = 0, max_iter = 30, randomize = FALSE)

These lines will be truncated in the PDF manual.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘count_compare’
heal_data: no visible global function definition for ‘optimum_k’
heal_data: no visible global function definition for ‘optimum_w’
heal_data: no visible global function definition for ‘pred_for_w’
Undefined global functions or variables:
  optimum_k optimum_w pred_for_w
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp4F9IrB/R.INSTALL4daa5b6bb710/imputeR/man/CubistR.Rd:29: file link ‘cubist’ in package ‘Cubist’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4F9IrB/R.INSTALL4daa5b6bb710/imputeR/man/pcrR.Rd:28: file link ‘pcr’ in package ‘pls’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4F9IrB/R.INSTALL4daa5b6bb710/imputeR/man/plsR.Rd:28: file link ‘plsr’ in package ‘pls’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/imputeR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpPmG9Ti/R.INSTALL28eb164b2a6d/imputeTS/man/na.kalman.Rd:38: file link ‘KalmanSmooth’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPmG9Ti/R.INSTALL28eb164b2a6d/imputeTS/man/na.kalman.Rd:39: file link ‘KalmanRun’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPmG9Ti/R.INSTALL28eb164b2a6d/imputeTS/man/na_kalman.Rd:38: file link ‘KalmanSmooth’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPmG9Ti/R.INSTALL28eb164b2a6d/imputeTS/man/na_kalman.Rd:39: file link ‘KalmanRun’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPmG9Ti/R.INSTALL28eb164b2a6d/imputeTS/man/na_kalman.Rd:64: file link ‘KalmanSmooth’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPmG9Ti/R.INSTALL28eb164b2a6d/imputeTS/man/plotNA.distributionBar.Rd:15: file link ‘nclass.Sturges’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPmG9Ti/R.INSTALL28eb164b2a6d/imputeTS/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/imputeTS.Rcheck/00install.out’ for details.
Warning: no function found corresponding to methods exports from ‘IM’ for: ‘initialize’

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

Probably some imports need to be declared in the NAMESPACE file.
Packages in Depends field not imported from:
  ‘bmp’ ‘jpeg’ ‘methods’ ‘png’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'MultiIm-class.Rd':
  \examples lines wider than 100 characters:
     #create MultiIm object, calculate generalized Pseudo-Zernike moments, invariants, and reconstruction for all images
             #create MultiIm object, calculate discrete Chebyshev moments, invariants, and reconstruction for all images
             #create MultiIm object, calculate continuous Chebyshev - Legendre moments, invariants, and reconstruction for all images

Rd file 'demoPoly.Rd':
  \examples lines wider than 100 characters:
             #display generalized Pseudo-Zernike polynomials of order and repetition (3,2), (4,2), (5,3), (6,3) 

Rd file 'momentObj.Rd':
  \examples lines wider than 100 characters:
             #calculate bivariate Legendre/Gegenbauer moments up to orders 50 and 100 with parameter 1 for Gegenbauer moments.
             #compute Radial Harmonic-Fourier moment invariants of a list of images, using up to order 10 and repetition 10

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpgKtynu/R.INSTALL38bd2438a600/IMWatson/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IMWatson.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmptDQmAi/R.INSTALL2d92673be66d/INCATome/man/INCATome.Rd:19: file link ‘eBayes’ in package ‘limma’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/INCATome.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpl5iij6/R.INSTALL4ed4ec3e4c7/incidence/man/incidence.Rd:280: file link ‘fit_optim_split’ in package ‘incidence’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpl5iij6/R.INSTALL4ed4ec3e4c7/incidence/man/incidence.Rd:285: file link ‘as.data.frame.incidence’ in package ‘incidence’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpl5iij6/R.INSTALL4ed4ec3e4c7/incidence/man/plot.incidence.Rd:43: file link ‘scale_x_date’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpl5iij6/R.INSTALL4ed4ec3e4c7/incidence/man/plot.incidence.Rd:44: file link ‘scale_x_datetime’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpl5iij6/R.INSTALL4ed4ec3e4c7/incidence/man/plot.incidence.Rd:44: file link ‘scale_x_continuous’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/incidence.Rcheck/00install.out’ for details.
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.
Rd file 'IDM.bootCI.Rd':
  \examples lines wider than 100 characters:
     #a built-in dataset fish is used. This data gives sizes of 53 female stickleback measured at the age of 17, 45, 80, and 115 days.
     #figure showing first two trajectories and percentages of variations accounted for by each trajectory.
     barplot(out$Percent.trajectory,ylim=c(0,105),las=1,names.arg=c("1","2","3","4"), ylab="Percentage of variation",cex.lab=1.35,cex.axis=1 ... [TRUNCATED]
     plot(age,out$Trajectories97.5CI[,1],type="l",lty=2,ylim=c(-1,1),las=1,ylab="Trajectory value",xlab="Age (days)",cex.lab=1.35,cex.axis=1 ... [TRUNCATED]
     plot(age,out$Trajectories97.5CI[,2],type="l",lty=2,ylim=c(-1,1),las=1,ylab="Trajectory value",xlab="Age (days)",cex.lab=1.35,cex.axis=1 ... [TRUNCATED]

Rd file 'p.function.Rd':
  \examples lines wider than 100 characters:
     temp2b=(-1)^i*factorial(j)/(factorial(i)*factorial(j-i))*factorial(2*j-2*i)/(factorial(j)*factorial(2*j-2*i-j))*x^(j-2*i)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpwlOu47/R.INSTALL3f6250d646c2/inference/man/transform.inference.Rd:17: file link ‘exp’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/inference.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpl1lPvy/R.INSTALL7507473b55b8/infer/man/pipe.Rd:11: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/infer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp6x8dFy/R.INSTALL40703d72dcbd/infix/man/except.Rd:28: file link ‘tryCatch’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6x8dFy/R.INSTALL40703d72dcbd/infix/man/funlogic.Rd:25: file link ‘Negate’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6x8dFy/R.INSTALL40703d72dcbd/infix/man/nomatch.Rd:16: file link ‘%in%’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6x8dFy/R.INSTALL40703d72dcbd/infix/man/pipes.Rd:27: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6x8dFy/R.INSTALL40703d72dcbd/infix/man/pipes.Rd:27: file link ‘%<>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6x8dFy/R.INSTALL40703d72dcbd/infix/man/pipes.Rd:27: file link ‘%$%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6x8dFy/R.INSTALL40703d72dcbd/infix/man/pipes.Rd:27: file link ‘%T>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/infix.Rcheck/00install.out’ for details.
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.
Found the following files/directories:
  ‘c.txt’ ‘rho.txt’ ‘sta.txt’ ‘topo.txt’
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.
Found the following files/directories:
  ‘bingFileContents.txt’ ‘japanInfraBing.png’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpBP2rox/R.INSTALL7c1b7cf8b8ad/Infusion/man/plot.SLik.Rd:30: file link ‘filled.mapMM’ in package ‘spaMM’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBP2rox/R.INSTALL7c1b7cf8b8ad/Infusion/man/plot.SLik.Rd:33: file link ‘filled.mapMM’ in package ‘spaMM’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBP2rox/R.INSTALL7c1b7cf8b8ad/Infusion/man/plot.SLik.Rd:53: file link ‘filled.mapMM’ in package ‘spaMM’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Infusion.Rcheck/00install.out’ for details.
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.
Rd file 'Jeffreys.Rd':
  \usage lines wider than 90 characters:
     Jeffreys(ltm.obj = NULL, inf.mat = NULL, inf.func = NULL, return = "prior", spl.method = "natural", range.int = c(-Inf, Inf))

Rd file 'iota.Rd':
  \usage lines wider than 90 characters:
     iota(ltm.obj, logL.fun, fscore.obj = NULL, data = NULL, prior = NULL, theta0 = NULL, range.int = c(-Inf, Inf), range.theta = c(-10, 10) ... [TRUNCATED]

Rd file 'iota.c.Rd':
  \usage lines wider than 90 characters:
     iota.c(ltm.obj, M = NULL, prior = NULL, logL.fun = NULL, rirm = NULL, range.int = c(-Inf, Inf))

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpwzbh91/R.INSTALL759f1407d64d/ingredients/man/bind_plots.Rd:20: file link ‘grid.arrange’ in package ‘gridExtra’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ingredients.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Malformed Title field: should not end in a period.
'library' or 'require' calls to packages already attached by Depends:
  ‘compiler’ ‘deSolve’ ‘lattice’ ‘nlme’
  Please remove these calls from your code.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘insideRODE/R/zzz.r’:
  .First.lib calls:
    require(nlme)
    require(lattice)
    require(deSolve)
    require(compiler)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

cfLSODE: no visible global function definition for ‘deriv’
cfODE: no visible global function definition for ‘deriv’
cfVODE: no visible global function definition for ‘deriv’
cpLSODE: no visible global function definition for ‘deriv’
cpODE: no visible global function definition for ‘deriv’
cpVODE: no visible global function definition for ‘deriv’
nlmLSODE: no visible global function definition for ‘deriv’
nlmLSODEcp: no visible global function definition for ‘deriv’
nlmODE: no visible global function definition for ‘deriv’
nlmODEcp: no visible global function definition for ‘deriv’
nlmVODE: no visible global function definition for ‘deriv’
nlmVODEcp: 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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpLWlL9P/R.INSTALL7d27c613cc4/insurancerating/man/model_performance.Rd:22: file link ‘BIC’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLWlL9P/R.INSTALL7d27c613cc4/insurancerating/man/reexports.Rd:17: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/insurancerating.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Error_Estimation_Response_1.tiff’ ‘Error_Estimation_Response_2.tiff’
  ‘Error_Estimation_Response_3.tiff’
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
  ‘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 rect strheight strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "polygon",
             "rect", "strheight", "strwidth", "text")
to your NAMESPACE file.
Rd file 'InteractiveIGraph.Rd':
  \examples lines wider than 100 characters:
     # this is an 'InteractiveIGraph' object, up till now there is not much difference. Just some extra attributes.

Rd file 'MenuAddItems.Rd':
  \examples lines wider than 100 characters:
       Item = list(list(label=msg, RegionParams=list(XBufCof = 0, YBufCof=0.2), RecParams=list(lwd = NA, border=NA), TextParams=list(cex=0.8 ... [TRUNCATED]

These lines will be truncated in the PDF manual.
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.
Malformed Description field: should contain one or more complete sentences.
compute_design_performance: no visible global function definition for
  ‘read.csv’
compute_design_performance : get_power: no visible global function
  definition for ‘rnorm’
compute_design_performance : power_curve_plot: no visible global
  function definition for ‘lines’
compute_design_performance : power_curve_plot: no visible global
  function definition for ‘legend’
compute_design_performance : expected_sample_size_plot: no visible
  global function definition for ‘lines’
compute_design_performance : expected_sample_size_plot: no visible
  global function definition for ‘legend’
compute_design_performance : expected_duration_plot: no visible global
  function definition for ‘lines’
compute_design_performance : expected_duration_plot: no visible global
  function definition for ‘legend’
compute_design_performance : boundary_adapt_plot: no visible global
  function definition for ‘matplot’
compute_design_performance : boundary_adapt_plot: no visible global
  function definition for ‘legend’
compute_design_performance : boundary_standard_H0C_plot: no visible
  global function definition for ‘matplot’
compute_design_performance : boundary_standard_H0C_plot: no visible
  global function definition for ‘legend’
compute_design_performance : boundary_standard_H01_plot: no visible
  global function definition for ‘matplot’
compute_design_performance : boundary_standard_H01_plot: no visible
  global function definition for ‘legend’
Undefined global functions or variables:
  legend lines matplot read.csv rnorm
Consider adding
  importFrom("graphics", "legend", "lines", "matplot")
  importFrom("stats", "rnorm")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpeC2nvi/R.INSTALL350227e02182/intergraph/man/as.matrix.igraph.Rd:41: file link ‘get.adjacency’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpeC2nvi/R.INSTALL350227e02182/intergraph/man/as.matrix.igraph.Rd:41: file link ‘get.edgelist’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpeC2nvi/R.INSTALL350227e02182/intergraph/man/as.matrix.igraph.Rd:52: file link ‘get.adjacency’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpeC2nvi/R.INSTALL350227e02182/intergraph/man/as.matrix.igraph.Rd:53: file link ‘get.edgelist’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpeC2nvi/R.INSTALL350227e02182/intergraph/man/asDF.Rd:65: file link ‘get.edgelist’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpeC2nvi/R.INSTALL350227e02182/intergraph/man/asIgraph.Rd:43: file link ‘graph.data.frame’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpeC2nvi/R.INSTALL350227e02182/intergraph/man/asIgraph.Rd:95: file link ‘graph.data.frame’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpeC2nvi/R.INSTALL350227e02182/intergraph/man/asNetwork.Rd:40: file link ‘graph.data.frame’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpeC2nvi/R.INSTALL350227e02182/intergraph/man/asNetwork.Rd:69: file link ‘graph.data.frame’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/intergraph.Rcheck/00install.out’ for details.
Interpol: no visible global function definition for ‘splinefun’
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘Interpol/R/AAdescriptor.R’:
  data(AAindex)
See section ‘Good practice’ in ‘?data’.
prepare_Rd: AAdescriptor.Rd:25-27: Dropping empty section \details
prepare_Rd: AAdescriptor.Rd:39-41: Dropping empty section \note
prepare_Rd: AAdescriptor.Rd:45-47: Dropping empty section \seealso
prepare_Rd: AAindex.Rd:11-12: Dropping empty section \format
prepare_Rd: AAindex.Rd:1080-1081: Dropping empty section \source
prepare_Rd: AAindex.Rd:1085-1086: Dropping empty section \examples
prepare_Rd: Interpol.Rd:35-37: Dropping empty section \details
prepare_Rd: Interpol.Rd:47-49: Dropping empty section \note
prepare_Rd: Interpol.Rd:53-55: Dropping empty section \seealso
prepare_Rd: V3.Rd:11-12: Dropping empty section \format
prepare_Rd: V3.Rd:13-14: Dropping empty section \details
prepare_Rd: V3.Rd:15-16: Dropping empty section \source
prepare_Rd: V3.Rd:20-21: Dropping empty section \examples
Rd file 'Interpol.Rd':
  \examples lines wider than 100 characters:
             plot(unlist(b), type="l", col="darkgreen", ylim=c(-3,3), ylab="descriptor value", xlab="sequence position", lwd=2)
             lines(seq(1,length(unlist(b)),(length(unlist(b))/length(as.vector(c)))),as.vector(c), col="red", lwd=2)

These lines will be truncated in the PDF manual.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpXNOiyp/R.INSTALL62a11a51b993/interval/man/methodRuleIC1.Rd:21: file link ‘permTS’ in package ‘perm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/interval.Rcheck/00install.out’ for details.
icScoreTest: no visible global function definition for ‘pnorm’
icScoreTest: no visible global function definition for ‘pchisq’
icfit.formula: no visible global function definition for ‘terms’
icfit.formula: no visible global function definition for
  ‘model.extract’
icfitBootCI: no visible global function definition for ‘binom.test’
ictest.formula: no visible global function definition for
  ‘model.extract’
plot.icfit: no visible global function definition for ‘gray’
plot.icfit: no visible global function definition for ‘axis’
plot.icfit : polygon.icfit: no visible global function definition for
  ‘polygon’
scoresFromFit: no visible global function definition for ‘dnorm’
scoresFromFit: no visible global function definition for ‘qnorm’
wsrHLYpclt: no visible global function definition for ‘model.matrix’
wsrHLYpclt: no visible global function definition for ‘pchisq’
wsrHLYpclt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  axis binom.test dnorm gray model.extract model.matrix pchisq pnorm
  polygon qnorm terms
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "axis", "polygon")
  importFrom("stats", "binom.test", "dnorm", "model.extract",
             "model.matrix", "pchisq", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
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.
'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.
Running examples in ‘inTrees-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getFreqPattern
> ### Title: calculate frequent variable interactions
> ### Aliases: getFreqPattern
> ### Keywords: variable interaction
> 
> ### ** Examples
> 
> library(RRF)
RRF 1.9.1
Type rrfNews() to see new features/changes/bug fixes.
> library(arules)
Loading required package: Matrix

Attaching package: ‘arules’

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

    abbreviate, write

> data(iris)
> X <- iris[,1:(ncol(iris)-1)]
> target <- iris[,"Species"] 
> rf <- RRF(X,as.factor(target),ntree=100) # build an ordinary RF 
> treeList <- RF2List(rf)
> ruleExec <- extractRules(treeList,X) # transform to R-executable rules
705 rules (length<=6) were extracted from the first 100 trees.
> ruleMetric <- getRuleMetric(ruleExec,X,target) 
> freqPattern <- getFreqPattern(ruleMetric)
Warning in Ops.factor(c(i), 1L) : ‘-’ not meaningful for factors
Error in validObject(.Object) : 
  invalid class “ngCMatrix” object: invalid object for slot "i" in class "ngCMatrix": got class "logical", should be or extend class "integer"
Calls: getFreqPattern ... initialize -> callNextMethod -> .nextMethod -> validObject
Execution halted
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp9OOoW1/R.INSTALL67358071c51/intRvals/man/intervalpdf.Rd:65: file link ‘dgamma’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9OOoW1/R.INSTALL67358071c51/intRvals/man/intervalpdf.Rd:71: file link ‘dnorm’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/intRvals.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpRcIWdV/R.INSTALL7fcb3ffa474f/intsurv/man/cox_cure.Rd:57: file link ‘model.matrix.default’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpRcIWdV/R.INSTALL7fcb3ffa474f/intsurv/man/cox_cure_net.Rd:66: file link ‘model.matrix.default’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpRcIWdV/R.INSTALL7fcb3ffa474f/intsurv/man/iCoxph.Rd:25: file link ‘na.omit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpRcIWdV/R.INSTALL7fcb3ffa474f/intsurv/man/iCoxph.Rd:26: file link ‘na.exclude’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpRcIWdV/R.INSTALL7fcb3ffa474f/intsurv/man/iCoxph.Rd:27: file link ‘na.pass’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpRcIWdV/R.INSTALL7fcb3ffa474f/intsurv/man/iCoxph.Rd:33: file link ‘model.matrix.default’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/intsurv.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘intubate.Rmd’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpIDaaLl/R.INSTALL1745bbc3343/invctr/man/is.wholenumber.Rd:21: file link ‘is.integer’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/invctr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmphGqso0/R.INSTALL76e919c13004/investr/man/plotFit.Rd:133: file link ‘plotfit’ in package ‘nlstools’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/investr.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpAqzjba/R.INSTALL51b91b8067c9/invLT/man/ivLT.plot.Rd:19: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/invLT.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘iNZightPlots’
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.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘beta’
Warning: no function found corresponding to methods exports from ‘ipdmeta’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
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.
ipd.meta.power.base.function : power: no visible global function
  definition for ‘qnorm’
ipd.meta.power.base.function : power: no visible global function
  definition for ‘pnorm’
ipd.meta.power.base.function: no visible global function definition for
  ‘qnorm’
ipdlme.hetero: no visible global function definition for ‘new’
ipdlme.homo: no visible global function definition for ‘new’
plot_ipdlme: no visible global function definition for ‘par’
plot_ipdlme: no visible global function definition for ‘abline’
plot_ipdlme: no visible global function definition for ‘axis’
plot_ipdlme: no visible global function definition for ‘segments’
confint,ipdlme: no visible global function definition for ‘qt’
plot,ipdlme: no visible global function definition for ‘par’
plot,ipdlme: no visible global function definition for ‘abline’
plot,ipdlme: no visible global function definition for ‘axis’
plot,ipdlme: no visible global function definition for ‘segments’
summary,ipdlme: no visible global function definition for ‘pt’
Undefined global functions or variables:
  abline axis new par pnorm pt qnorm qt segments
Consider adding
  importFrom("graphics", "abline", "axis", "par", "segments")
  importFrom("methods", "new")
  importFrom("stats", "pnorm", "pt", "qnorm", "qt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-standard file/directory found at top level:
  ‘version’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpGrU8BO/R.INSTALL68204cf6fb74/ips/man/descendants.Rd:12: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGrU8BO/R.INSTALL68204cf6fb74/ips/man/fixNodes.Rd:24: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGrU8BO/R.INSTALL68204cf6fb74/ips/man/forceEqualTipHeights.Rd:10: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGrU8BO/R.INSTALL68204cf6fb74/ips/man/forceEqualTipHeights.Rd:16: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGrU8BO/R.INSTALL68204cf6fb74/ips/man/oi.Rd:15: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ips.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpBspY8o/R.INSTALL5d4ff865507/IRdisplay/man/display_-less-than-image-greater-than.Rd:22: file link ‘connection’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBspY8o/R.INSTALL5d4ff865507/IRdisplay/man/display_-less-than-text-greater-than.Rd:25: file link ‘connection’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IRdisplay.Rcheck/00install.out’ for details.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpTNkpzJ/R.INSTALL56812495f4ab/irr/man/bhapkar.Rd:37: file link ‘stuart.maxwell.mh’ in package ‘irr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/irr.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘irtoys-vignette.Rmd’
Malformed Description field: should contain one or more complete sentences.
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
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.
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.
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
'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.
Found the following files/directories:
  ‘RMTplot.pdf’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpNNkVGL/R.INSTALL40f77e1a96e/ItemResponseTrees/man/augment.irtree_fit.Rd:20: file link ‘IRT.factor.scores.tam.mml’ in package ‘TAM’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNNkVGL/R.INSTALL40f77e1a96e/ItemResponseTrees/man/augment.irtree_fit.Rd:24: file link ‘IRT.factor.scores.tam.mml’ in package ‘TAM’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNNkVGL/R.INSTALL40f77e1a96e/ItemResponseTrees/man/clps.Rd:11: file link ‘NA_character_’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNNkVGL/R.INSTALL40f77e1a96e/ItemResponseTrees/man/clps.Rd:20: file link ‘NA_character_’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ItemResponseTrees.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpaSRHda/R.INSTALL6ea7380102d1/itertools2/man/imap.Rd:24: file link ‘Map’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpaSRHda/R.INSTALL6ea7380102d1/itertools2/man/istarmap.Rd:27: file link ‘Map’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/itertools2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpwvDtb9/R.INSTALL1f4e228a34a0/itertools/man/iRNGStream.Rd:19: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpwvDtb9/R.INSTALL1f4e228a34a0/itertools/man/iRNGStream.Rd:19: file link ‘nextRNGStream’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpwvDtb9/R.INSTALL1f4e228a34a0/itertools/man/iRNGStream.Rd:20: file link ‘nextRNGSubStream’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/itertools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp1cSfbc/R.INSTALL63c1169012ce/itsadug/man/fvisgam.Rd:235: file link ‘mgcv’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp1cSfbc/R.INSTALL63c1169012ce/itsadug/man/gamtabs.Rd:19: file link ‘mgcv’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp1cSfbc/R.INSTALL63c1169012ce/itsadug/man/info.Rd:24: file link ‘R.version’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp1cSfbc/R.INSTALL63c1169012ce/itsadug/man/itsadug.Rd:10: file link ‘mgcv’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp1cSfbc/R.INSTALL63c1169012ce/itsadug/man/pvisgam.Rd:214: file link ‘mgcv’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp1cSfbc/R.INSTALL63c1169012ce/itsadug/man/resid_gam.Rd:98: file link ‘resid’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/itsadug.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp8gdkOu/R.INSTALL709517f22b2d/iva/man/mra.Rd:69: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8gdkOu/R.INSTALL709517f22b2d/iva/man/mra.Rd:71: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8gdkOu/R.INSTALL709517f22b2d/iva/man/mra.Rd:71: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/iva.Rcheck/00install.out’ for details.
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: ‘gurobi’
Malformed Title field: should not end in a period.
ARsensitivity.ci: no visible global function definition for ‘residuals’
ARsensitivity.ci: no visible global function definition for ‘lm’
ARsensitivity.ci: no visible global function definition for ‘qf’
ARsensitivity.ci: no visible global function definition for ‘fitted’
ARsensitivity.power: no visible global function definition for ‘qf’
ARsensitivity.power: no visible global function definition for ‘pf’
ARsensitivity.size: no visible global function definition for ‘qf’
ARsensitivity.size: no visible global function definition for ‘pf’
anderson.rubin.ci: no visible global function definition for ‘qf’
anderson.rubin.ci: no visible global function definition for ‘fitted’
anderson.rubin.ci: no visible global function definition for ‘lm’
power.iv: no visible global function definition for ‘qf’
power.iv: no visible global function definition for ‘pf’
Undefined global functions or variables:
  fitted lm pf qf residuals
Consider adding
  importFrom("stats", "fitted", "lm", "pf", "qf", "residuals")
to your NAMESPACE file.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmphyYEFl/R.INSTALL6ca677d957aa/ivx/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ivx.Rcheck/00install.out’ for details.
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.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpWG2nSR/R.INSTALL667a4f6b84a3/jack/man/ESF.Rd:10: file link ‘bigq’ in package ‘gmp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpWG2nSR/R.INSTALL667a4f6b84a3/jack/man/Jack.Rd:10: file link ‘bigq’ in package ‘gmp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpWG2nSR/R.INSTALL667a4f6b84a3/jack/man/MSF.Rd:10: file link ‘bigq’ in package ‘gmp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpWG2nSR/R.INSTALL667a4f6b84a3/jack/man/Schur.Rd:10: file link ‘bigq’ in package ‘gmp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpWG2nSR/R.INSTALL667a4f6b84a3/jack/man/Zonal.Rd:10: file link ‘bigq’ in package ‘gmp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpWG2nSR/R.INSTALL667a4f6b84a3/jack/man/ZonalQ.Rd:10: file link ‘bigq’ in package ‘gmp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jack.Rcheck/00install.out’ for details.
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.
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
Non-standard files/directories found at top level:
  ‘getsp.class’ ‘getsp.java’ ‘version’
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'.
getSysinfo: no visible global function definition for ‘sessionInfo’
getVecInfo: no visible global function definition for ‘sd’
isSeriesConstant: no visible global function definition for ‘median’
labelMargins: no visible global function definition for ‘mtext’
plotBG: no visible global function definition for ‘polygon’
plotBG: no visible global function definition for ‘par’
plotColorScale: no visible global function definition for ‘par’
plotColorScale: no visible global function definition for ‘text’
plotImageRotated: no visible global function definition for
  ‘heat.colors’
plotImageRotated: no visible global function definition for ‘par’
plotImageRotated: no visible global function definition for ‘image’
plotImageRotated: no visible global function definition for ‘axis’
plotNLines: no visible global function definition for ‘par’
plotNLines: no visible global function definition for ‘mtext’
plotNLines: no visible global function definition for ‘axis’
plotNLines: no visible global function definition for ‘points’
plotNLines: no visible global function definition for ‘sd’
userCoords: no visible global function definition for ‘par’
Undefined global functions or variables:
  axis heat.colors image median mtext par points polygon sd sessionInfo
  text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "axis", "image", "mtext", "par", "points",
             "polygon", "text")
  importFrom("stats", "median", "sd")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpviwGSy/R.INSTALL70964822265b/jcolors/man/jcolors_contin.Rd:20: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpviwGSy/R.INSTALL70964822265b/jcolors/man/jcolors_contin.Rd:21: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jcolors.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpGrVOSP/R.INSTALL629923b801bf/jetset/man/jmap.Rd:31: file link ‘org.Hs.egSYMBOL2EG’ in package ‘org.Hs.eg.db’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jetset.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmptuLlry/R.INSTALL7848314ac7e2/jipApprox/man/is.wholenumber.Rd:19: file link ‘is.integer’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jipApprox.Rcheck/00install.out’ for details.
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.
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.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmphdNO1q/R.INSTALL4a931414df0/joineRML/man/bootSE.Rd:129: file link ‘tryCatch’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphdNO1q/R.INSTALL4a931414df0/joineRML/man/fixef.mjoint.Rd:74: file link ‘fixef’ in package ‘nlme’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphdNO1q/R.INSTALL4a931414df0/joineRML/man/pbc2.Rd:62: file link ‘pbc2’ in package ‘JM’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphdNO1q/R.INSTALL4a931414df0/joineRML/man/ranef.mjoint.Rd:56: file link ‘ranef’ in package ‘nlme’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphdNO1q/R.INSTALL4a931414df0/joineRML/man/vcov.mjoint.Rd:86: file link ‘cov2cor’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/joineRML.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpTC8QGr/R.INSTALL6797f6f3546/joineR/man/lines.jointdata.Rd:16: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpTC8QGr/R.INSTALL6797f6f3546/joineR/man/plot.jointdata.Rd:16: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpTC8QGr/R.INSTALL6797f6f3546/joineR/man/plot.jointdata.Rd:29: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpTC8QGr/R.INSTALL6797f6f3546/joineR/man/points.jointdata.Rd:16: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpTC8QGr/R.INSTALL6797f6f3546/joineR/man/points.jointdata.Rd:20: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/joineR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpLUFHa5/R.INSTALL68242094b068/JointAI/man/MC_error.Rd:63: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLUFHa5/R.INSTALL68242094b068/JointAI/man/densplot.Rd:34: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLUFHa5/R.INSTALL68242094b068/JointAI/man/traceplot.Rd:58: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLUFHa5/R.INSTALL68242094b068/JointAI/man/traceplot.Rd:59: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/JointAI.Rcheck/00install.out’ for details.
PKG_CXXFLAGS set in ‘src/Makevars’ without any corresponding files
   PKG_CXXFLAGS set in ‘src/Makevars.win’ without any corresponding files
'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.
Packages in Depends field not imported from:
  ‘Rsolnp’ ‘dglm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpUULmia/R.INSTALL7e274ead855c/josaplay/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/josaplay.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp8naB4a/R.INSTALL2743156487c4/jose/man/jwt_encode.Rd:36: file link ‘read_pubkey’ in package ‘openssl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jose.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpCwHYuP/R.INSTALL33894bedbf78/jpmesh/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jpmesh.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp6an4xu/R.INSTALLb613d714c87/jpndistrict/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jpndistrict.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [175s/249s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(jpndistrict)
  This package provide map data is based on the Digital Map 25000 (Map
  Image) published by Geospatial Information Authority of Japan (Approval
  No.603FY2017 information usage <http://www.gsi.go.jp>)
  > 
  > test_check("jpndistrict")
  trying URL 'http://nlftp.mlit.go.jp/ksj/gml/data/P34/P34-14/P34-14_47_GML.zip'
  ── 1. Error: Collect administration offices data (@test-spdf_jpn.R#102)  ───────
  cannot open URL 'http://nlftp.mlit.go.jp/ksj/gml/data/P34/P34-14/P34-14_47_GML.zip'
  Backtrace:
    1. jpndistrict::jpn_admins(jis_code = 47)
    2. purrr::map_chr(., ~substr(.x, 1, 2))
    2. base::unique(.)
    9. purrr::map(., ~read_ksj_p34(pref_code = as.numeric(.x)))
   10. jpndistrict:::.f(.x[[i]], ...)
   11. jpndistrict:::read_ksj_p34(pref_code = as.numeric(.x))
   12. utils::download.file(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 94 | SKIPPED: 1 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: Collect administration offices data (@test-spdf_jpn.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpg4N3Z7/R.INSTALL676b139bfc7b/jsmodule/man/ROC_table.Rd:38: file link ‘data.table-package’ in package ‘data.table’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpg4N3Z7/R.INSTALL676b139bfc7b/jsmodule/man/jsPropensityExtAddin.Rd:30: file link ‘data.table-package’ in package ‘data.table’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpg4N3Z7/R.INSTALL676b139bfc7b/jsmodule/man/rocModule.Rd:137: file link ‘ggroc.roc’ in package ‘pROC’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpg4N3Z7/R.INSTALL676b139bfc7b/jsmodule/man/rocModule.Rd:146: file link ‘ggroc.roc’ in package ‘pROC’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpg4N3Z7/R.INSTALL676b139bfc7b/jsmodule/man/survIDINRI_helper.Rd:50: file link ‘data.table-package’ in package ‘data.table’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpg4N3Z7/R.INSTALL676b139bfc7b/jsmodule/man/timeROC_table.Rd:35: file link ‘data.table-package’ in package ‘data.table’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jsmodule.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpDGssyQ/R.INSTALL56766fffb310/jsonld/man/jsonld.Rd:44: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jsonld.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpeWuShr/R.INSTALLc9e5d9d856d/jstable/man/geeglm.display.Rd:32: file link ‘data.table-package’ in package ‘data.table’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jstable.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp4AV63t/R.INSTALL42587ec957c4/jstor/man/jst_get_chapters.Rd:30: file link ‘unnest’ in package ‘tidyr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4AV63t/R.INSTALL42587ec957c4/jstor/man/jst_get_ngram.Rd:21: file link ‘read_tsv’ in package ‘readr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4AV63t/R.INSTALL42587ec957c4/jstor/man/jst_import.Rd:76: file link ‘write_csv’ in package ‘readr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4AV63t/R.INSTALL42587ec957c4/jstor/man/jst_import.Rd:92: file link ‘write_csv’ in package ‘readr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4AV63t/R.INSTALL42587ec957c4/jstor/man/jst_re_import.Rd:27: file link ‘read_csv’ in package ‘readr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jstor.Rcheck/00install.out’ for details.
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘jumptest.Rmd’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpf01jk4/R.INSTALL5936162dd478/kableExtra/man/reexports.Rd:17: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kableExtra.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpzdeW0R/R.INSTALL2f266c9b9b0c/kangar00/man/pathway-class.Rd:114: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzdeW0R/R.INSTALL2f266c9b9b0c/kangar00/man/pathway-class.Rd:122: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzdeW0R/R.INSTALL2f266c9b9b0c/kangar00/man/pathway-class.Rd:83: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzdeW0R/R.INSTALL2f266c9b9b0c/kangar00/man/read_geno-character-method.Rd:21: file link ‘read.big.matrix’ in package ‘bigmemory’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzdeW0R/R.INSTALL2f266c9b9b0c/kangar00/man/read_geno-character-method.Rd:29: file link ‘read.big.matrix’ in package ‘bigmemory’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kangar00.Rcheck/00install.out’ for details.
expression_up : <anonymous>: no visible global function definition for
  ‘quantile’
expression_up : <anonymous>: no visible global function definition for
  ‘IQR’
expression_up : <anonymous>: no visible global function definition for
  ‘median’
expression_up : <anonymous>: no visible global function definition for
  ‘sd’
plot_up: no visible global function definition for ‘text’
Undefined global functions or variables:
  IQR median quantile sd text
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "IQR", "median", "quantile", "sd")
to your NAMESPACE file.
Found the following files/directories:
  ‘my.Mobius.set.func.csv’ ‘my.card.set.func.csv’ ‘my.set.func.csv’
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').
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpaQgpcb/R.INSTALL64942fde49ed/kaps/man/km.curve.Rd:16: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kaps.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘song.wav’ ‘song4karaoke.wav’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpUtj72b/R.INSTALL50b1257d68f9/kde1d/man/dkde1d.Rd:33: file link ‘sobol’ in package ‘randtoolbox’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kde1d.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpPj1HnX/R.INSTALL708e47211056/kdecopula/man/dkdecop.Rd:29: file link ‘ghalton’ in package ‘qrng’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPj1HnX/R.INSTALL708e47211056/kdecopula/man/dkdecop.Rd:82: file link ‘ghalton’ in package ‘qrng’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPj1HnX/R.INSTALL708e47211056/kdecopula/man/kdecop.Rd:163: file link ‘pkdecop’ in package ‘kdecopula’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPj1HnX/R.INSTALL708e47211056/kdecopula/man/kdecop.Rd:164: file link ‘rkdecop’ in package ‘kdecopula’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPj1HnX/R.INSTALL708e47211056/kdecopula/man/kdecopula.Rd:20: file link ‘pkdecop’ in package ‘kdecopula’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPj1HnX/R.INSTALL708e47211056/kdecopula/man/kdecopula.Rd:21: file link ‘rkdecop’ in package ‘kdecopula’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPj1HnX/R.INSTALL708e47211056/kdecopula/man/logLik.kdecopula.Rd:38: file link ‘BIC’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPj1HnX/R.INSTALL708e47211056/kdecopula/man/plot.kdecopula.Rd:60: file link ‘wireframe’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kdecopula.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp52QfMT/R.INSTALL64d31f8a8da2/kdevine/man/dkde1d.Rd:29: file link ‘ghalton’ in package ‘qrng’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp52QfMT/R.INSTALL64d31f8a8da2/kdevine/man/dkdevinecop.Rd:28: file link ‘ghalton’ in package ‘qrng’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp52QfMT/R.INSTALL64d31f8a8da2/kdevine/man/dkdevinecop.Rd:59: file link ‘rkdecop’ in package ‘kdecopula’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp52QfMT/R.INSTALL64d31f8a8da2/kdevine/man/dkdevinecop.Rd:60: file link ‘ghalton’ in package ‘qrng’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp52QfMT/R.INSTALL64d31f8a8da2/kdevine/man/kdevine-package.Rd:17: file link ‘kdecopula-package’ in package ‘kdecopula’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kdevine.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘KDVizGroup1.html’ ‘KDVizGroup1_files’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpReaWwh/R.INSTALL45555b0bb3ac/kedd/man/h.bcv.Rd:105: file link ‘bw.bcv’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpReaWwh/R.INSTALL45555b0bb3ac/kedd/man/h.ucv.Rd:122: file link ‘bw.ucv’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpReaWwh/R.INSTALL45555b0bb3ac/kedd/man/kernel.fun.Rd:71: file link ‘D’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kedd.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpkVv4ho/R.INSTALLcfa1a1e73c0/kelvin/man/Beir.Rd:38: file link ‘BesselJ’ in package ‘Bessel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpkVv4ho/R.INSTALLcfa1a1e73c0/kelvin/man/Beir.Rd:21: file link ‘BesselK’ in package ‘Bessel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpkVv4ho/R.INSTALLcfa1a1e73c0/kelvin/man/Beir.Rd:25: file link ‘BesselJ’ in package ‘Bessel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpkVv4ho/R.INSTALLcfa1a1e73c0/kelvin/man/Beir.Rd:65: file link ‘BesselJ’ in package ‘Bessel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpkVv4ho/R.INSTALLcfa1a1e73c0/kelvin/man/Keir.Rd:43: file link ‘BesselK’ in package ‘Bessel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpkVv4ho/R.INSTALLcfa1a1e73c0/kelvin/man/Keir.Rd:22: file link ‘BesselK’ in package ‘Bessel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpkVv4ho/R.INSTALLcfa1a1e73c0/kelvin/man/Keir.Rd:26: file link ‘BesselK’ in package ‘Bessel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpkVv4ho/R.INSTALLcfa1a1e73c0/kelvin/man/Keir.Rd:70: file link ‘BesselK’ in package ‘Bessel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kelvin.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpoFTJ8x/R.INSTALL70d8293a3176/keras/man/multi-assign.Rd:10: file link ‘%<-%’ in package ‘zeallot’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpoFTJ8x/R.INSTALL70d8293a3176/keras/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpoFTJ8x/R.INSTALL70d8293a3176/keras/man/reexports.Rd:33: file link ‘use_virtualenv’ in package ‘reticulate’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpoFTJ8x/R.INSTALL70d8293a3176/keras/man/reexports.Rd:33: file link ‘use_condaenv’ in package ‘reticulate’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpoFTJ8x/R.INSTALL70d8293a3176/keras/man/reexports.Rd:37: file link ‘flag_numeric’ in package ‘tfruns’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpoFTJ8x/R.INSTALL70d8293a3176/keras/man/reexports.Rd:37: file link ‘flag_integer’ in package ‘tfruns’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpoFTJ8x/R.INSTALL70d8293a3176/keras/man/reexports.Rd:37: file link ‘flag_string’ in package ‘tfruns’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpoFTJ8x/R.INSTALL70d8293a3176/keras/man/reexports.Rd:37: file link ‘flag_boolean’ in package ‘tfruns’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/keras.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpYXSOcd/R.INSTALL4409a71f1c7/kergp/man/covQualNested.Rd:96: file link ‘contr.helmert’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpYXSOcd/R.INSTALL4409a71f1c7/kergp/man/covQualNested.Rd:97: file link ‘contr.treatment’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kergp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpy95h5n/R.INSTALL11e2166d851a/kernelboot/man/kernelboot-class.Rd:40: file link ‘.Random.seed’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpy95h5n/R.INSTALL11e2166d851a/kernelboot/man/kernelboot.Rd:34: file link ‘bw.nrd0’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpy95h5n/R.INSTALL11e2166d851a/kernelboot/man/kernelboot.Rd:157: file link ‘runif’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpy95h5n/R.INSTALL11e2166d851a/kernelboot/man/kernelboot.Rd:157: file link ‘rnorm’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kernelboot.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpAltMdI/R.INSTALL44a12b76dc5/keyholder/man/keyed-df-one-tbl.Rd:60: file link ‘transmute’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpAltMdI/R.INSTALL44a12b76dc5/keyholder/man/keys-manipulate.Rd:51: file link ‘rename’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpAltMdI/R.INSTALL44a12b76dc5/keyholder/man/reexports.Rd:15: file link ‘%>%’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpAltMdI/R.INSTALL44a12b76dc5/keyholder/man/rename-keys-scoped.Rd:29: file link ‘rename_all’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpAltMdI/R.INSTALL44a12b76dc5/keyholder/man/rename-keys-scoped.Rd:29: file link ‘rename’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/keyholder.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpl8DnTt/R.INSTALL6632de99cc3/keyplayer/man/fragment.Rd:85: file link ‘shortest.paths’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpl8DnTt/R.INSTALL6632de99cc3/keyplayer/man/mreach.closeness.Rd:97: file link ‘shortest.paths’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpl8DnTt/R.INSTALL6632de99cc3/keyplayer/man/mreach.degree.Rd:83: file link ‘shortest.paths’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/keyplayer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpPEt6RC/R.INSTALL10ea4768db8/KFKSDS/man/KF.Rd:31: file link ‘KS.deriv’ in package ‘KFKSDS’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPEt6RC/R.INSTALL10ea4768db8/KFKSDS/man/KF.Rd:93: file link ‘KS.deriv’ in package ‘KFKSDS’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPEt6RC/R.INSTALL10ea4768db8/KFKSDS/man/KS.Rd:32: file link ‘KF.deriv’ in package ‘KFKSDS’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPEt6RC/R.INSTALL10ea4768db8/KFKSDS/man/KS.Rd:32: file link ‘KF.deriv.C’ in package ‘KFKSDS’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPEt6RC/R.INSTALL10ea4768db8/KFKSDS/man/KS.Rd:70: file link ‘KSDS’ in package ‘KFKSDS’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPEt6RC/R.INSTALL10ea4768db8/KFKSDS/man/predict-stsmSS.Rd:34: file link ‘predict.StructTS’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/KFKSDS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmptA4yb2/R.INSTALL12b1c1fcd1b/khroma/man/colour.Rd:23: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/khroma.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp6N9kRU/R.INSTALL17b2abe0e5c/kimisc/man/seconds.to.hms-deprecated.Rd:29: file link ‘strftime’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kimisc.Rcheck/00install.out’ for details.
kissmigDummyS: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpqeTZmw/R.INSTALL1494105d7e70/kitagawa/man/logsmoo.Rd:17: file link ‘loess.smooth’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpqeTZmw/R.INSTALL1494105d7e70/kitagawa/man/logsmoo.Rd:20: file link ‘loess.smooth’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpqeTZmw/R.INSTALL1494105d7e70/kitagawa/man/logsmoo.Rd:41: file link ‘loess.smooth’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kitagawa.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp9VKO7K/R.INSTALLf3746982a97/kknn/man/kknn.Rd:70: file link ‘simulation’ in package ‘kknn’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9VKO7K/R.INSTALLf3746982a97/kknn/man/train.kknn.Rd:62: file link ‘simulation’ in package ‘kknn’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kknn.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘rkward’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp53cwWk/R.INSTALL7392521dfc39/klausuR/man/klausur.Rd:170: file link ‘psychometric’ in package ‘psychometric’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp53cwWk/R.INSTALL7392521dfc39/klausuR/man/klausur.Rd:74: file link ‘plot’ in package ‘klausuR’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp53cwWk/R.INSTALL7392521dfc39/klausuR/man/klausur.Rd:261: file link ‘plot’ in package ‘klausuR’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp53cwWk/R.INSTALL7392521dfc39/klausuR/man/klausur.Rd:261: file link ‘psychometric’ in package ‘psychometric’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp53cwWk/R.INSTALL7392521dfc39/klausuR/man/klausur.report.Rd:41: file link ‘plot’ in package ‘klausuR’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/klausuR.Rcheck/00install.out’ for details.
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.
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.

