File 'pgam/libs/i386/pgam.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'pgam.o'
File 'pgam/libs/x64/pgam.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'pgam.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
fbins: no visible global function definition for 'quantile'
fhat: no visible global function definition for 'dnorm'
fhatgg: no visible global function definition for 'dnorm'
fhatnew: no visible global function definition for 'dnorm'
mica: no visible global function definition for 'cor'
trans: no visible binding for global variable 'sd'
weight.seq: no visible global function definition for 'dnorm'
weight.seq: no visible global function definition for 'nlm'
Undefined global functions or variables:
  cor dnorm nlm quantile sd
Consider adding
  importFrom("stats", "cor", "dnorm", "nlm", "quantile", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: working directory was changed to 'd:/Rcompile/CRANpkg/local/3.5/PGICA.Rcheck/Sim', resetting
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.
init_load: no visible global function definition for 'cov.wt'
pgmmEM: no visible global function definition for 'runif'
pgmmEM: no visible global function definition for 'kmeans'
plot.pgmm: no visible global function definition for 'par'
plot.pgmm: no visible global function definition for 'matplot'
plot.pgmm: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis cov.wt kmeans matplot par runif
Consider adding
  importFrom("graphics", "axis", "matplot", "par")
  importFrom("stats", "cov.wt", "kmeans", "runif")
to your NAMESPACE file.
dvol.mse.est: no visible global function definition for 'optim'
ellipsoidSurface: no visible global function definition for 'integrate'
latscale: no visible global function definition for 'uniroot'
covariogram,Segment-function: no visible global function definition for
  'integrate'
plot,FigLat-missing: no visible global function definition for 'par'
plot,PointPattern-matrix: no visible global function definition for
  'par'
plot,PointPattern-matrix: no visible global function definition for
  'lines'
plot,PointPattern-missing: no visible global function definition for
  'points'
plot,Quadrat-missing: no visible global function definition for 'lines'
plot,Segment-matrix: no visible global function definition for 'par'
plot,Segment-matrix: no visible global function definition for
  'polygon'
plot,Segment-missing: no visible global function definition for 'lines'
Undefined global functions or variables:
  integrate lines optim par points polygon uniroot
Consider adding
  importFrom("graphics", "lines", "par", "points", "polygon")
  importFrom("stats", "integrate", "optim", "uniroot")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   1.7Mb
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.
flowField: no visible global function definition for 'plot'
flowField: no visible global function definition for 'arrows'
nullclines: no visible global function definition for 'contour'
numericalSolution: no visible global function definition for 'locator'
numericalSolution: no visible global function definition for 'plot'
numericalSolution: no visible global function definition for 'lines'
phasePortrait: no visible global function definition for 'plot'
phasePortrait: no visible global function definition for 'arrows'
stability: no visible global function definition for 'locator'
trajectory: no visible global function definition for 'locator'
trajectory: no visible global function definition for 'plot'
trajectory: no visible global function definition for 'lines'
trajectory: no visible global function definition for 'points'
Undefined global functions or variables:
  arrows contour lines locator plot points
Consider adding
  importFrom("graphics", "arrows", "contour", "lines", "locator", "plot",
             "points")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'ggplot2' 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.phtMCMC: no visible global function definition for 'ggplot'
plot.phtMCMC: no visible global function definition for 'melt'
plot.phtMCMC: no visible global function definition for 'geom_line'
plot.phtMCMC: no visible global function definition for 'aes_string'
plot.phtMCMC: no visible global function definition for 'geom_smooth'
plot.phtMCMC: no visible global function definition for 'facet_wrap'
plot.phtMCMC: no visible global function definition for 'ggtitle'
plot.phtMCMC: no visible global function definition for 'xlab'
plot.phtMCMC: no visible global function definition for 'ylab'
plot.phtMCMC: no visible global function definition for 'geom_density'
Undefined global functions or variables:
  aes_string facet_wrap geom_density geom_line geom_smooth ggplot
  ggtitle melt xlab ylab
File 'PhaseType/libs/i386/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.o'
File 'PhaseType/libs/x64/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.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.
deforestation: no visible global function definition for 'model.frame'
deforestation: no visible global function definition for 'model.matrix'
deforestation: no visible global function definition for
  'model.response'
deforestation: no visible global function definition for 'vcov'
deforestation: no visible global function definition for 'glm'
demography: no visible global function definition for 'model.frame'
demography: no visible global function definition for 'model.matrix'
demography: no visible global function definition for 'model.response'
form.beta.start: no visible global function definition for 'coef'
form.beta.start: no visible global function definition for 'glm'
form.sigma2.start: no visible global function definition for 'var'
form.sigma2.start: no visible global function definition for
  'residuals'
form.sigma2.start: no visible global function definition for 'glm'
rinvgamma: no visible global function definition for 'rgamma'
rwish: no visible global function definition for 'rchisq'
rwish: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  coef glm model.frame model.matrix model.response rchisq residuals
  rgamma rnorm var vcov
Consider adding
  importFrom("stats", "coef", "glm", "model.frame", "model.matrix",
             "model.response", "rchisq", "residuals", "rgamma", "rnorm",
             "var", "vcov")
to your NAMESPACE file.