Found the following calls to data() loading into the global environment:
File ‘km.ci/R/epband.fun.R’:
  data(critical.value.nair.90, critical.value.nair.95, critical.value.nair.99)
File ‘km.ci/R/hall.wellner.fun.R’:
  data(critical.value.hall.90, critical.value.hall.95, critical.value.hall.99)
See section ‘Good practice’ in ‘?data’.
Malformed Description field: should contain one or more complete sentences.
noe.compute.pv: no visible global function definition for ‘punif’
Undefined global functions or variables:
  punif
Consider adding
  importFrom("stats", "punif")
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpy9tGdX/R.INSTALL883661dc792/kmer/man/cluster.Rd:57: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpy9tGdX/R.INSTALL883661dc792/kmer/man/kcount.Rd:58: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpy9tGdX/R.INSTALL883661dc792/kmer/man/kdistance.Rd:57: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpy9tGdX/R.INSTALL883661dc792/kmer/man/mbed.Rd:84: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpy9tGdX/R.INSTALL883661dc792/kmer/man/otu.Rd:77: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kmer.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘LogLikelihood.txt’ ‘pvalues.out’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpYgxoP8/R.INSTALL697c56cdd36c/kml3d/man/kml3d-package.Rd:107: file link ‘makeTriangles’ in package ‘misc3d’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpYgxoP8/R.INSTALL697c56cdd36c/kml3d/man/plot3d.Rd:51: file link ‘rgl’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpYgxoP8/R.INSTALL697c56cdd36c/kml3d/man/plot3dPdf.Rd:56: file link ‘makeTriangles’ in package ‘misc3d’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpYgxoP8/R.INSTALL697c56cdd36c/kml3d/man/plotMean3d.Rd:48: file link ‘rgl’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpYgxoP8/R.INSTALL697c56cdd36c/kml3d/man/plotTraj3d.Rd:48: file link ‘rgl’ in package ‘rgl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kml3d.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘cld1.Rdata’ ‘main.tex’ ‘myCld.Rdata’ ‘myCld3d.Rdata’ ‘scene.asy’
Warning: no function found corresponding to methods exports from ‘kmlcov’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
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.
Found the following files/directories:
  ‘cld1.Rdata’ ‘ld.Rdata’ ‘myCld.Rdata’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpZox5aq/R.INSTALL64bf2f64a4/knitcitations/man/citep.Rd:17: file link ‘Citep’ in package ‘RefManageR’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZox5aq/R.INSTALL64bf2f64a4/knitcitations/man/citep.Rd:52: file link ‘Citep’ in package ‘RefManageR’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZox5aq/R.INSTALL64bf2f64a4/knitcitations/man/citet.Rd:17: file link ‘Citet’ in package ‘RefManageR’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZox5aq/R.INSTALL64bf2f64a4/knitcitations/man/citet.Rd:52: file link ‘Citep’ in package ‘RefManageR’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/knitcitations.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Killed after ’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpmtLcL9/R.INSTALL494d7b68c97f/knitr/man/chunk_hook.Rd:59: file link ‘recordPlot’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpmtLcL9/R.INSTALL494d7b68c97f/knitr/man/hook_plot.Rd:48: file link ‘recordPlot’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpmtLcL9/R.INSTALL494d7b68c97f/knitr/man/knit.Rd:28: file link ‘Stangle’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpmtLcL9/R.INSTALL494d7b68c97f/knitr/man/knit2pandoc.Rd:29: file link ‘Stangle’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpmtLcL9/R.INSTALL494d7b68c97f/knitr/man/plot_crop.Rd:19: file link ‘image_trim’ in package ‘magick’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpmtLcL9/R.INSTALL494d7b68c97f/knitr/man/write_bib.Rd:37: file link ‘toBibtex’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/knitr.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dataFiller : central.value: no visible global function definition for
  ‘median’
dataFiller: no visible global function definition for ‘daisy’
dataFiller: no visible global function definition for ‘complete.cases’
knnMCN: no visible global function definition for ‘cov’
knnVCN: no visible global function definition for ‘dist’
Undefined global functions or variables:
  complete.cases cov daisy dist median
Consider adding
  importFrom("stats", "complete.cases", "cov", "dist", "median")
to your NAMESPACE file.
Rd file 'knnMCN.Rd':
  \examples lines wider than 100 characters:
                 ") ", "you have selected is bigger than the capacity of one class in your training data set", 
             stop("\nWarnings:\nsample variance-covariance matrix is singular,\nand larger class sample capacity is required ,\nor you can t ... [TRUNCATED]
                     stop("\nWarnings:\nsample variance-covariance matrix is singular,\nand larger class sample capacity is required ,\nor y ... [TRUNCATED]

Rd file 'knnVCN.Rd':
  \examples lines wider than 100 characters:
                 ") ", "you have selected is bigger than the capacity of one class in your training data set", 

These lines will be truncated in the PDF manual.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpzduF46/R.INSTALL747027c5f306/knockoff/man/stat.stability_selection.Rd:39: file link ‘glmnet.lasso_maxCoef’ in package ‘stabs’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/knockoff.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘Completeness.RData’ ‘Estimators.RData’ ‘Inf.txt’ ‘List of
  species.RData’ ‘Observed richness.RData’ ‘Records.RData’
  ‘Slope.RData’ ‘Standard error of the estimators.RData’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp22qE54/R.INSTALL45e46e6a5d40/kntnr/man/kntn_unnest.Rd:14: file link ‘unnest’ in package ‘tidyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kntnr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpN4OTRg/R.INSTALL469223b5ab3a/kokudosuuchi/man/getKSJData.Rd:25: file link ‘read_sf’ in package ‘sf’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kokudosuuchi.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
assign_clustpp: no visible global function definition for ‘kmeans’
kpod: no visible global function definition for ‘kmeans’
makeData: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  kmeans rnorm
Consider adding
  importFrom("stats", "kmeans", "rnorm")
to your NAMESPACE file.
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.
Found the following files/directories:
  ‘KSEA Bar Plot.tiff’ ‘KSEA Kinase Scores.csv’
  ‘KSEA.Merged.Heatmap.png’ ‘Kinase-Substrate Links.csv’
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.
Found the following files/directories:
  ‘DF7.bas’ ‘DF7.dat’ ‘DF7.rel’ ‘DF7.spc’ ‘DF7.struct’
Found the following hidden files and directories:
  .Rbuildindex.10034
  .Rbuildindex.31551
  .Rbuildindex.31678
  .Rbuildindex.9995
  inst/doc/.fr-hy2VZf
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘Biobase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'ROC.graphic.ktsp.Rd':
  \usage lines wider than 90 characters:
     ROC.graphic.ktsp(roc, m = 1, boxplot = TRUE, AUC = TRUE, auc.x = 0.55, auc.y = 0.25, box.col = "yellow", line.col = "red", multiple.col ... [TRUNCATED]

Rd file 'ROC.offset.Rd':
  \usage lines wider than 90 characters:
     ROC.offset(dat, grp, n = 200, healthy = NULL, seed = NULL, para1 = 200, para2 = 1, mult.cutoff = FALSE, length = 40, display = FALSE, m ... [TRUNCATED]

Rd file 'ROC.voting.Rd':
  \usage lines wider than 90 characters:
     ROC.voting(dat, grp, n = 200, healthy = NULL, seed = NULL, para1 = 200, para2 = 1, length = 40, display = FALSE, med = FALSE)

Rd file 'bootstrap.ktsp.Rd':
  \usage lines wider than 90 characters:
     bootstrap.ktsp(dat, grp, k = NULL, seed = NULL, n = 500, length = 40, display = FALSE, med = FALSE)

Rd file 'cv.Rd':
  \usage lines wider than 90 characters:
     cv(dat, grp, cross = 5, display = FALSE, length = 40, seed = NULL, med = FALSE, healthy = NULL)

Rd file 'cv2.Rd':
  \usage lines wider than 90 characters:
     cv2(indice, dat, grp, cross = 5, display = FALSE, length = 40, seed = NULL, med = FALSE, healthy = NULL)

Rd file 'ktspcalc.Rd':
  \usage lines wider than 90 characters:
     ktspcalc(dat, grp, k = NULL, cross = 5, performance = FALSE, healthy = NULL, seed = NULL, display = TRUE, length = 40, med = FALSE)

Rd file 'ktspcalc2.Rd':
  \usage lines wider than 90 characters:
     ktspcalc2(indice, dat, grp, length = 40, cross =5, display = display, med = FALSE, performance = FALSE, seed = NULL, healthy = NULL)

These lines will be truncated in the PDF manual.
S3 methods shown with full name in documentation object 'predict.ktsp':
  ‘predict.ktsp’

S3 methods shown with full name in documentation object 'print.ktsp':
  ‘print.ktsp’

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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.
Found the following files/directories:
  ‘mydata.xml’ ‘swarms.pdf’
Found the following significant warnings:
  Warning: namespace ‘leaflet’ is not available and has been replaced
  Rd warning: /home/hornik/tmp/scratch/RtmpSZkTh0/R.INSTALLb90228f9101/kuniezu/man/extreme_points.Rd:8: file link ‘st_sfc’ in package ‘sf’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpSZkTh0/R.INSTALLb90228f9101/kuniezu/man/jgd2011_bbox.Rd:19: file link ‘st_sf’ in package ‘sf’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpSZkTh0/R.INSTALLb90228f9101/kuniezu/man/jp47prefectural_offices.Rd:8: file link ‘st_sf’ in package ‘sf’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpSZkTh0/R.INSTALLb90228f9101/kuniezu/man/move_jpn_rs.Rd:10: file link ‘st_sf’ in package ‘sf’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpSZkTh0/R.INSTALLb90228f9101/kuniezu/man/move_jpn_rs.Rd:15: file link ‘st_sf’ in package ‘sf’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kuniezu.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘m.kvh’ ‘test.kvh’
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘readme.txt’
kztp: warning in rowMeans(kztp, dim = 2): partial argument match of
  ‘dim’ to ‘dims’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpHg4omA/R.INSTALL6f594ccbdfaf/labdsv/man/dga.Rd:28: file link ‘mgcv’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHg4omA/R.INSTALL6f594ccbdfaf/labdsv/man/homoteneity.Rd:15: file link ‘partition’ in package ‘cluster’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHg4omA/R.INSTALL6f594ccbdfaf/labdsv/man/importance.Rd:17: file link ‘partition’ in package ‘cluster’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/labdsv.Rcheck/00install.out’ for details.
Found the following hidden files and directories:
  .Rapp.history
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
License components which are templates and need '+ file LICENSE':
  MIT
Malformed Description field: should contain one or more complete sentences.
extended.figures: no visible global function definition for ‘par’
extended.figures: no visible global function definition for ‘runif’
extended.figures : figure2: no visible global function definition for
  ‘hist’
extended.figures : figure2: no visible global function definition for
  ‘axis’
extended.figures : figure3 : <anonymous>: no visible global function
  definition for ‘median’
extended.figures : figure3: no visible global function definition for
  ‘barplot’
Undefined global functions or variables:
  axis barplot hist median par runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "median", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpaCf7g5/R.INSTALL75e245fe617c/labelled/man/recode.haven_labelled.Rd:23: file link ‘tidy-dots’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpaCf7g5/R.INSTALL75e245fe617c/labelled/man/to_labelled.Rd:48: file link ‘data.set’ in package ‘memisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpaCf7g5/R.INSTALL75e245fe617c/labelled/man/to_labelled.Rd:106: file link ‘data.set’ in package ‘memisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpaCf7g5/R.INSTALL75e245fe617c/labelled/man/to_labelled.Rd:107: file link ‘importer’ in package ‘memisc’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/labelled.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpaAuiTk/R.INSTALL32ca320b76ed/labelmachine/man/lapplI.Rd:42: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpaAuiTk/R.INSTALL32ca320b76ed/labelmachine/man/lapplI.Rd:48: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpaAuiTk/R.INSTALL32ca320b76ed/labelmachine/man/lapplI.Rd:50: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpaAuiTk/R.INSTALL32ca320b76ed/labelmachine/man/lapplI.Rd:18: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpaAuiTk/R.INSTALL32ca320b76ed/labelmachine/man/lapplI.Rd:23: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpaAuiTk/R.INSTALL32ca320b76ed/labelmachine/man/named_lapply.Rd:13: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpaAuiTk/R.INSTALL32ca320b76ed/labelmachine/man/named_lapply.Rd:18: file link ‘sapply’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/labelmachine.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘labelrank.Rmd’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp6tWJ0u/R.INSTALL77b67ceb2411/LabRS/man/expchart.Rd:28: file link ‘dev.copy’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6tWJ0u/R.INSTALL77b67ceb2411/LabRS/man/expchart.Rd:11: file link ‘dev.copy’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6tWJ0u/R.INSTALL77b67ceb2411/LabRS/man/expchart.Rd:22: file link ‘dev.copy’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6tWJ0u/R.INSTALL77b67ceb2411/LabRS/man/percent.Rd:12: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6tWJ0u/R.INSTALL77b67ceb2411/LabRS/man/percent.Rd:14: file link ‘prop.table’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6tWJ0u/R.INSTALL77b67ceb2411/LabRS/man/tabcont.Rd:14: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6tWJ0u/R.INSTALL77b67ceb2411/LabRS/man/tabcont.Rd:16: file link ‘prop.table’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6tWJ0u/R.INSTALL77b67ceb2411/LabRS/man/tabfreq.Rd:12: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LabRS.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpn2iKgl/R.INSTALL75d87ce4928d/lacunaritycovariance/man/gblemp.Rd:45: file link ‘roll_sum’ in package ‘RcppRoll’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpn2iKgl/R.INSTALL75d87ce4928d/lacunaritycovariance/man/rbdd.Rd:33: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpn2iKgl/R.INSTALL75d87ce4928d/lacunaritycovariance/man/rbdr.Rd:22: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpn2iKgl/R.INSTALL75d87ce4928d/lacunaritycovariance/man/rblnd.Rd:21: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpn2iKgl/R.INSTALL75d87ce4928d/lacunaritycovariance/man/rbpto.Rd:42: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lacunaritycovariance.Rcheck/00install.out’ for details.
Running ‘run_testthattests.R’ [25s/37s]
Running the tests in ‘tests/run_testthattests.R’ failed.
Complete output:
  > library(testthat)
  > #library(lacunaritycovariance)
  > test_check("lacunaritycovariance")
  Loading required package: lacunaritycovariance
  Loading required package: spatstat
  Loading required package: spatstat.data
  Loading required package: nlme
  Loading required package: rpart
  
  spatstat 1.64-1       (nickname: 'Help you I can, yes!') 
  For an introduction to spatstat, type 'beginner' 
  
  ── 1. Failure: rbpto generates simulations that match covariance for big window 
  mean(abs(cvc.diff)) is not strictly less than cp * cvcreltol * 1.5. Difference: 0.0208
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 122 | SKIPPED: 13 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: rbpto generates simulations that match covariance for big window (@test-rbpto.R#38) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpyeXj9t/R.INSTALL46f13a462347/LAGOSNE/man/classifications.Rd:133: file link ‘lakes.geo’ in package ‘LAGOSNE’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpyeXj9t/R.INSTALL46f13a462347/LAGOSNE/man/conn.Rd:301: file link ‘lakes.geo’ in package ‘LAGOSNE’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpyeXj9t/R.INSTALL46f13a462347/LAGOSNE/man/lake_info.Rd:19: file link ‘agrepl’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpyeXj9t/R.INSTALL46f13a462347/LAGOSNE/man/lakes_limno.Rd:37: file link ‘lakes.geo’ in package ‘LAGOSNE’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpyeXj9t/R.INSTALL46f13a462347/LAGOSNE/man/locus.Rd:47: file link ‘lakes.geo’ in package ‘LAGOSNE’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpyeXj9t/R.INSTALL46f13a462347/LAGOSNE/man/lulc.Rd:107: file link ‘lakes.geo’ in package ‘LAGOSNE’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LAGOSNE.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘DiceOptim’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpFpUltr/R.INSTALL1b1533312062/laGP/man/optim.auglag.Rd:255: file link ‘optim.step.tgp’ in package ‘tgp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/laGP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpYqoow3/Rbuild5a5373a5f226/lagsarlmtree/man/lagsarlmtree.Rd:36: file link ‘lagsarlm’ in package ‘spdep’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpYqoow3/Rbuild5a5373a5f226/lagsarlmtree/man/lagsarlmtree.Rd:94: file link ‘lagsarlm’ in package ‘spdep’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lagsarlmtree.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘zipcode’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpbLQxXn/R.INSTALL18156fc0370b/LambertW/man/p_m1.Rd:58: file link ‘pgeom’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LambertW.Rcheck/00install.out’ for details.
Found the following sources/headers with CR or CRLF line endings:
  inst/include/lamW.h
  inst/include/lamW_RcppExports.h
Some Unix compilers require LF line endings.
GNU make is a SystemRequirements.
getGO: no visible global function definition for ‘new’
getGO: no visible global function definition for ‘getGeneric’
graph.kd: no visible global function definition for ‘as’
Undefined global functions or variables:
  as getGeneric new
Consider adding
  importFrom("methods", "as", "getGeneric", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
Found the following files/directories:
  ‘example.llo’
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.
Rd file 'cv.lars.Rd':
  \usage lines wider than 90 characters:
         trace = FALSE, plot.it = TRUE, se = TRUE,type = c("lasso", "lar", "forward.stagewise", "stepwise"),

Rd file 'lars.Rd':
  \usage lines wider than 90 characters:
         trace = FALSE, normalize = TRUE, intercept = TRUE, Gram, eps = .Machine$double.eps, max.steps, use.Gram = TRUE)

Rd file 'plot.lars.Rd':
  \usage lines wider than 90 characters:
     plot(x, xvar= c("norm", "df", "arc.length", "step"), breaks = TRUE, plottype = c("coefficients", 

These lines will be truncated in the PDF manual.
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.
Rd file 'lassoshooting.Rd':
  \usage lines wider than 90 characters:
     lassoshooting(X=NULL, y=NULL, lambda, XtX=NULL, Xty=NULL, thr=1.0e-6, maxit=1e4, nopenalize=NULL, penaltyweight=NULL, trace=0, ...)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpuBZEK7/R.INSTALL12064d5a9b78/latentnet/man/ergmm-terms.Rd:427: file link ‘terms-ergm’ in package ‘ergm’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuBZEK7/R.INSTALL12064d5a9b78/latentnet/man/gof.ergmm.Rd:43: file link ‘plot.gof’ in package ‘ergm’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuBZEK7/R.INSTALL12064d5a9b78/latentnet/man/gof.ergmm.Rd:93: file link ‘plot.gof’ in package ‘ergm’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuBZEK7/R.INSTALL12064d5a9b78/latentnet/man/mcmc.diagnostics.ergmm.Rd:71: file link ‘plot.mcmc.list’ in package ‘coda’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuBZEK7/R.INSTALL12064d5a9b78/latentnet/man/simulate.ergmm.Rd:70: file link ‘print.network’ in package ‘network’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/latentnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpZhgHI6/R.INSTALL7cb46053dab8/Laterality/man/Laterality-package.Rd:41: file link ‘ade4-package’ in package ‘ade4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZhgHI6/R.INSTALL7cb46053dab8/Laterality/man/laterAFCM.Rd:70: file link ‘ade4-package’ in package ‘ade4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZhgHI6/R.INSTALL7cb46053dab8/Laterality/man/laterAFCM.Rd:70: file link ‘acm.disjonctif’ in package ‘ade4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZhgHI6/R.INSTALL7cb46053dab8/Laterality/man/laterAFCM.Rd:70: file link ‘acm.burt’ in package ‘ade4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZhgHI6/R.INSTALL7cb46053dab8/Laterality/man/lvisAFCM.Rd:114: file link ‘ade4-package’ in package ‘ade4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZhgHI6/R.INSTALL7cb46053dab8/Laterality/man/lvisAFCM.Rd:114: file link ‘acm.disjonctif’ in package ‘ade4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZhgHI6/R.INSTALL7cb46053dab8/Laterality/man/lvisAFCM.Rd:114: file link ‘acm.burt’ in package ‘ade4’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Laterality.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘using-latex2exp.Rmd’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpVMtv70/R.INSTALL10013c301985/latte/man/reexports.Rd:14: file link ‘edit_r_environ’ in package ‘usethis’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/latte.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpKkaF2L/R.INSTALL4fd2372dbc1/lavaan/man/getCov.Rd:39: file link ‘cov2cor’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpKkaF2L/R.INSTALL4fd2372dbc1/lavaan/man/lavaan-class.Rd:127: file link ‘BIC’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lavaan.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: C:/Users/Slava/AppData/Local/Temp/RtmpEVrMpZ/Rbuild16e41de54b5b/lawstat/man/brunner.munzel.test.Rd:70: file link ‘pwilcox’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/Slava/AppData/Local/Temp/RtmpEVrMpZ/Rbuild16e41de54b5b/lawstat/man/laplace.test.Rd:50: file link ‘plaplace’ in package ‘VGAM’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/Slava/AppData/Local/Temp/RtmpEVrMpZ/Rbuild16e41de54b5b/lawstat/man/lorenz.curve.Rd:48: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/Slava/AppData/Local/Temp/RtmpEVrMpZ/Rbuild16e41de54b5b/lawstat/man/nig.parameter.Rd:59: file link ‘rnig’ in package ‘fBasics’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/Slava/AppData/Local/Temp/RtmpEVrMpZ/Rbuild16e41de54b5b/lawstat/man/rqq.Rd:51: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/Slava/AppData/Local/Temp/RtmpEVrMpZ/Rbuild16e41de54b5b/lawstat/man/rqq.Rd:99: file link ‘qqplot’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/Slava/AppData/Local/Temp/RtmpEVrMpZ/Rbuild16e41de54b5b/lawstat/man/rqq.Rd:99: file link ‘qqline’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lawstat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp2BNuPw/R.INSTALL69813b32e88f/lax/man/plot.retlev.Rd:30: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lax.Rcheck/00install.out’ for details.
Found the following calls to attach():
File ‘lazyData/R/requireData.R’:
  attach(NULL, pos = pos, name = searchDataName)
See section ‘Good practice’ in ‘?attach’.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpEDxARW/R.INSTALL1288deea11d/lcc/man/lccPlot.Rd:50: file link ‘marrangeGrob’ in package ‘gridExtra’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lcc.Rcheck/00install.out’ for details.
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.
Found the following files/directories:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
Found the following files/directories:
  ‘fitted.pdf’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpT0mRnI/R.INSTALL17044d1ce35/ldaPrototype/man/dendTopics.Rd:55: file link ‘labels.hclust’ in package ‘dendextend’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ldaPrototype.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpfxmNc2/R.INSTALL1b2258ce2a/LDheatmap/man/LDheatmap.addGrob.Rd:12: file link ‘grob’ in package ‘grid’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LDheatmap.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Non-standard file/directory found at top level:
  ‘LDOD.Rproj’
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.
core: no visible global function definition for ‘cov’
lad: no visible global function definition for ‘cov’
lad : InitialMatrix: no visible global function definition for ‘cov’
pfc : onepfc: no visible global function definition for ‘as.formula’
pfc : onepfc: no visible global function definition for ‘lm’
pfc: no visible global function definition for ‘cov’
pfc : aniso: no visible global function definition for ‘cov’
plot.lad: no visible global function definition for ‘lines’
plot.lad: no visible global function definition for ‘lowess’
plot.lad: no visible global function definition for ‘title’
plot.lad: no visible global function definition for ‘par’
plot.lad: no visible global function definition for ‘legend’
plot.pfc: no visible global function definition for ‘lines’
plot.pfc: no visible global function definition for ‘lowess’
plot.pfc: no visible global function definition for ‘title’
plot.pfc: no visible global function definition for ‘par’
plot.pfc: no visible global function definition for ‘legend’
screen.pfc : unipfc: no visible global function definition for
  ‘as.formula’
screen.pfc : unipfc: no visible global function definition for ‘lm’
screen.pfc : unipfc: no visible global function definition for ‘pf’
structure.test: no visible global function definition for ‘pchisq’
summary.core : lrtest: no visible global function definition for
  ‘pchisq’
summary.lad : lrtest: no visible global function definition for
  ‘pchisq’
summary.pfc : lrtest: no visible global function definition for
  ‘pchisq’
summary.pfc : r2: no visible global function definition for ‘lm’
Undefined global functions or variables:
  as.formula cov legend lines lm lowess par pchisq pf title
Consider adding
  importFrom("graphics", "legend", "lines", "par", "title")
  importFrom("stats", "as.formula", "cov", "lm", "lowess", "pchisq",
             "pf")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
prepare_Rd: HWE2sided.Rd:15-16: Dropping empty section \details
prepare_Rd: HWE2sided.table.Rd:17-18: Dropping empty section \details
prepare_Rd: LD2sided.pvals.Rd:13-14: Dropping empty section \details
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmppHKUAf/R.INSTALL13a2686a06e0/leafem/man/addStaticLabels.Rd:29: file link ‘addLabelOnlyMarkers’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmppHKUAf/R.INSTALL13a2686a06e0/leafem/man/addStaticLabels.Rd:23: file link ‘labelOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmppHKUAf/R.INSTALL13a2686a06e0/leafem/man/addStaticLabels.Rd:63: file link ‘addLabelOnlyMarkers’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmppHKUAf/R.INSTALL13a2686a06e0/leafem/man/addTileFolder.Rd:32: file link ‘tileOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/leafem.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpHaBVKE/R.INSTALL17fe49df1ff/leafletCN/man/leafletCN-imports.Rd:8: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/leafletCN.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpzvvalm/R.INSTALL17b839852bf1/leaflet.esri/man/addEsriBasemapLayer.Rd:21: file link ‘tileOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpzvvalm/R.INSTALL17b839852bf1/leaflet.esri/man/addEsriDynamicMapLayer.Rd:24: file link ‘popupOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpzvvalm/R.INSTALL17b839852bf1/leaflet.esri/man/addEsriFeatureLayer.Rd:47: file link ‘markerClusterOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpzvvalm/R.INSTALL17b839852bf1/leaflet.esri/man/addEsriFeatureLayer.Rd:91: file link ‘highlightOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpzvvalm/R.INSTALL17b839852bf1/leaflet.esri/man/addEsriImageMapLayer.Rd:24: file link ‘popupOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpzvvalm/R.INSTALL17b839852bf1/leaflet.esri/man/tiledMapLayerOptions.Rd:21: file link ‘tileOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/leaflet.esri.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpFXyJVW/R.INSTALL5ef057a2489/leaflet.extras/man/TileCaching.Rd:13: file link ‘tileOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpFXyJVW/R.INSTALL5ef057a2489/leaflet.extras/man/TileCaching.Rd:13: file link ‘addTiles’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpFXyJVW/R.INSTALL5ef057a2489/leaflet.extras/man/addGeodesicPolylines.Rd:67: file link ‘pathOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpFXyJVW/R.INSTALL5ef057a2489/leaflet.extras/man/omnivore.Rd:197: file link ‘addGeoJSON’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpFXyJVW/R.INSTALL5ef057a2489/leaflet.extras/man/omnivore.Rd:197: file link ‘addTopoJSON’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpFXyJVW/R.INSTALL5ef057a2489/leaflet.extras/man/omnivore.Rd:106: file link ‘markerClusterOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpFXyJVW/R.INSTALL5ef057a2489/leaflet.extras/man/omnivore.Rd:150: file link ‘highlightOptions’ in package ‘leaflet’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/leaflet.extras.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpjXDdGS/R.INSTALL6638505dd133/leaflet.minicharts/man/addMinicharts.Rd:166: file link ‘addPolygons’ in package ‘leaflet’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/leaflet.minicharts.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpSmmnLZ/R.INSTALL2cad7b286948/leaflet/man/leaflet-imports.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpSmmnLZ/R.INSTALL2cad7b286948/leaflet/man/map-shiny.Rd:16: file link ‘shinyWidgetOutput’ in package ‘htmlwidgets’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/leaflet.Rcheck/00install.out’ for details.
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.
AlternateSVD: no visible binding for global variable ‘sd’
IPOD: no visible global function definition for ‘mad’
IPOD: no visible global function definition for ‘pnorm’
Pvalue: no visible global function definition for ‘pf’
ROCplot: no visible global function definition for ‘png’
ROCplot: no visible global function definition for ‘matplot’
ROCplot: no visible global function definition for ‘legend’
ROCplot: no visible global function definition for ‘dev.off’
leapp: no visible global function definition for ‘png’
leapp: no visible global function definition for ‘dev.off’
ridge: no visible global function definition for ‘sd’
ridge: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dev.off legend mad matplot pf png pnorm sd
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "mad", "pf", "pnorm", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpjgNI6b/R.INSTALL4f0a5332099f/learnr/man/safe_env.Rd:10: file link ‘rcmd_safe_env’ in package ‘callr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/learnr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpgVAKHV/R.INSTALL34b3d62a8a3/leiden/man/leiden.Rd:21: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/leiden.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpk9DSNL/R.INSTALL235055172463/LeMaRns/man/calc_Q.Rd:138: file link ‘dlnorm’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LeMaRns.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpYXEjj1/R.INSTALL39b151b48f3/lenses/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lenses.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpPCBxLQ/R.INSTALL19667a6d1d89/lfl/man/frbe.Rd:53: file link ‘rwf’ in package ‘forecast’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lfl.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpqYBRH0/R.INSTALL5ee2fd407aa/lfstat/man/cdf_ev.Rd:26: file link ‘quagev’ in package ‘lmom’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpqYBRH0/R.INSTALL5ee2fd407aa/lfstat/man/cdf_ev.Rd:26: file link ‘pelgev’ in package ‘lmom’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lfstat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpHa2rsL/R.INSTALL5aa4721ca8f9/lgr/man/EventFilter.Rd:17: file link ‘Filter’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHa2rsL/R.INSTALL5aa4721ca8f9/lgr/man/LayoutDbi.Rd:124: file link ‘DBI’ in package ‘DBI’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHa2rsL/R.INSTALL5aa4721ca8f9/lgr/man/LayoutFormat.Rd:46: file link ‘format.POSIXct’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHa2rsL/R.INSTALL5aa4721ca8f9/lgr/man/LayoutJson.Rd:36: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHa2rsL/R.INSTALL5aa4721ca8f9/lgr/man/LogEvent.Rd:39: file link ‘POSIXct’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHa2rsL/R.INSTALL5aa4721ca8f9/lgr/man/get_logger.Rd:16: file link ‘R6’ in package ‘R6’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHa2rsL/R.INSTALL5aa4721ca8f9/lgr/man/system_infos.Rd:31: file link ‘sys.call’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lgr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpTOFYrr/R.INSTALL6867002cfd6/LICORS/man/wKDE.Rd:41: file link ‘approx’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LICORS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpwVGhay/R.INSTALL376667129eea/lifecycle/man/signal_experimental.Rd:28: file link ‘signal’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpwVGhay/R.INSTALL376667129eea/lifecycle/man/signal_experimental.Rd:29: file link ‘signalCondition’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lifecycle.Rcheck/00install.out’ for details.
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.
Non-standard files/directories found at top level:
  ‘LIHNPSD-manual.pdf’ ‘PSD-Paper.pdf’ ‘Rplots.pdf’
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.
Rd file 'LIHNPSD-package.Rd':
  \examples lines wider than 100 characters:
       dist <- list( sigma= 0.004625, alpha= 0.292645, gamma= 0.482744, beta= -0.154049, location= 0.002968 )

Rd file 'LIHNPSD_standardfit_fn.Rd':
  \usage lines wider than 90 characters:
     LIHNPSD_standardfit_fn(psd, data_stats, hist, plotqq = 1, weights = list(), merge_tails = c(0, 0), debug = 0)

Rd file 'prepare.Rd':
  \examples lines wider than 100 characters:
       dist <- list( sigma= 0.004625, alpha= 0.292645, gamma= 0.482744, beta= -0.154049, location= 0.002968 )

Rd file 'rawmean.Rd':
  \examples lines wider than 100 characters:
       dist <- list( sigma= 0.004625, alpha= 0.292645, gamma= 0.482744, beta= -0.154049, location= 0.002968 )

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpGed8Yd/R.INSTALL182e57108053/lime/man/plot_superpixels.Rd:11: file link ‘image_read’ in package ‘magick’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lime.Rcheck/00install.out’ for details.
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.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmplfKi78/R.INSTALL294667afa90/lineup/man/find.gene.pseudomarker.Rd:64: file link ‘find.pseudomarkerpos’ in package ‘qtl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplfKi78/R.INSTALL294667afa90/lineup/man/plot2dist.Rd:26: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplfKi78/R.INSTALL294667afa90/lineup/man/plot2dist.Rd:40: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplfKi78/R.INSTALL294667afa90/lineup/man/plotEGclass.Rd:28: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplfKi78/R.INSTALL294667afa90/lineup/man/summary.lineupdist.Rd:25: file link ‘print.data.frame’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lineup.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp7wxz1t/R.INSTALL1b654e6c2638/lingtypology/man/imports.Rd:8: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lingtypology.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpgYJQS1/R.INSTALL4b1b20ccfc2b/linguisticsdown/man/writeIPA.Rd:14: file link ‘insertText’ in package ‘rstudioapi’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/linguisticsdown.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpiNgFpo/R.INSTALL729723997c8c/LinkedMatrix/man/initialize-ColumnLinkedMatrix-method.Rd:14: file link ‘initialize’ in package ‘methods’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LinkedMatrix.Rcheck/00install.out’ for details.
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘linkspotterVignette.Rmd’
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.
Rd file 'idf.Rd':
  \usage lines wider than 90 characters:
     plot(x, y=NULL, ..., var = NULL, typ="hist", k.x = 1, k.y = 1, inf.margin=10, p.cex=1, col.lev=15, plot.grid=FALSE, x.adj = 0.5, x.padj ... [TRUNCATED]
  \examples lines wider than 100 characters:
     plot(pm.idf, typ="draft", k.x=10, k.y=20, p.cex=0.35, x.adj=0.5, x.padj=4, y.las=0, y.adj=0.5, y.padj=-4, x.lab="temperature", y.lab="p ... [TRUNCATED]

Rd file 's.linlir.Rd':
  \usage lines wider than 90 characters:
     plot(x, y=NULL, ..., typ, para.typ="polygon", b.grid=500, nb.func=1000, seed.func=NULL, pl.lrm=TRUE, pl.band=FALSE, lrm.col="blue", pl. ... [TRUNCATED]
  \examples lines wider than 100 characters:
     plot(test, typ="lrm", lrm.col="red", pl.band=TRUE, pl.dat=TRUE, pl.dat.typ="draft",k.x=10, k.y=10, y.las=1, y.adj=6)

These lines will be truncated in the PDF manual.
Non-standard file/directory found at top level:
  ‘pkg.Rproj’
'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
Found the following files/directories:
  ‘steinh.mps’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpI36vrc/R.INSTALL740715881df8/lintr/man/linters.Rd:217: file link ‘seq_len’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpI36vrc/R.INSTALL740715881df8/lintr/man/linters.Rd:218: file link ‘seq_along’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpI36vrc/R.INSTALL740715881df8/lintr/man/read_settings.Rd:24: file link ‘read.dcf’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lintr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpqhlXpT/R.INSTALL1c8d491ce1e7/lipidomeR/man/heatmap_lipidome_from_limma.Rd:91: file link ‘scale_shape_manual’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lipidomeR.Rcheck/00install.out’ for details.
Non-standard file/directory found at top level:
  ‘package.R’
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.
'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.
Rd file 'lle.Rd':
  \examples lines wider than 100 characters:
             plot( results$id, main="intrinsic dimension", type="l", xlab=expression(x[i]), ylab="id", lwd=2 )

These lines will be truncated in the PDF manual.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpQEefwg/R.INSTALL3d886e91dc7e/lme4/man/bootMer.Rd:71: file link ‘clusterExport’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQEefwg/R.INSTALL3d886e91dc7e/lme4/man/glmer.nb.Rd:9: file link ‘theta.ml’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQEefwg/R.INSTALL3d886e91dc7e/lme4/man/glmer.nb.Rd:32: file link ‘theta.ml’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQEefwg/R.INSTALL3d886e91dc7e/lme4/man/glmer.nb.Rd:63: file link ‘theta.ml’ in package ‘MASS’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lme4.Rcheck/00install.out’ for details.
'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.
Rd file 'lmec-package.Rd':
  \examples lines wider than 100 characters:
     X<- cbind((UTIdata$Fup==0)+0, (UTIdata$Fup==1)+0, (UTIdata$Fup==3)+0, (UTIdata$Fup==6)+0, (UTIdata$Fup==9)+0, (UTIdata$Fup==12)+0, (UTI ... [TRUNCATED]

Rd file 'lmec.Rd':
  \usage lines wider than 90 characters:
     lmec(yL, cens, X, Z, cluster, maxstep = 200, varstruct = "unstructured", init, method = "ML", epsstop = 0.001, abspmv = 0.001, mcmc0 =  ... [TRUNCATED]
  \examples lines wider than 100 characters:
     X = cbind((UTIdata$Fup==0)+0, (UTIdata$Fup==1)+0, (UTIdata$Fup==3)+0, (UTIdata$Fup==6)+0, (UTIdata$Fup==9)+0, (UTIdata$Fup==12)+0, (UTI ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp3zajF1/R.INSTALL2b5551b2cf58/lmeInfo/man/CI_g.Rd:15: file link ‘qt’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lmeInfo.Rcheck/00install.out’ for details.
mq.diagnostics : mq_missinggenotype_plot: no visible global function
  definition for ‘plot.missing’
Undefined global functions or variables:
  plot.missing
Package vignette with placeholder title ‘Vignette Title’:
  ‘lmem.qtler.Rmd’
Found the following files/directories:
  ‘cross.data.file.csv’ ‘qtl_analysis_reports’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpd1mpbK/R.INSTALL44a285c17d4/lmerTest/man/anova.lmerModLmerTest.Rd:69: file link ‘KRmodcomp’ in package ‘pbkrtest’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpd1mpbK/R.INSTALL44a285c17d4/lmerTest/man/lmer.Rd:52: file link ‘glmerControl’ in package ‘lme4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpd1mpbK/R.INSTALL44a285c17d4/lmerTest/man/lmerModLmerTest-class.Rd:10: file link ‘merMod’ in package ‘lme4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpd1mpbK/R.INSTALL44a285c17d4/lmerTest/man/lmerModLmerTest-class.Rd:34: file link ‘merMod’ in package ‘lme4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpd1mpbK/R.INSTALL44a285c17d4/lmerTest/man/summary.lmerModLmerTest.Rd:78: file link ‘KRmodcomp’ in package ‘pbkrtest’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lmerTest.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpkPciTG/R.INSTALL6a7f486883c1/lmf/man/rmnorm.Rd:49: file link ‘rmnorm’ in package ‘mnormt’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lmf.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpEfqqQq/R.INSTALL15b2b56c53b/lmmen/man/initialize_example.Rd:41: file link ‘rmvnorm’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lmmen.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘emulator’ ‘methods’ ‘miscTools’ ‘penalized’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'plot.lmmlasso.Rd':
  \examples lines wider than 100 characters:
     fit <- lmmlasso(x=classroomStudy$X,y=classroomStudy$y,z=classroomStudy$Z,grp=classroomStudy$grp,lambda=15,pdMat="pdIdent")

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpcOO9Ps/R.INSTALL1d0c214603d3/lmms/man/lmms-package.Rd:21: file link ‘investNoise’ in package ‘lmms’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcOO9Ps/R.INSTALL1d0c214603d3/lmms/man/lmms-package.Rd:21: file link ‘filterNoise’ in package ‘lmms’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcOO9Ps/R.INSTALL1d0c214603d3/lmms/man/lmms-package.Rd:22: file link ‘lmmSpline’ in package ‘lmms’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcOO9Ps/R.INSTALL1d0c214603d3/lmms/man/lmms-package.Rd:22: file link ‘lmmsDE’ in package ‘lmms’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lmms.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpXyEtOK/R.INSTALL2f175d2b2476/lmvar/man/fitted.lmvar.Rd:29: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXyEtOK/R.INSTALL2f175d2b2476/lmvar/man/fwbw.lm.Rd:87: file link ‘BIC’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXyEtOK/R.INSTALL2f175d2b2476/lmvar/man/fwbw.lmvar_no_fit.Rd:92: file link ‘BIC’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXyEtOK/R.INSTALL2f175d2b2476/lmvar/man/plot.lmvar.Rd:22: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lmvar.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘LN0SCIs-tutorial.Rmd’
Found the following files/directories:
  ‘basic_1_HOTAIR_MXI1_CD58.pdf’ ‘basic_2_HOTAIR_MXI1_PRKCE.pdf’
  ‘survival_1_HOTAIR_MXI1_CD58_exp_test.pdf’
  ‘survival_1_HOTAIR_MXI1_CD58_exp_train.pdf’
  ‘survival_1_HOTAIR_MXI1_CD58_test_curve.pdf’
  ‘survival_1_HOTAIR_MXI1_CD58_test_score.pdf’
  ‘survival_1_HOTAIR_MXI1_CD58_train_curve.pdf’
  ‘survival_1_HOTAIR_MXI1_CD58_train_score.pdf’
  ‘survival_2_HOTAIR_MXI1_PRKCE_exp_test.pdf’
  ‘survival_2_HOTAIR_MXI1_PRKCE_exp_train.pdf’
  ‘survival_2_HOTAIR_MXI1_PRKCE_test_curve.pdf’
  ‘survival_2_HOTAIR_MXI1_PRKCE_test_score.pdf’
  ‘survival_2_HOTAIR_MXI1_PRKCE_train_curve.pdf’
  ‘survival_2_HOTAIR_MXI1_PRKCE_train_score.pdf’
Found the following files/directories:
  ‘tTestTable.rda’
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.
Found the following significant warnings:
  Rd warning: C:/Users/KevinD/AppData/Local/Temp/Rtmpay2n4e/Rbuilde004e245770/lodr/man/coef.lod_lm.Rd:35: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/KevinD/AppData/Local/Temp/Rtmpay2n4e/Rbuilde004e245770/lodr/man/lod_lm.Rd:23: file link ‘as.numeric’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/KevinD/AppData/Local/Temp/Rtmpay2n4e/Rbuilde004e245770/lodr/man/lod_lm.Rd:70: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/KevinD/AppData/Local/Temp/Rtmpay2n4e/Rbuilde004e245770/lodr/man/residuals.lod_lm.Rd:39: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lodr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpE3S9Iv/R.INSTALL783a2983c3ee/LogConcDEAD/man/plot.LogConcDEAD.Rd:5: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpE3S9Iv/R.INSTALL783a2983c3ee/LogConcDEAD/man/plot.LogConcDEAD.Rd:38: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpE3S9Iv/R.INSTALL783a2983c3ee/LogConcDEAD/man/plot.LogConcDEAD.Rd:62: file link ‘heat_hcl’ in package ‘colorspace’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpE3S9Iv/R.INSTALL783a2983c3ee/LogConcDEAD/man/plot.LogConcDEAD.Rd:78: file link ‘heat_hcl’ in package ‘colorspace’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LogConcDEAD.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmptGfJq9/R.INSTALL78d440b04970/loggit/man/handlers.Rd:44: file link ‘getOption’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/loggit.Rcheck/00install.out’ for details.
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.
Found the following files/directories:
  ‘GCN4wt’
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.
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.
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.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:182:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:896:16: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:196:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpl5crdO/R.INSTALL4f896ba25c5/longitudinalData/man/makeLatexFile.Rd:44: file link ‘makeTriangles’ in package ‘misc3d’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpl5crdO/R.INSTALL4f896ba25c5/longitudinalData/man/parWindows.Rd:25: file link ‘split.screen’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpl5crdO/R.INSTALL4f896ba25c5/longitudinalData/man/plot3dPdf.Rd:58: file link ‘makeTriangles’ in package ‘misc3d’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpl5crdO/R.INSTALL4f896ba25c5/longitudinalData/man/plotTrajMeans3d.Rd:45: file link ‘rgl’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpl5crdO/R.INSTALL4f896ba25c5/longitudinalData/man/saveTrianglesAsASY.Rd:28: file link ‘makeTriangles’ in package ‘misc3d’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/longitudinalData.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘main.tex’ ‘scene.asy’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp63zz8E/R.INSTALL458f718b1237/longitudinal/man/dyn.cor.Rd:31: file link ‘cor.shrink’ in package ‘corpcor’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp63zz8E/R.INSTALL458f718b1237/longitudinal/man/dyn.cor.Rd:36: file link ‘var.shrink’ in package ‘corpcor’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/longitudinal.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ElemStatLearn’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp9pChxG/R.INSTALL14437f78a68/loon/man/l_nestedTclList2Rlist.Rd:11: file link ‘tcl’ in package ‘tcltk’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9pChxG/R.INSTALL14437f78a68/loon/man/l_nestedTclList2Rlist.Rd:12: file link ‘.Tcl’ in package ‘tcltk’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/loon.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Model_1.cm’ ‘dambacher.dot’ ‘levins.dot’
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.
Rd file 'fplot.Rd':
  \usage lines wider than 90 characters:
     fplot(gemat,type="both",metric="jaccard",addlabels=FALSE,scaled=TRUE,weighted=TRUE,pch=20,bg=1,pcex=3,pcol=4,lty=1,lcol=8,tfont=12,tcol ... [TRUNCATED]

Rd file 'fplot.foodweb.Rd':
  \usage lines wider than 90 characters:
     fplot.foodweb(gemat,ranks,addlabels=FALSE,scaled=TRUE,weighted=TRUE,pch=20,bg=1,pcex=3,pcol=4,lty=1,lcol=8,tfont=12,tcol=1)

Rd file 'groupplot.Rd':
  \usage lines wider than 90 characters:
     groupplot(gemat, groups, type = "both", metric = "jaccard", addlabels = FALSE, scaled = TRUE, pch = 20, bg = 1, pcex = 3, pcol = 4, lty ... [TRUNCATED]

Rd file 'groupplot.foodweb.Rd':
  \usage lines wider than 90 characters:
     groupplot.foodweb(gemat, ranks, groups, addlabels = FALSE, scaled = TRUE, pch = 20, bg = 1, pcex = 3, pcol = 4, lty = 1, lcol = 8, tfon ... [TRUNCATED]
  \examples lines wider than 100 characters:
     groupplot.foodweb(gemat=mat,ranks=rlist,groups=glist,pch=pch,lcol=lcol) #other parameters are set in default

These lines will be truncated in the PDF manual.
amendColumns: no visible global function definition for ‘setNames’
fillColumns: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpoSDHWg/R.INSTALL778b412b3e07/loo/man/print.loo.Rd:30: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/loo.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Overview.Rmd’
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmptXTn2Y/R.INSTALL3138435d7f0e/lotri/man/lotri.Rd:17: file link ‘sys.call’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lotri.Rcheck/00install.out’ for details.
Checking should be performed on sources prepared by ‘R CMD build’.
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.
'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
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmptPOe18/R.INSTALL25173c60a882/LSAfun/man/breakdown.Rd:33: file link ‘gsub’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmptPOe18/R.INSTALL25173c60a882/LSAfun/man/plot_doclist.Rd:36: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmptPOe18/R.INSTALL25173c60a882/LSAfun/man/plot_doclist.Rd:57: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmptPOe18/R.INSTALL25173c60a882/LSAfun/man/plot_neighbors.Rd:41: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmptPOe18/R.INSTALL25173c60a882/LSAfun/man/plot_wordlist.Rd:34: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmptPOe18/R.INSTALL25173c60a882/LSAfun/man/plot_wordlist.Rd:52: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LSAfun.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpPKqT7I/R.INSTALL133f1fa0132b/LSC/man/LSC-utils.Rd:110: file link ‘plot.mixed_LICORS’ in package ‘LICORS’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LSC.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘homer.bmp’ ‘homer.jpeg’ ‘homer.pdf’ ‘homer.png’ ‘homer.ps’
  ‘homer.tiff’
Found the following significant warnings:
  Rd warning: C:/Users/Marcelo/AppData/Local/Temp/Rtmp42WNqX/Rbuild347440411127/LSDsensitivity/man/ergod.test.lsd.rd:34: file link ‘PP.test’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/Marcelo/AppData/Local/Temp/Rtmp42WNqX/Rbuild347440411127/LSDsensitivity/man/ergod.test.lsd.rd:48: file link ‘PP.test’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LSDsensitivity.Rcheck/00install.out’ for details.
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.
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.
'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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpfdcORl/R.INSTALL103b21e2d835/lubridate/man/make_datetime.Rd:37: file link ‘ISOdate’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfdcORl/R.INSTALL103b21e2d835/lubridate/man/parse_date_time.Rd:59: file link ‘as.POSIXct’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfdcORl/R.INSTALL103b21e2d835/lubridate/man/reexports.Rd:16: file link ‘intersect’ in package ‘generics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfdcORl/R.INSTALL103b21e2d835/lubridate/man/reexports.Rd:16: file link ‘setdiff’ in package ‘generics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfdcORl/R.INSTALL103b21e2d835/lubridate/man/reexports.Rd:16: file link ‘union’ in package ‘generics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfdcORl/R.INSTALL103b21e2d835/lubridate/man/round_date.Rd:53: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfdcORl/R.INSTALL103b21e2d835/lubridate/man/round_date.Rd:179: file link ‘round’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lubridate.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpkhntb6/R.INSTALLf71df52eec/lumberjack/man/simple.Rd:28: file link ‘connection’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpkhntb6/R.INSTALLf71df52eec/lumberjack/man/simple.Rd:29: file link ‘write.csv’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lumberjack.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpxhwb6c/R.INSTALL6aad4342055f/Luminescence/man/fit_OSLLifeTimes.Rd:138: file link ‘FDist’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Luminescence.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpZyAn02/R.INSTALLff47bf26df9/lunar/man/lunar.distance.Rd:9: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZyAn02/R.INSTALLff47bf26df9/lunar/man/lunar.distance.mean.Rd:10: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZyAn02/R.INSTALLff47bf26df9/lunar/man/lunar.illumination.Rd:9: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZyAn02/R.INSTALLff47bf26df9/lunar/man/lunar.illumination.mean.Rd:10: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZyAn02/R.INSTALLff47bf26df9/lunar/man/lunar.metric.mean.Rd:10: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZyAn02/R.INSTALLff47bf26df9/lunar/man/lunar.phase.Rd:9: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZyAn02/R.INSTALLff47bf26df9/lunar/man/lunar.phase.Rd:48: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZyAn02/R.INSTALLff47bf26df9/lunar/man/lunar.phase.Rd:49: file link ‘POSIXct’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZyAn02/R.INSTALLff47bf26df9/lunar/man/terrestrial.season.Rd:9: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lunar.Rcheck/00install.out’ for details.
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').
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp2bGiDq/R.INSTALL26086e1c0670/lutz/man/tz_offset.Rd:12: file link ‘OlsonNames’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lutz.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘test’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpJOHjV6/R.INSTALL12da30737829/lvnet/man/lav2lvnet.Rd:25: file link ‘lavaanify’ in package ‘lavaan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lvnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpsQofoZ/R.INSTALL6e3b56455ef3/lwgeom/man/geod.Rd:45: file link ‘st_distance’ in package ‘sf’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpsQofoZ/R.INSTALL6e3b56455ef3/lwgeom/man/st_split.Rd:12: file link ‘st_combine’ in package ‘sf’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lwgeom.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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpV5UtOM/R.INSTALL28111ba7a3e6/m2r/man/reexports.Rd:14: file link ‘edit_r_environ’ in package ‘usethis’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/m2r.Rcheck/00install.out’ for details.
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
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.
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.
Package suggested but not available for checking: ‘R2wd’
'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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘maddison_project_database.Rmd’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmplM95cc/R.INSTALL16fd5b85c3cf/madness/man/extract-methods.Rd:21: file link ‘as.integer’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/madness.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpZTXj8T/R.INSTALL73994972b36/MADPop/man/hUM.post.Rd:20: file link ‘sampling’ in package ‘rstan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MADPop.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpVXzOFq/R.INSTALL8be39de1ece/madrat/man/madapply.Rd:38: file link ‘parallel’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpVXzOFq/R.INSTALL8be39de1ece/madrat/man/madlapply.Rd:29: file link ‘parallel’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/madrat.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘R2wd’
'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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpwcnUmr/R.INSTALL17ee64d1ede4/magclass/man/head.magpie.Rd:35: file link ‘tail’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/magclass.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp5BMIGn/R.INSTALL2875354f3b81/magick/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/magick.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction-to-package-majesticr--rmd.Rmd’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpYcD0z1/R.INSTALL3f464a08a71a/MakefileR/man/Concatenation.Rd:22: file link ‘+’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpYcD0z1/R.INSTALL3f464a08a71a/MakefileR/man/make_comment.Rd:20: file link ‘+’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpYcD0z1/R.INSTALL3f464a08a71a/MakefileR/man/make_def.Rd:27: file link ‘+’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpYcD0z1/R.INSTALL3f464a08a71a/MakefileR/man/make_group.Rd:26: file link ‘+’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpYcD0z1/R.INSTALL3f464a08a71a/MakefileR/man/make_rule.Rd:32: file link ‘+’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpYcD0z1/R.INSTALL3f464a08a71a/MakefileR/man/make_text.Rd:21: file link ‘+’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpYcD0z1/R.INSTALL3f464a08a71a/MakefileR/man/makefile.Rd:24: file link ‘+’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MakefileR.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘MyMetadata.Rdata’ ‘MyMetadata.csv’ ‘MyintMatrix.Rdata’
  ‘MyintMatrix.csv’ ‘int.Rdata’ ‘int.binary.nex’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpZLTLL1/R.INSTALL1a7e19be84dc/Mangrove/man/MangroveExamples.Rd:13: file link ‘Mangrove’ in package ‘Mangrove’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZLTLL1/R.INSTALL1a7e19be84dc/Mangrove/man/plotSampledPrev.Rd:41: file link ‘plot.MangroveSample’ in package ‘Mangrove’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Mangrove.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp5dXZ80/R.INSTALL22b57d94a922/manhattanly/man/manhattanr.Rd:84: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp5dXZ80/R.INSTALL22b57d94a922/manhattanly/man/qqr.Rd:62: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp5dXZ80/R.INSTALL22b57d94a922/manhattanly/man/volcanor.Rd:64: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/manhattanly.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpUA5Wc7/R.INSTALL2b3c36ff7f8/mapcan/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mapcan.Rcheck/00install.out’ for details.
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.
'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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpLgPwLP/R.INSTALL1ca73ef1ca4/mapplots/man/draw.shape.Rd:34: file link ‘read.shapefile’ in package ‘shapefiles’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLgPwLP/R.INSTALL1ca73ef1ca4/mapplots/man/write.grid.Rd:31: file link ‘write.shapefile’ in package ‘shapefiles’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mapplots.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpxcYiDg/R.INSTALL763340a93c57/mapStats/man/mapStats-internal.Rd:31: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpxcYiDg/R.INSTALL763340a93c57/mapStats/man/mapStats-internal.Rd:52: file link ‘brewer.pal’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpxcYiDg/R.INSTALL763340a93c57/mapStats/man/mapStats.Rd:63: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpxcYiDg/R.INSTALL763340a93c57/mapStats/man/mapStats.Rd:82: file link ‘brewer.pal’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpxcYiDg/R.INSTALL763340a93c57/mapStats/man/mapStats.Rd:152: file link ‘RColorBrewer’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mapStats.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpJ4rzvq/R.INSTALL752068a24a90/maptools/man/CCmaps.Rd:17: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJ4rzvq/R.INSTALL752068a24a90/maptools/man/CCmaps.Rd:36: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/maptools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpIdmriX/R.INSTALL1ed4419905ba/marcher/man/locate_shift.Rd:10: file link ‘POSIXt’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/marcher.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpa1PRKC/R.INSTALL1f3926b6b376/margins/man/cplot.Rd:112: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpa1PRKC/R.INSTALL1f3926b6b376/margins/man/cplot.Rd:136: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpa1PRKC/R.INSTALL1f3926b6b376/margins/man/cplot.Rd:138: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpa1PRKC/R.INSTALL1f3926b6b376/margins/man/dydx.Rd:61: file link ‘contr.poly’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpa1PRKC/R.INSTALL1f3926b6b376/margins/man/dydx.Rd:61: file link ‘contr.treatment’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/margins.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpWT0C3N/R.INSTALL5eee11bedb9d/marg/man/cond.rsm.Rd:135: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpWT0C3N/R.INSTALL5eee11bedb9d/marg/man/marg.object.Rd:88: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/marg.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpmbcXGb/R.INSTALL2c7a6f0fdf16/marmap/man/etopo.Rd:29: file link ‘heat.colors’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpmbcXGb/R.INSTALL2c7a6f0fdf16/marmap/man/etopo.Rd:29: file link ‘cm.colors’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpmbcXGb/R.INSTALL2c7a6f0fdf16/marmap/man/space.pies.Rd:58: file link ‘pointLabel’ in package ‘maptools’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpmbcXGb/R.INSTALL2c7a6f0fdf16/marmap/man/space.pies.Rd:68: file link ‘pointLabel’ in package ‘maptools’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/marmap.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpJRBQWW/R.INSTALL31f13d9890bd/mason/man/mason.Rd:11: file link ‘dplyr’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJRBQWW/R.INSTALL31f13d9890bd/mason/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJRBQWW/R.INSTALL31f13d9890bd/mason/man/polish.Rd:22: file link ‘gsub’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJRBQWW/R.INSTALL31f13d9890bd/mason/man/polish.Rd:43: file link ‘gsub’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJRBQWW/R.INSTALL31f13d9890bd/mason/man/polish.Rd:47: file link ‘grepl’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJRBQWW/R.INSTALL31f13d9890bd/mason/man/polish.Rd:51: file link ‘mutate_at’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mason.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpvN6YIZ/R.INSTALL271853b42913/Matching/man/GenMatch.Rd:314: file link ‘makePSOCKcluster’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Matching.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘WhatIf’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpbbtO6c/R.INSTALL29b178c48a14/matlib/man/arrows3d.Rd:35: file link ‘segments3d’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbbtO6c/R.INSTALL29b178c48a14/matlib/man/arrows3d.Rd:44: file link ‘rgl’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbbtO6c/R.INSTALL29b178c48a14/matlib/man/cone3d.Rd:20: file link ‘rgl.material’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbbtO6c/R.INSTALL29b178c48a14/matlib/man/plotEqn3d.Rd:50: file link ‘rgl.material’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbbtO6c/R.INSTALL29b178c48a14/matlib/man/showEig.Rd:55: file link ‘dataEllipse’ in package ‘car’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbbtO6c/R.INSTALL29b178c48a14/matlib/man/vectors3d.Rd:39: file link ‘text3d’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbbtO6c/R.INSTALL29b178c48a14/matlib/man/vectors3d.Rd:86: file link ‘texts3d’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbbtO6c/R.INSTALL29b178c48a14/matlib/man/vectors3d.Rd:86: file link ‘rgl.material’ in package ‘rgl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/matlib.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpncvP16/R.INSTALL266e27fba39d/matrixNormal/man/matrixNormal_Distribution.Rd:60: file link ‘rmvnorm’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/matrixNormal.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘plspm’
Unknown package ‘plspm’ in Rd xrefs
Running examples in ‘matrixpls-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: matrixplsboot
> ### Title: Bootstrapping of matrixpls function
> ### Aliases: matrixplsboot matrixpls.boot summary.matrixplsboot
> 
> ### ** Examples
> 
> library(plspm)
Error in library(plspm) : there is no package called ‘plspm’
Execution halted
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmprGOhWf/R.INSTALL2c9629a9c31c/Matrix/man/abIndex-class.Rd:80: file link ‘Ops’ in package ‘methods’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprGOhWf/R.INSTALL2c9629a9c31c/Matrix/man/image-methods.Rd:53: file link ‘panel.levelplot.raster’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprGOhWf/R.INSTALL2c9629a9c31c/Matrix/man/image-methods.Rd:81: file link ‘get.gpar’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprGOhWf/R.INSTALL2c9629a9c31c/Matrix/man/matrix-products.Rd:406: file link ‘tcrossprod’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Matrix.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpDjYWDu/R.INSTALL41c73c94fd05/matrixStats/man/rowCollapse.Rd:55: file link ‘[’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpDjYWDu/R.INSTALL41c73c94fd05/matrixStats/man/rowCumsums.Rd:83: file link ‘cumprod’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpDjYWDu/R.INSTALL41c73c94fd05/matrixStats/man/rowCumsums.Rd:84: file link ‘cummin’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpDjYWDu/R.INSTALL41c73c94fd05/matrixStats/man/rowCumsums.Rd:84: file link ‘cummax’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpDjYWDu/R.INSTALL41c73c94fd05/matrixStats/man/rowProds.Rd:66: file link ‘is.nan’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpDjYWDu/R.INSTALL41c73c94fd05/matrixStats/man/rowRanges.Rd:52: file link ‘pmin.int’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpDjYWDu/R.INSTALL41c73c94fd05/matrixStats/man/varDiff.Rd:143: file link ‘var’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpDjYWDu/R.INSTALL41c73c94fd05/matrixStats/man/varDiff.Rd:166: file link ‘var’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpDjYWDu/R.INSTALL41c73c94fd05/matrixStats/man/weightedVar.Rd:73: file link ‘var’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/matrixStats.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp80eywh/R.INSTALL27d52f8416bb/Matrix.utils/man/dMcast.Rd:115: file link ‘cast’ in package ‘reshape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Matrix.utils.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpKlxyuX/R.INSTALL78262ab582ff/matsbyname/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpKlxyuX/R.INSTALL78262ab582ff/matsbyname/man/quasi-quote-assign.Rd:10: file link ‘:=’ in package ‘rlang’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/matsbyname.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp49PLJp/R.INSTALL5e721d91f573/matsindf/man/data.Rd:10: file link ‘.data’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp49PLJp/R.INSTALL5e721d91f573/matsindf/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp49PLJp/R.INSTALL5e721d91f573/matsindf/man/quasi-quote-assign.Rd:10: file link ‘:=’ in package ‘rlang’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/matsindf.Rcheck/00install.out’ for details.
Rd file 'mat.dissim.Rd':
  \usage lines wider than 90 characters:
     mat.dissim(inFossil, inModern, llMod = c(), modTaxa = c(), llFoss = c(), fosTaxa = c(), numAnalogs = 1, counts = T, sitenames = 1:lengt ... [TRUNCATED]

Rd file 'mat.fossavg.Rd':
  \usage lines wider than 90 characters:
     mat.fossavg(dObj, modEnvCol, fossEnvCol = 0, fossCols = 0, cutoff = 0, distance = -1, wmethod = "none", numanalogs = length(dObj$positi ... [TRUNCATED]

Rd file 'mat.jumprecon.Rd':
  \usage lines wider than 90 characters:
     mat.jumprecon(dObj, modEnvCol, fossEnvCol, cutoff = 0, alpha = NULL, distance = -1, numanalogs = length(dObj$position[, 1]))

Rd file 'mat.mc.Rd':
  \usage lines wider than 90 characters:
     mat.mc(inModern, modTaxa = c(NULL, NULL), probs = c(0.05, 0.025, 0.01, 0.001), freqint = seq(0, 2, 0.02), sampleSize = length(inModern[ ... [TRUNCATED]

Rd file 'mat.roc.Rd':
  \usage lines wider than 90 characters:
     mat.roc(inModern, modTaxa = c(), colClasses = NULL, numAnalogs = 2, rocEvalSeq = seq(0, 2, 0.05), counts = F, aucmethod = "trap")

Rd file 'mat.roc.allpair.Rd':
  \usage lines wider than 90 characters:
     mat.roc.allpair(inModern, modTaxa = c(), colClasses = NULL, numAnalogs = 2, rocEvalSeq = seq(0, 2, 0.05), counts = F, aucmethod = "trap ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘utilities.R’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmplYL0PQ/R.INSTALL2fc4b93ffe/maxLik/man/maxBFGS.Rd:176: file link ‘MaxControl-class’ in package ‘maxLik’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplYL0PQ/R.INSTALL2fc4b93ffe/maxLik/man/maxLik-package.Rd:31: file link ‘coef.maxim’ in package ‘maxLik’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplYL0PQ/R.INSTALL2fc4b93ffe/maxLik/man/maxLik-package.Rd:32: file link ‘stdEr.maxLik’ in package ‘maxLik’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplYL0PQ/R.INSTALL2fc4b93ffe/maxLik/man/maxNR.Rd:254: file link ‘MaxControl-class’ in package ‘maxLik’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/maxLik.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpPI70yO/R.INSTALL22983dcd32c/MaxMC/man/mmc.Rd:219: file link ‘GA’ in package ‘GA’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MaxMC.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpQxIZm1/R.INSTALL3f2c5b096de9/maxstat/man/maxstat.test.Rd:74: file link ‘pperm’ in package ‘exactRankTests’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/maxstat.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘map_5.png’ ‘maze_5.html’
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp3kPgoZ/R.INSTALLec42c79b51a/mbest/man/effects.Rd:66: file link ‘fixef’ in package ‘nlme’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp3kPgoZ/R.INSTALLec42c79b51a/mbest/man/effects.Rd:66: file link ‘ranef’ in package ‘nlme’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mbest.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: C:/Users/hp17602/AppData/Local/Temp/Rtmp8mwkxH/Rbuild17fc1b0c6c48/MBNMAdose/man/inconsistency.loops.Rd:37: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpLmBygh/R.INSTALL559b36af3d68/MBNMAdose/man/mbnma.network.Rd:104: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MBNMAdose.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: C:/Users/hp17602/AppData/Local/Temp/RtmpmKFBZa/Rbuild459845806a11/MBNMAtime/man/inconsistency.loops.Rd:29: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpDB7QCM/R.INSTALL56755a80c067/MBNMAtime/man/mb.network.Rd:91: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/hp17602/AppData/Local/Temp/RtmpmKFBZa/Rbuild459845806a11/MBNMAtime/man/mb.nodesplit.comparisons.Rd:29: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MBNMAtime.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpurqIpB/Rbuild4de259836db4/mboost/man/baselearners.Rd:158: file link ‘stationary.cov’ in package ‘fields’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp1JX9WE/R.INSTALL56174ff445d0/mboost/man/cvrisk.Rd:35: file link ‘parLapply’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mboost.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpKD2jDq/R.INSTALL7fb71a878548/mboxr/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mboxr.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Rd file 'VegTypeChanges.Rd':
  \examples lines wider than 100 characters:
     ## vegChanges = VegTypeChanges(ncdf.th <- system.file("netcdf", "WW2100_HadGEM2-ES85_year_sample.nc", PACKAGE = "MC2toPath")path, base. ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘fireFracs.csv’ ‘fireProbabilityMultipliers.txt’
  ‘vegChangeProbabilityMultipliers.txt’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpsvlIjZ/R.INSTALL304a68c32255/mccf1/man/summary.mccf1.Rd:12: file link ‘signif’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mccf1.Rcheck/00install.out’ for details.
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.
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.
Found the following files/directories:
  ‘dnzcY3e.1’ ‘dnzcY3e.2’ ‘dnzcY3e.3’ ‘mcmc.1.csv’ ‘mcmc.10.csv’
  ‘mcmc.11.csv’ ‘mcmc.12.csv’ ‘mcmc.13.csv’ ‘mcmc.14.csv’ ‘mcmc.15.csv’
  ‘mcmc.16.csv’ ‘mcmc.17.csv’ ‘mcmc.18.csv’ ‘mcmc.19.csv’ ‘mcmc.2.csv’
  ‘mcmc.20.csv’ ‘mcmc.3.csv’ ‘mcmc.4.csv’ ‘mcmc.5.csv’ ‘mcmc.6.csv’
  ‘mcmc.7.csv’ ‘mcmc.8.csv’ ‘mcmc.9.csv’
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.
Found the following files/directories:
  ‘CarStats.pdf’ ‘CarStats_labels.pdf’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp4CWCB6/R.INSTALL24ac24f29409/mc.heterogeneity/man/mc.d.Rd:21: file link ‘rma’ in package ‘metafor’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4CWCB6/R.INSTALL24ac24f29409/mc.heterogeneity/man/mc.fcor.Rd:17: file link ‘rma’ in package ‘metafor’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4CWCB6/R.INSTALL24ac24f29409/mc.heterogeneity/man/mc.lnOR.Rd:24: file link ‘rma’ in package ‘metafor’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mc.heterogeneity.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpqB40Jl/R.INSTALL26f5313994ec/mcmcderive/man/mcmc_derive.Rd:45: file link ‘mcmcr’ in package ‘mcmcr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mcmcderive.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpwKMzNH/R.INSTALL365f40984ce9/MCMCglmm/man/rtnorm.Rd:20: file link ‘rtnorm’ in package ‘msm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MCMCglmm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmprLagrW/R.INSTALL50c81f832eed/MCMCpack/man/SSVSquantreg.Rd:166: file link ‘summary.qrssvs’ in package ‘MCMCpack’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MCMCpack.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpGOMdzh/R.INSTALL47a82022da09/mcmcr/man/anyNA.Rd:42: file link ‘anyNA’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGOMdzh/R.INSTALL47a82022da09/mcmcr/man/mcmcr_example.Rd:13: file link ‘line’ in package ‘coda’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mcmcr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpjzHXe5/R.INSTALL6f52671eb77e/MCMCtreeR/man/estimateSkewNormal.Rd:78: file link ‘qst’ in package ‘sn’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpjzHXe5/R.INSTALL6f52671eb77e/MCMCtreeR/man/estimateSkewT.Rd:79: file link ‘qst’ in package ‘sn’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MCMCtreeR.Rcheck/00install.out’ for details.
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.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘scatterplot3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.nsga2: no visible global function definition for ‘lines’
plot.nsga2: no visible global function definition for ‘pairs’
plot.nsga2.collection: no visible global function definition for
  ‘devAskNewPage’
Undefined global functions or variables:
  devAskNewPage lines pairs
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "lines", "pairs")
to your NAMESPACE file.
src/Makevars: incorrect macro SHLIB_OPENMP_CFLAGS included in PKG_CXXFLAGS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  src/Makevars.win: incorrect macro SHLIB_OPENMP_CFLAGS included in PKG_CXXFLAGS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpVTjqZC/R.INSTALL332a15013cc5/mcprofile/man/confint.mcprofile.Rd:26: file link ‘confint.glm’ in package ‘MASS’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpVTjqZC/R.INSTALL332a15013cc5/mcprofile/man/confint.mcprofile.Rd:26: file link ‘confint.glht’ in package ‘multcomp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpVTjqZC/R.INSTALL332a15013cc5/mcprofile/man/summary.mcprofile.Rd:22: file link ‘summary.glht’ in package ‘multcomp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mcprofile.Rcheck/00install.out’ for details.
'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.
Depends: includes the non-default packages:
  'lattice', 'locfit', 'maptools', 'quantreg', 'RANN', 'SparseM'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘lattice’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘RColorBrewer’ ‘car’ ‘spatstat’ ‘spdep’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘RANN’ ‘maptools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Checking should be performed on sources prepared by ‘R CMD build’.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpNtfERZ/R.INSTALL34032a0dffef/MDBED/man/CDF_3dPlot.Rd:47: file link ‘wireframe’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MDBED.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp2CM5n9/R.INSTALL3cc01769c23e/MDFS/man/plot.MDFS.Rd:14: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MDFS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpOnTE6o/R.INSTALL3d7c6240489b/mdftracks/man/read.mdf.Rd:28: file link ‘file’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpOnTE6o/R.INSTALL3d7c6240489b/mdftracks/man/write.mdf.Rd:46: file link ‘file’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mdftracks.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: C:/Users/sunpn563/AppData/Local/Temp/Rtmpg5tUOX/Rbuilded024453f7f/mdmb/man/frm.Rd:97: file link ‘lm.wfit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHhgk4h/R.INSTALL2aa0569bcd69/mdmb/man/offset_values_extract.Rd:49: file link ‘model.offset’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: C:/Users/sunpn563/AppData/Local/Temp/Rtmpg5tUOX/Rbuilded024453f7f/mdmb/man/yjt_dist.Rd:172: file link ‘dt’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mdmb.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [13s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mds)
  > 
  > test_check("mds")
  ── 1. Error: (unknown) (@test_da.R#446)  ───────────────────────────────────────
  'origin' must be supplied
  Backtrace:
    1. base::summary(a1)
    2. mds:::summary.mds_das(a1)
    5. base::c.Date(...)
    8. base::lapply(list(...), function(e) unclass(as.Date(e)))
    9. base:::FUN(X[[i]], ...)
   11. base::as.Date.numeric(e)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 319 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test_da.R#446) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mds_intro.Rmd’ using rmarkdown
Quitting from lines 146-147 (mds_intro.Rmd) 
Error: processing vignette 'mds_intro.Rmd' failed with diagnostics:
'origin' must be supplied
--- failed re-building ‘mds_intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'etl', 'macleish'
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpBqRQhM/R.INSTALL60af634efb56/mdsr/man/CholeraDeaths.Rd:8: file link ‘SpatialPointsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBqRQhM/R.INSTALL60af634efb56/mdsr/man/src_scidb.Rd:18: file link ‘src_mysql’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mdsr.Rcheck/00install.out’ for details.
Non-standard file/directory found at top level:
  ‘AUTHORS’
Authors information should be in file inst/AUTHORS
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpECzokF/R.INSTALL60ae54437c9f/MEDseq/man/MEDseq_control.Rd:115: file link ‘wcKMedoids’ in package ‘WeightedCluster’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MEDseq.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpvdEwCt/R.INSTALL6dd812236a36/mefa4/man/Mefa.Rd:77: file link ‘xtab’ in package ‘mefa4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpvdEwCt/R.INSTALL6dd812236a36/mefa4/man/Mefa.Rd:77: file link ‘taxa’ in package ‘mefa4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpvdEwCt/R.INSTALL6dd812236a36/mefa4/man/Melt.Rd:29: file link ‘melt’ in package ‘mefa’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mefa4.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Data_Correlation.txt’ ‘correlation_FDR_table.txt’
.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.
Found the following files/directories:
  ‘meme_data2.jpg’
'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
Package vignette with placeholder title ‘Vignette Title’:
  ‘README.Rmd’
Found the following files/directories:
  ‘Absolute Positions.txt’ ‘Epidemics 1.tiff’ ‘Epidemics 1.txt’
  ‘Epidemics 2.tiff’ ‘Epidemics 2.txt’ ‘Epidemics 3.tiff’ ‘Epidemics
  3.txt’ ‘Epidemics 4.tiff’ ‘Epidemics 4.txt’ ‘Epidemics 5.tiff’
  ‘Epidemics 5.txt’ ‘Epidemics 6.tiff’ ‘Epidemics 6.txt’ ‘Epidemics
  7.tiff’ ‘Epidemics 7.txt’ ‘Epidemics 8.tiff’ ‘Epidemics 8.txt’ ‘MAP
  Curve 1.tiff’ ‘MAP Curve 1.txt’ ‘MAP Curve 2.tiff’ ‘MAP Curve 2.txt’
  ‘MAP Curve 3.tiff’ ‘MAP Curve 3.txt’ ‘MAP Curve 4.tiff’ ‘MAP Curve
  4.txt’ ‘MAP Curve 5.tiff’ ‘MAP Curve 5.txt’ ‘MAP Curve 6.tiff’ ‘MAP
  Curve 6.txt’ ‘MAP Curve 7.tiff’ ‘MAP Curve 7.txt’ ‘MAP Curve 8.tiff’
  ‘MAP Curve 8.txt’ ‘MAP Curve Slope 1.tiff’ ‘MAP Curve Slope 1.txt’
  ‘MAP Curve Slope 2.tiff’ ‘MAP Curve Slope 2.txt’ ‘MAP Curve Slope
  3.tiff’ ‘MAP Curve Slope 3.txt’ ‘MAP Curve Slope 4.tiff’ ‘MAP Curve
  Slope 4.txt’ ‘MAP Curve Slope 5.tiff’ ‘MAP Curve Slope 5.txt’ ‘MAP
  Curve Slope 6.tiff’ ‘MAP Curve Slope 6.txt’ ‘MAP Curve Slope 7.tiff’
  ‘MAP Curve Slope 7.txt’ ‘MAP Curve Slope 8.tiff’ ‘MAP Curve Slope
  8.txt’ ‘MEM Model v1.tiff’ ‘MEM Model v1.txt’ ‘MEM Model v2.tiff’
  ‘MEM Model v2.txt’ ‘Moving Epidemics.tiff’ ‘Moving Epidemics.txt’
  ‘Relative Positions.txt’ ‘Summary.txt’ ‘graph 1.tiff’ ‘graph 2.tiff’
  ‘graph 3.tiff’ ‘graph 4.tiff’ ‘graph 5.tiff’ ‘series graph.png’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpawLNTm/R.INSTALL5880327ac696/messaging/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/messaging.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp1dpkMR/R.INSTALL4cda4865b1f6/metaBMA/man/plot.meta_pred.Rd:21: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp1dpkMR/R.INSTALL4cda4865b1f6/metaBMA/man/plot.prior.Rd:16: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp1dpkMR/R.INSTALL4cda4865b1f6/metaBMA/man/plot_default.Rd:19: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp1dpkMR/R.INSTALL4cda4865b1f6/metaBMA/man/plot_forest.Rd:30: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp1dpkMR/R.INSTALL4cda4865b1f6/metaBMA/man/plot_posterior.Rd:23: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/metaBMA.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmplpT3QD/R.INSTALL2eac22764670/metagam/man/tidyeval.Rd:17: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplpT3QD/R.INSTALL2eac22764670/metagam/man/tidyeval.Rd:18: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplpT3QD/R.INSTALL2eac22764670/metagam/man/tidyeval.Rd:20: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplpT3QD/R.INSTALL2eac22764670/metagam/man/tidyeval.Rd:21: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplpT3QD/R.INSTALL2eac22764670/metagam/man/tidyeval.Rd:25: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/metagam.Rcheck/00install.out’ for details.
bcgVaccineData: no visible global function definition for ‘data’
bcgVaccineData: no visible global function definition for ‘qnorm’
hConfidence: no visible global function definition for ‘qchisq’
intervalEstimates_OneSgnf : crt: no visible global function definition
  for ‘qt’
intervalEstimates_OneSgnf: no visible binding for global variable
  ‘qnorm’
metagenGeneralised: no visible binding for global variable ‘quantile’
performancePointH : property: no visible global function definition for
  ‘var’
performancePointR : property: no visible global function definition for
  ‘var’
pfunc : pfun: no visible global function definition for ‘uniroot’
pivotalStream: no visible global function definition for ‘rchisq’
pivotalStream : <anonymous>: no visible global function definition for
  ‘rchisq’
pivotalStream: no visible global function definition for ‘rnorm’
rBinomGauss: no visible global function definition for ‘rnorm’
rBinomGauss: no visible global function definition for ‘rbinom’
rD: no visible global function definition for ‘rchisq’
rY: no visible global function definition for ‘rnorm’
render: no visible global function definition for ‘pdf’
render: no visible global function definition for ‘dev.off’
renderSVG: no visible global function definition for ‘svg’
renderSVG: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  data dev.off pdf qchisq qnorm qt quantile rbinom rchisq rnorm svg
  uniroot var
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "svg")
  importFrom("stats", "qchisq", "qnorm", "qt", "quantile", "rbinom",
             "rchisq", "rnorm", "uniroot", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
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.
MAPE: no visible global function definition for ‘is’
MAPE: no visible global function definition for ‘new’
Undefined global functions or variables:
  is new
Consider adding
  importFrom("methods", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘doSMP’
Package in Depends field not imported from: ‘foreach’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  ‘pcaPP:::l1median_HoCr’ ‘pcaPP:::l1median_VaZh’
  See the note in ?`:::` about the use of this operator.
prepare_Rd: DropDupGenes.Rd:29-31: Dropping empty section \details
prepare_Rd: DropDupGenes.Rd:41-43: Dropping empty section \note
prepare_Rd: DropDupGenes.Rd:47-49: Dropping empty section \seealso
prepare_Rd: MetaPCA-package.Rd:29-30: Dropping empty section \seealso
prepare_Rd: MetaPCA.Rd:76-78: Dropping empty section \details
prepare_Rd: MetaPCA.Rd:88-90: Dropping empty section \note
prepare_Rd: MetaPCA.Rd:94-96: Dropping empty section \seealso
prepare_Rd: PlotPC2D.Rd:80-82: Dropping empty section \details
prepare_Rd: PlotPC2D.Rd:92-94: Dropping empty section \note
prepare_Rd: PlotPC2D.Rd:98-100: Dropping empty section \seealso
prepare_Rd: PreprocessMetaAnalysis.Rd:39-41: Dropping empty section \details
prepare_Rd: PreprocessMetaAnalysis.Rd:51-53: Dropping empty section \note
prepare_Rd: PreprocessMetaAnalysis.Rd:57-59: Dropping empty section \seealso
prepare_Rd: requireAll.Rd:19-21: Dropping empty section \details
prepare_Rd: requireAll.Rd:31-33: Dropping empty section \note
prepare_Rd: requireAll.Rd:25-27: Dropping empty section \references
prepare_Rd: requireAll.Rd:37-39: Dropping empty section \seealso
Package vignette with placeholder title ‘Vignette Title’:
  ‘how_to_use_crosshairs.Rmd’
fishercomb: no visible global function definition for ‘pchisq’
fishercomb: no visible global function definition for ‘p.adjust’
invnorm : <anonymous>: no visible global function definition for
  ‘qnorm’
invnorm: no visible global function definition for ‘pnorm’
invnorm: no visible global function definition for ‘p.adjust’
sim.function : <anonymous>: no visible global function definition for
  ‘rnorm’
sim.function : <anonymous>: no visible global function definition for
  ‘rnbinom’
Undefined global functions or variables:
  p.adjust pchisq pnorm qnorm rnbinom rnorm
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "pnorm", "qnorm", "rnbinom",
             "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpBfMXpV/R.INSTALL5b5f1a9491a8/metaSEM/man/lavaan2RAM.Rd:38: file link ‘lavaanify’ in package ‘lavaan’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBfMXpV/R.INSTALL5b5f1a9491a8/metaSEM/man/lavaan2RAM.Rd:43: file link ‘lavaanify’ in package ‘lavaan’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBfMXpV/R.INSTALL5b5f1a9491a8/metaSEM/man/lavaan2RAM.Rd:45: file link ‘lavaanify’ in package ‘lavaan’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBfMXpV/R.INSTALL5b5f1a9491a8/metaSEM/man/lavaan2RAM.Rd:48: file link ‘lavaanify’ in package ‘lavaan’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBfMXpV/R.INSTALL5b5f1a9491a8/metaSEM/man/uniR1.Rd:49: file link ‘uniR2mx’ in package ‘metaSEM’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBfMXpV/R.INSTALL5b5f1a9491a8/metaSEM/man/uniR1.Rd:49: file link ‘uniR2lavaan’ in package ‘metaSEM’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/metaSEM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpq6ScqJ/R.INSTALL174646ece8ea/metasens/man/funnel.limitmeta.Rd:125: file link ‘funnel.meta’ in package ‘meta’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/metasens.Rcheck/00install.out’ for details.
Unexported objects imported by ':::' calls:
  ‘SKAT:::Get_Davies_PVal’ ‘SKAT:::Get_Lambda’ ‘SKAT:::Get_Liu_PVal’
  ‘SKAT:::SKAT_Check_Method’ ‘SKAT:::SKAT_Optimal_Each_Q’
  ‘SKAT:::SKAT_Optimal_PValue_Davies’ ‘SKAT:::SKAT_Optimal_PValue_Liu’
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpUSGJTg/R.INSTALL2f5370e2ac73/metathis/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/metathis.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmphThC2c/R.INSTALL3dc95bc2cde7/metawho/man/deft_do.Rd:29: file link ‘rma’ in package ‘metafor’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphThC2c/R.INSTALL3dc95bc2cde7/metawho/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphThC2c/R.INSTALL3dc95bc2cde7/metawho/man/tidyeval.Rd:17: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphThC2c/R.INSTALL3dc95bc2cde7/metawho/man/tidyeval.Rd:18: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphThC2c/R.INSTALL3dc95bc2cde7/metawho/man/tidyeval.Rd:20: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphThC2c/R.INSTALL3dc95bc2cde7/metawho/man/tidyeval.Rd:21: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphThC2c/R.INSTALL3dc95bc2cde7/metawho/man/tidyeval.Rd:25: file link ‘quotation’ in package ‘rlang’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/metawho.Rcheck/00install.out’ for details.
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.
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.
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
MetSizeR : sim.pilot.data: no visible global function definition for
  ‘rnorm’
MetSizeR : sim.pilot: no visible global function definition for
  ‘rgamma’
MetSizeR : sim.pilot: no visible global function definition for ‘rnorm’
MetSizeR : samp.dist: no visible global function definition for ‘var’
MetSizeR : metsize: no visible global function definition for ‘qnorm’
MetSizeR : metsize: no visible global function definition for
  ‘quantile’
MetSizeR : metsize: no visible global function definition for ‘lm’
MetSizeR : metsize: no visible global function definition for ‘par’
MetSizeR : metsize: no visible global function definition for ‘lines’
MetSizeR : metsize: no visible global function definition for ‘abline’
MetSizeR : metsize: no visible global function definition for ‘legend’
MetSizeR : metsize: no visible global function definition for ‘arrows’
MetSizeR : metsize: no visible global function definition for ‘title’
MetSizeR : metsize: no visible global function definition for ‘text’
MetSizeR : pilot.open: no visible global function definition for
  ‘read.table’
MetSizeR : cov.open: no visible global function definition for
  ‘read.table’
MetSizeR : demo.pilot.open: no visible global function definition for
  ‘read.table’
MetSizeR : ssize.est : up.size: no visible global function definition
  for ‘pdf’
MetSizeR : ssize.est : up.size: no visible global function definition
  for ‘dev.off’
MetSizeR : <anonymous>: no visible global function definition for
  ‘help’
Undefined global functions or variables:
  abline arrows dev.off help legend lines lm par pdf qnorm quantile
  read.table rgamma rnorm text title var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "arrows", "legend", "lines", "par",
             "text", "title")
  importFrom("stats", "lm", "qnorm", "quantile", "rgamma", "rnorm",
             "var")
  importFrom("utils", "help", "read.table")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpKWVhnZ/R.INSTALL71b145fc1f61/metsyn/man/make_metdes.Rd:54: file link ‘metsyn’ in package ‘metsyn’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpKWVhnZ/R.INSTALL71b145fc1f61/metsyn/man/make_metdes.Rd:56: file link ‘metsta’ in package ‘metsyn’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpKWVhnZ/R.INSTALL71b145fc1f61/metsyn/man/make_metsta.Rd:55: file link ‘metsyn’ in package ‘metsyn’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpKWVhnZ/R.INSTALL71b145fc1f61/metsyn/man/make_metsta.Rd:57: file link ‘metdes’ in package ‘metsyn’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpKWVhnZ/R.INSTALL71b145fc1f61/metsyn/man/make_metsyn.Rd:26: file link ‘download_monthly_synop’ in package ‘metsyn’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpKWVhnZ/R.INSTALL71b145fc1f61/metsyn/man/make_metsyn.Rd:34: file link ‘metdes’ in package ‘metsyn’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpKWVhnZ/R.INSTALL71b145fc1f61/metsyn/man/make_metsyn.Rd:60: file link ‘download_monthly_synop’ in package ‘metsyn’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpKWVhnZ/R.INSTALL71b145fc1f61/metsyn/man/make_metsyn.Rd:61: file link ‘metdes’ in package ‘metsyn’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpKWVhnZ/R.INSTALL71b145fc1f61/metsyn/man/make_metsyn.Rd:63: file link ‘metsta’ in package ‘metsyn’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/metsyn.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpXX8zFU/R.INSTALL557b14ab1f46/mev/man/rmev.Rd:31: file link ‘rmvevd’ in package ‘evd’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXX8zFU/R.INSTALL557b14ab1f46/mev/man/rmev.Rd:74: file link ‘rbvevd’ in package ‘evd’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXX8zFU/R.INSTALL557b14ab1f46/mev/man/rmev.Rd:119: file link ‘rmvevd’ in package ‘evd’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXX8zFU/R.INSTALL557b14ab1f46/mev/man/rmev.Rd:119: file link ‘rbvevd’ in package ‘evd’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mev.Rcheck/00install.out’ for details.
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.
GNU make is a SystemRequirements.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpMnrXgL/R.INSTALL328d14d7443/mgcViz/man/l_fitRaster.Rd:11: file link ‘geom_raster’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMnrXgL/R.INSTALL328d14d7443/mgcViz/man/l_gridCheck2D.Rd:21: file link ‘stat_summary_hex’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMnrXgL/R.INSTALL328d14d7443/mgcViz/man/l_gridQCheck2D.Rd:22: file link ‘stat_summary_hex’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMnrXgL/R.INSTALL328d14d7443/mgcViz/man/l_vline.Rd:17: file link ‘geom_vline’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMnrXgL/R.INSTALL328d14d7443/mgcViz/man/print.checkGam.Rd:12: file link ‘grid.arrange’ in package ‘gridExtra’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMnrXgL/R.INSTALL328d14d7443/mgcViz/man/print.plotGam.Rd:23: file link ‘grid.arrange’ in package ‘gridExtra’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mgcViz.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmphUOy8B/R.INSTALL3c9172468b67/mgcv/man/bam.Rd:14: file link ‘parallel’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphUOy8B/R.INSTALL3c9172468b67/mgcv/man/bam.Rd:129: file link ‘parLapply’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphUOy8B/R.INSTALL3c9172468b67/mgcv/man/bam.Rd:188: file link ‘makeForkCluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphUOy8B/R.INSTALL3c9172468b67/mgcv/man/mgcv-parallel.Rd:11: file link ‘parallel’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphUOy8B/R.INSTALL3c9172468b67/mgcv/man/predict.bam.Rd:77: file link ‘parLapply’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mgcv.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpX9a657/R.INSTALL31e610dd5367/MGDrivE/man/Network.Rd:75: file link ‘connection’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpX9a657/R.INSTALL31e610dd5367/MGDrivE/man/Network.Rd:76: file link ‘connection’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpX9a657/R.INSTALL31e610dd5367/MGDrivE/man/get_conF_Network.Rd:10: file link ‘connection’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpX9a657/R.INSTALL31e610dd5367/MGDrivE/man/get_conM_Network.Rd:10: file link ‘connection’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpX9a657/R.INSTALL31e610dd5367/MGDrivE/man/oneDay_migrationOut_stochastic_Patch.Rd:17: file link ‘rmultinom’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpX9a657/R.INSTALL31e610dd5367/MGDrivE/man/oneDay_migrationOut_stochastic_Patch.Rd:18: file link ‘rbinom’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpX9a657/R.INSTALL31e610dd5367/MGDrivE/man/oneDay_migrationOut_stochastic_Patch.Rd:21: file link ‘rbinom’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MGDrivE.Rcheck/00install.out’ for details.
maglm: no visible global function definition for ‘combn’
maglm: no visible global function definition for ‘glm’
maglm: no visible global function definition for ‘logLik’
mamglm: no visible global function definition for ‘combn’
mamglm: no visible global function definition for ‘logLik’
ses.maglm: no visible global function definition for ‘rnorm’
ses.maglm: no visible binding for global variable ‘sd’
ses.mamglm: no visible global function definition for ‘rnorm’
ses.mamglm: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  combn glm logLik rnorm sd
Consider adding
  importFrom("stats", "glm", "logLik", "rnorm", "sd")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘mglm_vignette.rmd’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpMec1GB/R.INSTALL37f86fd51c22/mgsub/man/mgsub.Rd:19: file link ‘regexpr’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMec1GB/R.INSTALL37f86fd51c22/mgsub/man/mgsub.Rd:20: file link ‘sub’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMec1GB/R.INSTALL37f86fd51c22/mgsub/man/mgsub_censor.Rd:22: file link ‘regexpr’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMec1GB/R.INSTALL37f86fd51c22/mgsub/man/mgsub_censor.Rd:23: file link ‘sub’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mgsub.Rcheck/00install.out’ for details.
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.
Package suggested but not available for checking: ‘structSSI’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpjfuVa0/R.INSTALL5935554babd7/MHTmult/man/gbonf.p.adjust.Rd:10: file link ‘as.numeric’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpjfuVa0/R.INSTALL5935554babd7/MHTmult/man/gsidak.p.adjust.Rd:10: file link ‘as.numeric’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MHTmult.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpB4m4gN/R.INSTALL33f32214aea6/micEconCES/man/cesEst.Rd:307: file link ‘linear.hypothesis’ in package ‘car’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/micEconCES.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpNe81Vr/R.INSTALL59e74f01acbd/michelRodange/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/michelRodange.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpa70T26/R.INSTALL5ee538078977/microbenchmark/man/find_prefix.Rd:13: file link ‘min’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/microbenchmark.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmplrVZcU/R.INSTALL443a476d351f/micromap/man/mmplot.Rd:81: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplrVZcU/R.INSTALL443a476d351f/micromap/man/mmplot.Rd:143: file link ‘scale_x_continuous’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/micromap.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Ex01-WFLung-2000-2004-State-Dot-County-Box.pdf’
  ‘Ex02-WmLung50-70-Arrow-Bar.pdf’ ‘Ex03-Time-Series-with-Conf.pdf’
  ‘Ex04-Scatter-Dots.pdf’ ‘Ex05-Stkd-Bar-var-height.pdf’
  ‘Ex06-Stkd-Bar-fixedheight-nodot.pdf’ ‘Ex07-Educ-Centered-Bar.pdf’
  ‘Ex08-DotSignificants.pdf’ ‘Ex09-Kansas Population and
  Inc-8.5x14-sn.pdf’ ‘Ex10-Kansas Population and Inc-11x17.pdf’
  ‘Ex11-New York Pop 2010 and Change-sn colSize.pdf’ ‘Ex12-MD Pop 1970
  and 2010 plus change-map.pdf’ ‘Ex13-China 2013 Population.pdf’
  ‘Ex14-Seoul 2012 Population.pdf’ ‘Ex15-Utah Population.pdf’
  ‘Ex16_state.x77_no_DC.pdf’ ‘Ex17_state.x77_DCasNA_D.pdf’ ‘Ex18_Africa
  Micromap-11x17.pdf’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpsUSXbR/R.INSTALL733c2fbae5c8/migui/man/migui.Rd:32: file link ‘mi-package’ in package ‘mi’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/migui.Rcheck/00install.out’ for details.
.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').
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpaT6qDX/R.INSTALL41e838dc3e15/MIIVsem/man/miivs.Rd:11: file link ‘lavaanify’ in package ‘lavaan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MIIVsem.Rcheck/00install.out’ for details.
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.
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.
Rd file 'MImix.Rd':
  \usage lines wider than 90 characters:
     MImix(results,variances,weights = 1/length(results), percentiles = c(0.025, 0.5, 0.975), ...) 