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
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'
fox: no visible global function definition for 'plot'
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'
kang: no visible global function definition for 'plot'
nahu: no visible global function definition for 'interaction.plot'
nahu: no visible global function definition for 'reorder'
nahu: no visible global function definition for 'plot'
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'
thsu: no visible global function definition for 'plot'
Undefined global functions or variables:
  cor interaction.plot median plot reorder sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "interaction.plot", "median", "reorder",
             "sd", "var")
to your NAMESPACE file.
markersCorPlot: no visible global function definition for 'rgb'
plotMarkerDistribution: no visible global function definition for 'rgb'
Undefined global functions or variables:
  rgb
Consider adding
  importFrom("grDevices", "rgb")
to your NAMESPACE file.
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').
Package in Depends field not imported from: 'raster'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
inf: no visible global function definition for 'tail'
phyfromnewick: no visible global function definition for 'head'
phyreg : inphyreg : merge.formulae.ag: no visible global function
  definition for 'update'
phyreg : inphyreg : merge.formula.test.ag: no visible global function
  definition for 'reformulate'
phyreg : inphyreg: no visible global function definition for
  'as.formula'
phyreg : inphyreg: no visible global function definition for
  'model.frame'
phyreg : inphyreg: no visible binding for global variable 'na.omit'
phyreg : inphyreg: no visible global function definition for
  'model.matrix'
phyreg : inphyreg: no visible global function definition for 'lm'
phyreg : inphyreg: no visible global function definition for 'lm.wfit'
phyreg : inphyreg: no visible global function definition for 'pf'
phyreg : inphyreg: no visible global function definition for 'coef'
Undefined global functions or variables:
  as.formula coef head lm lm.wfit model.frame model.matrix na.omit pf
  reformulate tail update
Consider adding
  importFrom("stats", "as.formula", "coef", "lm", "lm.wfit",
             "model.frame", "model.matrix", "na.omit", "pf",
             "reformulate", "update")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Found the following hidden files and directories:
  data/.Rhistory
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
plotData: no visible global function definition for 'plot'
plotData: no visible global function definition for 'abline'
plotData: no visible global function definition for 'text'
Undefined global functions or variables:
  abline plot text
Consider adding
  importFrom("graphics", "abline", "plot", "text")
to your NAMESPACE file.
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.
'library' or 'require' calls in package code:
  'brglm' 'quantreg'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File which contains pragma(s) suppressing diagnostics:
  'src/pijavski.cpp'
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  y[2]: "<chr>         "
  
  x[3]: "<U+6210><U+4EA4>    "
  y[3]: "\"\\u6210\\u4ea4\""
  
  x[4]: "<NA>    "
  y[4]: "<NA>          "
  
  == testthat results  ===========================================================
  OK: 135 SKIPPED: 2 FAILED: 2
  1. Failure: output test (@test-format_character.R#70) 
  2. Failure: output test (@test-format_character.R#71) 
  
  Error: testthat unit tests failed
  Execution halted
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'
'library' or 'require' calls in package code:
  'argparse' 'devtools' 'knitr'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
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.