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp6X1mkI/R.INSTALL467066387a7f/MIMSunit/man/iir.Rd:43: file link ‘cheby2’ in package ‘signal’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6X1mkI/R.INSTALL467066387a7f/MIMSunit/man/interpolate_signal.Rd:19: file link ‘spline’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6X1mkI/R.INSTALL467066387a7f/MIMSunit/man/interpolate_signal.Rd:20: file link ‘approx’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MIMSunit.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpbvx9hd/R.INSTALL1a2431f08c81/miniCRAN/man/getCranDescription.Rd:23: file link ‘CRAN_package_db’ in package ‘tools’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpbvx9hd/R.INSTALL1a2431f08c81/miniCRAN/man/plot.pkgDepGraph.Rd:24: file link ‘igraph.plotting’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpbvx9hd/R.INSTALL1a2431f08c81/miniCRAN/man/plot.pkgDepGraph.Rd:27: file link ‘igraph.plotting’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/miniCRAN.Rcheck/00install.out’ for details.
rminimax: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpz1S574/R.INSTALL37af276bcbc3/miniMeta/man/plotOptions.Rd:14: file link ‘forest.meta’ in package ‘meta’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/miniMeta.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpktYEoN/R.INSTALL320a5637fc9d/miniUI/man/miniContentPanel.Rd:13: file link ‘fillCol’ in package ‘shiny’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/miniUI.Rcheck/00install.out’ for details.
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.
Found the following files/directories:
  ‘glycolysis.xml’ ‘glycolysis_desc.tsv’ ‘glycolysis_met.tsv’
  ‘glycolysis_react.tsv’
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.
Rd file 'minxent.multiple.Rd':
  \examples lines wider than 100 characters:
     minxent.multiple(q=q,G=G,eta=eta,c(0,0)) #estimates of lagrangian multipliers and MinxEnt distribution

Rd file 'minxent.single.Rd':
  \examples lines wider than 100 characters:
     minxent.single(q=q,G=G,eta=eta,c(0)) # estimate of lagrangian multipliers and Kullback minimimum cross entropy distribution

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpvoAJnW/R.INSTALL5e93683d4df0/mipfp/man/CompareMaxDev.Rd:42: file link ‘error.margins.mipfp’ in package ‘mipfp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpvoAJnW/R.INSTALL5e93683d4df0/mipfp/man/Estimate.Rd:142: file link ‘gof.estimates.mipfp’ in package ‘mipfp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpvoAJnW/R.INSTALL5e93683d4df0/mipfp/man/Estimate.Rd:145: file link ‘print.mipfp’ in package ‘mipfp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpvoAJnW/R.INSTALL5e93683d4df0/mipfp/man/ObtainModelEstimates.Rd:50: file link ‘Rsolnp’ in package ‘Rsolnp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpvoAJnW/R.INSTALL5e93683d4df0/mipfp/man/ObtainModelEstimates.Rd:110: file link ‘Rsolnp’ in package ‘Rsolnp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpvoAJnW/R.INSTALL5e93683d4df0/mipfp/man/confint.mipfp.Rd:61: file link ‘confint.default’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mipfp.Rcheck/00install.out’ for details.
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.

Found the following calls to attach():
File ‘MIPHENO/R/cdf.pval.R’:
  attach(sample.cdf)
See section ‘Good practice’ in ‘?attach’.
.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.
Found the following files/directories:
  ‘GGplots.pdf’ ‘Heatmap.pdf’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpI03ZwT/R.INSTALL506b605fa27/mi/man/bounded.Rd:12: file link ‘rtruncnorm’ in package ‘truncnorm’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpI03ZwT/R.INSTALL506b605fa27/mi/man/rdata.frame.Rd:42: file link ‘rmsn’ in package ‘sn’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mi.Rcheck/00install.out’ for details.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Malformed Description field: should contain one or more complete sentences.
fisher.combination: no visible global function definition for ‘pchisq’
gs.test: no visible global function definition for ‘ks.test’
gs.test: no visible global function definition for ‘wilcox.test’
gs.test: no visible global function definition for ‘fisher.test’
inverse.normal.combination: no visible global function definition for
  ‘qnorm’
inverse.normal.combination: no visible global function definition for
  ‘pnorm’
limma.one.sided: no visible global function definition for ‘pt’
Undefined global functions or variables:
  fisher.test ks.test pchisq pnorm pt qnorm wilcox.test
Consider adding
  importFrom("stats", "fisher.test", "ks.test", "pchisq", "pnorm", "pt",
             "qnorm", "wilcox.test")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpBWEAym/R.INSTALL398f5ea26092/misc3d/man/contour3d.Rd:61: file link ‘drawScene.rgl’ in package ‘misc3d’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBWEAym/R.INSTALL398f5ea26092/misc3d/man/drawScene.Rd:28: file link ‘panel.3dwire’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBWEAym/R.INSTALL398f5ea26092/misc3d/man/parametric3d.Rd:52: file link ‘drawScene.rgl’ in package ‘misc3d’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/misc3d.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘rgl’ ‘tkrplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘canonicalizeAndMergeScene’ ‘colorScene’ ‘t2ve’ ‘vertexNormals’
  ‘vertexTriangles’
Found the following files/directories:
  ‘nmix.off’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpxw2vdh/R.INSTALL3acb5a782f91/miscF/man/curve.polynomial.rjmcmc.Rd:68: file link ‘sm.spline’ in package ‘pspline’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpxw2vdh/R.INSTALL3acb5a782f91/miscF/man/rMultinom.Rd:25: file link ‘rmultinom’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/miscF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpawNpe1/R.INSTALL48a05378667/miscset/man/ggplotGrid.Rd:46: file link ‘grid.arrange’ in package ‘gridExtra’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpawNpe1/R.INSTALL48a05378667/miscset/man/info.Rd:23: file link ‘session_info’ in package ‘devtools’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpawNpe1/R.INSTALL48a05378667/miscset/man/strextr.Rd:34: file link ‘str_extract_all’ in package ‘stringr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/miscset.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpCAeoDn/R.INSTALL10213302e953/miscTools/man/compPlot.Rd:18: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpCAeoDn/R.INSTALL10213302e953/miscTools/man/ddnorm.Rd:30: file link ‘dnorm’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/miscTools.Rcheck/00install.out’ for details.
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.
AndersonDarling: no visible global function definition for ‘spline’
Hawkins: no visible global function definition for ‘cov’
Hawkins: no visible global function definition for ‘pf’
Impute: no visible global function definition for ‘cov’
Mimpute: no visible global function definition for ‘rnorm’
SimNey: no visible global function definition for ‘runif’
TestMCARNormality: no visible global function definition for ‘cov’
TestMCARNormality: no visible global function definition for ‘pchisq’
TestUNey: no visible global function definition for ‘pchisq’
boxplot.testhomosc: no visible global function definition for ‘par’
boxplot.testhomosc: no visible global function definition for ‘title’
boxplot.testhomosc: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cov par pchisq pf rnorm runif spline title
Consider adding
  importFrom("graphics", "abline", "par", "title")
  importFrom("stats", "cov", "pchisq", "pf", "rnorm", "runif", "spline")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp2zpNyT/R.INSTALL69d641c11b10/missMethods/man/evaluate_imputed_values.Rd:84: file link ‘is.na’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp2zpNyT/R.INSTALL69d641c11b10/missMethods/man/median.factor.Rd:29: file link ‘median.default’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/missMethods.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [6s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(missMethods)
  > 
  > 
  > test_check("missMethods")
  ── 1. Error: delete_MAR_censoring() and delete_cutoff(), which is called by
      
  missing values are not allowed in subscripted assignments of data frames
  Backtrace:
    1. testthat::expect_equal(...)
    7. missMethods::delete_MAR_censoring(...)
    8. missMethods:::delete_censoring(...)
   10. base::`[<-.data.frame`(`*tmp*`, na_indices, miss_cols[i], value = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 539 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: delete_MAR_censoring() and delete_cutoff(), which is called by
            delete_MAR_censoring(), work (@test-delete_censoring.R#104) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpLVir4j/R.INSTALL48be2f20a2cc/missSBM/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/missSBM.Rcheck/00install.out’ for details.
'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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpQaMZAK/R.INSTALL5bc73504ddbe/mistr/man/fdist.Rd:21: file link ‘FDist’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQaMZAK/R.INSTALL5bc73504ddbe/mistr/man/fdist.Rd:29: file link ‘FDist’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQaMZAK/R.INSTALL5bc73504ddbe/mistr/man/multinomdist.Rd:21: file link ‘Multinomial’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQaMZAK/R.INSTALL5bc73504ddbe/mistr/man/multinomdist.Rd:29: file link ‘Multinomial’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQaMZAK/R.INSTALL5bc73504ddbe/mistr/man/q.default.Rd:37: file link ‘q’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQaMZAK/R.INSTALL5bc73504ddbe/mistr/man/q_approxfun.Rd:27: file link ‘approx’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQaMZAK/R.INSTALL5bc73504ddbe/mistr/man/summary_comp_fit.Rd:15: file link ‘mle2-class’ in package ‘bbmle’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQaMZAK/R.INSTALL5bc73504ddbe/mistr/man/summary_comp_fit.Rd:21: file link ‘mle2-class’ in package ‘bbmle’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mistr.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘imputation.R’ ‘imputation.dat’ ‘imputation.inp’ ‘imputation.sav’
  ‘imputation.sps’ ‘imputation1.dat’ ‘imputation2.dat’
  ‘imputation3.dat’ ‘imputation4.dat’ ‘imputation5.dat’
  ‘imputationlist.dat’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmppkhtkM/R.INSTALL43745e4961f/miWQS/man/impute.multivariate.bayesian.Rd:17: file link ‘J’ in package ‘matrixNormal’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmppkhtkM/R.INSTALL43745e4961f/miWQS/man/impute.multivariate.bayesian.Rd:19: file link ‘I’ in package ‘matrixNormal’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmppkhtkM/R.INSTALL43745e4961f/miWQS/man/make.quantile.matrix.Rd:28: file link ‘.bincode’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmppkhtkM/R.INSTALL43745e4961f/miWQS/man/plot.wqs.Rd:5: file link ‘ggplot2’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/miWQS.Rcheck/00install.out’ for details.
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpqHYnKa/R.INSTALL1d7f1fd71e07/MixedPsy/man/xplode.Rd:53: file link ‘lme4’ in package ‘lme4’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MixedPsy.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpWe8FMV/R.INSTALL1e284e505156/mixggm/man/control-parameters.Rd:68: file link ‘GA’ in package ‘GA’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpWe8FMV/R.INSTALL1e284e505156/mixggm/man/searchGGM.Rd:87: file link ‘GA’ in package ‘GA’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mixggm.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpoyvL3t/R.INSTALL13211db6a584/mixsqp/man/mixkwdual.Rd:37: file link ‘mosek’ in package ‘Rmosek’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mixsqp.Rcheck/00install.out’ for details.
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.
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.
Found the following files/directories:
  ‘ascii3d.txt’ ‘condor_3dMKDE.dat’ ‘condor_3dMKDE.vtk’
  ‘condor_3dMKDE.xdmf’ ‘condor_dem.dat’ ‘condor_dem.vtk’
  ‘condor_dem.xdmf’ ‘condor_locations.vtk’ ‘condor_path.vtk’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpADoufe/R.INSTALL1ef23386159a/mkin/man/loftest.Rd:21: file link ‘lrtest.default’ in package ‘lmtest’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpADoufe/R.INSTALL1ef23386159a/mkin/man/lrtest.mkinfit.Rd:32: file link ‘lrtest.default’ in package ‘lmtest’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mkin.Rcheck/00install.out’ for details.
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.
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘developing-with-mlapi.Rmd’
Non-standard file/directory found at top level:
  ‘Data-Administration.R’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpFdvUAB/R.INSTALL61d05eefa125/mlearning/man/confusion.Rd:137: file link ‘cm.colors’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mlearning.Rcheck/00install.out’ for details.
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.
Non-standard file/directory found at top level:
  ‘CONTENTS’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpCc1Qd0/R.INSTALL78ed727709df/mle.tools/man/coxsnell.bc.Rd:127: file link ‘D’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpCc1Qd0/R.INSTALL78ed727709df/mle.tools/man/expected.varcov.Rd:125: file link ‘D’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpCc1Qd0/R.INSTALL78ed727709df/mle.tools/man/observed.varcov.Rd:95: file link ‘D’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mle.tools.Rcheck/00install.out’ for details.
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').
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpG7diGN/R.INSTALL1f3c2b67b6a1/mlflow/man/reexports.Rd:16: file link ‘%>%’ in package ‘purrr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpG7diGN/R.INSTALL1f3c2b67b6a1/mlflow/man/reexports.Rd:18: file link ‘%||%’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpG7diGN/R.INSTALL1f3c2b67b6a1/mlflow/man/reexports.Rd:20: file link ‘%<-%’ in package ‘zeallot’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mlflow.Rcheck/00install.out’ for details.
Non-standard file/directory found at top level:
  ‘CHANGELOG.txt’
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.
Rd file 'SortModes.Rd':
  \examples lines wider than 100 characters:
             # A) Computation of relative data power. Store values in vector of size H=ncp. Could use different criterion here.

Rd file 'mlica.rd':
  \examples lines wider than 100 characters:
                 print("Consider either increasing the threshold for pca eigenvalues to perform ICA on a smaller subspace or increasing maxi ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpgpP65H/R.INSTALL3cadeb440cf/mlogitBMA/man/summary.bic.mlogit.Rd:26: file link ‘summary.bic.glm’ in package ‘BMA’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpgpP65H/R.INSTALL3cadeb440cf/mlogitBMA/man/summary.bic.mlogit.Rd:28: file link ‘plot.bic.glm’ in package ‘BMA’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpgpP65H/R.INSTALL3cadeb440cf/mlogitBMA/man/summary.bic.mlogit.Rd:30: file link ‘imageplot.bma’ in package ‘BMA’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mlogitBMA.Rcheck/00install.out’ for details.
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.
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy

Found the following assignments to the global environment:
File ‘mlPhaser/R/mlPhaser.R’:
  assign("validHaploGroups", c(get("validHaploGroups", globalenv()), 
    groupStoreList), globalenv())
  assign("validHaploGroups", list(), globalenv())
Rd file 'phaseReport.Rd':
  \examples lines wider than 100 characters:
     phaseReport(my.genotypes,haplotypes, haploFreqs, outFormat="all")       # outFormat="all" is the default

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpDSsJUQ/R.INSTALL227e7c9fd65a/mlr3filters/man/mlr_filters_variance.Rd:8: file link ‘var’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mlr3filters.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpNYA013/R.INSTALL231f1411ba81/mlr3pipelines/man/Graph.Rd:93: file link ‘htmlwidgets’ in package ‘htmlwidgets’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNYA013/R.INSTALL231f1411ba81/mlr3pipelines/man/Graph.Rd:94: file link ‘htmlwidgets’ in package ‘htmlwidgets’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNYA013/R.INSTALL231f1411ba81/mlr3pipelines/man/mlr_pipeops_histbin.Rd:48: file link ‘nclass.Sturges’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mlr3pipelines.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpGi7phA/R.INSTALL3cfa7dec8850/mlr3/man/mlr_measures_classif.fbeta.Rd:7: file link ‘precision’ in package ‘mlr3measures’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGi7phA/R.INSTALL3cfa7dec8850/mlr3/man/mlr_measures_classif.fbeta.Rd:8: file link ‘recall’ in package ‘mlr3measures’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGi7phA/R.INSTALL3cfa7dec8850/mlr3/man/mlr_measures_classif.precision.Rd:15: file link ‘precision’ in package ‘mlr3measures’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGi7phA/R.INSTALL3cfa7dec8850/mlr3/man/mlr_measures_classif.recall.Rd:15: file link ‘recall’ in package ‘mlr3measures’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGi7phA/R.INSTALL3cfa7dec8850/mlr3/man/mlr_measures_classif.sensitivity.Rd:15: file link ‘sensitivity’ in package ‘mlr3measures’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGi7phA/R.INSTALL3cfa7dec8850/mlr3/man/mlr_measures_classif.specificity.Rd:15: file link ‘specificity’ in package ‘mlr3measures’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGi7phA/R.INSTALL3cfa7dec8850/mlr3/man/mlr_tasks_boston_housing.Rd:10: file link ‘BostonHousing2’ in package ‘mlbench’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGi7phA/R.INSTALL3cfa7dec8850/mlr3/man/mlr_tasks_pima.Rd:10: file link ‘PimaIndiansDiabetes2’ in package ‘mlbench’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mlr3.Rcheck/00install.out’ for details.
Depends: includes the non-default packages:
  'mlr3', 'mlr3db', 'mlr3filters', 'mlr3learners', 'mlr3pipelines',
  'mlr3tuning', 'mlr3viz', 'paradox'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package suggested but not available for checking: ‘DiceOptim’
Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.pdf’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpDMd0Q9/R.INSTALL25312104f88/mmcm/man/reexports.Rd:14: file link ‘GenzBretz’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mmcm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpo8kdEP/R.INSTALL4f545bbca8a9/mmetrics/man/define.Rd:16: file link ‘quos’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpo8kdEP/R.INSTALL4f545bbca8a9/mmetrics/man/define.Rd:12: file link ‘quo’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpo8kdEP/R.INSTALL4f545bbca8a9/mmetrics/man/define.Rd:19: file link ‘quos’ in package ‘rlang’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mmetrics.Rcheck/00install.out’ for details.
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.
Namespace with empty importFrom: ‘gee’
Malformed Description field: should contain one or more complete sentences.
mmm: no visible global function definition for ‘model.frame’
mmm: no visible global function definition for ‘model.matrix’
mmm: no visible global function definition for ‘model.response’
mmm: no visible global function definition for ‘as.formula’
mmm: no visible global function definition for ‘gee’
Undefined global functions or variables:
  as.formula gee 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').
Checking should be performed on sources prepared by ‘R CMD build’.
sadmvng: no visible global function definition for ‘cov2cor’
sadmvng: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cov2cor pnorm
Consider adding
  importFrom("stats", "cov2cor", "pnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpV0y2MZ/R.INSTALL92f2f1218f3/mnt/man/SR.Rd:19: file link ‘mvnorm.e’ in package ‘energy’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpV0y2MZ/R.INSTALL92f2f1218f3/mnt/man/SR.Rd:29: file link ‘mvnorm.e’ in package ‘energy’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mnt.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘MoBPSmaps’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpbCY1dy/R.INSTALL50b628b2a872/model4you/man/objfun.pmtree.Rd:22: file link ‘predict.party’ in package ‘partykit’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbCY1dy/R.INSTALL50b628b2a872/model4you/man/pmforest.Rd:137: file link ‘gettree’ in package ‘partykit’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbCY1dy/R.INSTALL50b628b2a872/model4you/man/print.pmtree.Rd:30: file link ‘print.party’ in package ‘partykit’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbCY1dy/R.INSTALL50b628b2a872/model4you/man/varimp.pmforest.Rd:36: file link ‘varimp.cforest’ in package ‘partykit’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/model4you.Rcheck/00install.out’ for details.
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.
Found the following files/directories:
  ‘BIO_TCandNLCD_NLCD.jpg’ ‘BIO_TCandNLCD_TCB.jpg’
  ‘BIO_TCandNLCD_TCG.jpg’ ‘BIO_TCandNLCD_TCW.jpg’
  ‘BIO_TCandNLCD_corrplot.jpg’ ‘BIO_TCandNLCD_mask_all_predictors.jpg’
  ‘BIO_TCandNLCD_projections.txt’ ‘RF_BIO_TCandNLCD_01.img’
  ‘RF_BIO_TCandNLCD_01.img.aux.xml’
  ‘RF_BIO_TCandNLCD_01_mapmake_arguments.txt’
  ‘RF_BIO_TCandNLCD_01_projections.txt’ ‘RF_BIO_TCandNLCD_OOB.csv’
  ‘RF_BIO_TCandNLCD_OOB_corrplot.jpg’
  ‘RF_BIO_TCandNLCD_OOB_corrplot.pdf’ ‘RF_BIO_TCandNLCD_OOB_error.jpg’
  ‘RF_BIO_TCandNLCD_OOB_error.pdf’
  ‘RF_BIO_TCandNLCD_OOB_importance.jpg’
  ‘RF_BIO_TCandNLCD_OOB_importance.pdf’
  ‘RF_BIO_TCandNLCD_OOB_scatterplot.jpg’
  ‘RF_BIO_TCandNLCD_OOB_scatterplot.pdf’
  ‘RF_BIO_TCandNLCD_model_building_arguments.txt’
  ‘RF_Bio_TC_model_building_arguments.txt’ ‘example.test.csv’
  ‘example.train.csv’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpadwAVT/R.INSTALL59fa4700b068/modelr/man/na.warn.Rd:15: file link ‘na.exclude’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpadwAVT/R.INSTALL59fa4700b068/modelr/man/permute.Rd:18: file link ‘select_helpers’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/modelr.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(modelr)
  > 
  > test_check("modelr")
  ── 1. Failure: typical.ordered works as expected (@test-typical.R#36)  ─────────
  typical(ordered(c("d", "d", "a", "b"))) not identical to "b".
  1/1 mismatches
  x[1]: NA
  y[1]: "b"
  
  ── 2. Failure: typical.ordered works as expected (@test-typical.R#37)  ─────────
  typical(ordered(c("d", "d", "a", "b", NA))) not identical to "b".
  1/1 mismatches
  x[1]: NA
  y[1]: "b"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 120 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: typical.ordered works as expected (@test-typical.R#36) 
  2. Failure: typical.ordered works as expected (@test-typical.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp7vUIin/R.INSTALL51afa379ab5/modelsummary/man/pipe.Rd:18: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/modelsummary.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpIu3bcs/R.INSTALL64492ec1374b/modeltests/man/augment_data_helper.Rd:33: file link ‘rownames_to_column’ in package ‘tibble’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpIu3bcs/R.INSTALL64492ec1374b/modeltests/man/check_arguments.Rd:38: file link ‘expect_true’ in package ‘testthat’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/modeltests.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpbBWxnx/R.INSTALL16b26bffc265/modeltools/man/StatModel-class.Rd:63: file link ‘lm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbBWxnx/R.INSTALL16b26bffc265/modeltools/man/StatModel-class.Rd:63: file link ‘glm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/modeltools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpzLgPvw/R.INSTALL51d8615f0da2/moderndive/man/get_regression_points.Rd:65: file link ‘augment’ in package ‘broom’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzLgPvw/R.INSTALL51d8615f0da2/moderndive/man/get_regression_summaries.Rd:33: file link ‘glance’ in package ‘broom’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzLgPvw/R.INSTALL51d8615f0da2/moderndive/man/get_regression_table.Rd:36: file link ‘tidy’ in package ‘broom’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzLgPvw/R.INSTALL51d8615f0da2/moderndive/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/moderndive.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpi8hMj2/R.INSTALL45f0252ce11b/modiscloud/man/get_date_from_POSIXct.Rd:48: file link ‘as.POSIXct’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpi8hMj2/R.INSTALL45f0252ce11b/modiscloud/man/make_POSIXct_date.Rd:54: file link ‘as.POSIXct’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/modiscloud.Rcheck/00install.out’ for details.
'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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpCtbxxv/R.INSTALL47696d592ea1/modTempEff/man/modTempEff-package.Rd:61: file link ‘mgcv’ in package ‘mgcv’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/modTempEff.Rcheck/00install.out’ for details.
.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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp8ZjMAR/R.INSTALL6b206133b47e/MoEClust/man/MoE_plotLogLik.Rd:17: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8ZjMAR/R.INSTALL6b206133b47e/MoEClust/man/MoE_plotLogLik.Rd:19: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8ZjMAR/R.INSTALL6b206133b47e/MoEClust/man/plot.MoEClust.Rd:19: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8ZjMAR/R.INSTALL6b206133b47e/MoEClust/man/plot.MoEClust.Rd:24: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MoEClust.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpqqQNrr/R.INSTALL8971f432ee6/momentuHMM/man/crawlWrap.Rd:40: file link ‘SpatialPointsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpqqQNrr/R.INSTALL8971f432ee6/momentuHMM/man/plot.miHMM.Rd:61: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpqqQNrr/R.INSTALL8971f432ee6/momentuHMM/man/plot.miSum.Rd:61: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpqqQNrr/R.INSTALL8971f432ee6/momentuHMM/man/plot.momentuHMM.Rd:59: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpqqQNrr/R.INSTALL8971f432ee6/momentuHMM/man/plotStationary.Rd:28: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpqqQNrr/R.INSTALL8971f432ee6/momentuHMM/man/prepData.Rd:62: file link ‘setZ’ in package ‘raster’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpqqQNrr/R.INSTALL8971f432ee6/momentuHMM/man/simData.Rd:127: file link ‘setZ’ in package ‘raster’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/momentuHMM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpfMdyXu/R.INSTALL43e542468c38/Momocs/man/as_df.Rd:30: file link ‘data_frame’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfMdyXu/R.INSTALL43e542468c38/Momocs/man/layers.Rd:159: file link ‘bw.nrd0’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfMdyXu/R.INSTALL43e542468c38/Momocs/man/reexports.Rd:17: file link ‘%<>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfMdyXu/R.INSTALL43e542468c38/Momocs/man/reexports.Rd:17: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfMdyXu/R.INSTALL43e542468c38/Momocs/man/reexports.Rd:17: file link ‘%$%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfMdyXu/R.INSTALL43e542468c38/Momocs/man/reexports.Rd:17: file link ‘%T>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfMdyXu/R.INSTALL43e542468c38/Momocs/man/rename.Rd:18: file link ‘rename’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Momocs.Rcheck/00install.out’ for details.
Warning: no function found corresponding to methods exports from ‘mondate’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
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.
.date.to.mondate: no visible global function definition for ‘new’
as.character.mondate: no visible global function definition for ‘slot’
Arith,array-mondate: no visible global function definition for
  ‘callGeneric’
Arith,mondate-array: no visible global function definition for
  ‘callGeneric’
Arith,mondate-mondate: no visible global function definition for
  ‘callGeneric’
Arith,mondate-numeric: no visible global function definition for
  ‘callGeneric’
Arith,numeric-mondate: no visible global function definition for
  ‘callGeneric’
Compare,mondate-ANY: no visible global function definition for
  ‘callGeneric’
Compare,mondate-ANY: no visible global function definition for
  ‘getDataPart’
Summary,mondate: no visible global function definition for
  ‘callGeneric’
[,mondate: no visible global function definition for ‘callNextMethod’
[,mondate: no visible global function definition for ‘new’
array,mondate: no visible global function definition for
  ‘callNextMethod’
as.numeric,mondate: no visible global function definition for ‘slot’
c,mondate: no visible global function definition for ‘new’
c,mondate: no visible binding for global variable ‘getDataPart’
c,mondate: no visible global function definition for ‘getDataPart’
matrix,mondate: no visible global function definition for
  ‘callNextMethod’
mondate,Date: no visible global function definition for ‘new’
mondate,POSIXt: no visible global function definition for ‘new’
mondate,missing: no visible global function definition for ‘new’
mondate,mondate: no visible global function definition for ‘new’
mondate,numeric: no visible global function definition for ‘new’
Undefined global functions or variables:
  callGeneric callNextMethod getDataPart new slot
Consider adding
  importFrom("methods", "callGeneric", "callNextMethod", "getDataPart",
             "new", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpUuOGS3/R.INSTALL14241170a0bf/Mondrian/man/mondrian.Rd:25: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpUuOGS3/R.INSTALL14241170a0bf/Mondrian/man/mondrian.Rd:49: file link ‘brewer.pal’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Mondrian.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘MonetDBLite’
Missing or unexported objects:
  ‘dplyr::base_agg’ ‘dplyr::base_scalar’ ‘dplyr::build_sql’
  ‘dplyr::is.ident’ ‘dplyr::sql_infix’ ‘dplyr::sql_prefix’
  ‘dplyr::sql_translator’ ‘dplyr::sql_variant’ ‘dplyr::src_sql’
  ‘dplyr::tbl_sql’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpBXYenb/R.INSTALL47f666b25aa1/mongolite/man/mongo.Rd:55: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpBXYenb/R.INSTALL47f666b25aa1/mongolite/man/ssl_options.Rd:19: file link ‘read_cert’ in package ‘openssl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mongolite.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpSgp9dB/R.INSTALL67572aad1855/monitoR/man/fileCopyRename.Rd:50: file link ‘OlsonNames’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpSgp9dB/R.INSTALL67572aad1855/monitoR/man/specCols.Rd:40: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpSgp9dB/R.INSTALL67572aad1855/monitoR/man/specCols.Rd:40: file link ‘topo.colors’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpSgp9dB/R.INSTALL67572aad1855/monitoR/man/specCols.Rd:40: file link ‘terrain.colors’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpSgp9dB/R.INSTALL67572aad1855/monitoR/man/templateMatching.Rd:78: file link ‘OlsonNames’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/monitoR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpwI85or/R.INSTALL489876f991ee/monographaR/man/monographaR-package.Rd:41: file link ‘sp’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/monographaR.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘test.csv’ ‘test1.csv’ ‘testsummary.csv’ ‘testsummary1.csv’
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.
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.
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.
Rd file 'cor.gen.Rd':
  \usage lines wider than 90 characters:
     cor.gen(num.subj, x.mean, x.sd, y.mean, y.sd, correlation, data.dec = 2, x.name = "Variable X", y.name = "Variable Y")

Rd file 'stat.gen.Rd':
  \usage lines wider than 90 characters:
     stat.gen(num.subj, target.mean, target.sd, data.dec = 2, neg.data = TRUE, x.name = "Variable X")

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘BMI BISS Correlation MorseGen Results.txt’ ‘Control MorseGen
  Results.txt’ ‘Massage MorseGen Results.txt’ ‘Variable X MorseGen
  Results.txt’ ‘Variable X Variable Y Correlation MorseGen Results.txt’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpk85ywd/R.INSTALL53b0ba194c9/morse/man/morse-package.Rd:92: file link ‘rjags’ in package ‘rjags’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpk85ywd/R.INSTALL53b0ba194c9/morse/man/morse-package.Rd:93: file link ‘ggplot2’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpk85ywd/R.INSTALL53b0ba194c9/morse/man/plot.reproData.Rd:42: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpk85ywd/R.INSTALL53b0ba194c9/morse/man/plot.reproFitTT.Rd:67: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpk85ywd/R.INSTALL53b0ba194c9/morse/man/plotDoseResponse.reproData.Rd:47: file link ‘pois.exact’ in package ‘epitools’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpk85ywd/R.INSTALL53b0ba194c9/morse/man/plotDoseResponse.reproData.Rd:54: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpk85ywd/R.INSTALL53b0ba194c9/morse/man/plotDoseResponse.reproData.Rd:74: file link ‘pois.exact’ in package ‘epitools’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpk85ywd/R.INSTALL53b0ba194c9/morse/man/plotDoseResponse.survDataCstExp.Rd:48: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/morse.Rcheck/00install.out’ for details.
Mort1Dsmooth: no visible global function definition for ‘time’
Mort1Dsmooth: no visible global function definition for ‘glm’
Mort1Dsmooth: no visible binding for global variable ‘poisson’
Mort1Dsmooth_optimize: no visible global function definition for
  ‘median’
Mort2Dsmooth: no visible global function definition for ‘glm’
Mort2Dsmooth: no visible binding for global variable ‘poisson’
Mort2Dsmooth: no visible global function definition for ‘median’
Mort2Dsmooth_optimize: no visible global function definition for
  ‘median’
plot.Mort1Dsmooth: no visible global function definition for ‘matplot’
plot.Mort2Dsmooth: no visible global function definition for ‘quantile’
predict.Mort1Dsmooth: no visible global function definition for ‘glm’
predict.Mort1Dsmooth: no visible binding for global variable ‘poisson’
predict.Mort2Dsmooth: no visible global function definition for ‘glm’
predict.Mort2Dsmooth: no visible binding for global variable ‘poisson’
print.summary.Mort1Dsmooth: no visible global function definition for
  ‘quantile’
print.summary.Mort2Dsmooth: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  glm matplot median poisson quantile time
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "glm", "median", "poisson", "quantile", "time")
to your NAMESPACE file.
Running ‘testthat.R’ [3s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mortyr)
  > 
  > test_check("mortyr")
  ── 1. Error: (unknown) (@test_returned_data.R#1)  ──────────────────────────────
  argument is of length zero
  Backtrace:
   1. mortyr::get_characters()
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test_returned_data.R#1) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp86ynl3/R.INSTALL62324184d6/mosaicCalc/man/connector.Rd:8: file link ‘connector’ in package ‘mosaic’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp86ynl3/R.INSTALL62324184d6/mosaicCalc/man/smoother.Rd:8: file link ‘smoother’ in package ‘mosaic’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp86ynl3/R.INSTALL62324184d6/mosaicCalc/man/spliner.Rd:8: file link ‘spliner’ in package ‘mosaic’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mosaicCalc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp4jORKp/R.INSTALL6eaa2c10e490/mosaicCore/man/na.warn.Rd:15: file link ‘na.exclude’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mosaicCore.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘fastR’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmphP8qVt/R.INSTALLa3ebeed67d/mosmafs/man/slickEcr.Rd:83: file link ‘replaceMuPlusLambda’ in package ‘ecr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mosmafs.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpl1ID3L/R.INSTALL1be04575f479/mosum/man/plot.mosum.cpts.Rd:27: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpl1ID3L/R.INSTALL1be04575f479/mosum/man/plot.mosum.stat.Rd:21: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mosum.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp4E6k9V/R.INSTALL274d239f4d98/move/man/move.Rd:25: file link ‘ltraj’ in package ‘adehabitatLT’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4E6k9V/R.INSTALL274d239f4d98/move/man/move.Rd:45: file link ‘ltraj’ in package ‘adehabitatLT’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4E6k9V/R.INSTALL274d239f4d98/move/man/move2ade.Rd:24: file link ‘ltraj’ in package ‘adehabitatLT’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4E6k9V/R.INSTALL274d239f4d98/move/man/turnAngleGc.Rd:23: file link ‘finalBearing’ in package ‘geosphere’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/move.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpjavIIK/R.INSTALL44bc6f01ea01/moveVis/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/moveVis.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
Package vignette with placeholder title ‘Vignette Title’:
  ‘mozzie.Rmd’
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘mpa-Ex.R’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpVLJjlC/R.INSTALL20697bc3cf34/mpath/man/predict.zipath.Rd:64: file link ‘fitted’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mpath.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpYRSf7X/R.INSTALL1f662e275ee8/MPDiR/man/panel.psyfun.Rd:6: file link ‘panel.lmline’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MPDiR.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpFqi1ab/R.INSTALL56605b65df24/mpMap2/man/detailedPedigree-class.Rd:53: file link ‘detailedPedigree’ in package ‘mpMap2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpFqi1ab/R.INSTALL56605b65df24/mpMap2/man/estimateMap.Rd:27: file link ‘qtl-package’ in package ‘qtl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mpMap2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp0NASTc/R.INSTALL27ad28654f42/mpmcorrelogram/man/mpmcorrelogram.Rd:103: file link ‘mantel.partial’ in package ‘vegan’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp0NASTc/R.INSTALL27ad28654f42/mpmcorrelogram/man/mpmcorrelogram.Rd:164: file link ‘mantel.partial’ in package ‘vegan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mpmcorrelogram.Rcheck/00install.out’ for details.
Dependence on R version ‘3.6.2’ not with patchlevel 0
'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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpx0Y1MW/R.INSTALL20ff1b4488a9/mppa/man/place.Rd:4: file link ‘plot,mproc-method’ in package ‘mppa’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpx0Y1MW/R.INSTALL20ff1b4488a9/mppa/man/place.Rd:7: file link ‘plot,mproc-method’ in package ‘mppa’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpx0Y1MW/R.INSTALL20ff1b4488a9/mppa/man/place.Rd:23: file link ‘plot,mproc-method’ in package ‘mppa’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mppa.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpPk46tB/R.INSTALL4d68231a2660/MPTinR/man/bmpt.fia.Rd:94: file link ‘sfInit’ in package ‘snowfall’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPk46tB/R.INSTALL4d68231a2660/MPTinR/man/bmpt.fia.Rd:94: file link ‘sfClusterSplit’ in package ‘snowfall’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MPTinR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp2fYC8V/R.INSTALL56ee784e1b1/MPTmultiverse/man/fit_mpt.Rd:89: file link ‘unnest’ in package ‘tidyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MPTmultiverse.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp2aYVud/R.INSTALL45962460fc95/mptools/man/mp_animate.Rd:87: file link ‘im.convert’ in package ‘animation’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mptools.Rcheck/00install.out’ for details.
ppersp: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette
Consider adding
  importFrom("grDevices", "colorRampPalette")
to your NAMESPACE file.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpXkTCHW/R.INSTALL45fc22efda9/MRFcov/man/MRFcov.Rd:31: file link ‘makePSOCKcluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXkTCHW/R.INSTALL45fc22efda9/MRFcov/man/MRFcov_spatial.Rd:31: file link ‘makePSOCKcluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXkTCHW/R.INSTALL45fc22efda9/MRFcov/man/MRFcov_spatial.Rd:51: file link ‘smooth.construct2’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXkTCHW/R.INSTALL45fc22efda9/MRFcov/man/MRFcov_spatial.Rd:96: file link ‘smooth.construct2’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXkTCHW/R.INSTALL45fc22efda9/MRFcov/man/bootstrap_MRF.Rd:35: file link ‘makePSOCKcluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXkTCHW/R.INSTALL45fc22efda9/MRFcov/man/cv_MRF_diag.Rd:38: file link ‘makePSOCKcluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXkTCHW/R.INSTALL45fc22efda9/MRFcov/man/cv_MRF_diag.Rd:99: file link ‘createFolds’ in package ‘caret’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXkTCHW/R.INSTALL45fc22efda9/MRFcov/man/predict_MRFnetworks.Rd:59: file link ‘graph.adjacency’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MRFcov.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘MRH_lung’
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.
Malformed Title field: should not end in a period.
MRwarp: no visible global function definition for ‘dev.new’
MRwarp: no visible global function definition for ‘lines’
MRwarp: no visible global function definition for ‘points’
MRwarp: no visible global function definition for ‘hist’
Undefined global functions or variables:
  dev.new hist lines points
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "lines", "points")
to your NAMESPACE file.
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpIQcKEC/R.INSTALL518a1b33cf94/msaenet/man/predict.msaenet.Rd:17: file link ‘predict.ncvreg’ in package ‘ncvreg’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpIQcKEC/R.INSTALL518a1b33cf94/msaenet/man/predict.msaenet.Rd:18: file link ‘predict.ncvsurv’ in package ‘ncvreg’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/msaenet.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpu8Ukpv/R.INSTALL58df2b7232f9/MSCMT/man/ggplot.mscmt.Rd:34: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpu8Ukpv/R.INSTALL58df2b7232f9/MSCMT/man/ggplot.mscmt.Rd:37: file link ‘Date’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpu8Ukpv/R.INSTALL58df2b7232f9/MSCMT/man/improveSynth.Rd:30: file link ‘mscmt’ in package ‘MSCMT’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpu8Ukpv/R.INSTALL58df2b7232f9/MSCMT/man/improveSynth.Rd:33: file link ‘mscmt’ in package ‘MSCMT’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpu8Ukpv/R.INSTALL58df2b7232f9/MSCMT/man/plot.mscmt.Rd:66: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MSCMT.Rcheck/00install.out’ for details.
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').
Found the following files/directories:
  ‘test.txt’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpn3EzkX/R.INSTALL6fd5ba8746b/msgr/man/try_pmap.Rd:47: file link ‘pmap’ in package ‘purrr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/msgr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpTYVqkt/R.INSTALL726332e21869/msigdbr/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/msigdbr.Rcheck/00install.out’ for details.
MSIseq.classify: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpSP8lud/R.INSTALL56958bc7f71/msmtools/man/survplot.Rd:25: file link ‘absorbing.msm’ in package ‘msm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/msmtools.Rcheck/00install.out’ for details.
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.
'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.
Found the following files/directories:
  ‘mtkMCDesigner.R’ ‘mtkRegressionTestAnalyser.R’ ‘mtkWWEvaluator.R’
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').
Rd file 'CrossValidationMuFicokmAll.Rd':
  \examples lines wider than 100 characters:
                     apply(matrix(1:DNest$n),1,function(x) CrossValidationMuFicokmAll(mymodel,x)$CVerrall)