plot.burndown: no visible global function definition for 'par'
plot.burndown: no visible global function definition for 'hcl'
plot.burndown: no visible global function definition for 'plot'
plot.burndown: no visible global function definition for 'polygon'
plot.burndown: no visible global function definition for 'lm'
plot.burndown: no visible global function definition for 'abline'
plot.burndown: no visible global function definition for 'lines'
plot.burndown: no visible global function definition for 'points'
plot.burndown: no visible global function definition for 'legend'
plot.burndown: no visible global function definition for 'mtext'
plot.gantt: no visible global function definition for 'gray'
plot.gantt: no visible global function definition for 'par'
plot.gantt: no visible global function definition for 'strheight'
plot.gantt: no visible global function definition for 'strwidth'
plot.gantt: no visible global function definition for 'plot'
plot.gantt: no visible global function definition for 'box'
plot.gantt: no visible global function definition for 'mtext'
plot.gantt: no visible global function definition for 'axis.POSIXct'
plot.gantt: no visible global function definition for 'rug'
plot.gantt: no visible global function definition for 'abline'
plot.gantt: no visible global function definition for 'axis'
plot.gantt: no visible global function definition for 'lines'
plot.gantt: no visible global function definition for 'rect'
Undefined global functions or variables:
  abline axis axis.POSIXct box gray hcl legend lines lm mtext par plot
  points polygon rect rug strheight strwidth
Consider adding
  importFrom("grDevices", "gray", "hcl")
  importFrom("graphics", "abline", "axis", "axis.POSIXct", "box",
             "legend", "lines", "mtext", "par", "plot", "points",
             "polygon", "rect", "rug", "strheight", "strwidth")
  importFrom("stats", "lm")
to your NAMESPACE file.
Package suggested but not available for checking: 'latticist'
'library' or 'require' call to 'lattice' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'latticist' 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:
  'cairoDevice' 'gWidgetsRGtk2' 'grid' 'lattice'
  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:
  'lattice:::lattice.getStatus' 'stats:::biplot.prcomp'
  See the note in ?`:::` about the use of this operator.
S3 methods shown with full name in documentation object 'plotCoords':
  'plotCoords.plot' 'plotCoords.biplot'

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.
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.
Packages in Depends field not imported from:
  'R.oo' 'limma' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fitBspline: no visible global function definition for 'median'
fitBspline: no visible global function definition for 'quantile'
fitGAPLM: no visible global function definition for 'poisson'
fitGAPLM: no visible global function definition for 'quantile'
fitGAPLM: no visible global function definition for 'anova'
fitGAPLM: no visible global function definition for 'as.formula'
fitGAPLM: no visible global function definition for 'glm'
fitGAPLM: no visible global function definition for 'pf'
fitGAPLM: no visible global function definition for 'lm'
fitGAPLM: no visible global function definition for 'p.adjust'
head.DEresults: no visible global function definition for 'head'
head.plmDE: no visible global function definition for 'head'
hist.DEresults: no visible global function definition for 'hist'
hist.DEresults: no visible global function definition for 'colors'
hist.DEresults: no visible global function definition for 'box'
limmaPLM: no visible global function definition for 'quantile'
plot.DEresults: no visible global function definition for 'as.formula'
plot.DEresults: no visible global function definition for 'lm'
plot.DEresults: no visible global function definition for 'glm'
plot.DEresults: no visible global function definition for 'plot'
plot.DEresults: no visible global function definition for 'lines'
plot.DEresults: no visible global function definition for 'points'
plot.DEresults: no visible global function definition for 'predict'
Undefined global functions or variables:
  anova as.formula box colors glm head hist lines lm median p.adjust pf
  plot points poisson predict quantile
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "box", "hist", "lines", "plot", "points")
  importFrom("stats", "anova", "as.formula", "glm", "lm", "median",
             "p.adjust", "pf", "poisson", "predict", "quantile")
  importFrom("utils", "head")
to your NAMESPACE file.
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.
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.
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 'plot'
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 plot quantile tail title
  var window
Consider adding
  importFrom("graphics", "axis", "box", "bxp", "lines", "matplot",
             "pairs", "par", "plot", "title")
  importFrom("stats", "median", "quantile", "var", "window")
  importFrom("utils", "tail")
to your NAMESPACE file.
generateEnvelope: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
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.
compute.lower.bound: no visible global function definition for 'cor'
kernel.pls.fit: no visible binding for global variable 'sd'
linear.pls.fit: no visible binding for global variable 'sd'
pcr: no visible binding for global variable 'sd'
pcr: no visible global function definition for 'cor'
pcr.cv: no visible global function definition for 'cor'
pcr.cv: no visible global function definition for 'plot'
pls.model: no visible binding for global variable 'sd'
ridge.cv: no visible global function definition for 'coef'
ridge.cv: no visible global function definition for 'cor'
ridge.cv: no visible global function definition for 'plot'
Undefined global functions or variables:
  coef cor plot sd
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "cor", "sd")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'plsdof'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
print.densityEHpi: no visible global function definition for 'str'
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'rbind.fill':
  'rbind.fill'

S3 methods shown with full name in documentation object 'rbind.fill.matrix':
  'rbind.fill.matrix'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Packages in Depends field not imported from:
  'impute' 'plyr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.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 'plot'
.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 plot rexp rmultinom
  runif
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "kmeans", "mahalanobis", "optimize", "rexp",
             "rmultinom", "runif")
  importFrom("utils", "alarm")
to your NAMESPACE file.