Rd file 'MuFicokm.Rd':
  \usage lines wider than 90 characters:
                     noise.var = NULL, estim.method = "MLE", penalty = NULL, optim.method = "BFGS", 

Rd file 'predict.MuFicokm.Rd':
  \examples lines wider than 100 characters:
                                                     rev(predictionsSK_UK$mean-2*sqrt(predictionsSK_UK$sig2))),

These lines will be truncated in the PDF manual.
Package vignette with placeholder title ‘Vignette Title’:
  ‘MullerPlot.Rmd’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp2njzTw/R.INSTALL71ed4ffa8167/multbxxc/man/mult_bxxc.Rd:12: file link ‘simple_triplet_matrix’ in package ‘slam’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multbxxc.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpD4TJuZ/R.INSTALL34106e244b67/multfisher/man/plot.multfisher.Rd:20: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multfisher.Rcheck/00install.out’ for details.
plotOptionValues: no visible global function definition for ‘persp’
Undefined global functions or variables:
  persp
Consider adding
  importFrom("graphics", "persp")
to your NAMESPACE file.
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.
calculate_direction: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpawsp0V/R.INSTALL68715593c71f/multicolor/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multicolor.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpxeCOPF/R.INSTALL733a4f0f3630/multicon/man/multicon-package.Rd:51: file link ‘psych’ in package ‘psych’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multicon.Rcheck/00install.out’ for details.
betas_plot: no visible global function definition for ‘cov2cor’
betas_plot: no visible global function definition for
  ‘colorRampPalette’
betas_plot: no visible global function definition for ‘pdf’
betas_plot: no visible global function definition for ‘dev.off’
mhplot: no visible global function definition for ‘read.table’
mhplot: no visible global function definition for ‘pdf’
mhplot: no visible global function definition for ‘points’
mhplot: no visible global function definition for ‘abline’
mhplot: no visible global function definition for ‘axis’
mhplot: no visible global function definition for ‘dev.off’
multi_meta: no visible global function definition for ‘write.table’
multi_meta: no visible global function definition for ‘read.table’
multi_meta: no visible global function definition for ‘pchisq’
qqplotter: no visible global function definition for ‘read.table’
qqplotter: no visible global function definition for ‘qchisq’
qqplotter: no visible global function definition for ‘ppoints’
qqplotter: no visible global function definition for ‘median’
qqplotter: no visible global function definition for ‘pchisq’
qqplotter: no visible global function definition for ‘pdf’
qqplotter: no visible global function definition for ‘abline’
qqplotter: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  abline axis colorRampPalette cov2cor dev.off median pchisq pdf points
  ppoints qchisq read.table write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "points")
  importFrom("stats", "cov2cor", "median", "pchisq", "ppoints", "qchisq")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘Output_from_running_example.txt’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpH40MK2/R.INSTALL5cabd3e75e5/multimode/man/locmodes.Rd:26: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpH40MK2/R.INSTALL5cabd3e75e5/multimode/man/locmodes.Rd:33: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpH40MK2/R.INSTALL5cabd3e75e5/multimode/man/plot.gtmod.Rd:32: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpH40MK2/R.INSTALL5cabd3e75e5/multimode/man/plot.gtmod.Rd:34: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpH40MK2/R.INSTALL5cabd3e75e5/multimode/man/plot.gtmod.Rd:36: file link ‘image.default’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpH40MK2/R.INSTALL5cabd3e75e5/multimode/man/plot.gtmod.Rd:36: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multimode.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp0JDlcw/R.INSTALL5e3e135fb4ec/multinets/man/is_multilevel.Rd:43: file link ‘is_bipartite’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multinets.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rPorta’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpkrvbha/R.INSTALL611128e0b3b5/multipanelfigure/man/fill_panel.Rd:34: file link ‘gList’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpkrvbha/R.INSTALL611128e0b3b5/multipanelfigure/man/fill_panel.Rd:35: file link ‘grob’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpkrvbha/R.INSTALL611128e0b3b5/multipanelfigure/man/fill_panel.Rd:53: file link ‘textGrob’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpkrvbha/R.INSTALL611128e0b3b5/multipanelfigure/man/fill_panel.Rd:87: file link ‘grob’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpkrvbha/R.INSTALL611128e0b3b5/multipanelfigure/man/fill_panel.Rd:87: file link ‘gList’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpkrvbha/R.INSTALL611128e0b3b5/multipanelfigure/man/fill_panel.Rd:88: file link ‘gTree’ in package ‘grid’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpkrvbha/R.INSTALL611128e0b3b5/multipanelfigure/man/grapes-greater-than-grapes.Rd:7: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpkrvbha/R.INSTALL611128e0b3b5/multipanelfigure/man/grapes-less-than-greater-than-grapes.Rd:7: file link ‘%<>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpkrvbha/R.INSTALL611128e0b3b5/multipanelfigure/man/grob_dimensions.Rd:17: file link ‘grob’ in package ‘grid’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multipanelfigure.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp4ZZaZi/R.INSTALL5ecd5704f253/multiPIM/man/Candidates.Rd:31: file link ‘profL1’ in package ‘penalized’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4ZZaZi/R.INSTALL5ecd5704f253/multiPIM/man/multiPIMboot.Rd:31: file link ‘parallel’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4ZZaZi/R.INSTALL5ecd5704f253/multiPIM/man/multiPIMboot.Rd:33: file link ‘RNGkind’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4ZZaZi/R.INSTALL5ecd5704f253/multiPIM/man/multiPIMboot.Rd:33: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multiPIM.Rcheck/00install.out’ for details.
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 vignette with placeholder title ‘Vignette Title’:
  ‘Sensitivity_analysis.Rmd’
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.
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.
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.
'library' or 'require' calls to packages already attached by Depends:
  ‘car’ ‘gplots’ ‘pdist’ ‘pls’ ‘rrcov’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘bitops’ ‘caTools’ ‘car’ ‘gplots’ ‘gtools’ ‘mvtnorm’ ‘pcaPP’ ‘pdist’
  ‘pls’ ‘robustbase’ ‘rrcov’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'Plot.pca.score.Rd':
  \examples lines wider than 100 characters:
             ylab = ylab, xlim = lim, ylim = lim, pch = 19, sub = paste("Cumulative Proportion of Variance Explained = ", 

Rd file 'oplsda.Rd':
  \examples lines wider than 100 characters:
             ylab = ylab, xlim = lim, ylim = lim, pch = 19, sub = paste("Cumulative Proportion of Variance Explained = ", 

Rd file 'univariate.Rd':
  \usage lines wider than 90 characters:
     univariate(file, imputation = FALSE, imput, normalize = TRUE, multi.test = TRUE, plot.volcano = FALSE, save.boxplot=TRUE)

Rd file 'volcano.Rd':
  \examples lines wider than 100 characters:
                         sep = ""), sub = "(Variables in Blue are significant (Pvalue<0.05) and showed Fold Changes >1.2 or <0.8)")
                           j, sep = ""), sub = "(Variables in Blue are significant (Pvalue<0.05) and showed Fold Changes >1.2 or <0.8)")

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpfPpsDB/R.INSTALL5ec4320ca6c3/MuMIn/man/AICc.Rd:56: file link ‘AICc’ in package ‘bbmle’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfPpsDB/R.INSTALL5ec4320ca6c3/MuMIn/man/AICc.Rd:57: file link ‘aicc’ in package ‘glmulti’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MuMIn.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpJ0NZZQ/R.INSTALL773628ca349e/munsellinterpol/man/MunsellNameFromHVC.Rd:31: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJ0NZZQ/R.INSTALL773628ca349e/munsellinterpol/man/MunsellNameFromHVC.Rd:38: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJ0NZZQ/R.INSTALL773628ca349e/munsellinterpol/man/MunsellNameFromHVC.Rd:53: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJ0NZZQ/R.INSTALL773628ca349e/munsellinterpol/man/MunsellNameFromHVC.Rd:69: file link ‘formatC’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/munsellinterpol.Rcheck/00install.out’ for details.
plotFID: no visible global function definition for ‘points’
Undefined global functions or variables:
  points
Consider adding
  importFrom("graphics", "points")
to your NAMESPACE file.
Found the following files/directories:
  ‘audio.wav’
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').
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmplCRAma/R.INSTALL2dfa76ceeb02/mvabund/man/manyany.Rd:107: file link ‘residuals.manyany’ in package ‘mvabund’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplCRAma/R.INSTALL2dfa76ceeb02/mvabund/man/manyglm.Rd:222: file link ‘plot.manyglm’ in package ‘mvabund’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplCRAma/R.INSTALL2dfa76ceeb02/mvabund/man/residuals.manyglm.Rd:37: file link ‘plot.manyglm’ in package ‘mvabund’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mvabund.Rcheck/00install.out’ for details.
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.
Found the following sources/headers not terminated with a newline:
  src/sitmo/sitmo.hpp
Some compilers warn on such files.
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.
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.
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.
prepare_Rd: mvsf.Rd:16-17: Dropping empty section \details
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpnzzMKq/R.INSTALL4f84d1986e/mvSLOUCH/man/parametric.bootstrap.Rd:219: file link ‘bootstrap’ in package ‘ouch’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mvSLOUCH.Rcheck/00install.out’ for details.
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.
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 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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpuCG6h9/R.INSTALL6d4f64e59680/mycor/man/mycor.Rd:35: file link ‘parallelplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuCG6h9/R.INSTALL6d4f64e59680/mycor/man/plot.mycor.Rd:13: file link ‘parallelplot’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mycor.Rcheck/00install.out’ for details.
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.
Rd file 'myepisodes_feed_url.Rd':
  \examples lines wider than 100 characters:
     ## Not run: myepisodes_feed_url("foouser", "321654321654321", feed = "mylist", onlyunacquired = TRUE, showignored = FALSE)

Rd file 'shows_from_myepisodes.Rd':
  \examples lines wider than 100 characters:
     ## Not run: shows_from_myepisodes("foouser", "321654321654321", feed = "mylist", onlyunacquired = TRUE, showignored = FALSE)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmplJ1T2O/R.INSTALL66375e35ed92/myTAI/man/DiffGenes.Rd:73: file link ‘exactTestDoubleTail’ in package ‘edgeR’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplJ1T2O/R.INSTALL66375e35ed92/myTAI/man/DiffGenes.Rd:74: file link ‘exactTestBySmallP’ in package ‘edgeR’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/myTAI.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpgTXRWG/R.INSTALL4d0d73fb8eb4/naaccr/man/read_naaccr.Rd:18: file link ‘connection’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpgTXRWG/R.INSTALL4d0d73fb8eb4/naaccr/man/read_naaccr.Rd:40: file link ‘file’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/naaccr.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘asreml’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpzUXdgU/R.INSTALLb6757f8fa90/nadiv/man/numPed.Rd:25: file link ‘[’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzUXdgU/R.INSTALLb6757f8fa90/nadiv/man/numPed.Rd:63: file link ‘[’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzUXdgU/R.INSTALLb6757f8fa90/nadiv/man/proLik.Rd:54: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzUXdgU/R.INSTALLb6757f8fa90/nadiv/man/proLik.Rd:56: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nadiv.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘re2r’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp2KevNe/R.INSTALL6b5a1b00f645/namer/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/namer.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpH3P63W/R.INSTALL50ae4d35f1ae/naniar/man/reexports.Rd:17: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpH3P63W/R.INSTALL50ae4d35f1ae/naniar/man/reexports.Rd:19: file link ‘is_na’ in package ‘rlang’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/naniar.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘NanoStringNorm_Example_Plots_All.pdf’
  ‘NanoStringNorm_Interactive_Plot’
NAPPA: no visible binding for global variable ‘sd’
NAPPA: no visible global function definition for ‘sd’
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for ‘coef’
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for ‘lm’
calibrate.sigmoid.curve: no visible global function definition for
  ‘nls’
calibrate.sigmoid.curve: no visible binding for global variable
  ‘weights’
calibrate.sigmoid.curve: no visible global function definition for
  ‘coef’
calibrate.sigmoid.curve: no visible global function definition for
  ‘rgb’
calibrate.sigmoid.curve: no visible global function definition for
  ‘box’
calibrate.sigmoid.curve: no visible global function definition for
  ‘axis’
calibrate.sigmoid.curve: no visible global function definition for
  ‘abline’
calibrate.sigmoid.curve: no visible global function definition for
  ‘lines’
calibrate.sigmoid.curve: no visible global function definition for
  ‘predict’
calibrate.sigmoid.curve: no visible global function definition for
  ‘smooth.spline’
calibrate.sigmoid.curve : <anonymous>: no visible global function
  definition for ‘nls’
calibrate.sigmoid.curve : <anonymous>: no visible binding for global
  variable ‘weights’
calibrate.sigmoid.curve: no visible binding for global variable ‘coef’
calibrate.sigmoid.curve: no visible global function definition for ‘pf’
calibrate.sigmoid.curve: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  abline axis box coef legend lines lm nls pf predict rgb sd
  smooth.spline weights
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines")
  importFrom("stats", "coef", "lm", "nls", "pf", "predict", "sd",
             "smooth.spline", "weights")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmprt4L6w/R.INSTALL67c07a193cee/nat.nblast/man/fill_pairs_sparse_score_mat.Rd:33: file link ‘spam’ in package ‘spam’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nat.nblast.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpVBfVmm/R.INSTALL67f24523ba9a/nat.templatebrains/man/nat.templatebrains-package.Rd:44: file link ‘Rprofile’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpVBfVmm/R.INSTALL67f24523ba9a/nat.templatebrains/man/nat.templatebrains-package.Rd:97: file link ‘nat’ in package ‘nat’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nat.templatebrains.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpTDFpo2/R.INSTALL691e61d04f06/NBLDA/man/generateCountData.Rd:17: file link ‘rnbinom’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NBLDA.Rcheck/00install.out’ for details.
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.
Found the following files/directories:
  ‘sample_data.txt’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpgtwswr/R.INSTALL53db2284337c/ncappc/man/read_nm_table.Rd:26: file link ‘dplyr’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpgtwswr/R.INSTALL53db2284337c/ncappc/man/read_nm_table.Rd:40: file link ‘dplyr’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ncappc.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmphsyBe3/R.INSTALL1cf97c2ff36c/ncdf4/man/ncdf4-package.Rd:57: file link ‘ncvar_put’ in package ‘ncdf4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphsyBe3/R.INSTALL1cf97c2ff36c/ncdf4/man/ncdf4-package.Rd:74: file link ‘ncvar_put’ in package ‘ncdf4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphsyBe3/R.INSTALL1cf97c2ff36c/ncdf4/man/ncvar_def.Rd:67: file link ‘ncvar_put’ in package ‘ncdf4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphsyBe3/R.INSTALL1cf97c2ff36c/ncdf4/man/ncvar_def.Rd:108: file link ‘ncvar_put’ in package ‘ncdf4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphsyBe3/R.INSTALL1cf97c2ff36c/ncdf4/man/ncvar_def.Rd:114: file link ‘ncvar_put’ in package ‘ncdf4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphsyBe3/R.INSTALL1cf97c2ff36c/ncdf4/man/ncvar_get.Rd:80: file link ‘ncvar_put’ in package ‘ncdf4’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ncdf4.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpldIxHy/R.INSTALL681014441032/ncdf.tools/man/classR2Ncdf.Rd:17: file link ‘RNetCDF’ in package ‘RNetCDF’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpldIxHy/R.INSTALL681014441032/ncdf.tools/man/readNcdfVarName.Rd:18: file link ‘RNetCDF’ in package ‘RNetCDF’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ncdf.tools.Rcheck/00install.out’ for details.
infoNcdfVars: no visible global function definition for ‘na.omit’
modifyNcdfDefAtts: no visible global function definition for ‘na.omit’
plotDatacube: no visible global function definition for ‘runif’
plotDatacube: no visible global function definition for
  ‘colorRampPalette’
plotDatacube: no visible global function definition for ‘dev.cur’
plotDatacube: no visible global function definition for ‘dev.new’
plotDatacube: no visible global function definition for ‘layout’
plotDatacube: no visible global function definition for ‘par’
plotDatacube: no visible global function definition for ‘points’
plotDatacube: no visible global function definition for ‘text’
plotDatacube: no visible global function definition for ‘plot.new’
plotDatacube: no visible global function definition for ‘mtext’
plotDatacube: no visible global function definition for ‘rgb’
plotDatacube: no visible global function definition for ‘legend’
transNcdfRotate: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  colorRampPalette dev.cur dev.new layout legend mtext na.omit par
  plot.new points rgb runif text
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.cur", "dev.new",
             "rgb")
  importFrom("graphics", "layout", "legend", "mtext", "par", "plot.new",
             "points", "text")
  importFrom("stats", "na.omit", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘test.nc’
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: ‘re2r’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpa3ovZd/R.INSTALL1ea45949cef/ncvreg/man/auc.Rd:28: file link ‘survConcordance’ in package ‘survival’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ncvreg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpdtqskt/R.INSTALL1c579de740b/ndtv/man/render.d3movie.Rd:152: file link ‘htmlwidgets’ in package ‘htmlwidgets’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ndtv.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘testNet.dot’ ‘toy_epi_sim.net’
data.reduction: no visible global function definition for ‘prcomp’
data.reduction: no visible global function definition for ‘hclust’
data.reduction: no visible global function definition for ‘as.dist’
data.reduction: no visible global function definition for ‘cor’
data.reduction: no visible global function definition for ‘dist’
heatmap1: no visible global function definition for ‘sd’
lineplot: no visible global function definition for ‘sd’
normalize: no visible global function definition for ‘sd’
profileplot3d : ColorFunction: no visible global function definition
  for ‘rgb’
profileplot3d : ColorFunction: no visible global function definition
  for ‘colorRamp’
profileplot3d: no visible global function definition for ‘sd’
profileplot3d: no visible global function definition for ‘gray’
Undefined global functions or variables:
  as.dist colorRamp cor dist gray hclust prcomp rgb sd
Consider adding
  importFrom("grDevices", "colorRamp", "gray", "rgb")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "prcomp", "sd")
to your NAMESPACE file.
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpbu6bTR/R.INSTALL36be4adcc3c8/neldermead/man/costf.transposex.Rd:27: file link ‘neldermead.costf’ in package ‘neldermead’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpbu6bTR/R.INSTALL36be4adcc3c8/neldermead/man/neldermead.restart.Rd:25: file link ‘neldermead.updatesimp’ in package ‘neldermead’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/neldermead.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpYacM8j/R.INSTALL6fb25370cfe6/neo4r/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/neo4r.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
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.
The following files look like leftovers/mistakes:
  ‘Rplots.pdf’, ‘Rplots.ps’
Please remove them from your package.
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.
Non-standard file/directory found at top level:
  ‘buildcmds’
EnvInd: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘fastshp’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpijAxkE/R.INSTALL6385280da004/NetLogoR/man/quickPlot-methods.Rd:66: file link ‘gpar’ in package ‘quickPlot’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NetLogoR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpq2uor7/R.INSTALL3405c99024a/networkDynamic/man/activate.Rd:105: file link ‘get.edge.attribute’ in package ‘network’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpq2uor7/R.INSTALL3405c99024a/networkDynamic/man/activity.attribute.Rd:54: file link ‘get.edge.attribute’ in package ‘network’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpq2uor7/R.INSTALL3405c99024a/networkDynamic/man/add.methods.networkDynamic.Rd:60: file link ‘add.edge’ in package ‘network’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpq2uor7/R.INSTALL3405c99024a/networkDynamic/man/network.extensions.Rd:83: file link ‘get.edgeIDs’ in package ‘network’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/networkDynamic.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘map.png’ ‘maze.html’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpTxzMp3/R.INSTALL6e7e57d133d4/NetworkRiskMeasures/man/communicability_matrix.Rd:10: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpTxzMp3/R.INSTALL6e7e57d133d4/NetworkRiskMeasures/man/contagion.Rd:20: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpTxzMp3/R.INSTALL6e7e57d133d4/NetworkRiskMeasures/man/criticality.Rd:15: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpTxzMp3/R.INSTALL6e7e57d133d4/NetworkRiskMeasures/man/impact_susceptibility.Rd:40: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpTxzMp3/R.INSTALL6e7e57d133d4/NetworkRiskMeasures/man/risk_matrix.Rd:32: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NetworkRiskMeasures.Rcheck/00install.out’ for details.
simulate.sisnetwork: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmptYZGGX/R.INSTALL35c472968ef6/neurocInstall/man/neuro_install.Rd:42: file link ‘install_github’ in package ‘devtools’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmptYZGGX/R.INSTALL35c472968ef6/neurocInstall/man/neuro_install.Rd:47: file link ‘install_github’ in package ‘devtools’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/neurocInstall.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘correlation_table.csv’ ‘mycorrplot.png’
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.
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.
Found the following files/directories:
  ‘Hgraph.dot’ ‘Igraph.dot’
Package suggested but not available for checking: ‘NFPdata’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpTG8R4d/R.INSTALL709175cf485d/NFP/man/calc_sim_score.Rd:11: file link ‘graphNEL’ in package ‘graph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NFP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp6pEqzo/R.INSTALL4de7edfbfe0/ngramrr/man/dtmwrappers.Rd:41: file link ‘DocumentTermMatrix’ in package ‘tm’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp6pEqzo/R.INSTALL4de7edfbfe0/ngramrr/man/dtmwrappers.Rd:41: file link ‘TermDocumentMatrix’ in package ‘tm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ngramrr.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘icd’
Malformed Description field: should contain one or more complete sentences.
Package vignette with placeholder title ‘Vignette Title’:
  ‘nitrcbot.Rmd’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpxAqRQt/R.INSTALL65442f0b0374/nixmass/man/plot.nixmass.Rd:10: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nixmass.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpU9j9ts/R.INSTALL377f28d6c2bd/nlcv/man/nldaI.Rd:21: file link ‘ldaI’ in package ‘MLInterfaces’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpU9j9ts/R.INSTALL377f28d6c2bd/nlcv/man/pamrI.Rd:31: file link ‘MLearn’ in package ‘MLInterfaces’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nlcv.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpfYyVKz/R.INSTALL70e57c8c6d69/nlist/man/nchains.Rd:28: file link ‘nlist_object’ in package ‘nlist’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfYyVKz/R.INSTALL70e57c8c6d69/nlist/man/nchains.Rd:32: file link ‘nlists_object’ in package ‘nlist’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nlist.Rcheck/00install.out’ for details.
nlmeODE: no visible global function definition for ‘deriv’
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpuNvgiQ/R.INSTALL2ddb4e279a6e/nlme/man/plot.intervals.lmList.Rd:34: file link ‘dotplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuNvgiQ/R.INSTALL2ddb4e279a6e/nlme/man/plot.intervals.lmList.Rd:21: file link ‘dotplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuNvgiQ/R.INSTALL2ddb4e279a6e/nlme/man/plot.ranef.lme.Rd:25: file link ‘dotplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuNvgiQ/R.INSTALL2ddb4e279a6e/nlme/man/plot.ranef.lme.Rd:65: file link ‘dotplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuNvgiQ/R.INSTALL2ddb4e279a6e/nlme/man/plot.ranef.lme.Rd:71: file link ‘dotplot’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nlme.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmphe0HSG/R.INSTALL59f753c61777/nlmixr/man/asHux.nlmixrFitCore.Rd:45: file link ‘tidy’ in package ‘broom’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmphe0HSG/R.INSTALL59f753c61777/nlmixr/man/reexports.Rd:66: file link ‘as_hux’ in package ‘huxtable’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmphe0HSG/R.INSTALL59f753c61777/nlmixr/man/reexports.Rd:68: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmphe0HSG/R.INSTALL59f753c61777/nlmixr/man/reexports.Rd:70: file link ‘fixef’ in package ‘nlme’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmphe0HSG/R.INSTALL59f753c61777/nlmixr/man/reexports.Rd:70: file link ‘ranef’ in package ‘nlme’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmphe0HSG/R.INSTALL59f753c61777/nlmixr/man/reexports.Rd:72: file link ‘rxParam’ in package ‘RxODE’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nlmixr.Rcheck/00install.out’ for details.
Missing or unexported object: ‘cleanNLP::cnlp_get_token’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpEx1DId/R.INSTALL5ac4626a7f3a/nlpred/man/xgboost_wrapper.Rd:25: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEx1DId/R.INSTALL5ac4626a7f3a/nlpred/man/xgboost_wrapper.Rd:27: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEx1DId/R.INSTALL5ac4626a7f3a/nlpred/man/xgboost_wrapper.Rd:29: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEx1DId/R.INSTALL5ac4626a7f3a/nlpred/man/xgboost_wrapper.Rd:31: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEx1DId/R.INSTALL5ac4626a7f3a/nlpred/man/xgboost_wrapper.Rd:33: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEx1DId/R.INSTALL5ac4626a7f3a/nlpred/man/xgboost_wrapper.Rd:35: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEx1DId/R.INSTALL5ac4626a7f3a/nlpred/man/xgboost_wrapper.Rd:37: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEx1DId/R.INSTALL5ac4626a7f3a/nlpred/man/xgboost_wrapper.Rd:39: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEx1DId/R.INSTALL5ac4626a7f3a/nlpred/man/xgboost_wrapper.Rd:59: file link ‘xgboost’ in package ‘xgboost’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nlpred.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpMFqXIV/R.INSTALL71e56513e055/nlreg/man/nlreg.Rd:133: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMFqXIV/R.INSTALL71e56513e055/nlreg/man/nlreg.contours.object.Rd:18: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMFqXIV/R.INSTALL71e56513e055/nlreg/man/nlreg.profile.objects.Rd:20: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMFqXIV/R.INSTALL71e56513e055/nlreg/man/plot.nlreg.contours.Rd:7: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMFqXIV/R.INSTALL71e56513e055/nlreg/man/plot.nlreg.diag.Rd:12: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMFqXIV/R.INSTALL71e56513e055/nlreg/man/plot.nlreg.profiles.Rd:104: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMFqXIV/R.INSTALL71e56513e055/nlreg/man/profile.nlreg.Rd:104: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nlreg.Rcheck/00install.out’ for details.
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.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpi9dAVY/R.INSTALL76729749a0b/nlstimedist/man/reexports.Rd:15: file link ‘%>%’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nlstimedist.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpai4a4c/R.INSTALL64bd6fe2fcc1/nlstools/man/confint2.Rd:26: file link ‘confint.nls’ in package ‘MASS’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nlstools.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpXgWZOZ/R.INSTALL73c2313bebe8/Nmisc/man/is.POSIXct.Rd:16: file link ‘is.POSIXt’ in package ‘lubridate’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXgWZOZ/R.INSTALL73c2313bebe8/Nmisc/man/keep_at.Rd:17: file link ‘select_helpers’ in package ‘tidyselect’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Nmisc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpMOS5uf/R.INSTALL3a11ed0f7dd/nmixgof/man/chat.Rd:10: file link ‘unmarkedFit’ in package ‘unmarked’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMOS5uf/R.INSTALL3a11ed0f7dd/nmixgof/man/nmixgof.Rd:10: file link ‘unmarked’ in package ‘unmarked’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMOS5uf/R.INSTALL3a11ed0f7dd/nmixgof/man/residcov.Rd:10: file link ‘unmarkedFit’ in package ‘unmarked’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMOS5uf/R.INSTALL3a11ed0f7dd/nmixgof/man/residqq.Rd:11: file link ‘unmarkedFit’ in package ‘unmarked’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMOS5uf/R.INSTALL3a11ed0f7dd/nmixgof/man/rqresiduals.Rd:10: file link ‘unmarkedFit’ in package ‘unmarked’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMOS5uf/R.INSTALL3a11ed0f7dd/nmixgof/man/shoveler.Rd:18: file link ‘unmarked’ in package ‘unmarked’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nmixgof.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘hurricaneexposuredata’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpEH1HcU/R.INSTALL708d3fd7957e/nofrills/man/as_fn.Rd:13: file link ‘quasiquotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEH1HcU/R.INSTALL708d3fd7957e/nofrills/man/curry.Rd:42: file link ‘quasiquotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEH1HcU/R.INSTALL708d3fd7957e/nofrills/man/curry.Rd:19: file link ‘quasiquotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEH1HcU/R.INSTALL708d3fd7957e/nofrills/man/fn.Rd:30: file link ‘quasiquotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEH1HcU/R.INSTALL708d3fd7957e/nofrills/man/fn.Rd:11: file link ‘quasiquotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEH1HcU/R.INSTALL708d3fd7957e/nofrills/man/fn.Rd:45: file link ‘quasiquotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEH1HcU/R.INSTALL708d3fd7957e/nofrills/man/fn.Rd:58: file link ‘quasiquotation’ in package ‘rlang’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nofrills.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpp6rsko/R.INSTALL69263b8d40/nonlinearTseries/man/corrDim.Rd:132: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpp6rsko/R.INSTALL69263b8d40/nonlinearTseries/man/infDim.Rd:166: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpp6rsko/R.INSTALL69263b8d40/nonlinearTseries/man/maxLyapunov.Rd:116: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpp6rsko/R.INSTALL69263b8d40/nonlinearTseries/man/sampleEntropy.Rd:66: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpp6rsko/R.INSTALL69263b8d40/nonlinearTseries/man/spaceTimePlot.Rd:80: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nonlinearTseries.Rcheck/00install.out’ for details.
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.
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.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpNi5PKg/R.INSTALLe0e1c25e127/nos/man/NOSM_POT_dir.Rd:14: file link ‘bipartite’ in package ‘bipartite’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNi5PKg/R.INSTALLe0e1c25e127/nos/man/NOSM_POT_undir.Rd:14: file link ‘bipartite’ in package ‘bipartite’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNi5PKg/R.INSTALLe0e1c25e127/nos/man/NOSM_bip.Rd:16: file link ‘bipartite’ in package ‘bipartite’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNi5PKg/R.INSTALLe0e1c25e127/nos/man/NOSM_dir.Rd:17: file link ‘bipartite’ in package ‘bipartite’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNi5PKg/R.INSTALLe0e1c25e127/nos/man/NOSM_undir.Rd:14: file link ‘bipartite’ in package ‘bipartite’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNi5PKg/R.INSTALLe0e1c25e127/nos/man/freqMat_2_edge.Rd:48: file link ‘bipartite’ in package ‘bipartite’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNi5PKg/R.INSTALLe0e1c25e127/nos/man/nos-package.Rd:49: file link ‘bipartite’ in package ‘bipartite’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nos.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpcKnE49/R.INSTALLbac6849c587/NostalgiR/man/nos.density.Rd:51: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcKnE49/R.INSTALLbac6849c587/NostalgiR/man/nos.density.Rd:51: file link ‘txtdensity’ in package ‘txtplot’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcKnE49/R.INSTALLbac6849c587/NostalgiR/man/nos.ecdf.Rd:42: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcKnE49/R.INSTALLbac6849c587/NostalgiR/man/nos.qqnorm.Rd:44: file link ‘qqline’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcKnE49/R.INSTALLbac6849c587/NostalgiR/man/nos.qqplot.Rd:53: file link ‘qqplot’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcKnE49/R.INSTALLbac6849c587/NostalgiR/man/nos.qqplot.Rd:53: file link ‘qqline’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcKnE49/R.INSTALLbac6849c587/NostalgiR/man/nos.xyplot.Rd:56: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NostalgiR.Rcheck/00install.out’ for details.
Rd file 'notifyR-package.Rd':
  \examples lines wider than 100 characters:
     send_push(userkey,message="finished.",title="World Simulation",url="http://www.myRresults.com/",url_title="View Results online.",priori ... [TRUNCATED]

Rd file 'send_push.Rd':
  \usage lines wider than 90 characters:
     send_push(user, message, title = "", device = "", url = "", url_title = "", priority = FALSE, timestamp = Sys.time())
  \examples lines wider than 100 characters:
     send_push(userkey,message="finished.",title="World Simulation",url="http://www.myRresults.com/",url_title="View Results online.",priori ... [TRUNCATED]

These lines will be truncated in the PDF 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.
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.
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘tmp.R’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpH8t3kA/R.INSTALLe05522c7515/np/man/np.quantile.Rd:154: file link ‘qlogspline’ in package ‘logspline’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpH8t3kA/R.INSTALLe05522c7515/np/man/np.quantile.Rd:155: file link ‘qkde’ in package ‘ks’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/np.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpNAxO4Z/R.INSTALLd025363899b/npsf/man/nptestrts.Rd:43: file link ‘performParallel’ in package ‘snowFT’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNAxO4Z/R.INSTALLd025363899b/npsf/man/nptestrts.Rd:46: file link ‘makeClusterFT’ in package ‘snowFT’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNAxO4Z/R.INSTALLd025363899b/npsf/man/nptestrts.Rd:46: file link ‘performParallel’ in package ‘snowFT’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNAxO4Z/R.INSTALLd025363899b/npsf/man/teradialbc.Rd:59: file link ‘performParallel’ in package ‘snowFT’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNAxO4Z/R.INSTALLd025363899b/npsf/man/teradialbc.Rd:62: file link ‘makeClusterFT’ in package ‘snowFT’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNAxO4Z/R.INSTALLd025363899b/npsf/man/teradialbc.Rd:62: file link ‘performParallel’ in package ‘snowFT’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/npsf.Rcheck/00install.out’ for details.
Found the following hidden files and directories:
  .Rapp.history
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
File ‘NPsimex/R/onload.R’:
  .onLoad calls:
    packageStartupMessage("NPsimex 0.2-1 loaded")

See section ‘Good practice’ in '?.onAttach'.

lambda.select: no visible global function definition for ‘bw.nrd0’
lambda.select: no visible global function definition for ‘bw.nrd’
lambda.select: no visible global function definition for ‘bw.ucv’
lambda.select: no visible global function definition for ‘bw.bcv’
lambda.select: no visible global function definition for ‘bw.SJ’
plot.NPsimex: no visible global function definition for ‘plot.default’
simex.H.density : simex1.est: no visible global function definition for
  ‘lm’
simex.density : simex1.est: no visible global function definition for
  ‘lm’
span.H.select: no visible global function definition for ‘density’
span.H.select : conden : <anonymous>: no visible global function
  definition for ‘dnorm’
span.select: no visible global function definition for ‘density’
span.select : conden : <anonymous>: no visible global function
  definition for ‘dnorm’
Undefined global functions or variables:
  bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv density dnorm lm plot.default
Consider adding
  importFrom("graphics", "plot.default")
  importFrom("stats", "bw.SJ", "bw.bcv", "bw.nrd", "bw.nrd0", "bw.ucv",
             "density", "dnorm", "lm")
to your NAMESPACE file.
prepare_Rd: lambda.select.Rd:19-20: Dropping empty section \details
prepare_Rd: lambda.select.Rd:21-22: Dropping empty section \value
prepare_Rd: simex.H.density.Rd:28-29: Dropping empty section \details
prepare_Rd: simex.density.Rd:28-29: Dropping empty section \details
prepare_Rd: span.H.select.Rd:28-29: Dropping empty section \details
prepare_Rd: span.H.select.Rd:30-31: Dropping empty section \value
prepare_Rd: span.select.Rd:27-28: Dropping empty section \details
prepare_Rd: span.select.Rd:29-30: Dropping empty section \value
Rd file 'simex.H.density.Rd':
  \examples lines wider than 100 characters:
     set.seed(123); X <- c(rnorm(N/2, mean=-2), rnorm(N/2,mean=2)); U <- rnorm(N,sd=1); msigma <- runif(N,min=0.3,max=0.5)

Rd file 'span.H.select.Rd':
  \usage lines wider than 90 characters:
      span.H.select(W, msigma, span=c(2,4,6,8,10,12,25), approx=FALSE, from=min(W), to=max(W), n.user=128, n.lambda=50, lambda="SJ", bw="SJ" ... [TRUNCATED]
  \examples lines wider than 100 characters:
     set.seed(123); X <- c(rnorm(N/2, mean=-2), rnorm(N/2,mean=2)); U <- rnorm(N,sd=1); msigma <- runif(N,min=0.3,max=0.5)
     X.simex <- simex.H.density(W, msigma=msigma, adjust=1, n.lambda=50, span=spans$span[order(spans$ISE)[1]])
     # X.simex <- simex.H.density(W, msigma=msigma, adjust=1, n.lambda=50, span=spans$span[order(spans$ISE)[1]])

Rd file 'span.select.Rd':
  \usage lines wider than 90 characters:
      span.select(W, msigma, span=c(2,4,6,8,10,12,25), from=min(W), to=max(W), n.user=128, n.lambda=50, lambda="SJ", bw="SJ", adjust=1, na.r ... [TRUNCATED]
  \examples lines wider than 100 characters:
     X.simex <- simex.density(W, msigma=msigma, adjust=1, n.lambda=50, span=spans$span[order(spans$ISE)[1]])

These lines will be truncated in the PDF manual.
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.
'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
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpAyeEIf/R.INSTALL8fe55e63e46/nseval/man/compat.Rd:15: file link ‘as.lazy_dots’ in package ‘lazyeval’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nseval.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpYB9ciE/R.INSTALL61c32a9cfdd6/nsga3/man/nsga3fs.Rd:25: file link ‘low’ in package ‘rPref’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nsga3.Rcheck/00install.out’ for details.
.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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpkn2HBM/R.INSTALLbf79c13c4f/nvctr/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nvctr.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of ‘env’ to ‘envir’
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of ‘env’ to ‘envir’
logMsg: no visible global function definition for ‘flush.console’
nwsPkgInfo: no visible global function definition for
  ‘packageDescription’
initialize,nwsServer: no visible global function definition for
  ‘make.socket’
initialize,nwsServer: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘nws/R/workerLoop.R’:
  assign("SleighName", displayName, globalenv())
  assign("SleighNws", nws, globalenv())
  assign("SleighUserNws", userNws, globalenv())
  assign("SleighRank", rank, globalenv())
  assign("SleighWorkerCount", workerCount, globalenv())
Rd file 'nwsVariable-methods.Rd':
  \usage lines wider than 90 characters:
     nwsVariable(.Object, xName, mode=c('fifo','lifo','multi','single'),env=parent.frame(),force=FALSE,quietly=FALSE)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp1KIbiF/R.INSTALLe7d10ae6b5e/OAIHarvester/man/serialize.Rd:24: file link ‘saveRDS’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OAIHarvester.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpQRACee/R.INSTALLdf31e39c642/objectProperties/man/PropertySet-class.Rd:9: file link ‘setRefClass’ in package ‘methods’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpQRACee/R.INSTALLdf31e39c642/objectProperties/man/PropertySet-class.Rd:20: file link ‘setRefClass’ in package ‘methods’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/objectProperties.Rcheck/00install.out’ for details.
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.
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').
Rd file 'Enum-class.Rd':
  \examples lines wider than 100 characters:
     PointSizeSingleEnum.gen <- setGlyphEnum("PointSize", levels = c("1", "2", "5", "10"), contains = "GlyphEnum")

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpz3lj3y/R.INSTALL1023722ccabe/objectSignals/man/fieldWithPrototype.Rd:7: file link ‘prototype’ in package ‘methods’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/objectSignals.Rcheck/00install.out’ for details.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
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').
obliclus: no visible global function definition for ‘rnorm’
obliclus: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans rnorm
Consider adding
  importFrom("stats", "kmeans", "rnorm")
to your NAMESPACE file.
File ‘obliclus/libs/obliclus.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpofMvyL/R.INSTALL18843c6df3a0/Observation/man/manual_data_collection_program.Rd:45: file link ‘diff.POSIXt’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Observation.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpuRBNeM/R.INSTALL10b752c2b055/observer/man/check_that.Rd:77: file link ‘check_that’ in package ‘ensurer’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuRBNeM/R.INSTALL10b752c2b055/observer/man/check_that.Rd:77: file link ‘ensure_that’ in package ‘ensurer’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuRBNeM/R.INSTALL10b752c2b055/observer/man/observations.Rd:37: file link ‘observe_if_’ in package ‘observer’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuRBNeM/R.INSTALL10b752c2b055/observer/man/reobserve.Rd:34: file link ‘ensure_that’ in package ‘observer’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/observer.Rcheck/00install.out’ for details.
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.
Rd file 'obsSensCCC.Rd':
  \usage lines wider than 90 characters:
     obsSensCCC(model, which = 2, g0 = c(2, 6, 10), g1, p0 = seq(0, 1, 0.2), p1 = p0, logOdds = FALSE, method = c("approx", "sim"))
     obsSensCCN(model, which = 2, gamma = round(seq(0, 2 * bstar, length = 6), 4), delta = seq(0, 3, 0.5), logOdds = FALSE, method = c("appr ... [TRUNCATED]
     obsSensCNN(model, which = 2, gamma = round(seq(0, 2 * bstar, length = 6), 4), rho = c(0, 0.5, 0.75, 0.85, 0.9, 0.95, 0.98, 0.99), sdx,  ... [TRUNCATED]
     obsSensNCC(model, which = 2, g0 = c(2, 6, 10), g1, p0 = seq(0, 1, 0.2), p1 = p0, log = TRUE, method = c("approx", "sim"))
     obsSensNCN(model, which = 2, gamma = round(seq(0, 3, length = 6), 4), delta = seq(0, 3, 0.5), log = TRUE, method = c("approx", "sim"))
     6), 4), rho = c(0, 0.5, 0.75, 0.85, 0.9, 0.95, 0.98, 0.99), sdx, log = TRUE, method = c("approx", "sim"))
     obsSensSCC(model, which = 2, g0 = c(2, 6, 10), g1, p0 = seq(0, 1, 0.2), p1 = p0, logHaz = FALSE, method = c("approx", "sim"))
     obsSensSCN(model, which = 2, gamma = round(seq(0, 3, length = 6), 4), delta = seq(0, 3, 0.5), logHaz = FALSE, method = c("approx", "sim ... [TRUNCATED]
     obsSensSNN(model, which = 2, gamma = round(seq(0, 3, length = 6), 4), rho = c(0, 0.5, 0.75, 0.85, 0.9, 0.95, 0.98, 0.99), sdx, logHaz = ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpQRAfcO/R.INSTALL7c04d29c230/oceanmap/man/empty.plot.Rd:16: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/oceanmap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmptRrPWg/R.INSTALL18b26b3a2baa/oce/man/mapPlot.Rd:140: file link ‘CRS’ in package ‘sp’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmptRrPWg/R.INSTALL18b26b3a2baa/oce/man/oceProject.Rd:42: file link ‘rawTransform’ in package ‘rgdal’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmptRrPWg/R.INSTALL18b26b3a2baa/oce/man/topoWorld.Rd:27: file link ‘coastlineWorldFine’ in package ‘ocedata’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/oce.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpUaDH5S/R.INSTALL6f0d8ce25f1/odbc/man/dbConnect-OdbcDriver-method.Rd:50: file link ‘integer64’ in package ‘bit64’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/odbc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpfGKC6t/R.INSTALL31d2334f476/oddstream/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/oddstream.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp9R5LYj/R.INSTALL63a84389bfdf/ODEsensitivity/man/ODEmorris.default.Rd:87: file link ‘sensitivity’ in package ‘sensitivity’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9R5LYj/R.INSTALL63a84389bfdf/ODEsensitivity/man/ODEsobol.default.Rd:89: file link ‘sensitivity’ in package ‘sensitivity’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9R5LYj/R.INSTALL63a84389bfdf/ODEsensitivity/man/ODEsobol.default.Rd:92: file link ‘sensitivity’ in package ‘sensitivity’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ODEsensitivity.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpPUUaZP/R.INSTALL7cb01e661746/OHPL/man/OHPL.Rd:34: file link ‘plsr’ in package ‘pls’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPUUaZP/R.INSTALL7cb01e661746/OHPL/man/cv.OHPL.Rd:37: file link ‘plsr’ in package ‘pls’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OHPL.Rcheck/00install.out’ for details.
Found the following hidden files and directories:
  .Rapp.history
  data/.Rapp.history
  data/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘RCurl’ ‘maps’
A package should be listed in only one of these fields.
mapvar: no visible global function definition for ‘data’
mapvar: no visible binding for global variable ‘state.fips’
mapvar: no visible global function definition for ‘rgb’
mapvar: no visible global function definition for ‘rect’
mapvar: no visible global function definition for ‘text’
rowScrape: no visible global function definition for ‘tail’
rowScrape: no visible global function definition for ‘head’
scrapeTable: no visible binding for global variable ‘tail’
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘OIdata/R/mapvar.R’:
  data(state.fips)
See section ‘Good practice’ in ‘?data’.
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.
Malformed Description field: should contain one or more complete sentences.
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.
fhcor: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor
Consider adding
  importFrom("stats", "cor")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Omu_vignette.Rmd’
GNU make is a SystemRequirements.
Found an obsolete/platform-specific call in the following function:
  ‘comp.freq’
Found the platform-specific device:
  ‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
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.
Rd file 'oncomodel-package.Rd':
  \examples lines wider than 100 characters:
       #plot.phylog(y.phyl, cnodes =1,  clabel.n=0.6, f=0.75, sub="Oncogenetic tree of given aberrations")

These lines will be truncated in the PDF 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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpTx6Pef/R.INSTALL46d4508c3eda/onelogin/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/onelogin.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpt1FUpQ/R.INSTALL91314ecb559/onemap/man/set_map_fun.Rd:26: file link ‘kosambi’ in package ‘onemap’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpt1FUpQ/R.INSTALL91314ecb559/onemap/man/set_map_fun.Rd:26: file link ‘haldane’ in package ‘onemap’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/onemap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpkkwUdX/R.INSTALL471f5294a5bf/onlinePCA/man/batchpca.Rd:22: file link ‘eigs_sym’ in package ‘RSpectra’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/onlinePCA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpI2aeBn/R.INSTALL65d546ba2961/OOBCurve/man/OOBCurve.Rd:18: file link ‘makeClassifTask’ in package ‘mlr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpI2aeBn/R.INSTALL65d546ba2961/OOBCurve/man/OOBCurve.Rd:18: file link ‘makeRegrTask’ in package ‘mlr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpI2aeBn/R.INSTALL65d546ba2961/OOBCurve/man/OOBCurvePars.Rd:14: file link ‘makeClassifTask’ in package ‘mlr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpI2aeBn/R.INSTALL65d546ba2961/OOBCurve/man/OOBCurvePars.Rd:14: file link ‘makeRegrTask’ in package ‘mlr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OOBCurve.Rcheck/00install.out’ for details.
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.
Package suggested but not available for checking: ‘Segmentor3IsBack’
Error(s) in re-building vignettes:
  ...
--- re-building ‘opart_gaussian.Rmd’ using rmarkdown
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to 'opart_gaussian.utf8' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".
--- finished re-building ‘opart_gaussian.Rmd’

--- re-building ‘opart_poisson.Rmd’ using rmarkdown
Quitting from lines 140-142 (opart_poisson.Rmd) 
Error: processing vignette 'opart_poisson.Rmd' failed with diagnostics:
there is no package called 'Segmentor3IsBack'
--- failed re-building ‘opart_poisson.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package vignette with placeholder title ‘Vignette Title’:
  ‘opencage.Rmd’
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpnIQf3D/R.INSTALL2abf496ebd6c/opencv/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/opencv.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpUN4XSX/R.INSTALL771d42240f7f/opendatatoronto/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/opendatatoronto.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp0T2BV4/R.INSTALL7b168153246/openEBGM/man/openEBGM.Rd:60: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/openEBGM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmprUk7t2/R.INSTALL2bf469d9fc6c/openintro/man/loop.Rd:7: file link ‘setTxtProgressBar’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/openintro.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpdaOghw/R.INSTALL4910a336be5/OpenML/man/OMLDataSetDescription.Rd:46: file link ‘POSIXt’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OpenML.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘openNLPmodels.en’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp4UbIj2/R.INSTALL433342486389/openssl/man/openssl.Rd:11: file link ‘signature_verify’ in package ‘openssl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4UbIj2/R.INSTALL433342486389/openssl/man/openssl.Rd:12: file link ‘cert_verify’ in package ‘openssl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4UbIj2/R.INSTALL433342486389/openssl/man/openssl.Rd:17: file link ‘rsa_keygen’ in package ‘openssl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4UbIj2/R.INSTALL433342486389/openssl/man/openssl.Rd:17: file link ‘md5’ in package ‘openssl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4UbIj2/R.INSTALL433342486389/openssl/man/openssl.Rd:18: file link ‘sha1’ in package ‘openssl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4UbIj2/R.INSTALL433342486389/openssl/man/openssl.Rd:18: file link ‘sha256’ in package ‘openssl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/openssl.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpLA1Tks/R.INSTALL138a65919e28/openSTARS/man/openSTARS.Rd:10: file link ‘SSN’ in package ‘SSN’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/openSTARS.Rcheck/00install.out’ for details.
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 suggested but not available for checking: ‘nbc4va’
Package suggested but not available for checking: ‘gurobi’
prepare_Rd: distance.Rd:21-22: Dropping empty section \details
prepare_Rd: distance.Rd:32-33: Dropping empty section \note
prepare_Rd: filter.Rd:26-27: Dropping empty section \details
prepare_Rd: filter.Rd:28-29: Dropping empty section \value
prepare_Rd: filter.Rd:36-37: Dropping empty section \note
prepare_Rd: findP.Rd:21-22: Dropping empty section \details
prepare_Rd: findP.Rd:34-35: Dropping empty section \note
prepare_Rd: ops-package.Rd:30-31: Dropping empty section \seealso
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.
Rd file 'optAUC-package.Rd':
  \examples lines wider than 100 characters:
     Y1Y2<-mvrnorm(n, c(y1.mean,y2.mean), matrix(c(y1.sd^2,rho*y1.sd*y2.sd, rho*y1.sd*y2.sd, y2.sd^2),2,2))
     # two markers in the model, the AUC from GCV is smaller than just first marker in the model, because the second marker is noise
     # the AUC from ACV (apearent estimate by substituting the estimated beta into the model) is larger than previous model, because overfit ... [TRUNCATED]

Rd file 'optAUC.Rd':
  \examples lines wider than 100 characters:
     Y1Y2<-mvrnorm(n, c(y1.mean,y2.mean), matrix(c(y1.sd^2,rho*y1.sd*y2.sd, rho*y1.sd*y2.sd, y2.sd^2),2,2))
     # two markers in the model, the AUC from GCV is smaller than just first marker in the model, because the second marker is noise
     # the AUC from ACV (apearent estimate by substituting the estimated beta into the model) is larger than previous model, because overfit ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
Malformed Description field: should contain one or more complete sentences.
avg2Lower: no visible global function definition for ‘optimize’
classificationError.data.frame: no visible binding for global variable
  ‘na.omit’
classificationError.data.frame: no visible global function definition
  for ‘terms’
classificationError.data.frame: no visible binding for global variable
  ‘predict’
classpredict.lda: no visible global function definition for ‘predict’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
simData: no visible global function definition for ‘var’
tnormAvg: no visible global function definition for ‘dnorm’
tnormAvg: no visible global function definition for ‘pnorm’
yapprox: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dnorm na.omit optimize pnorm predict rnorm runif terms var
Consider adding
  importFrom("stats", "approx", "dnorm", "na.omit", "optimize", "pnorm",
             "predict", "rnorm", "runif", "terms", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpPExLQ8/R.INSTALL12c066c4c50/optCluster/man/optCluster.Rd:22: file link ‘ExpressionSet’ in package ‘Biobase’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPExLQ8/R.INSTALL12c066c4c50/optCluster/man/optCluster.Rd:266: file link ‘som’ in package ‘kohonen’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/optCluster.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmprk2wyL/R.INSTALL7fa14814a6d6/opticut/man/opticut.Rd:305: file link ‘rspf’ in package ‘ResourceSelection’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/opticut.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘gurobi’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpXQe9bd/R.INSTALL1c24818da07/optimalThreshold/man/cdf.Rd:74: file link ‘pnorm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXQe9bd/R.INSTALL1c24818da07/optimalThreshold/man/cdf.Rd:74: file link ‘plnorm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXQe9bd/R.INSTALL1c24818da07/optimalThreshold/man/cdf.Rd:74: file link ‘pgamma’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXQe9bd/R.INSTALL1c24818da07/optimalThreshold/man/cdf.Rd:74: file link ‘plogis’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXQe9bd/R.INSTALL1c24818da07/optimalThreshold/man/gradient.Rd:74: file link ‘dnorm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXQe9bd/R.INSTALL1c24818da07/optimalThreshold/man/gradient.Rd:74: file link ‘dlnorm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXQe9bd/R.INSTALL1c24818da07/optimalThreshold/man/gradient.Rd:74: file link ‘dgamma’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXQe9bd/R.INSTALL1c24818da07/optimalThreshold/man/gradient.Rd:74: file link ‘dlogis’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/optimalThreshold.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpzmaHVS/R.INSTALL675b20234d7f/optimbase/man/optimbase.destroy.Rd:30: file link ‘optimbase.logshutdown’ in package ‘optimbase’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/optimbase.Rcheck/00install.out’ for details.
print.optimbase: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmppIkCxx/R.INSTALL203475fbc2d6/optimParallel/man/optimParallel.Rd:50: file link ‘setDefaultCluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmppIkCxx/R.INSTALL203475fbc2d6/optimParallel/man/optimParallel.Rd:89: file link ‘clusterExport’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmppIkCxx/R.INSTALL203475fbc2d6/optimParallel/man/optimParallel.Rd:182: file link ‘setDefaultCluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmppIkCxx/R.INSTALL203475fbc2d6/optimParallel/man/optimParallel.Rd:183: file link ‘stopCluster’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/optimParallel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpYoy4v5/R.INSTALL6268173e56ec/optimsimplex/man/optimsimplex.gradientfv.Rd:66: file link ‘optimsimplex.dirmat’ in package ‘optimsimplex’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpYoy4v5/R.INSTALL6268173e56ec/optimsimplex/man/optimsimplex.gradientfv.Rd:67: file link ‘optimsimplex.deltafv’ in package ‘optimsimplex’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/optimsimplex.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp4hBveM/R.INSTALL142d55641d65/optimus/man/find_optimal.Rd:13: file link ‘as.factor’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4hBveM/R.INSTALL142d55641d65/optimus/man/get_characteristic.Rd:13: file link ‘as.factor’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4hBveM/R.INSTALL142d55641d65/optimus/man/merge_clusters.Rd:13: file link ‘as.factor’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp4hBveM/R.INSTALL142d55641d65/optimus/man/plot.aicsums.Rd:16: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/optimus.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Rd file 'TestStage.Rd':
  \examples lines wider than 100 characters:
     object1 <- OptimDes(B.init,m.init,alpha,beta,param,x,target="EDA",sf="futility",num.arm=1,num.stage=2)
     mda <- ifelse(l>1,B.init[l-1]+(B.init[l]-B.init[l-1])*(n-sum(m.init[1:(l-1)]))/m.init[l],B.init[l]*(n/m.init[l]))

Rd file 'np.OptimDes.Rd':
  \examples lines wider than 100 characters:
     object14 <- np.OptimDes(B.init,m.init,alpha,beta,param,x,pt=1.1,target="ETSL",sf="futility",num.arm=1,num.stage=2)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp2nbEng/R.INSTALL18e745aba1b/optinterv/man/plot_change.Rd:23: file link ‘densityplot’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/optinterv.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘UserGuide.Rmd’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpOkMxao/R.INSTALL28b51e845d5/optpart/man/classmatch.Rd:48: file link ‘partition’ in package ‘cluster’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpOkMxao/R.INSTALL28b51e845d5/optpart/man/clique.test.Rd:29: file link ‘mss.test’ in package ‘optpart’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpOkMxao/R.INSTALL28b51e845d5/optpart/man/lambda.Rd:34: file link ‘partition’ in package ‘cluster’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpOkMxao/R.INSTALL28b51e845d5/optpart/man/mergeclust.Rd:28: file link ‘partition’ in package ‘cluster’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/optpart.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpoAEL7V/R.INSTALL3802f0003a0/opusminer/man/opus.Rd:13: file link ‘transactions’ in package ‘arules’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpoAEL7V/R.INSTALL3802f0003a0/opusminer/man/opus.Rd:47: file link ‘transactions’ in package ‘arules’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpoAEL7V/R.INSTALL3802f0003a0/opusminer/man/opus.Rd:34: file link ‘itemsets’ in package ‘arules’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpoAEL7V/R.INSTALL3802f0003a0/opusminer/man/read_transactions.Rd:19: file link ‘transactions’ in package ‘arules’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/opusminer.Rcheck/00install.out’ for details.
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.
'library' or 'require' call to ‘psych’ which was already attached by Depends.
  Please remove these calls from your code.
Rd file 'dmes.Rd':
  \examples lines wider than 100 characters:
     > #cf. Efron, B. & Tibshirani (1993). An Introduction to the Bootstrap. New York/London: Chapman&Hall.
     > #Ruscio, J. & Mullen, T. (2012). Confidence Intervals for the Probability of Superiority Effect Size Measure and the Area Under a Rec ... [TRUNCATED]

Rd file 'orddom_f.Rd':
  \examples lines wider than 100 characters:
     orddom_f(ex_pre,ex_post,alpha=0.025,paired=TRUE,decimalpt=",",description="EXP 01: Within exp 01 to 02") 
     orddom_f(con_pre,con_post,alpha=0.025,paired=TRUE,decimalpt=",",description="EXP 01: Within con 01 to 02") 

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘orddom_csv.txt’ ‘orddom_csv_tab.txt’ ‘tmp_r.txt’
'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.
Found the following significant warnings:
  Rd warning: /private/var/folders/pn/mz1zt3vs765b7x5ldr8bckvj8064w7/T/RtmpKjXmks/Rbuild89c341f210bf/ordinalgmifs/man/ordinalgmifs-package.Rd:26: file link ‘VGAM’ in package ‘VGAM’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ordinalgmifs.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [8s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(ordinalNet)
  > testthatInst <- require(testthat)
  Loading required package: testthat
  > 
  > if (testthatInst) test_check("ordinalNet")
  ── 1. Error: Elastic net sratio matches glmnetcr::glmnet.cr (@test-ordinalNet.R#
  argument "exclude" is missing, with no default
  Backtrace:
   1. glmnetcr::glmnetcr(x, y, alpha = 0.5, lambda = 0.1/2, method = "forward")
   2. glmnet::glmnet(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 33 | SKIPPED: 0 | WARNINGS: 722 | FAILED: 1 ]
  1. Error: Elastic net sratio matches glmnetcr::glmnet.cr (@test-ordinalNet.R#202) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpMUsopa/R.INSTALL5177c377325/ordinal/man/addtermOld.Rd:71: file link ‘clm2’ in package ‘ordinal’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMUsopa/R.INSTALL5177c377325/ordinal/man/anovaOld.Rd:48: file link ‘clm2’ in package ‘ordinal’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMUsopa/R.INSTALL5177c377325/ordinal/man/predictOld.Rd:40: file link ‘clm2’ in package ‘ordinal’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpMUsopa/R.INSTALL5177c377325/ordinal/man/predictOld.Rd:40: file link ‘clmm2’ in package ‘ordinal’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ordinal.Rcheck/00install.out’ for details.
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘intro.Rmd’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpbGesaH/R.INSTALL15ac3e242db8/orgutils/man/readOrg.Rd:56: file link ‘read.csv’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbGesaH/R.INSTALL15ac3e242db8/orgutils/man/readOrg.Rd:71: file link ‘read.csv’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/orgutils.Rcheck/00install.out’ for details.
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.
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
boat3d: no visible global function definition for ‘rgl.cur’
boat3d: no visible global function definition for ‘open3d’
boat3d: no visible global function definition for ‘clear3d’
boat3d: no visible global function definition for ‘bg3d’
boat3d: no visible global function definition for ‘rgl.set’
boat3d: no visible global function definition for ‘triangles3d’
boat3d: no visible global function definition for ‘quads3d’
boat3d: no visible global function definition for ‘decorate3d’
boat3d: no visible global function definition for ‘scatterplot3d’
orientlm: no visible global function definition for ‘model.matrix’
orientlm: no visible global function definition for ‘lm’
Undefined global functions or variables:
  bg3d clear3d decorate3d lm model.matrix open3d quads3d rgl.cur
  rgl.set scatterplot3d triangles3d
Consider adding
  importFrom("stats", "lm", "model.matrix")
to your NAMESPACE file.
File ‘OriGen/libs/OriGen.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Object: ‘OriGen.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ 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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpqa62dc/R.INSTALL56ff60c86b3c/oro.dicom/man/dicom2analyze.Rd:53: file link ‘convert.datatype.anlz’ in package ‘oro.nifti’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpqa62dc/R.INSTALL56ff60c86b3c/oro.dicom/man/dicom2nifti.Rd:71: file link ‘convert.datatype’ in package ‘oro.nifti’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/oro.dicom.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘dcemriS4’
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘genefilter’ ‘gtools’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of ‘ties’ to ‘ties.method’
est.lme : <anonymous>: no visible global function definition for ‘lme’
est.lme : <anonymous>: no visible global function definition for
  ‘VarCorr’
guo: no visible global function definition for ‘p.adjust’
guo: no visible global function definition for ‘na.omit’
pttest : ptest: no visible global function definition for ‘na.omit’
srt : <anonymous>: no visible global function definition for
  ‘rowttests’
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpKxiSV0/R.INSTALL15f23a45f718/orsifronts/man/orsifronts.Rd:7: file link ‘SpatialLinesDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/orsifronts.Rcheck/00install.out’ for details.
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.
'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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmputV0CD/R.INSTALL129f5deea745/osmplotr/man/add_osm_groups.Rd:44: file link ‘shape’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmputV0CD/R.INSTALL129f5deea745/osmplotr/man/add_osm_objects.Rd:27: file link ‘shape’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/osmplotr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpEfRHRf/R.INSTALL6bb675d70de8/OSMscale/man/proj.Rd:26: file link ‘CRS’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OSMscale.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘OTclust.Rmd’
Found the following significant warnings:
  moves.c:440:38: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/outbreaker.Rcheck/00install.out’ for details.
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.
Found the following files/directories:
  ‘result.txt’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpUhORIz/R.INSTALL165642b99624/owdbr/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/owdbr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpvBQDrC/R.INSTALL790f7d995485/owmr/man/reexports.Rd:15: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpvBQDrC/R.INSTALL790f7d995485/owmr/man/reexports.Rd:15: file link ‘%<>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/owmr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpZBCPuv/R.INSTALL4fa075561fd2/ozmaps/man/oz.Rd:13: file link ‘ozRegion’ in package ‘oz’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZBCPuv/R.INSTALL4fa075561fd2/ozmaps/man/oz.Rd:25: file link ‘ozRegion’ in package ‘oz’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZBCPuv/R.INSTALL4fa075561fd2/ozmaps/man/oz.Rd:27: file link ‘ozRegion’ in package ‘oz’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ozmaps.Rcheck/00install.out’ for details.
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.
Missing or unexported objects:
  ‘devtools::use_build_ignore’ ‘devtools::use_travis’
Malformed Description field: should contain one or more complete sentences.
Non-standard files/directories found at top level:
  ‘DESCRIPTION_EX’ ‘divers’ ‘main.R’ ‘testsDev’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpIOZ9RI/R.INSTALL685455461592/packrat/man/lockfile-metadata.Rd:18: file link ‘package_version’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/packrat.Rcheck/00install.out’ for details.
[,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’
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.
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.
Rd file 'CalGIF.Rd':
  \examples lines wider than 100 characters:
     ###calculate the global influence factor (GIF) by using the random walk with restart (RWR) algorithm###

Rd file 'PAGI.Main.Rd':
  \examples lines wider than 100 characters:
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",

These lines will be truncated in the PDF manual.
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.
Rd file 'paired.Loc.Rd':
  \usage lines wider than 90 characters:
     paired.Loc(x, y, method = "parametric", exact = FALSE, conf.level = 0.95, alternative = "two.sided")
  \examples lines wider than 100 characters:
     astra <- c(2.4, 4.8, 4, 4.9, 3.9, 4.1, 3.8, 3.5, 4.6, 2.9, 4.9, 3.7, 4.8, 3.7, 3.8, 4.1, 4.2, 4.3, 3.9, 3.8)
     flame <- c(2.4, 4.8, 4, 4.7, 3.9, 4.2, 3.8, 3.3, 4.6, 3, 5, 3.6, 4.9, 3.8, 3.9, 4.6, 4.2, 4.4, 4, 3.4)

Rd file 'paired.Scale.Rd':
  \examples lines wider than 100 characters:
     astra <- c(2.4, 4.8, 4, 4.9, 3.9, 4.1, 3.8, 3.5, 4.6, 2.9, 4.9, 3.7, 4.8, 3.7, 3.8, 4.1, 4.2, 4.3, 3.9, 3.8)
     flame <- c(2.4, 4.8, 4, 4.7, 3.9, 4.2, 3.8, 3.3, 4.6, 3, 5, 3.6, 4.9, 3.8, 3.9, 4.6, 4.2, 4.4, 4, 3.4)

Rd file 'pairedCI-package.Rd':
  \examples lines wider than 100 characters:
     astra <- c(2.4, 4.8, 4, 4.9, 3.9, 4.1, 3.8, 3.5, 4.6, 2.9, 4.9, 3.7, 4.8, 3.7, 3.8, 4.1, 4.2, 4.3, 3.9, 3.8)
     flame <- c(2.4, 4.8, 4, 4.7, 3.9, 4.2, 3.8, 3.3, 4.6, 3, 5, 3.6, 4.9, 3.8, 3.9, 4.6, 4.2, 4.4, 4, 3.4)

These lines will be truncated in the PDF manual.
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.
Rd file 'pairheatmap.Rd':
  \examples lines wider than 100 characters:
              groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),
              groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),
              groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),

These lines will be truncated in the PDF manual.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpv5HceV/R.INSTALL1668348aea58/pairwiseComparisons/man/reexports.Rd:25: file link ‘%$%’ in package ‘ipmisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpv5HceV/R.INSTALL1668348aea58/pairwiseComparisons/man/reexports.Rd:25: file link ‘%<-%’ in package ‘ipmisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpv5HceV/R.INSTALL1668348aea58/pairwiseComparisons/man/reexports.Rd:25: file link ‘%<>%’ in package ‘ipmisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpv5HceV/R.INSTALL1668348aea58/pairwiseComparisons/man/reexports.Rd:25: file link ‘%>%’ in package ‘ipmisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpv5HceV/R.INSTALL1668348aea58/pairwiseComparisons/man/reexports.Rd:25: file link ‘as_tibble’ in package ‘ipmisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpv5HceV/R.INSTALL1668348aea58/pairwiseComparisons/man/reexports.Rd:25: file link ‘enframe’ in package ‘ipmisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpv5HceV/R.INSTALL1668348aea58/pairwiseComparisons/man/reexports.Rd:25: file link ‘tibble’ in package ‘ipmisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpv5HceV/R.INSTALL1668348aea58/pairwiseComparisons/man/reexports.Rd:27: file link ‘%|%’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpv5HceV/R.INSTALL1668348aea58/pairwiseComparisons/man/reexports.Rd:27: file link ‘%||%’ in package ‘rlang’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pairwiseComparisons.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘GDPgrowthRESULTS.csv’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpOOzqrb/R.INSTALL7203f40e4a3/palaeoSig/man/centipede_plot.Rd:26: file link ‘caterpillar’ in package ‘analogue’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpOOzqrb/R.INSTALL7203f40e4a3/palaeoSig/man/obs.cor.Rd:28: file link ‘rda’ in package ‘vegan’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpOOzqrb/R.INSTALL7203f40e4a3/palaeoSig/man/obs.cor.Rd:116: file link ‘rda’ in package ‘vegan’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpOOzqrb/R.INSTALL7203f40e4a3/palaeoSig/man/palaeoSig-package.Rd:46: file link ‘rioja-package’ in package ‘rioja’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpOOzqrb/R.INSTALL7203f40e4a3/palaeoSig/man/randomTF.Rd:35: file link ‘rda’ in package ‘vegan’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpOOzqrb/R.INSTALL7203f40e4a3/palaeoSig/man/randomTF.Rd:107: file link ‘rda’ in package ‘vegan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/palaeoSig.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘CorShrink’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpy5gAij/R.INSTALL49c7734f4328/palasso/man/methods.Rd:52: file link ‘coef.cv.glmnet’ in package ‘glmnet’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/palasso.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpJ4PIyR/R.INSTALL159434528d0f/paleofire/man/pfSimpleGrid.Rd:101: file link ‘Raster-class’ in package ‘raster’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJ4PIyR/R.INSTALL159434528d0f/paleofire/man/plot.pfGridding.Rd:45: file link ‘brewer.pal’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJ4PIyR/R.INSTALL159434528d0f/paleofire/man/plot.pfSiteSel.Rd:30: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/paleofire.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpFh8CzF/R.INSTALL53a93c1e8a84/paleoMAS/man/analog.mult.Rd:45: file link ‘wireframe’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpFh8CzF/R.INSTALL53a93c1e8a84/paleoMAS/man/analog.mult.Rd:47: file link ‘wireframe’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpFh8CzF/R.INSTALL53a93c1e8a84/paleoMAS/man/analog.mult.Rd:50: file link ‘wireframe’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/paleoMAS.Rcheck/00install.out’ for details.
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.
Rd file 'syas.Rd':
  \examples lines wider than 100 characters:
     bcrossv.sa(modernq[,1],perq2,a.d,delta=25,method="canberra",quant=0.05,trials=c(5, 0.05),detrend=FALSE)

Rd file 'vcrossv.all.Rd':
  \examples lines wider than 100 characters:
     #build a dummy factor assuming that the first 10 species belong to group1 and the send ten belong to group 2

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘Dispersion.pdf’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpE9oGeK/R.INSTALL1cf51605930b/pammtools/man/dplyr_verbs.Rd:181: file link ‘quo’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpE9oGeK/R.INSTALL1cf51605930b/pammtools/man/dplyr_verbs.Rd:183: file link ‘quasiquotation’ in package ‘rlang’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpE9oGeK/R.INSTALL1cf51605930b/pammtools/man/dplyr_verbs.Rd:213: file link ‘summarize_all’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpE9oGeK/R.INSTALL1cf51605930b/pammtools/man/geom_hazard.Rd:129: file link ‘geom_line’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpE9oGeK/R.INSTALL1cf51605930b/pammtools/man/geom_hazard.Rd:130: file link ‘geom_step’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpE9oGeK/R.INSTALL1cf51605930b/pammtools/man/pamm.Rd:30: file link ‘ti’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpE9oGeK/R.INSTALL1cf51605930b/pammtools/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpE9oGeK/R.INSTALL1cf51605930b/pammtools/man/tidy_smooth.Rd:20: file link ‘qqline’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pammtools.Rcheck/00install.out’ for details.
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.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpieR4mt/R.INSTALL7432606743cc/panelr/man/reexports.Rd:18: file link ‘%<>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpieR4mt/R.INSTALL7432606743cc/panelr/man/reexports.Rd:18: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/panelr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpF63JNx/R.INSTALL6bc85d2c7cb1/papeR/man/confint.Rd:29: file link ‘mcmcsamp’ in package ‘lme4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpF63JNx/R.INSTALL6bc85d2c7cb1/papeR/man/confint.Rd:35: file link ‘mcmcsamp’ in package ‘lme4’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpF63JNx/R.INSTALL6bc85d2c7cb1/papeR/man/prettify.Rd:132: file link ‘mcmcsamp’ in package ‘lme4’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/papeR.Rcheck/00install.out’ for details.
Warning: no function found corresponding to methods exports from ‘parallelize.dynamic’ for: ‘initialize’

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' call to ‘package’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘methods’ ‘parallel’ ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Codoc mismatches from documentation object 'Apply':
Apply
  Code: function(X, MARGIN, FUN, ..., simplify = TRUE)
  Docs: function(X, MARGIN, FUN, ...)
  Argument names in code not in docs:
    simplify
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp70Uk7z/R.INSTALL150c10971415/parallelMap/man/parallelRegisterLevels.Rd:24: file link ‘.onLoad’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp70Uk7z/R.INSTALL150c10971415/parallelMap/man/parallelStart.Rd:157: file link ‘makePSOCKcluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp70Uk7z/R.INSTALL150c10971415/parallelMap/man/parallelStart.Rd:159: file link ‘mcmapply’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp70Uk7z/R.INSTALL150c10971415/parallelMap/man/parallelStart.Rd:180: file link ‘clusterMap’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp70Uk7z/R.INSTALL150c10971415/parallelMap/man/parallelStop.Rd:16: file link ‘stopCluster’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/parallelMap.Rcheck/00install.out’ for details.
parallelSVM.default: no visible binding for global variable ‘na.omit’
parallelSVM.formula: no visible binding for global variable ‘na.omit’
predict.parallelSVM: no visible binding for global variable ‘predict’
Undefined global functions or variables:
  na.omit predict
Consider adding
  importFrom("stats", "na.omit", "predict")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpIClnHE/R.INSTALL694e597e96d3/parameters/man/p_value.Rd:64: file link ‘convert_pd_to_p’ in package ‘bayestestR’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/parameters.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpRSXA59/R.INSTALL14a95bd8bc07/ParamHelpers/man/evaluateParamExpressions.Rd:10: file link ‘ParamSet’ in package ‘ParamHelpers’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpRSXA59/R.INSTALL14a95bd8bc07/ParamHelpers/man/evaluateParamExpressions.Rd:21: file link ‘ParamSet’ in package ‘ParamHelpers’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpRSXA59/R.INSTALL14a95bd8bc07/ParamHelpers/man/getParamSet.Rd:14: file link ‘ParamSet’ in package ‘ParamHelpers’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpRSXA59/R.INSTALL14a95bd8bc07/ParamHelpers/man/hasExpression.Rd:10: file link ‘ParamSet’ in package ‘ParamHelpers’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ParamHelpers.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘example.csv’ ‘example.tsv’ ‘example.xlsx’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpYH9qni/R.INSTALL75a27a5b013b/parboost/man/parboost.Rd:56: file link ‘mboost’ in package ‘mboost’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpYH9qni/R.INSTALL75a27a5b013b/parboost/man/parboost.Rd:62: file link ‘mboost’ in package ‘mboost’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpYH9qni/R.INSTALL75a27a5b013b/parboost/man/parboost.Rd:63: file link ‘boost_control’ in package ‘mboost’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/parboost.Rcheck/00install.out’ for details.
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction-to-parcoords-.Rmd’
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘NUL’
Malformed Title field: should not end in a period.
Calls with DUP:
   .C("aracne", as.double(t(mis)), as.integer(n), as.double(eps), 
       as.double(eta), res = double(n * n), PACKAGE = "parmigene", 
       DUP = FALSE)
   .C("clr", as.double(t(mis)), as.integer(n), res = double(n * 
       n), PACKAGE = "parmigene", DUP = FALSE)
   .C("mrnet", as.double(t(mis)), as.integer(n), res = double(n * 
       n), PACKAGE = "parmigene", DUP = FALSE)
DUP is no longer supported and will be ignored.
File ‘parmigene/libs/parmigene.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpAKHJwl/R.INSTALL539855aadf3/parsetools/man/get_parse_data.Rd:69: file link ‘srcref’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpAKHJwl/R.INSTALL539855aadf3/parsetools/man/pd_identify.Rd:29: file link ‘srcref’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/parsetools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp2PXYkk/R.INSTALL77c140bf5ef5/parsnip/man/reexports.Rd:20: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/parsnip.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmprlRlUx/R.INSTALL76867093dcc2/partialCI/man/fit.pci.Rd:140: file link ‘partialAR’ in package ‘partialAR’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprlRlUx/R.INSTALL76867093dcc2/partialCI/man/hedge.pci.Rd:153: file link ‘partialAR’ in package ‘partialAR’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprlRlUx/R.INSTALL76867093dcc2/partialCI/man/loglik.pci.Rd:99: file link ‘partialAR’ in package ‘partialAR’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprlRlUx/R.INSTALL76867093dcc2/partialCI/man/multigetYahooPrices.Rd:39: file link ‘getYahooData’ in package ‘TTR’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprlRlUx/R.INSTALL76867093dcc2/partialCI/man/statehistory.pci.Rd:51: file link ‘partialAR’ in package ‘partialAR’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/partialCI.Rcheck/00install.out’ for details.
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.
Malformed Description field: should contain one or more complete sentences.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpxKEb7E/R.INSTALL19a6281b0a1a/partition/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/partition.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘co2’ ‘co2.1’ ‘co2.2’ ‘co2s.1’ ‘co2s.2’ ‘ctm.1’ ‘ctm.2’ ‘m’ ‘m.1’
  ‘m.2’ ‘test’ ‘test.1’ ‘test.2’ ‘testa.1’ ‘testa.2’ ‘xfile.1’
  ‘xfile.2’
Warning: no function found corresponding to methods exports from ‘partsm’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpVctzEn/R.INSTALL7512222e162f/partykit/man/ctree_control.Rd:43: file link ‘GenzBretz’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpVctzEn/R.INSTALL7512222e162f/partykit/man/glmtree.Rd:44: file link ‘glm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpVctzEn/R.INSTALL7512222e162f/partykit/man/lmtree.Rd:41: file link ‘lm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpVctzEn/R.INSTALL7512222e162f/partykit/man/lmtree.Rd:42: file link ‘lm.wfit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpVctzEn/R.INSTALL7512222e162f/partykit/man/prune.modelparty.Rd:31: file link ‘prune’ in package ‘rpart’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpVctzEn/R.INSTALL7512222e162f/partykit/man/prune.modelparty.Rd:58: file link ‘prune’ in package ‘rpart’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/partykit.Rcheck/00install.out’ for details.
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.
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.
Found the following files/directories:
  ‘pastis_data_1’ ‘pastis_data_2’ ‘pastis_data_3’
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘e1071’
  Please remove these calls from your code.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpSqZDND/R.INSTALL6a574c5f41d3/patchwork/man/wrap_elements.Rd:32: file link ‘ggtitle’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/patchwork.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpbqQScj/R.INSTALL1fd4726a988b/pathfindR/man/enrichment_chart.Rd:45: file link ‘ggplot2’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbqQScj/R.INSTALL1fd4726a988b/pathfindR/man/visualize_hsa_KEGG.Rd:39: file link ‘gravity_types’ in package ‘magick’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbqQScj/R.INSTALL1fd4726a988b/pathfindR/man/visualize_hsa_KEGG.Rd:42: file link ‘gravity_types’ in package ‘magick’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbqQScj/R.INSTALL1fd4726a988b/pathfindR/man/visualize_term_interactions.Rd:29: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpbqQScj/R.INSTALL1fd4726a988b/pathfindR/man/visualize_term_interactions.Rd:33: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pathfindR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpdDrAK5/R.INSTALL1c4e5eb436d2/pathlibr/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pathlibr.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘pathlibr.Rmd’
Checking should be performed on sources prepared by ‘R CMD build’.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpOyxrqQ/R.INSTALL7bea49676e6/patrick/man/with_parameters_test_that.Rd:32: file link ‘!!!’ in package ‘rlang’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/patrick.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpuhKmPE/R.INSTALL76f234fc2ed9/patternize/man/lanArray.Rd:5: file link ‘Morpho’ in package ‘Morpho’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuhKmPE/R.INSTALL76f234fc2ed9/patternize/man/lanArray.Rd:23: file link ‘Morpho’ in package ‘Morpho’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuhKmPE/R.INSTALL76f234fc2ed9/patternize/man/patRDA.Rd:7: file link ‘rda’ in package ‘vegan’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuhKmPE/R.INSTALL76f234fc2ed9/patternize/man/patRDA.Rd:118: file link ‘rda’ in package ‘vegan’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpuhKmPE/R.INSTALL76f234fc2ed9/patternize/man/patternize.Rd:86: file link ‘rda’ in package ‘vegan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/patternize.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PAutilities)
  package 'PAutilities' was built under R version 3.5.0
  > 
  > test_check("PAutilities")
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.
Warning: no function found corresponding to methods exports from ‘PAWL’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘foreach’ ‘ggplot2’ ‘reshape’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘foreach’ ‘ggplot2’ ‘methods’ ‘mvtnorm’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'createAdaptiveRandomWalkProposal.Rd':
  \usage lines wider than 90 characters:
         createAdaptiveRandomWalkProposal(nchains, targetdimension, adaptiveproposal, adaptationrate, sigma_init)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpfHSVQp/R.INSTALL225d6e498934/pbapply/man/pbapply.Rd:79: file link ‘parLapply’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfHSVQp/R.INSTALL225d6e498934/pbapply/man/pbapply.Rd:94: file link ‘makeForkCluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpfHSVQp/R.INSTALL225d6e498934/pbapply/man/pbapply.Rd:122: file link ‘parLapply’ in package ‘parallel’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pbapply.Rcheck/00install.out’ for details.
Found the following sources/headers with CR or CRLF line endings:
  src/zmqsrc/src/condition_variable.hpp
Some Unix compilers require LF line endings.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpz3zYfp/R.INSTALL5ff120a67001/pbo/man/dotplot.pbo.Rd:16: file link ‘dotplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpz3zYfp/R.INSTALL5ff120a67001/pbo/man/dotplot.pbo.Rd:19: file link ‘dotplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpz3zYfp/R.INSTALL5ff120a67001/pbo/man/dotplot.pbo.Rd:22: file link ‘dotplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpz3zYfp/R.INSTALL5ff120a67001/pbo/man/dotplot.pbo.Rd:32: file link ‘dotplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpz3zYfp/R.INSTALL5ff120a67001/pbo/man/histogram.pbo.Rd:29: file link ‘densityplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpz3zYfp/R.INSTALL5ff120a67001/pbo/man/histogram.pbo.Rd:29: file link ‘panel.abline’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpz3zYfp/R.INSTALL5ff120a67001/pbo/man/histogram.pbo.Rd:36: file link ‘densityplot’ in package ‘lattice’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpz3zYfp/R.INSTALL5ff120a67001/pbo/man/histogram.pbo.Rd:37: file link ‘panel.abline’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pbo.Rcheck/00install.out’ for details.
'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.
a_get_native: no visible global function definition for ‘par’
a_get_relative: no visible global function definition for ‘par’
brackets: no visible global function definition for ‘par’
brackets: no visible global function definition for ‘dist’
brackets: no visible global function definition for ‘lines’
Undefined global functions or variables:
  dist lines par
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "dist")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpKLE1Ul/R.INSTALL503c5204c6cf/PBSddesolve/man/dde.Rd:66: file link ‘pastgradient’ in package ‘PBSddesolve’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PBSddesolve.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp3cOwt8/R.INSTALL359f499d2d07/PBSmapping/man/plotMap.Rd:83: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PBSmapping.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
draw.pcaBootPlot: no visible global function definition for ‘grid’
draw.pcaBootPlot: no visible global function definition for ‘points’
draw.pcaBootPlot: no visible global function definition for ‘symbols’
draw.pcaBootPlot: no visible global function definition for ‘legend’
pcaBootPlot: no visible global function definition for ‘prcomp’
pcaBootPlot: no visible global function definition for ‘cor’
pcaBootPlot: no visible global function definition for ‘quantile’
pcaBootPlot: no visible global function definition for ‘pdf’
pcaBootPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  cor dev.off grid legend pdf points prcomp quantile symbols
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "grid", "legend", "points", "symbols")
  importFrom("stats", "cor", "prcomp", "quantile")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpjIS5sV/R.INSTALL68b3270e92e8/pcalg/man/randDAG.Rd:85: file link ‘graphNEL’ in package ‘graph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpjIS5sV/R.INSTALL68b3270e92e8/pcalg/man/randDAG.Rd:99: file link ‘random.graph.game’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpjIS5sV/R.INSTALL68b3270e92e8/pcalg/man/randDAG.Rd:99: file link ‘barabasi.game’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pcalg.Rcheck/00install.out’ for details.
PCDReg.wf: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp8QphCs/R.INSTALL6ab14b6db8f7/pcensmix/man/mixgen.Rd:27: file link ‘rnorm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8QphCs/R.INSTALL6ab14b6db8f7/pcensmix/man/mixgen.Rd:27: file link ‘rlnorm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8QphCs/R.INSTALL6ab14b6db8f7/pcensmix/man/mixgen.Rd:28: file link ‘rweibull’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8QphCs/R.INSTALL6ab14b6db8f7/pcensmix/man/mixgen.Rd:28: file link ‘rgamma’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8QphCs/R.INSTALL6ab14b6db8f7/pcensmix/man/mixgen.Rd:29: file link ‘rcauchy’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8QphCs/R.INSTALL6ab14b6db8f7/pcensmix/man/mixgen.Rd:29: file link ‘rbeta’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pcensmix.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpkSHtwP/R.INSTALL202a424df31c/pcFactorStan/man/pcStan.Rd:23: file link ‘sampling’ in package ‘rstan’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpkSHtwP/R.INSTALL202a424df31c/pcFactorStan/man/pcStan.Rd:31: file link ‘sampling’ in package ‘rstan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pcFactorStan.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘AbsolutePlot_Absolute Risk.pdf’ ‘ContrastPlot_OR.pdf’
Package suggested but not available for checking: ‘FFTrees’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpPMa8no/R.INSTALL2081493aecbb/PCRedux/man/earlyreg.Rd:46: file link ‘coefficients’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpPMa8no/R.INSTALL2081493aecbb/PCRedux/man/winklR.Rd:69: file link ‘acos’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PCRedux.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp8BQd4o/R.INSTALL7cfa7e1521e6/pcts/man/autocovariances-methods.Rd:76: file link ‘autocovariances’ in package ‘sarima’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pcts.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpn9ZjSB/R.INSTALL70e653379f7/pdfCluster/man/plot.kepdf.Rd:87: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpn9ZjSB/R.INSTALL70e653379f7/pdfCluster/man/plot.pdfCluster.Rd:81: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pdfCluster.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpK3UpKN/R.INSTALL21183325b3ca/pdftools/man/qpdf.Rd:24: file link ‘pdf_combine’ in package ‘qpdf’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpK3UpKN/R.INSTALL21183325b3ca/pdftools/man/qpdf.Rd:24: file link ‘pdf_compress’ in package ‘qpdf’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpK3UpKN/R.INSTALL21183325b3ca/pdftools/man/qpdf.Rd:24: file link ‘pdf_length’ in package ‘qpdf’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpK3UpKN/R.INSTALL21183325b3ca/pdftools/man/qpdf.Rd:24: file link ‘pdf_split’ in package ‘qpdf’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpK3UpKN/R.INSTALL21183325b3ca/pdftools/man/qpdf.Rd:24: file link ‘pdf_subset’ in package ‘qpdf’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pdftools.Rcheck/00install.out’ for details.
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').
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpnJqlGO/R.INSTALL73212ef49df2/pdqr/man/meta.Rd:69: file link ‘runif’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpnJqlGO/R.INSTALL73212ef49df2/pdqr/man/summ_interval.Rd:52: file link ‘qnorm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpnJqlGO/R.INSTALL73212ef49df2/pdqr/man/summ_roc.Rd:86: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pdqr.Rcheck/00install.out’ for details.
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘peakPick-vignette.Rmd’
peacf: no visible global function definition for ‘is.ts’
peacf: no visible global function definition for ‘cycle’
peacf: no visible global function definition for ‘ts.intersect’
peacf: no visible global function definition for ‘lag’
peacf: no visible global function definition for ‘ts’
peacf: no visible global function definition for ‘pchisq’
peacf.plot: no visible global function definition for ‘segments’
peacf.plot: no visible global function definition for ‘title’
pear: no visible global function definition for ‘cycle’
pear: no visible global function definition for ‘pchisq’
peboxplot: no visible global function definition for ‘cycle’
peboxplot: no visible global function definition for ‘boxplot’
peboxplot: no visible global function definition for ‘title’
peplot: no visible global function definition for ‘par’
peplot: no visible global function definition for ‘cycle’
peplot: no visible global function definition for ‘identify’
peplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  boxplot cycle identify is.ts lag mtext par pchisq segments title ts
  ts.intersect
Consider adding
  importFrom("graphics", "boxplot", "identify", "mtext", "par",
             "segments", "title")
  importFrom("stats", "cycle", "is.ts", "lag", "pchisq", "ts",
             "ts.intersect")
to your NAMESPACE file.
The following files should probably not be installed:
  ‘addendum.tex’, ‘slplot.tex’, ‘table1.tex’, ‘table3.tex’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
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.
Rd file 'PearsonICA.Rd':
  \usage lines wider than 90 characters:
     PearsonICA(X, n.comp = 0, row.norm = FALSE, maxit = 200, tol = 1e-04, border.base = c(2.6, 4), border.slope = c(0, 1), verbose = FALSE, ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘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').
Found the following files/directories:
  ‘A.txt’ ‘Ainv.txt’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpIDVnur/R.INSTALL3cd17a7824b8/pegas/man/geod.Rd:33: file link ‘as.dist’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpIDVnur/R.INSTALL3cd17a7824b8/pegas/man/na.omit.loci.Rd:5: file link ‘na.omit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpIDVnur/R.INSTALL3cd17a7824b8/pegas/man/nuc.div.Rd:48: file link ‘GC.content’ in package ‘ape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pegas.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpvTQYbT/R.INSTALL80b38d1d25b/peperr/man/complexity.LASSO.Rd:22: file link ‘optL1’ in package ‘penalized’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/peperr.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘CoxBoost’ ‘codetools’ ‘locfit’ ‘penalized’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
complexity.LASSO: no visible global function definition for ‘profL1’
complexity.ipec.CoxBoost: no visible global function definition for
  ‘CoxBoost’
complexity.ipec.CoxBoost: no visible global function definition for
  ‘locfit’
complexity.mincv.CoxBoost: no visible global function definition for
  ‘cv.CoxBoost’
complexity.ripec.CoxBoost: no visible global function definition for
  ‘CoxBoost’
complexity.ripec.CoxBoost: no visible global function definition for
  ‘locfit’
extract: no visible global function definition for ‘findGlobals’
fit.CoxBoost: no visible global function definition for ‘CoxBoost’
fit.LASSO: no visible global function definition for ‘penalized’
Undefined global functions or variables:
  CoxBoost cv.CoxBoost findGlobals locfit penalized profL1
Rd file 'aggregation.brier.Rd':
  \usage lines wider than 90 characters:
     aggregation.brier(full.data=NULL, response, x, model, cplx=NULL,  type=c("apparent", "noinf"), 

Rd file 'aggregation.misclass.Rd':
  \usage lines wider than 90 characters:
     aggregation.misclass(full.data=NULL, response, x, model, cplx=NULL,  type=c("apparent", "noinf"), 

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘PARMA21del1_ident’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpGTqC6h/R.INSTALL453a40cb3324/PerformanceAnalytics/man/PerformanceAnalytics-package.Rd:180: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGTqC6h/R.INSTALL453a40cb3324/PerformanceAnalytics/man/Return.read.Rd:22: file link ‘as.yearmon’ in package ‘zoo’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGTqC6h/R.INSTALL453a40cb3324/PerformanceAnalytics/man/Return.read.Rd:23: file link ‘as.yearqtr’ in package ‘zoo’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGTqC6h/R.INSTALL453a40cb3324/PerformanceAnalytics/man/chart.QQPlot.Rd:183: file link ‘qqplot’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGTqC6h/R.INSTALL453a40cb3324/PerformanceAnalytics/man/chart.StackedBar.Rd:109: file link ‘barchart’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PerformanceAnalytics.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpUkEGmx/R.INSTALL699c23755779/performance/man/model_performance.lavaan.Rd:35: file link ‘fitmeasures’ in package ‘lavaan’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpUkEGmx/R.INSTALL699c23755779/performance/man/model_performance.lm.Rd:28: file link ‘BIC’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpUkEGmx/R.INSTALL699c23755779/performance/man/model_performance.rma.Rd:28: file link ‘BIC’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpUkEGmx/R.INSTALL699c23755779/performance/man/performance_accuracy.Rd:34: file link ‘auc’ in package ‘bayestestR’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/performance.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘dendextendRcpp’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmphw52IH/R.INSTALL258866bf45b2/periscope/man/downloadablePlotUI.Rd:66: file link ‘graphics’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/periscope.Rcheck/00install.out’ for details.
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').
Found the following files/directories:
  ‘permus_per_dist_4’ ‘permus_per_shape_bin_4_0’
  ‘permus_per_shape_bin_4_1’ ‘permus_per_shape_bin_4_2’
  ‘permus_per_shape_bin_4_3’
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.
Rd file 'perm-internal.Rd':
  \usage lines wider than 90 characters:
     ksample.exact.mc(scores, group, nmc = 10^4 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED = TRUE)
     trend.exact.mc(scores, group, alternative = "two.sided", nmc = 10^3 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED = TR ... [TRUNCATED]
     twosample.exact.mc(scores, group, alternative = "two.sided", nmc = 10^4 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED  ... [TRUNCATED]

Rd file 'perm.Rd':
  \usage lines wider than 90 characters:
     permKS(x, g, exact = NULL, method = NULL, methodRule = methodRuleKS1, control=permControl(), ...)
     permTREND(x, y, alternative = c("two.sided", "less", "greater"), exact = NULL, method = NULL, methodRule = methodRuleTREND1, control=pe ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpzQJzxA/R.INSTALL635c4cfcafc4/perry/man/perryPlot.Rd:89: file link ‘geom_pointrange’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzQJzxA/R.INSTALL635c4cfcafc4/perry/man/perryPlot.Rd:90: file link ‘geom_line’ in package ‘ggplot2’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzQJzxA/R.INSTALL635c4cfcafc4/perry/man/perryPlot.Rd:156: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/perry.Rcheck/00install.out’ for details.
hasMethod: no visible global function definition for ‘getS3method’
Undefined global functions or variables:
  getS3method
Consider adding
  importFrom("utils", "getS3method")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpqYavdk/R.INSTALL2a0f45353ea7/PerseusR/man/as.ExpressionSet.matrixData.Rd:19: file link ‘ExpressionSet’ in package ‘Biobase’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpqYavdk/R.INSTALL2a0f45353ea7/PerseusR/man/as.ExpressionSet.matrixData.Rd:13: file link ‘ExpressionSet’ in package ‘Biobase’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpqYavdk/R.INSTALL2a0f45353ea7/PerseusR/man/as.matrixData.ExpressionSet.Rd:16: file link ‘ExpressionSet’ in package ‘Biobase’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpqYavdk/R.INSTALL2a0f45353ea7/PerseusR/man/as.matrixData.ExpressionSet.Rd:10: file link ‘ExpressionSet’ in package ‘Biobase’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PerseusR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpkPP5rv/R.INSTALL7dc120481ec6/persiandictionary/man/dictionary-package.Rd:38: file link ‘as.roman’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/persiandictionary.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpiEyJK8/R.INSTALL21d5162cc1d2/peRspective/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/peRspective.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘neural_network-s0000r1000.html’ ‘neural_network-s1000r1000.html’
  ‘neural_network-s2000r1000.html’ ‘neural_network-s3000r1000.html’
Found the following files/directories:
  ‘Myfile.txt’
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
pGLS: no visible global function definition for ‘model.response’
pGLS: no visible global function definition for ‘model.matrix’
pGLS: no visible global function definition for ‘pt’
Undefined global functions or variables:
  model.matrix model.response pt
Consider adding
  importFrom("stats", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
prepare_Rd: data_fs.Rd:11: Dropping empty section \source
prepare_Rd: var_fs.Rd:12-14: Dropping empty section \references
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp9t9Jj0/R.INSTALL28141d240119/PGRdup/man/DataClean.Rd:68: file link ‘gsub’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9t9Jj0/R.INSTALL28141d240119/PGRdup/man/DataClean.Rd:103: file link ‘gsub’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9t9Jj0/R.INSTALL28141d240119/PGRdup/man/DisProbDup.Rd:30: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9t9Jj0/R.INSTALL28141d240119/PGRdup/man/ProbDup.Rd:305: file link ‘stringdistmatrix’ in package ‘stringdist’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9t9Jj0/R.INSTALL28141d240119/PGRdup/man/ReviewProbDup.Rd:74: file link ‘write.csv’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PGRdup.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘animation.gif’
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpDtxPw0/R.INSTALL5f5a26b5a265/phangorn/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp878fip/R.INSTALL60e13799b1d/phaseR/man/flowField.Rd:78: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp878fip/R.INSTALL60e13799b1d/phaseR/man/flowField.Rd:166: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp878fip/R.INSTALL60e13799b1d/phaseR/man/nullclines.Rd:64: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp878fip/R.INSTALL60e13799b1d/phaseR/man/nullclines.Rd:153: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp878fip/R.INSTALL60e13799b1d/phaseR/man/numericalSolution.Rd:62: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp878fip/R.INSTALL60e13799b1d/phaseR/man/phasePortrait.Rd:100: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp878fip/R.INSTALL60e13799b1d/phaseR/man/trajectory.Rd:145: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phaseR.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘test.pdf’
Error(s) in re-building vignettes:
  ...
--- re-building ‘NER-MetaMAP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building ‘NER-MetaMAP.Rmd’

--- re-building ‘NLP-NILE.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building ‘NLP-NILE.Rmd’

--- re-building ‘example1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 69-71 (example1.Rmd) 
Error: processing vignette 'example1.Rmd' failed with diagnostics:
argument "subject_weight" is missing, with no default
--- failed re-building ‘example1.Rmd’

--- re-building ‘example2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 40-41 (example2.Rmd) 
Error: processing vignette 'example2.Rmd' failed with diagnostics:
argument "subject_weight" is missing, with no default
--- failed re-building ‘example2.Rmd’

--- re-building ‘main.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building ‘main.Rmd’

SUMMARY: processing the following files failed:
  ‘example1.Rmd’ ‘example2.Rmd’

Error: Vignette re-building failed.
Execution halted
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpZh6ssc/R.INSTALL5b7d5834e254/pheno/man/pheno.ddm.Rd:38: file link ‘matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pheno.Rcheck/00install.out’ for details.
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').
Rd file 'pheno.mlm.fit.Rd':
  \examples lines wider than 100 characters:
             R <- pheno.mlm.fit(DWD)                                                         # parameter estimation
             summary(tr)$coef[2]                                                                     # slope of trend
             summary(tr)$coef[4]                                                                     # standard error of trend

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp3Te5Kh/R.INSTALL7f581f25c3c8/PhenotypeSimulator/man/correlatedBgEffects.Rd:59: file link ‘rmvnorm’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PhenotypeSimulator.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpvm8YZe/R.INSTALL2e154ab4f76/phonR/man/normVowels.Rd:50: file link ‘exp’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpvm8YZe/R.INSTALL2e154ab4f76/phonR/man/normVowels.Rd:66: file link ‘colMeans’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpvm8YZe/R.INSTALL2e154ab4f76/phonR/man/repulsiveForce.Rd:26: file link ‘log’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phonR.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
Package suggested but not available for checking: ‘hyperSpec’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpalW8Rm/R.INSTALL29da266b0d94/photobiologyWavebands/man/NDVI.Rd:42: file link ‘NDxI’ in package ‘photobiology’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/photobiologyWavebands.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpihUCR4/R.INSTALL7fe712523b9a/photosynthesis/man/constants.Rd:12: file link ‘tleaf’ in package ‘tealeaves’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpihUCR4/R.INSTALL7fe712523b9a/photosynthesis/man/enviro_par.Rd:12: file link ‘tleaf’ in package ‘tealeaves’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpihUCR4/R.INSTALL7fe712523b9a/photosynthesis/man/leaf_par.Rd:12: file link ‘tleaf’ in package ‘tealeaves’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpihUCR4/R.INSTALL7fe712523b9a/photosynthesis/man/make_parameters.Rd:23: file link ‘tleaf’ in package ‘tealeaves’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpihUCR4/R.INSTALL7fe712523b9a/photosynthesis/man/parameter_names.Rd:12: file link ‘tleaf’ in package ‘tealeaves’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpihUCR4/R.INSTALL7fe712523b9a/photosynthesis/man/photosynthesis.Rd:25: file link ‘tleaf’ in package ‘tealeaves’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpihUCR4/R.INSTALL7fe712523b9a/photosynthesis/man/photosynthesis.Rd:95: file link ‘crossing’ in package ‘tidyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/photosynthesis.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘photosynthesis-introduction.Rmd’
Package suggested but not available for checking: ‘OutbreakTools’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpIP2t9a/R.INSTALL5d0a20af0ddc/phybreak/man/get.phybreak.Rd:52: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpIP2t9a/R.INSTALL5d0a20af0ddc/phybreak/man/sim.phybreak.Rd:54: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpIP2t9a/R.INSTALL5d0a20af0ddc/phybreak/man/sim.phybreak.Rd:63: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phybreak.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘output_values’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpHe5pkE/R.INSTALL2d9613364675/phylocanvas/man/as_tree-methods.Rd:23: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHe5pkE/R.INSTALL2d9613364675/phylocanvas/man/as_tree-methods.Rd:24: file link ‘phylo4’ in package ‘phylobase’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHe5pkE/R.INSTALL2d9613364675/phylocanvas/man/get.descendants.Rd:10: file link ‘phylo4’ in package ‘phylobase’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHe5pkE/R.INSTALL2d9613364675/phylocanvas/man/load.tree.Rd:23: file link ‘phylo4’ in package ‘phylobase’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHe5pkE/R.INSTALL2d9613364675/phylocanvas/man/load.tree.Rd:25: file link ‘phylo4’ in package ‘phylobase’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHe5pkE/R.INSTALL2d9613364675/phylocanvas/man/load.tree.Rd:15: file link ‘phylo4’ in package ‘phylobase’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHe5pkE/R.INSTALL2d9613364675/phylocanvas/man/phylocanvas.Rd:13: file link ‘phylo’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpHe5pkE/R.INSTALL2d9613364675/phylocanvas/man/phylocanvas.Rd:14: file link ‘phylo4’ in package ‘phylobase’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phylocanvas.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpl2HALo/R.INSTALL24d84f7d7373/phyloclim/man/hypothesis.tests.Rd:28: file link ‘SpatialPointsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phyloclim.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp8kAedF/R.INSTALL1366031f62c/phylogram/man/ladder.Rd:24: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8kAedF/R.INSTALL1366031f62c/phylogram/man/ladder.Rd:42: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8kAedF/R.INSTALL1366031f62c/phylogram/man/prune.Rd:45: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8kAedF/R.INSTALL1366031f62c/phylogram/man/read.dendrogram.Rd:26: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8kAedF/R.INSTALL1366031f62c/phylogram/man/read.dendrogram.Rd:54: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp8kAedF/R.INSTALL1366031f62c/phylogram/man/write.dendrogram.Rd:45: file link ‘ape’ in package ‘ape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phylogram.Rcheck/00install.out’ for details.
Unknown packages ‘surface’, ‘bayou’ in Rd xrefs
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpntK47s/R.INSTALL22ad735e7862/phylopath/man/plot.DAG.Rd:32: file link ‘create_layout’ in package ‘ggraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpntK47s/R.INSTALL22ad735e7862/phylopath/man/plot.fitted_DAG.Rd:38: file link ‘create_layout’ in package ‘ggraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpntK47s/R.INSTALL22ad735e7862/phylopath/man/plot_model_set.Rd:32: file link ‘create_layout’ in package ‘ggraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phylopath.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpNkVTdc/R.INSTALL23da40a29d7c/phyloregion/man/phylobuilder.Rd:66: file link ‘stripLabel’ in package ‘ape’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phyloregion.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘INLA’
Found the following files/directories:
  ‘subj_slp_sum.csv’ ‘wa_ps_V811043_sum.csv’
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.
File which contains pragma(s) suppressing diagnostics:
  ‘src/pijavski.cpp’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpvLF9kf/R.INSTALL418f66d54c05/pillar/man/deprecated.Rd:16: file link ‘vec_is’ in package ‘vctrs’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpvLF9kf/R.INSTALL418f66d54c05/pillar/man/type_sum.Rd:21: file link ‘vec_ptype_abbr’ in package ‘vctrs’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpvLF9kf/R.INSTALL418f66d54c05/pillar/man/type_sum.Rd:28: file link ‘vec_ptype_abbr’ in package ‘vctrs’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pillar.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpnXLlwh/R.INSTALLcd164182e1/pim/man/Extract.pim.summary.Rd:20: file link ‘as.integer’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpnXLlwh/R.INSTALLcd164182e1/pim/man/estimators.Rd:121: file link ‘glm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pim.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpjP8GW4/R.INSTALL2fef1ec39766/pinbasic/man/pin_confint.Rd:29: file link ‘set.seed’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmp8r4vU7/Rbuild34455ee0dd49/pinbasic/man/pinbasic.Rd:23: file link ‘lubridate’ in package ‘lubridate’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pinbasic.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpgwlFQp/R.INSTALL7d214369d290/pins/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pins.Rcheck/00install.out’ for details.
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.
Package suggested but not available for checking: ‘ggsubplot’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpNWl6Hv/R.INSTALL2d4579642ca1/pixiedust/man/dust.Rd:195: file link ‘glance’ in package ‘broom’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNWl6Hv/R.INSTALL2d4579642ca1/pixiedust/man/dust.Rd:234: file link ‘tidy’ in package ‘broom’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pixiedust.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpzC8Wty/R.INSTALL390057914792/pkgbuild/man/rcmd_build_tools.Rd:14: file link ‘rcmd_safe_env’ in package ‘callr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pkgbuild.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpnemeli/R.INSTALL10d967cce366/pkgcond/man/dot-underscore.Rd:23: file link ‘gettextf’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pkgcond.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpKvEYja/R.INSTALL16d56383e8b9/pkgload/man/help.Rd:33: file link ‘?’ in package ‘utils’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pkgload.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpxbegg8/R.INSTALL25a861216b5/pkgnet/man/DirectedGraph.Rd:9: file link ‘igraph-package’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpxbegg8/R.INSTALL25a861216b5/pkgnet/man/DirectedGraph.Rd:102: file link ‘neighborhood.size’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpxbegg8/R.INSTALL25a861216b5/pkgnet/man/DirectedGraph.Rd:106: file link ‘neighborhood.size’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpxbegg8/R.INSTALL25a861216b5/pkgnet/man/DirectedGraphMeasures.Rd:29: file link ‘neighborhood.size’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpxbegg8/R.INSTALL25a861216b5/pkgnet/man/DirectedGraphMeasures.Rd:33: file link ‘neighborhood.size’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpxbegg8/R.INSTALL25a861216b5/pkgnet/man/InheritanceReporter.Rd:21: file link ‘ReferenceClasses’ in package ‘methods’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpxbegg8/R.INSTALL25a861216b5/pkgnet/man/InheritanceReporter.Rd:24: file link ‘ReferenceClasses’ in package ‘methods’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pkgnet.Rcheck/00install.out’ for details.
Depends: includes the non-default packages:
  'RGtk2', 'gWidgetsRGtk2', 'cairoDevice', 'lattice', 'rggobi',
  'ggplot2', 'proto'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘RGtk2’ ‘gWidgetsRGtk2’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘cairoDevice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
prepare_Rd: PKgraph.Rd:11-13: Dropping empty section \arguments
prepare_Rd: PKgraph.Rd:17-19: Dropping empty section \examples
prepare_Rd: pkdata.Rd:9-11: Dropping empty section \format
prepare_Rd: pkdata.Rd:14-16: Dropping empty section \examples
prepare_Rd: pkdata2.Rd:9-11: Dropping empty section \format
prepare_Rd: pkdata2.Rd:14-16: Dropping empty section \examples
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpJCKS4c/R.INSTALL334c57cfeda9/PKPDmisc/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PKPDmisc.Rcheck/00install.out’ for details.
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.
Found the following files/directories:
  ‘Indometh_Bolus_Linear_CoreOutput.txt’
  ‘Indometh_Bolus_Log_CoreOutput.txt’
  ‘Indometh_Infusion_Linear_CoreOutput.txt’
  ‘Indometh_Infusion_Log_CoreOutput.txt’ ‘Output’
  ‘Theoph_Linear_CoreOutput.txt’ ‘Theoph_Log_CoreOutput.txt’
Package suggested but not available for checking: ‘BradleyTerryScalable’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpWfaGQD/R.INSTALL295a698e5e05/plainview/man/plainView.Rd:89: file link ‘SpatialPixelsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plainview.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
Malformed Description field: should contain one or more complete sentences.
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.
Rd file 'em.hmm.Rd':
  \examples lines wider than 100 characters:
     #all.Rlts=cbind(rbind(chr1.data,chr6.data), LIS=c(chr1.L2rlts$LIS,chr6.L2rlts$LIS), gFDR=plis.rlts$aLIS, fdr001state=plis.rlts$States)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpetZUbq/R.INSTALL5a47a2e95a7/PLMIX/man/as.top_ordering.Rd:73: file link ‘as.rankings’ in package ‘PlackettLuce’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpetZUbq/R.INSTALL5a47a2e95a7/PLMIX/man/gsPLMIX_to_mcmc.Rd:34: file link ‘as.mcmc’ in package ‘coda’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PLMIX.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /tmp/RtmpIT3Jjp/Rbuild471d6d602ab5/plm/man/detect.lindep.Rd:89: file link ‘alias.lm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpIT3Jjp/Rbuild471d6d602ab5/plm/man/detect.lindep.Rd:52: file link ‘alias.lm’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp1tRu3D/R.INSTALL51da35ad4a9f/plm/man/pdata.frame.Rd:140: file link ‘as.list.data.frame’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpralL02/R.INSTALL371d5c8e58d8/PLNmodels/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PLNmodels.Rcheck/00install.out’ for details.
nrmlepln: no visible global function definition for ‘pchisq’
nrmlerasch: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpVje63y/R.INSTALL379b677068f0/plot3logit/man/deprecated-functions.Rd:19: file link ‘ggtern-package’ in package ‘ggtern’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpVje63y/R.INSTALL379b677068f0/plot3logit/man/effect.Rd:14: file link ‘graphical parameters’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /private/var/folders/h1/d3zt9jvn19s5_2kr3qm5ggjc0000gn/T/Rtmpfh0NLv/Rbuild2624e187dde/plot3logit/man/field3logit.Rd:114: file link ‘ggtern-package’ in package ‘ggtern’ does not exist and so has been treated as a topic
  Rd warning: /private/var/folders/h1/d3zt9jvn19s5_2kr3qm5ggjc0000gn/T/Rtmpfh0NLv/Rbuild2624e187dde/plot3logit/man/plot3logit-package.Rd:30: file link ‘ggtern-package’ in package ‘ggtern’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plot3logit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpvmBtyL/R.INSTALL5f8c30ee6b/plotdap/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plotdap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpJrj5MG/R.INSTALL25e47b7b5612/plotluck/man/plotluck.Rd:159: file link ‘RColorBrewer’ in package ‘RColorBrewer’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJrj5MG/R.INSTALL25e47b7b5612/plotluck/man/plotluck.Rd:171: file link ‘plot.data.frame’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plotluck.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpIpQKP6/R.INSTALL7dfe5082e84d/plot.matrix/man/assignColors.Rd:44: file link ‘heat.colors’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpIpQKP6/R.INSTALL7dfe5082e84d/plot.matrix/man/plot.matrix.Rd:22: file link ‘heat.colors’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpIpQKP6/R.INSTALL7dfe5082e84d/plot.matrix/man/plot.matrix.Rd:52: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpIpQKP6/R.INSTALL7dfe5082e84d/plot.matrix/man/plot.matrix.Rd:80: file link ‘heat.colors’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plot.matrix.Rcheck/00install.out’ for details.
plotAuto: no visible global function definition for ‘window’
plotAuto: no visible global function definition for ‘title’
plotAuto: no visible global function definition for ‘axis’
plotAuto: no visible global function definition for ‘box’
plotCumu: no visible global function definition for ‘title’
plotCumu: no visible global function definition for ‘axis’
plotCumu: no visible global function definition for ‘box’
plotDens : panel.dens: no visible global function definition for ‘var’
plotDens : panel.dens: no visible global function definition for
  ‘quantile’
plotDens : panel.dens: no visible global function definition for
  ‘median’
plotDens: no visible global function definition for ‘tail’
plotQuant: no visible global function definition for ‘par’
plotQuant: no visible binding for global variable ‘quantile’
plotQuant: no visible global function definition for ‘lines’
plotQuant: no visible global function definition for ‘bxp’
plotQuant: no visible global function definition for ‘matplot’
plotQuant: no visible global function definition for ‘axis’
plotQuant: no visible global function definition for ‘box’
plotQuant: no visible global function definition for ‘title’
plotSplom: no visible global function definition for ‘pairs’
plotTrace : panel.trace: no visible global function definition for
  ‘var’
plotTrace : panel.trace: no visible global function definition for
  ‘median’
plotTrace: no visible global function definition for ‘tail’
Undefined global functions or variables:
  axis box bxp lines matplot median pairs par quantile tail title var
  window
Consider adding
  importFrom("graphics", "axis", "box", "bxp", "lines", "matplot",
             "pairs", "par", "title")
  importFrom("stats", "median", "quantile", "var", "window")
  importFrom("utils", "tail")
to your NAMESPACE file.
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.
Rd file 'envelopeArea_and_Perimeter.Rd':
  \examples lines wider than 100 characters:
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")

Rd file 'generateEnvelope.Rd':
  \examples lines wider than 100 characters:
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")
     grid.polygon(envelopeXY[,1], envelopeXY[,2], gp=gpar(fill="pink", col="transparent", lwd=5), default.units="npc")

Rd file 'tangentLine.Rd':
  \examples lines wider than 100 characters:
                     tangent <- tangentLine(centers[1,], centers[2,], r0, r[2], k=k)  # compute coefficients for the tangent line, if NA, th ... [TRUNCATED]
                             grid.abline(-tangent["c"] / tangent["b"], -tangent["a"] / tangent["b"], gp=gpar(col="blue", lwd=ii), units="npc ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp3PKx7B/R.INSTALL1f121f75a3f5/plotscale/man/plotsize.default.Rd:35: file link ‘current.vpTree’ in package ‘grid’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plotscale.Rcheck/00install.out’ for details.
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: ‘plspm’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpLTPp7n/R.INSTALL81f514c22fb/plsmod/man/reexports.Rd:18: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plsmod.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpXcBxbY/R.INSTALL272561f1af4d/plsmselect/man/gamlasso.Rd:87: file link ‘ti’ in package ‘mgcv’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXcBxbY/R.INSTALL272561f1af4d/plsmselect/man/summary.gamlasso.Rd:79: file link ‘coef.cv.glmnet’ in package ‘glmnet’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plsmselect.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpjzvDJc/R.INSTALL26203b0eb87f/plsRglm/man/plots.confints.bootpls.Rd:21: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpjzvDJc/R.INSTALL26203b0eb87f/plsRglm/man/plots.confints.bootpls.Rd:22: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpjzvDJc/R.INSTALL26203b0eb87f/plsRglm/man/plots.confints.bootpls.Rd:27: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plsRglm.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction.Rmd’
print.densityEHpi: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Rd file 'predict.plus.Rd':
  \examples lines wider than 100 characters:
     extracted.values <- predict(object, lam = sort(object$lam.path[1:10],decreasing=TRUE), newx=object$x)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp69E4jF/R.INSTALL3a592052c092/plyr/man/rbind.fill.matrix.Rd:48: file link ‘rbind’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plyr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpF5drYB/R.INSTALL91056daea13/pm4py/man/reexports.Rd:15: file link ‘py_to_r’ in package ‘reticulate’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpF5drYB/R.INSTALL91056daea13/pm4py/man/reexports.Rd:15: file link ‘r_to_py’ in package ‘reticulate’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pm4py.Rcheck/00install.out’ for details.
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.
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').
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.
Non-standard file/directory found at top level:
  ‘TODO.md’
'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
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpCQxWMw/R.INSTALL3c19744c5d57/poio/man/plural_forms.Rd:36: file link ‘ISO_639_2’ in package ‘ISOcodes’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpCQxWMw/R.INSTALL3c19744c5d57/poio/man/po.Rd:28: file link ‘ngettext’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpCQxWMw/R.INSTALL3c19744c5d57/poio/man/po.Rd:32: file link ‘R6’ in package ‘R6’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpCQxWMw/R.INSTALL3c19744c5d57/poio/man/summary.po.Rd:12: file link ‘print.data.frame’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/poio.Rcheck/00install.out’ for details.
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.
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.
Found the following files/directories:
  ‘pow.txt’
rpoistweedie: no visible global function definition for ‘runif’
testOmegaPT: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
prepare_Rd: poistweedie.Rd:51: Dropping empty section \references
prepare_Rd: ppoistweedie.Rd:37: Dropping empty section \references
prepare_Rd: qpoistweedie.Rd:40: Dropping empty section \references
prepare_Rd: rpoistweedie.Rd:36: Dropping empty section \references
prepare_Rd: varpt.Rd:31: Dropping empty section \references
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmptgYAeP/R.INSTALL26356aae5a3d/poliscidata/man/available.imported.functions.Rd:146: file link ‘svytable’ in package ‘survey’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmptgYAeP/R.INSTALL26356aae5a3d/poliscidata/man/available.imported.functions.Rd:147: file link ‘svytable’ in package ‘survey’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/poliscidata.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Table.Output.html’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpYvaU7M/R.INSTALL4c86fddbc79/polite/man/nullcoalesce.Rd:11: file link ‘%||%’ in package ‘purrr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpYvaU7M/R.INSTALL4c86fddbc79/polite/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/polite.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘pollimetrydata’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpog5jJB/R.INSTALL63ac556ffd0d/polmineR/man/reexports.Rd:14: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/polmineR.Rcheck/00install.out’ for details.
Running examples in ‘polspline-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: beta.polyclass
> ### Title: Polyclass: polychotomous regression and multiple classification
> ### Aliases: beta.polyclass
> ### Keywords: smooth nonlinear
> 
> ### ** Examples
> 
> data(iris)
> fit.iris <- polyclass(iris[,5], iris[,1:4])
Warning in Ops.factor(as.integer(data), data) :
  ‘-’ not meaningful for factors
Error in if (max(abs(as.integer(data) - data)) < 0.001) data <- as.integer(data) else stop("not-integer data") : 
  missing value where TRUE/FALSE needed
Calls: polyclass
Execution halted
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.
Found the following files/directories:
  ‘polyfreqs-mcmc.out’
Package vignette with placeholder title ‘Vignette Title’:
  ‘polynomials.Rmd’
Found the following files/directories:
  ‘AbsorbedDrugMetabolites’ ‘CorrelationResults’
  ‘EndogenousMetabolites’ ‘HeatMap’ ‘PKresults’
  ‘SecondAbsorbedMetabolites’ ‘preprocessed-data’
Found the following files/directories:
  ‘SPAGfreqExample2.txt’ ‘SpagInputExample.txt’ ‘SpagOutExample.txt’
  ‘SpagTemp.txt’ ‘TetrasatExample.txt’ ‘atetraexample.txt’
  ‘atetratest.txt’ ‘exampleGMoutput.txt’ ‘forPOPDIST.txt’
  ‘genodiveExample.txt’ ‘readGMtest.txt’ ‘strtemp.txt’ ‘structtest.txt’
  ‘testGenoDive2.txt’ ‘testGenoDive3.txt’ ‘testPOPDIST.txt’
  ‘tetrasattest.txt’
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmps1AJyV/R.INSTALL2e536d954cf3/polywog/man/plot.polywog.Rd:35: file link ‘wireframe’ in package ‘lattice’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/polywog.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpsoJxRv/R.INSTALL2eaa7550aa93/pomdp/man/plot_policy_graph.Rd:49: file link ‘visIgraph’ in package ‘visNetwork’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpsoJxRv/R.INSTALL2eaa7550aa93/pomdp/man/plot_policy_graph.Rd:109: file link ‘visIgraph’ in package ‘visNetwork’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pomdp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp8hpCuL/R.INSTALL2f254a01d3c7/pomp/man/reexports.Rd:15: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pomp.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpiYZMIk/R.INSTALL32383b140e28/poorman/man/print.grouped_data.Rd:36: file link ‘getOption’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/poorman.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpNrqEdc/R.INSTALL6a6b4eb8212f/PopED/man/median_hilow_poped.Rd:13: file link ‘median_hilow’ in package ‘ggplot2’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PopED.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘PopED_output_summary_D_cont_opt_1.txt’ ‘PopED_output_summary_RS.txt’
  ‘PopED_output_summary_mfea_opt_1.txt’ ‘test.csv’
Non-standard file/directory found at top level:
  ‘extdata’
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Rd file 'popgen.Rd':
  \usage lines wider than 90 characters:
     popgen(datafile, ndigit = 3, freq.overall = T, freq.by.pop = T, genetic.stats = T, pairwise.fst = T)

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘WhopGenome’
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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpeqxgSH/R.INSTALL68045f41d81d/popprxl/man/read.genalexcel.Rd:17: file link ‘genclone’ in package ‘poppr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/popprxl.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpedHoB3/R.INSTALL30c27927c03/poptrend/man/poptrend.Rd:17: file link ‘mgcv’ in package ‘mgcv’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/poptrend.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpqhH1Zq/R.INSTALLda64bd4ec66/portalr/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/portalr.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘TSA’
Unknown package ‘TSA’ in Rd xrefs
'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:
  ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘portfolioSim/R/AllClasses.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

contributionSummaryDf,simResult : <anonymous>: no visible global
  function definition for ‘aggregate’
getSimTrades,stiFromSignal-orderable-portfolio-simData-logical: no
  visible binding for global variable ‘shares’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.freq’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.errors’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.type’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.summary.interface’
loadIn,simResultSinglePeriod-character-missing: no visible binding for
  global variable ‘x’
plot,simResult-missing: no visible global function definition for
  ‘xyplot’
runSim,portfolioSim-logical: no visible binding for global variable
  ‘id’
runSim,portfolioSim-logical: no visible global function definition for
  ‘updateSummary’
securityPerfSummaryDf,simResult: no visible global function definition
  for ‘aggregate’
summary,simResult: no visible global function definition for ‘sd’
summary,simResult: no visible global function definition for ‘head’
summary,simResult: no visible global function definition for ‘tail’
Undefined global functions or variables:
  aggregate head id master.errors master.freq master.summary.interface
  master.type sd shares tail updateSummary x xyplot
Consider adding
  importFrom("stats", "aggregate", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp581o4N/R.INSTALL41f3434642e1/postGIStools/man/get_postgis_query.Rd:30: file link ‘sp’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/postGIStools.Rcheck/00install.out’ for details.
'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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpT4a3DN/R.INSTALL3c0f5ca8282c/ppcc/man/ppccTest.Rd:268: file link ‘qgumbel’ in package ‘VGAM’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpT4a3DN/R.INSTALL3c0f5ca8282c/ppcc/man/ppccTest.Rd:269: file link ‘qgev’ in package ‘VGAM’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ppcc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpoTGsez/R.INSTALL67f559aab492/ppcong/man/P.Rd:10: file link ‘%P%’ in package ‘tfse’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ppcong.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Quad1.RData’ ‘Sp Env Data.RData’ ‘Sp PPM Data.RData’
  ‘SpEnvData.RData’ ‘Test.RData’ ‘TestPPM.RData’ ‘TestSP.RData’
pps1: no visible global function definition for ‘runif’
ppss: no visible global function definition for ‘runif’
ppswr: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
prepare_Rd: calif.Rd:5-6: Dropping empty section \arguments
prepare_Rd: calif.Rd:8-9: Dropping empty section \examples
prepare_Rd: califcty.Rd:5-6: Dropping empty section \arguments
prepare_Rd: califcty.Rd:8-9: Dropping empty section \examples
prepare_Rd: sizesok.Rd:12-13: Dropping empty section \examples
prepare_Rd: stratumsizes.Rd:11-12: Dropping empty section \examples
Malformed Description field: should contain one or more complete sentences.
LDA.Tree : Find.proj: no visible binding for global variable ‘var’
LDA.Tree : Find.proj: no visible binding for global variable ‘IQR’
LDA.Tree : Find.proj: no visible binding for global variable ‘median’
PDA.Tree : Find.proj: no visible binding for global variable ‘var’
PDA.Tree : Find.proj: no visible binding for global variable ‘median’
PDA.Tree : Find.proj: no visible binding for global variable ‘IQR’
PP.Tree : Find.proj: no visible binding for global variable ‘var’
PP.Tree : Find.proj: no visible binding for global variable ‘median’
PP.Tree : Find.proj: no visible binding for global variable ‘IQR’
PP.optimize.Huber: no visible binding for global variable ‘sd’
PP.optimize.anneal: no visible binding for global variable ‘sd’
PP.optimize.plot: no visible binding for global variable ‘sd’
PP.optimize.plot: no visible global function definition for ‘hist’
PP.optimize.plot: no visible global function definition for ‘text’
PP.optimize.plot: no visible global function definition for ‘par’
PP.optimize.plot: no visible global function definition for ‘colors’
PP.optimize.plot: no visible global function definition for ‘pairs’
PP.optimize.random: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  IQR colors hist median pairs par sd text var
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "hist", "pairs", "par", "text")
  importFrom("stats", "IQR", "median", "sd", "var")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘dev’
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.
PKG_CXXFLAGS set in ‘src/Makevars.win’ without any corresponding files
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.
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘DESCRIPTION.bck’
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘predmixcor/R/firstlib.r’:
  .First.lib calls:
    cat("predmixcor loaded\n", "COPY RIGHT: Longhai Li\n", "http://math.usask.ca/~longhai\n",     "Type ?begin.predmixcor for help\n", sep = "")

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

Predict.mix: no visible global function definition for ‘dbinom’
abs_cor: no visible global function definition for ‘cor’
gen.alpha.IGamma: no visible global function definition for ‘qgamma’
gendata.mix: no visible global function definition for ‘runif’
gendata.mix: no visible global function definition for ‘rbeta’
mh1.unif: no visible global function definition for ‘runif’
train_predict_mix: no visible global function definition for ‘dbinom’
training: no visible global function definition for ‘runif’
training: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  cor dbinom qgamma rbeta runif
Consider adding
  importFrom("stats", "cor", "dbinom", "qgamma", "rbeta", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmprZNb12/R.INSTALL350c4dae69e6/pre/man/coef.gpe.Rd:22: file link ‘coef.cv.glmnet’ in package ‘glmnet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprZNb12/R.INSTALL350c4dae69e6/pre/man/coef.pre.Rd:22: file link ‘coef.cv.glmnet’ in package ‘glmnet’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmprZNb12/R.INSTALL350c4dae69e6/pre/man/corplot.Rd:55: file link ‘colorRampPalette’ in package ‘grDevices’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pre.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Non-standard file/directory found at top level:
  ‘COPYRIGHTS’
Copyright information should be in file inst/COPYRIGHTS
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpXigXOT/R.INSTALL48b961cfa0d5/presser/man/presser_response.Rd:42: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXigXOT/R.INSTALL48b961cfa0d5/presser/man/presser_response.Rd:43: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/presser.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
Package suggested but not available for checking: ‘INLA’
Found the following significant warnings:
  zhegv.c:216:27: warning: ‘strncpy’ output may be truncated copying 2 bytes from a string of length 5 [-Wstringop-truncation]
  zhegv.c:216:27: warning: ‘strncpy’ output may be truncated copying 3 bytes from a string of length 3 [-Wstringop-truncation]
  zhegv.c:216:27: warning: ‘strncpy’ output may be truncated copying 2 bytes from a string of length 2 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PRIMME.Rcheck/00install.out’ for details.
basisplot: no visible global function definition for ‘abline’
basisplot: no visible global function definition for ‘text’
basisplot: no visible global function definition for ‘par’
plot.prinsimp: no visible global function definition for ‘screeplot’
plot.simpart: no visible global function definition for ‘par’
position_text: no visible global function definition for ‘par’
position_text: no visible global function definition for ‘strwidth’
simpart.formula: no visible global function definition for ‘terms’
simpart.formula: no visible global function definition for
  ‘model.matrix’
varperc: no visible global function definition for ‘lines’
varperc: no visible global function definition for ‘text’
varsimp: no visible global function definition for ‘points’
varsimp: no visible global function definition for ‘text’
varsimp: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline lines model.matrix par points screeplot strwidth terms text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "points", "strwidth",
             "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘priorcd.Rmd’
Found the following files/directories:
  ‘network.html’ ‘network_files’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpCrak3U/R.INSTALL397c709006ec/prioritizrdata/man/salt_data.Rd:12: file link ‘RasterStack-class’ in package ‘raster’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpCrak3U/R.INSTALL397c709006ec/prioritizrdata/man/salt_data.Rd:13: file link ‘RasterLayer-class’ in package ‘raster’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpCrak3U/R.INSTALL397c709006ec/prioritizrdata/man/tas_data.Rd:12: file link ‘RasterStack-class’ in package ‘raster’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpCrak3U/R.INSTALL397c709006ec/prioritizrdata/man/tas_data.Rd:13: file link ‘SpatialPolygonsDataFrame’ in package ‘sp’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/prioritizrdata.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘gurobi’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpsmvhEM/R.INSTALL39f173826be0/prioritylasso/man/pl_data.Rd:24: file link ‘rmvnorm’ in package ‘mvtnorm’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/prioritylasso.Rcheck/00install.out’ for details.
pr.conditional: no visible global function definition for ‘qnorm’
pr.marginal: no visible global function definition for ‘qnorm’
prLogisticDelta: no visible global function definition for ‘glm’
prLogisticDelta: no visible binding for global variable ‘binomial’
Undefined global functions or variables:
  binomial glm qnorm
Consider adding
  importFrom("stats", "binomial", "glm", "qnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpFNGqBT/R.INSTALL81810036936/probably/man/reexports.Rd:15: file link ‘as.factor’ in package ‘generics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpFNGqBT/R.INSTALL81810036936/probably/man/reexports.Rd:15: file link ‘as.ordered’ in package ‘generics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/probably.Rcheck/00install.out’ for details.
.pfda.fstep: no visible global function definition for ‘dist’
.pfda.mstep: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov dist
Consider adding
  importFrom("stats", "cov", "dist")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpcuGTnL/R.INSTALL3adf2c4e28e6/ProbForecastGOP/man/Field.sim.Rd:142: file link ‘GaussRF’ in package ‘RandomFields’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ProbForecastGOP.Rcheck/00install.out’ for details.
prepare_Rd: ProbForecastGOP-package.Rd:42-43: Dropping empty section \seealso
Rd file 'Emp.variog.Rd':
  \usage lines wider than 90 characters:
     Emp.variog(day, obs, forecast, id, coord1, coord2, cut.points=NULL, max.dist=NULL, nbins=300)

Rd file 'EmpDir.variog.Rd':
  \usage lines wider than 90 characters:
     EmpDir.variog(day, obs, forecast, id, coord1, coord2, tol.angle1=45, tol.angle2=135, cut.points=NULL, max.dist=NULL, nbins=300, type) 
  \examples lines wider than 100 characters:
     plot(dir.variog$bin.midpoints,dir.variog$dir.variog,xlab="Distance",ylab="Semi-variance",main="Empirical Directional variogram")

Rd file 'Field.sim.Rd':
  \usage lines wider than 90 characters:
     Field.sim(obs, forecast, coord1.grid, coord2.grid, forecast.grid,variog.model="exponential", param.est, n.sim=99, n.displ=4, 

Rd file 'avg.variog.Rd':
  \examples lines wider than 100 characters:
     variogram <- avg.variog(day=day, coord1=coord1,coord2=coord2,id=id,variable=obs,cut.points=NULL,max.dist=NULL,nbins=NULL) 
     plot(variogram$bin.midpoints,variogram$empir.variog,xlab="Distance", ylab="Semi-variance",main="Empirical variogram")

Rd file 'avg.variog.dir.Rd':
  \examples lines wider than 100 characters:
     dir.variog <- avg.variog.dir(day,coord1,coord2,id,variable=obs, tol.angle1=NULL,tol.angle2=NULL,cut.points=NULL,max.dist=NULL, nbins=NU ... [TRUNCATED]
     plot(dir.variog$bin.midpoints,dir.variog$dir.variog,xlab="Distance", ylab="Semi-variance",main="Empirical Directional variogram")

Rd file 'linesmodel.Rd':
  \examples lines wider than 100 characters:
     lines(variogram$bin.midpoints,linesmodel(distance=variogram$bin.midpoints,variog.model="exponential",param=c(param.variog$nugget,

These lines will be truncated in the PDF manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ProbitSpatial.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpR5s6da/R.INSTALL69f4599abe00/prob/man/CharFunc.Rd:108: file link ‘kummerM’ in package ‘fAsianOptions’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpR5s6da/R.INSTALL69f4599abe00/prob/man/CharFunc.Rd:155: file link ‘kummerU’ in package ‘fAsianOptions’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpR5s6da/R.INSTALL69f4599abe00/prob/man/CharFunc.Rd:318: file link ‘kummerM’ in package ‘fAsianOptions’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpR5s6da/R.INSTALL69f4599abe00/prob/man/CharFunc.Rd:319: file link ‘kummerU’ in package ‘fAsianOptions’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/prob.Rcheck/00install.out’ for details.
Running examples in ‘processcontrol-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: six_sigma_ctrl_chart
> ### Title: Generate IndX and mR charts.
> ### Aliases: six_sigma_ctrl_chart
> 
> ### ** Examples
> 
> data("spcTimeSeries")
> six_sigma_ctrl_chart(spcTimeSeries)
Error in plot.window(...) : invalid 'xlim' value
Calls: six_sigma_ctrl_chart ... <Anonymous> -> plot.default -> localWindow -> plot.window
Execution halted
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp5Qsica/R.INSTALL341247910ff5/processx/man/curl_fds.Rd:11: file link ‘multi_fdset’ in package ‘curl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/processx.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpKeqdMr/R.INSTALL3bfd7a866a67/ProcMod/man/names.procmod_corls.Rd:30: file link ‘corls’ in package ‘ProcMod’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpKeqdMr/R.INSTALL3bfd7a866a67/ProcMod/man/print.procmod_corls.Rd:32: file link ‘corls’ in package ‘ProcMod’ does not exist and so has been treated as a topic
  Rd warning: /private/var/folders/jx/vdgsg8jj7qv6gxrlbl_bwlpr0000gn/T/RtmphJi8Rz/Rbuild1409462a272a6/ProcMod/man/varls.Rd:83: file link ‘cov2cor’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ProcMod.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpTKJhln/R.INSTALL63eb7b6ce7b8/pROC/man/cov.Rd:93: file link ‘cov’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpTKJhln/R.INSTALL63eb7b6ce7b8/pROC/man/var.Rd:85: file link ‘var’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pROC.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
GPois: no visible global function definition for ‘dnorm’
GPois: no visible binding for global variable ‘poisson’
GPois: no visible global function definition for ‘predict’
GPois: no visible global function definition for ‘fitted’
GPois: no visible global function definition for ‘residuals’
GPois: no visible global function definition for ‘smooth.spline’
ProDenICA: no visible global function definition for ‘rnorm’
d.gaussmix: no visible global function definition for ‘dnorm’
djordan: no visible global function definition for ‘dt’
djordan: no visible global function definition for ‘dunif’
mixmat: no visible global function definition for ‘rnorm’
mixmat: no visible global function definition for ‘runif’
r.gaussmix: no visible global function definition for ‘rmultinom’
r.gaussmix: no visible global function definition for ‘rnorm’
rjordan: no visible global function definition for ‘rt’
rjordan: no visible global function definition for ‘runif’
rmix.dexp: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm dt dunif fitted poisson predict residuals rmultinom rnorm rt
  runif smooth.spline
Consider adding
  importFrom("stats", "dnorm", "dt", "dunif", "fitted", "poisson",
             "predict", "residuals", "rmultinom", "rnorm", "rt", "runif",
             "smooth.spline")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages in Depends field not imported from:
  ‘splines’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
IndividualPROC: no visible global function definition for ‘survfit’
IndividualPROC: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile survfit
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmph6iXXm/R.INSTALL2ff34ece51c7/projects/man/display_metadata.Rd:81: file link ‘left_join’ in package ‘dplyr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmph6iXXm/R.INSTALL2ff34ece51c7/projects/man/export_project.Rd:15: file link ‘zipr’ in package ‘zip’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmph6iXXm/R.INSTALL2ff34ece51c7/projects/man/export_project.Rd:31: file link ‘zipr’ in package ‘zip’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmph6iXXm/R.INSTALL2ff34ece51c7/projects/man/file_management.Rd:82: file link ‘openProject’ in package ‘rstudioapi’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmph6iXXm/R.INSTALL2ff34ece51c7/projects/man/file_management.Rd:116: file link ‘openProject’ in package ‘rstudioapi’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmph6iXXm/R.INSTALL2ff34ece51c7/projects/man/new_edit_delete.Rd:151: file link ‘as_datetime’ in package ‘lubridate’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmph6iXXm/R.INSTALL2ff34ece51c7/projects/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmph6iXXm/R.INSTALL2ff34ece51c7/projects/man/save_session_info.Rd:12: file link ‘dir_create’ in package ‘fs’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/projects.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpqer5ZA/R.INSTALL303850c55783/projmgr/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/projmgr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpzteKkp/R.INSTALL3f58317be3df/promises/man/is.promise.Rd:32: file link ‘Future’ in package ‘future’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzteKkp/R.INSTALL3f58317be3df/promises/man/reexports.Rd:15: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpzteKkp/R.INSTALL3f58317be3df/promises/man/reexports.Rd:15: file link ‘%T>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/promises.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘SDMTools’
addpi: no visible global function definition for ‘lines’
genPerms: no visible global function definition for ‘combn’
getVar: no visible global function definition for ‘glm’
getVar: no visible global function definition for ‘binomial’
getVar: no visible global function definition for ‘var’
pba: no visible global function definition for ‘glm’
pba: no visible global function definition for ‘binomial’
pba: no visible global function definition for ‘predict’
pba: no visible global function definition for ‘rbinom’
pcr: no visible global function definition for ‘quantile’
plotpi: no visible global function definition for ‘axis’
plotpi: no visible global function definition for ‘abline’
plotpi: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline axis binomial combn glm lines predict quantile rbinom var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "binomial", "glm", "predict", "quantile", "rbinom",
             "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
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.
addIonSatistics: no visible binding for global variable ‘median’
adjustOne: no visible binding for global variable ‘median’
attachModifications: no visible global function definition for
  ‘na.omit’
avrgLoadingCalculation: no visible binding for global variable ‘median’
channelResponses : estimate: no visible binding for global variable
  ‘var’
responseStatisics : func: no visible global function definition for
  ‘aggregate’
testing: no visible global function definition for ‘aov’
testingOneshot: no visible global function definition for ‘anova’
testingTukey: no visible global function definition for ‘TukeyHSD’
Undefined global functions or variables:
  TukeyHSD aggregate anova aov median na.omit var
Consider adding
  importFrom("stats", "TukeyHSD", "aggregate", "anova", "aov", "median",
             "na.omit", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘class’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘class’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
addcircle: no visible global function definition for ‘lines’
addclassifierboundary: no visible global function definition for ‘par’
addclassifierboundary: no visible global function definition for
  ‘contour’
plot.protoclass: no visible global function definition for ‘box’
plot.protoclass: no visible global function definition for ‘rgb2hsv’
plot.protoclass: no visible global function definition for ‘col2rgb’
plot.protoclass: no visible global function definition for ‘points’
plot.protoclass: no visible global function definition for ‘hsv’
predict.protoclass: no visible global function definition for ‘knn1’
Undefined global functions or variables:
  box col2rgb contour hsv knn1 lines par points rgb2hsv
Consider adding
  importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
  importFrom("graphics", "box", "contour", "lines", "par", "points")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘doc’
Extract_plant_grapevine_function: 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.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpdITnnl/R.INSTALL7cb74f7a3da2/protolite/man/geobuf.Rd:21: file link ‘toJSON’ in package ‘jsonlite’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/protolite.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpu7UHGy/R.INSTALL4b99310eb4fc/ProTrackR/man/playWave.Rd:25: file link ‘$.audioInstance’ in package ‘audio’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpu7UHGy/R.INSTALL4b99310eb4fc/ProTrackR/man/read.module.Rd:22: file link ‘file’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpu7UHGy/R.INSTALL4b99310eb4fc/ProTrackR/man/read.module.Rd:22: file link ‘url’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpu7UHGy/R.INSTALL4b99310eb4fc/ProTrackR/man/resample.Rd:18: file link ‘approx’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpu7UHGy/R.INSTALL4b99310eb4fc/ProTrackR/man/resample.Rd:32: file link ‘approx’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmpu7UHGy/R.INSTALL4b99310eb4fc/ProTrackR/man/write.module.Rd:18: file link ‘file’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ProTrackR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp0lrlz4/R.INSTALL574c1edbe333/protViz/man/mascot.rd:72: file link ‘xmlParse’ in package ‘XML’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/protViz.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package vignette with placeholder title ‘Vignette Title’:
  ‘TargetDecoyFDR_Example.Rmd’
Package in Depends field not imported from: ‘rpart’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mahalanobisComposite: no visible global function definition for
  ‘princomp’
prepareComposite: no visible global function definition for ‘cov’
winsorizor : f: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cov princomp quantile
Consider adding
  importFrom("stats", "cov", "princomp", "quantile")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘PSF_vignette.Rmd’
Malformed Description field: should contain one or more complete sentences.
candidate.overlap: no visible global function definition for
  ‘write.table’
fisher: no visible global function definition for ‘fisher.test’
fisher.iteration: no visible global function definition for
  ‘download.file’
fisher.iteration: no visible global function definition for
  ‘read.table’
pSI.list: no visible global function definition for ‘write.table’
specificity.index: no visible global function definition for ‘png’
specificity.index: no visible global function definition for ‘par’
specificity.index: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off download.file fisher.test par png read.table write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par")
  importFrom("stats", "fisher.test")
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘gene_count_1.csv’
'library' or 'require' call to ‘numDeriv’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
test.problem : g: no visible global function definition for ‘grad’
test.problem: no visible global function definition for ‘new’
psoptim,test.problem-missing-missing-missing-missing: no visible global
  function definition for ‘new’
show,test.result: no visible global function definition for ‘show’
show,test.result: no visible global function definition for ‘sd’
Undefined global functions or variables:
  grad new sd show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
pspearman: no visible global function definition for ‘pt’
spearman.test: no visible global function definition for
  ‘complete.cases’
spearman.test: no visible global function definition for ‘cor’
Undefined global functions or variables:
  complete.cases cor pt
Consider adding
  importFrom("stats", "complete.cases", "cor", "pt")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘orig’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpCtFu7o/R.INSTALL5c88210daf52/PSSMCOOL/man/Discrete_Cosine_Transform.Rd:17: file link ‘dct’ in package ‘dtt’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpCtFu7o/R.INSTALL5c88210daf52/PSSMCOOL/man/dwt_PSSM.Rd:16: file link ‘dwt.nondyadic’ in package ‘waveslim’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PSSMCOOL.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘EffectsRelBaseline’ ‘boot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catEffectBootAdaptor: no visible binding for global variable ‘sumSqCat’
compExclusionFraction: no visible global function definition for
  ‘rpois’
compExclusionFraction: no visible global function definition for
  ‘t.test’
compExclusionFraction: no visible global function definition for ‘glm’
compExclusionFraction: no visible global function definition for
  ‘anova’
compPowerCatSelectivity: no visible binding for global variable
  ‘fRatioStat’
compPowerGeneralRespDetection: no visible binding for global variable
  ‘sumSqCat’
compPowerRespDetection: no visible binding for global variable
  ‘sumSqCat’
compRejectionFraction: no visible global function definition for
  ‘rpois’
compRejectionFraction: no visible global function definition for
  ‘t.test’
compRejectionFraction: no visible global function definition for ‘glm’
compRejectionFraction: no visible global function definition for
  ‘anova’
simCatResp: no visible global function definition for ‘rpois’
simNormCatResp: no visible global function definition for ‘rnorm’
testCatEffectBoot: no visible global function definition for ‘boot’
Undefined global functions or variables:
  anova boot fRatioStat glm rnorm rpois sumSqCat t.test
Consider adding
  importFrom("stats", "anova", "glm", "rnorm", "rpois", "t.test")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpC8lR2F/R.INSTALL50fa2460844b/psychmeta/man/correct_d_bias.Rd:31: file link ‘gamma’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpC8lR2F/R.INSTALL50fa2460844b/psychmeta/man/correct_glass_bias.Rd:33: file link ‘gamma’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpC8lR2F/R.INSTALL50fa2460844b/psychmeta/man/print.Rd:13: file link ‘print.tbl’ in package ‘tibble’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpC8lR2F/R.INSTALL50fa2460844b/psychmeta/man/print.Rd:15: file link ‘print.tbl’ in package ‘tibble’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpC8lR2F/R.INSTALL50fa2460844b/psychmeta/man/print.Rd:17: file link ‘print.tbl’ in package ‘tibble’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/psychmeta.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘multilevel’ ‘nlme’
A package should be listed in only one of these fields.
Non-standard file/directory found at top level:
  ‘README.txt’
'library' or 'require' calls to packages already attached by Depends:
  ‘multilevel’ ‘nlme’
  Please remove these calls from your code.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpH3BgyY/R.INSTALL5f1840b41010/psychomix/man/raschmix.Rd:66: file link ‘RaschModel.fit’ in package ‘psychotools’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/psychomix.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpI9w2CW/R.INSTALL6fe27bc584b9/psychotools/man/btmodel.Rd:38: file link ‘glm.fit’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpl02l2r/Rbuild2449d39c0f9d7/psychotools/man/gpcmodel.Rd:30: file link ‘as.matrix’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpI9w2CW/R.INSTALL6fe27bc584b9/psychotools/man/pcmodel.Rd:28: file link ‘as.matrix’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /tmp/Rtmpl02l2r/Rbuild2449d39c0f9d7/psychotools/man/plmodel.Rd:32: file link ‘as.matrix’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpI9w2CW/R.INSTALL6fe27bc584b9/psychotools/man/raschmodel.Rd:28: file link ‘as.matrix’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpI9w2CW/R.INSTALL6fe27bc584b9/psychotools/man/rsmodel.Rd:28: file link ‘as.matrix’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/psychotools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /tmp/RtmpPdonRx/Rbuild2d34729a18258/psychotree/man/bttree.Rd:31: file link ‘na.pass’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPdonRx/Rbuild2d34729a18258/psychotree/man/mpttree.Rd:31: file link ‘na.pass’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPdonRx/Rbuild2d34729a18258/psychotree/man/pctree.Rd:60: file link ‘plot.modelparty’ in package ‘partykit’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPdonRx/Rbuild2d34729a18258/psychotree/man/pctree.Rd:60: file link ‘plot.party’ in package ‘partykit’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPdonRx/Rbuild2d34729a18258/psychotree/man/raschtree.Rd:57: file link ‘plot.modelparty’ in package ‘partykit’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPdonRx/Rbuild2d34729a18258/psychotree/man/raschtree.Rd:57: file link ‘plot.party’ in package ‘partykit’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPdonRx/Rbuild2d34729a18258/psychotree/man/rstree.Rd:60: file link ‘plot.modelparty’ in package ‘partykit’ does not exist and so has been treated as a topic
  Rd warning: /tmp/RtmpPdonRx/Rbuild2d34729a18258/psychotree/man/rstree.Rd:60: file link ‘plot.party’ in package ‘partykit’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/psychotree.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmphGH0Xe/R.INSTALL608e6fd2f9c9/psychTools/man/cubits.Rd:25: file link ‘table2df’ in package ‘psych’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphGH0Xe/R.INSTALL608e6fd2f9c9/psychTools/man/heights.Rd:19: file link ‘table2df’ in package ‘psych’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmphGH0Xe/R.INSTALL608e6fd2f9c9/psychTools/man/psychTools.Rd:7: file link ‘psych’ in package ‘psych’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/psychTools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpb7GqTC/R.INSTALL4240cff7f68/psymonitor/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/psymonitor.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpxuGoFE/R.INSTALL3169196901d9/psyosphere/man/about_common_mistakes.Rd:36: file link ‘wtd.mean’ in package ‘Hmisc’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/psyosphere.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpOTdrFt/R.INSTALL61c15f8de491/PtProcess/man/Changes.Rd:89: file link ‘makePSOCKcluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpOTdrFt/R.INSTALL61c15f8de491/PtProcess/man/makeSOCKcluster.Rd:20: file link ‘makePSOCKcluster’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpOTdrFt/R.INSTALL61c15f8de491/PtProcess/man/plot.Rd:8: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PtProcess.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpBDvEwF/R.INSTALLb3c60a1192f/ptstem/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ptstem.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘R.utils’ ‘rmeta’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ChisqTest_expect: no visible global function definition for ‘pchisq’
plot_chase_observed_expected: no visible global function definition for
  ‘meta.MH’
plot_chase_observed_expected: no visible global function definition for
  ‘txtProgressBar’
plot_chase_observed_expected: no visible global function definition for
  ‘setTxtProgressBar’
test.one.treated: no visible global function definition for
  ‘fisher.test’
test_one: no visible global function definition for ‘rbinom’
test_one: no visible global function definition for ‘fisher.test’
Undefined global functions or variables:
  fisher.test meta.MH pchisq rbinom setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "fisher.test", "pchisq", "rbinom")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmperl0ra/R.INSTALL321c13b8c271/publipha/man/ExtractParameters.Rd:45: file link ‘extract’ in package ‘rstan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/publipha.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
PurBayes: no visible global function definition for ‘update’
PurBayes: no visible global function definition for ‘sd’
plot.PurBayes: no visible global function definition for ‘quantile’
plot.PurBayes: no visible global function definition for ‘lines’
summary.PurBayes : <anonymous>: no visible global function definition
  for ‘quantile’
Undefined global functions or variables:
  lines quantile sd update
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "quantile", "sd", "update")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpOAjaGN/R.INSTALL2677719d6288/purrrlyr/man/by_slice.Rd:53: file link ‘mutate_each’ in package ‘dplyr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/purrrlyr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpHZPeIe/R.INSTALL33f9470f9d69/pushbar/man/pushbar.Rd:21: file link ‘tags’ in package ‘shiny’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pushbar.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpS7nV82/R.INSTALL13435d0b3011/pvclust/man/pvclust.Rd:154: file link ‘package_version’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pvclust.Rcheck/00install.out’ for details.
CandidateBio.getBio : <anonymous>: no visible global function
  definition for ‘na.omit’
Committee.getCommittee : <anonymous>: no visible global function
  definition for ‘na.omit’
getAllBios: no visible global function definition for ‘txtProgressBar’
getAllBios: no visible global function definition for
  ‘setTxtProgressBar’
getAllLocalOfficials: no visible global function definition for
  ‘txtProgressBar’
getAllLocalOfficials: no visible global function definition for
  ‘setTxtProgressBar’
getAllVotes: no visible global function definition for ‘txtProgressBar’
getAllVotes: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  na.omit setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp5348x1/R.INSTALL19c54cc62696/PWFSLSmoke/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PWFSLSmoke.Rcheck/00install.out’ for details.
.grid.matrix: no visible global function definition for ‘slot’
.matrix2grid: no visible global function definition for ‘as’
.poly2grid: no visible global function definition for ‘is’
.poly2grid: no visible global function definition for ‘slot’
.poly2grid: no visible global function definition for ‘as’
.pycno.core : smooth2D : s1d: no visible global function definition for
  ‘filter’
.pycno.core: no visible global function definition for ‘flush.console’
.pycno2matrix: no visible global function definition for ‘slot’
Undefined global functions or variables:
  as filter flush.console is slot
Consider adding
  importFrom("methods", "as", "is", "slot")
  importFrom("stats", "filter")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package vignette with placeholder title ‘Vignette Title’:
  ‘qaig-introduction.Rmd’
Found the following files/directories:
  ‘exampleplot_1_blockdist_1.png’ ‘exampleplot_1_blockdist_2.png’
  ‘exampleplot_1_blockdist_3.png’ ‘exampleplot_1_bootdist.png’
  ‘exampleplot_1_dist.png’ ‘exampleplot_1_histogramtest_EMD.png’
  ‘exampleplot_1_roc_dynamic.png’ ‘exampleplot_1_slidedist_1.png’
  ‘exampleplot_1_slidedist_2.png’ ‘exampleplot_1_slidedist_3.png’
  ‘exampleplot_1_trimmeddist.png’ ‘exampleplot_blockdist_1.png’
  ‘exampleplot_blockdist_2.png’ ‘exampleplot_blockdist_3.png’
  ‘exampleplot_bootdist.png’ ‘exampleplot_dist.png’
  ‘exampleplot_lim_dyn.png’ ‘exampleplot_lim_sig.png’
  ‘exampleplot_lim_sta.png’ ‘exampleplot_noc.png’
  ‘exampleplot_roc_dyn.png’ ‘exampleplot_roc_sta.png’
  ‘exampleplot_slidedist_1.png’ ‘exampleplot_slidedist_2.png’
  ‘exampleplot_slidedist_3.png’ ‘exampleplot_trimmeddist.png’
  ‘myworkflow_result.xml’ ‘test_2_roc_dynamic.png’ ‘test_4_dist.png’
  ‘test_5_blockdist_1.png’ ‘test_5_blockdist_2.png’
  ‘test_5_blockdist_3.png’ ‘test_6_slidedist_1.png’
  ‘test_6_slidedist_2.png’ ‘test_6_slidedist_3.png’
  ‘test_7_trimmeddist.png’ ‘test_8_bootdist.png’ ‘test_emd_1d.png’
  ‘test_emd_2d.png’ ‘test_jsd_1d.png’ ‘test_jsd_2d.png’
  ‘test_kld_1d.png’ ‘test_kld_2d.png’ ‘test_ms_1d.png’ ‘test_ms_2d.png’
  ‘test_rms_1d.png’ ‘test_rms_2d.png’
csQCAbinTest: no visible global function definition for ‘p.adjust’
fsQCApermTest: no visible global function definition for ‘p.adjust’
mvQCAbinTest: no visible global function definition for ‘p.adjust’
p.threshold.adjust: no visible global function definition for
  ‘p.adjust’
plot.fsQCApt: no visible global function definition for ‘dev.cur’
plot.fsQCApt: no visible global function definition for ‘dev.new’
plot.fsQCApt: no visible global function definition for ‘par’
plot.fsQCApt: no visible global function definition for ‘density’
plot.fsQCApt: no visible global function definition for ‘axis’
plot.fsQCApt: no visible global function definition for ‘polygon’
plot.fsQCApt: no visible global function definition for ‘points’
plot.fsQCApt: no visible global function definition for ‘hist’
summary.csQCAbt: no visible global function definition for
  ‘printCoefmat’
summary.fsQCApt: no visible global function definition for
  ‘printCoefmat’
summary.mvQCAbt: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  axis density dev.cur dev.new hist p.adjust par points polygon
  printCoefmat
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new")
  importFrom("graphics", "axis", "hist", "par", "points", "polygon")
  importFrom("stats", "density", "p.adjust", "printCoefmat")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpGELB1Q/R.INSTALL32f1883a92b/QCA/man/chartFunctions.Rd:46: file link ‘translate’ in package ‘admisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGELB1Q/R.INSTALL32f1883a92b/QCA/man/generate.Rd:33: file link ‘expand’ in package ‘admisc’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpGELB1Q/R.INSTALL32f1883a92b/QCA/man/pof.Rd:144: file link ‘translate’ in package ‘admisc’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/QCA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpSft9Qe/R.INSTALL54003ab99dfd/QCAtools/man/plot.qca.Rd:10: file link ‘eqmcc’ in package ‘QCA’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/QCAtools.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘EWAS_QC_graph_effectsize.png’ ‘EWAS_QC_graph_precision.png’
  ‘EWAS_QC_legend.txt’ ‘sample1.txt.gz’ ‘sample2.txt.gz’
  ‘sample_map.txt.gz’ ‘sample_output.graph_M.png’
  ‘sample_output.graph_QQ.png’ ‘sample_output.graph_p.png’
  ‘sample_output.graph_volcano.png’ ‘sample_output.histo.png’
  ‘sample_output.txt’ ‘sample_output1.graph_M.png’
  ‘sample_output1.graph_QQ.png’ ‘sample_output1.graph_p.png’
  ‘sample_output1.graph_volcano.png’ ‘sample_output1.histo.png’
  ‘sample_output2.graph_M.png’ ‘sample_output2.graph_QQ.png’
  ‘sample_output2.graph_p.png’ ‘sample_output2.graph_volcano.png’
  ‘sample_output2.histo.png’ ‘translation_table.txt’
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘sample_QQ.png’ ‘sample_QQ1.png’ ‘sample_QQ2.png’ ‘sample_QQ3.png’
  ‘sample_distribution.png’ ‘sample_graph_p-correlation.png’
  ‘sample_histogram.png’ ‘sample_histogram1.png’
  ‘sample_histogram2.png’ ‘sample_histogram3.png’
  ‘sample_plots_graph_M.png’ ‘sample_plots_graph_QQ.png’
  ‘sample_precision.png’ ‘sample_regional_association.png’
  ‘sample_skewness_kurtosis.png’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpJjmv3w/R.INSTALLed83b91cdbe/qdapTools/man/id.Rd:26: file link ‘ncol’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJjmv3w/R.INSTALLed83b91cdbe/qdapTools/man/lookup_e.Rd:97: file link ‘new.env’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJjmv3w/R.INSTALLed83b91cdbe/qdapTools/man/mtabulate.Rd:41: file link ‘counts2list’ in package ‘qdapTools’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJjmv3w/R.INSTALLed83b91cdbe/qdapTools/man/split_vector.Rd:24: file link ‘grepl’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpJjmv3w/R.INSTALLed83b91cdbe/qdapTools/man/timeconv.Rd:32: file link ‘times’ in package ‘chron’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qdapTools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmplf1eQE/R.INSTALL3f345122917a/qgraph/man/centrality_auto.Rd:9: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmplf1eQE/R.INSTALL3f345122917a/qgraph/man/clustcoef_auto.Rd:34: file link ‘igraph’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmplf1eQE/R.INSTALL3f345122917a/qgraph/man/qgraph.Rd:36: file link ‘cov2cor’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmplf1eQE/R.INSTALL3f345122917a/qgraph/man/qgraph.Rd:41: file link ‘corr.p’ in package ‘psych’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qgraph.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp8bAENO/R.INSTALL71943312a911/qiitr/man/qiita_api.Rd:28: file link ‘httr’ in package ‘httr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qiitr.Rcheck/00install.out’ for details.
Running examples in ‘qiitr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: qiita_util
> ### Title: Generate Payload And Tag For Qiita API
> ### Aliases: qiita_util qiita_util_payload qiita_util_tag
> 
> ### ** Examples
> 
> qiita_util_tag(name = "R", versions = ">3.1")
$name
[1] "R"

$versions
[1] ">3.1"

attr(,"class")
[1] "qiita_tag" "list"     
> 
> qiita_util_payload(body = "foo",
+                    title = "test",
+                    tags = list(
+                      qiita_util_tag(name = "R", versions = ">3.1"),
+                      qiita_util_tag(name = "dplyr")
+                    ),
+                    private = TRUE)
Error in `class<-`(x, unique.default(c("AsIs", oldClass(x)))) : 
  attempt to set an attribute on NULL
Calls: qiita_util_payload -> qiita_util_tag -> I
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(qiitr)
  > 
  > test_check("qiitr")
  ── 1. Error: qiita_util_tag test without versions (@test-qiita-util.R#11)  ─────
  attempt to set an attribute on NULL
  Backtrace:
   1. testthat::expect_equal(...)
   4. qiitr::qiita_util_tag(name = "R")
   5. base::I(versions)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 4 | SKIPPED: 12 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: qiita_util_tag test without versions (@test-qiita-util.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
chooseMDoubleBootstrap: no visible global function definition for
  ‘model.matrix’
chooseMDoubleBootstrap: no visible global function definition for
  ‘as.formula’
chooseMDoubleBootstrap: no visible global function definition for
  ‘model.frame’
chooseMDoubleBootstrap: no visible global function definition for ‘lm’
chooseMDoubleBootstrap: no visible global function definition for
  ‘coef’
chooseMDoubleBootstrap: no visible global function definition for
  ‘quantile’
chooseMDoubleBootstrap: no visible global function definition for
  ‘qnorm’
getModel: no visible global function definition for ‘lm’
getModel: no visible global function definition for ‘model.matrix’
getModel: no visible global function definition for ‘as.formula’
getModel: no visible global function definition for ‘model.frame’
getModel: no visible global function definition for ‘model.response’
getModel: no visible global function definition for ‘coef’
getModel: no visible global function definition for ‘qnorm’
qLearn: no visible global function definition for ‘model.matrix’
qLearn: no visible global function definition for ‘as.formula’
qLearn: no visible global function definition for ‘model.frame’
qLearn: no visible global function definition for ‘coef’
qLearn: no visible global function definition for ‘lm’
qLearn: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  as.formula coef lm model.frame model.matrix model.response qnorm
  quantile
Consider adding
  importFrom("stats", "as.formula", "coef", "lm", "model.frame",
             "model.matrix", "model.response", "qnorm", "quantile")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpXircRO/R.INSTALL46e9167b97b3/qmethod/man/import.htmlq.Rd:9: file link ‘read.csv2’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXircRO/R.INSTALL46e9167b97b3/qmethod/man/plot.QmethodRes.Rd:18: file link ‘rainbow’ in package ‘grDevices’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpXircRO/R.INSTALL46e9167b97b3/qmethod/man/plot.QmethodRes.Rd:27: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qmethod.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpbeSPNS/R.INSTALL33067ceef5c5/qmix/man/plot_trace.qmix.Rd:12: file link ‘traceplot’ in package ‘rstan’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qmix.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
pcAxisCubeMake: no visible global function definition for ‘aggregate’
pcAxisCubeToCSV: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  aggregate write.csv
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘datInSFexample6_1pxCube.csv’ ‘datInSFexample6_1pxCubeA0.csv ’
  ‘datInSFexample6_1pxCubeA1.csv ’ ‘datInSFexample6_1pxCubeData.csv ’
  ‘datInSFexample6_1pxCubeVariable.csv’
  ‘datInSFexample6_1pxCubeVariableDomain.csv’
Found the following files/directories:
  ‘lambda.pdf’ ‘qqplot.pdf’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpOXEVaA/R.INSTALL3bd710fb2cc7/qqplotr/man/stat_qq_band.Rd:116: file link ‘s_Qn’ in package ‘robustbase’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qqplotr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp9mCvye/R.INSTALL730c5f5efb63/QRegVCM/man/AHeVT.Rd:82: file link ‘as.matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9mCvye/R.INSTALL730c5f5efb63/QRegVCM/man/AHeVXT.Rd:84: file link ‘as.matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9mCvye/R.INSTALL730c5f5efb63/QRegVCM/man/QRIndiv.Rd:74: file link ‘as.matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9mCvye/R.INSTALL730c5f5efb63/QRegVCM/man/QRSimul.Rd:79: file link ‘as.matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9mCvye/R.INSTALL730c5f5efb63/QRegVCM/man/QRStepwise.Rd:80: file link ‘as.matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9mCvye/R.INSTALL730c5f5efb63/QRegVCM/man/QRWSimul.Rd:81: file link ‘as.matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9mCvye/R.INSTALL730c5f5efb63/QRegVCM/man/simul_shapetest.Rd:101: file link ‘as.matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp9mCvye/R.INSTALL730c5f5efb63/QRegVCM/man/test_variability.Rd:113: file link ‘as.matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/QRegVCM.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qtbase.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘qtl2’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpakR4sg/R.INSTALL56a316bb6fd3/qtl2pleio/man/pipe.Rd:10: file link ‘%>%’ in package ‘magrittr’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qtl2pleio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp3N0O89/R.INSTALL49d267ba7dc7/qtlcharts/man/iplotRF.Rd:54: file link ‘plotRF’ in package ‘qtl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qtlcharts.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
ci.length: no visible global function definition for ‘qexp’
detectable.bc: no visible global function definition for ‘uniroot’
detectable.f2: no visible global function definition for ‘uniroot’
detectable.ri: no visible global function definition for ‘uniroot’
nu: no visible global function definition for ‘pnorm’
nullinfo: no visible global function definition for ‘qnorm’
nullinfo: no visible global function definition for ‘dnorm’
optselection.bc: no visible global function definition for ‘optimize’
optselection.f2: no visible global function definition for ‘optimize’
optspacing.bc: no visible global function definition for ‘optim’
optspacing.bc: no visible global function definition for ‘optimize’
optspacing.f2: no visible global function definition for ‘optim’
optspacing.f2: no visible global function definition for ‘optimize’
powercalc.bc: no visible global function definition for ‘pchisq’
powercalc.f2: no visible global function definition for ‘pchisq’
samplesize.bc: no visible global function definition for ‘uniroot’
samplesize.f2: no visible global function definition for ‘uniroot’
samplesize.ri: no visible global function definition for ‘uniroot’
tailprob: no visible global function definition for ‘pchisq’
thresh: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  dnorm optim optimize pchisq pnorm qexp qnorm uniroot
Consider adding
  importFrom("stats", "dnorm", "optim", "optimize", "pchisq", "pnorm",
             "qexp", "qnorm", "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpcDcTIt/R.INSTALL7f1933897bce/qtlnet/man/igraph.Rd:50: file link ‘graph.data.frame’ in package ‘igraph’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpcDcTIt/R.INSTALL7f1933897bce/qtlnet/man/igraph.Rd:66: file link ‘graph.data.frame’ in package ‘igraph’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qtlnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmplvMkhw/R.INSTALL366a63136392/qtl/man/addmarker.Rd:28: file link ‘read.csv’ in package ‘utils’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplvMkhw/R.INSTALL366a63136392/qtl/man/effectscan.Rd:38: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplvMkhw/R.INSTALL366a63136392/qtl/man/mqmplotmultitrait.Rd:26: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplvMkhw/R.INSTALL366a63136392/qtl/man/plot.map.Rd:39: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplvMkhw/R.INSTALL366a63136392/qtl/man/plot.pxg.Rd:37: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplvMkhw/R.INSTALL366a63136392/qtl/man/plot.scanone.Rd:50: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplvMkhw/R.INSTALL366a63136392/qtl/man/plot.scanone.Rd:61: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplvMkhw/R.INSTALL366a63136392/qtl/man/plotLodProfile.Rd:43: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmplvMkhw/R.INSTALL366a63136392/qtl/man/plotModel.Rd:37: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qtl.Rcheck/00install.out’ for details.
Package required but not available: ‘qtbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'library' or 'require' call to ‘Rmpfr’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
adjacencyMatrix: no visible global function definition for ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpZwDjGD/R.INSTALL52bb6bc9167/quadmesh/man/quadmesh.Rd:52: file link ‘qmesh3d’ in package ‘rgl’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpZwDjGD/R.INSTALL52bb6bc9167/quadmesh/man/triangmesh.Rd:73: file link ‘tmesh3d’ in package ‘rgl’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/quadmesh.Rcheck/00install.out’ for details.
quadp: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
alphaf: no visible global function definition for ‘pchisq’
alphaf: no visible global function definition for ‘dbinom’
conout: no visible global function definition for ‘sd’
ibgaout: no visible global function definition for ‘qnorm’
ibgaout: no visible global function definition for ‘pnorm’
plot.qualint: no visible global function definition for ‘qnorm’
powerval: no visible global function definition for ‘rnorm’
powerval: no visible global function definition for ‘qnorm’
powerval: no visible global function definition for ‘pnorm’
print.expplot: no visible global function definition for ‘gray’
print.expplot: no visible binding for global variable ‘coef’
print.outplot: no visible global function definition for ‘gray’
print.outplot: no visible binding for global variable ‘coef’
qualint: no visible global function definition for ‘qnorm’
qualval: no visible global function definition for ‘qnorm’
surout: no visible global function definition for ‘tail’
surout: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef dbinom gray pchisq pnorm qnorm rnorm sd tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("stats", "coef", "dbinom", "pchisq", "pnorm", "qnorm",
             "rnorm", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp0uMGeD/R.INSTALL54be73b250cf/qualpalr/man/plot.qualpal.Rd:13: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/Rtmp0uMGeD/R.INSTALL54be73b250cf/qualpalr/man/plot.qualpal.Rd:26: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qualpalr.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpyZxzi2/R.INSTALL4af38578512/QUALYPSO/man/plotQUALYPSOTotalVarianceByScenario.Rd:30: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpyZxzi2/R.INSTALL4af38578512/QUALYPSO/man/plotQUALYPSOTotalVarianceDecomposition.Rd:25: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpyZxzi2/R.INSTALL4af38578512/QUALYPSO/man/plotQUALYPSOeffect.Rd:30: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpyZxzi2/R.INSTALL4af38578512/QUALYPSO/man/plotQUALYPSOgrandmean.Rd:26: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/QUALYPSO.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpSUPf17/R.INSTALL4b9319b32dae/qualypsoss/man/plotQUALYPSOSSClimateChangeResponse.Rd:22: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpSUPf17/R.INSTALL4b9319b32dae/qualypsoss/man/plotQUALYPSOSSClimateResponse.Rd:21: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpSUPf17/R.INSTALL4b9319b32dae/qualypsoss/man/plotQUALYPSOSSTotalVarianceByScenario.Rd:30: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpSUPf17/R.INSTALL4b9319b32dae/qualypsoss/man/plotQUALYPSOSSTotalVarianceDecomposition.Rd:23: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpSUPf17/R.INSTALL4b9319b32dae/qualypsoss/man/plotQUALYPSOSSeffect.Rd:31: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpSUPf17/R.INSTALL4b9319b32dae/qualypsoss/man/plotQUALYPSOSSgrandmean.Rd:26: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qualypsoss.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp8SyZGw/R.INSTALL1e721572122e/quanteda.textmodels/man/as.matrix.csr.dfm.Rd:13: file link ‘matrix.csr’ in package ‘SparseM’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/quanteda.textmodels.Rcheck/00install.out’ for details.
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.
Non-standard file/directory found at top level:
  ‘README.txt’
Rd file 'graph.mod.Rd':
  \usage lines wider than 90 characters:
     graph.mod(ssmod, x, y, data, title = "", xlab = "Centered X", ylab = "Raw Y", ylimit = 1.5, ...)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘Judge.pdf’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmplP6K2g/R.INSTALL3b6a35dc775a/quantreg/man/plot.rqs.Rd:29: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/quantreg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmpg7Fujw/R.INSTALL77812c7ca39/quantspec/man/ClippedFT-class.Rd:21: file link ‘mvfft’ in package ‘stats’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/quantspec.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpNnL7kn/R.INSTALL365b579dd00e/QuantTools/man/plot_ts.Rd:21: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpNnL7kn/R.INSTALL365b579dd00e/QuantTools/man/plot_ts.Rd:25: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/QuantTools.Rcheck/00install.out’ for details.
Found the following sources/headers with CR or CRLF line endings:
  inst/include/BackTest.h
Some Unix compilers require LF line endings.
Found the following files/directories:
  ‘Example’
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp1Ma5xE/R.INSTALL36f0102906d3/Quartet/man/PlotQuartet.Rd:26: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Quartet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/Rtmp1aVRDr/R.INSTALL5b3e3016609f/questionr/man/addNAstr.Rd:40: file link ‘addNA’ in package ‘base’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/questionr.Rcheck/00install.out’ for details.