pmlr: no visible global function definition for 'model.response'
pmlr: no visible global function definition for 'model.matrix'
pmlr: no visible global function definition for 'model.weights'
pmlr: no visible global function definition for 'pchisq'
pmlr: no visible global function definition for 'qnorm'
profileCIs: no visible global function definition for 'qchisq'
test.LR: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  model.matrix model.response model.weights pchisq qchisq qnorm
Consider adding
  importFrom("stats", "model.matrix", "model.response", "model.weights",
             "pchisq", "qchisq", "qnorm")
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').
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pnmtrem1: no visible global function definition for 'pnorm'
pnmtrem1: no visible global function definition for 'dnorm'
pnmtrem1: no visible global function definition for 'ginv'
pnmtrem1 : fun: no visible global function definition for 'pnorm'
pnmtrem1 : derf: no visible global function definition for 'dnorm'
pnmtrem1 : derf: no visible global function definition for 'pnorm'
pnmtrem1 : fun: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm ginv pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
'library' or 'require' call to 'rgenoud' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.sigma: no visible global function definition for 'plot'
smooth: no visible global function definition for 'genoud'
Undefined global functions or variables:
  genoud plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
pocrm.imp: no visible global function definition for 'optimize'
pocrm.sim : crm: no visible global function definition for 'optimize'
pocrm.sim : twostgcrm: no visible global function definition for
  'runif'
Undefined global functions or variables:
  optimize runif
Consider adding
  importFrom("stats", "optimize", "runif")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
ppoibin: no visible global function definition for 'pnorm'
ppoibin: no visible global function definition for 'dnorm'
rpoibin: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm pnorm runif
Consider adding
  importFrom("stats", "dnorm", "pnorm", "runif")
to your NAMESPACE file.
ColorDendrogram: no visible global function definition for 'plot'
ColorDendrogram: no visible global function definition for 'segments'
CountDataSet: no visible global function definition for 'rexp'
CountDataSet: no visible global function definition for 'runif'
CountDataSet: no visible global function definition for 'rnorm'
CountDataSet: no visible global function definition for 'rnbinom'
NullModel: no visible binding for global variable 'quantile'
NullModel : <anonymous>: no visible global function definition for
  'median'
NullModelTest: no visible binding for global variable 'quantile'
NullModelTest : <anonymous>: no visible global function definition for
  'median'
PoissonDistance: no visible global function definition for 'as.dist'
permute.rows: no visible global function definition for 'runif'
print.poiclacv: no visible global function definition for 'write.table'
se: no visible global function definition for 'sd'
Undefined global functions or variables:
  as.dist median plot quantile rexp rnbinom rnorm runif sd segments
  write.table
Consider adding
  importFrom("graphics", "plot", "segments")
  importFrom("stats", "as.dist", "median", "quantile", "rexp", "rnbinom",
             "rnorm", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
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.
pointdensity: no visible global function definition for
  'txtProgressBar'
pointdensity: no visible global function definition for
  'setTxtProgressBar'
pointdensity: no visible global function definition for 'flush.console'
Undefined global functions or variables:
  flush.console setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "flush.console", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
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.
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.
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.
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.
Packages suggested but not available for checking:
  'polmineR.Rcpp' 'europarl.en' 'rcqp'
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.
DistributionPlotBinomial: no visible global function definition for
  'qbinom'
DistributionPlotBinomial: no visible global function definition for
  'plot'
DistributionPlotBinomial: no visible global function definition for
  'dbinom'
DistributionPlotBinomial: no visible global function definition for
  'points'
DistributionPlotBinomial: no visible global function definition for
  'abline'
DistributionPlotGamma: no visible global function definition for
  'qgamma'
DistributionPlotGamma: no visible global function definition for 'plot'
DistributionPlotGamma: no visible global function definition for
  'dgamma'
DistributionPlotGamma: no visible global function definition for
  'abline'
DistributionPlotNorm: no visible global function definition for 'qnorm'
DistributionPlotNorm: no visible global function definition for 'plot'
DistributionPlotNorm: no visible global function definition for 'dnorm'
DistributionPlotNorm: no visible global function definition for
  'abline'
calculateDIC: no visible global function definition for 'pnorm'
plot.segratioMCMC: no visible global function definition for 'plot'
plotFitted: no visible global function definition for 'nclass.Sturges'
plotFitted : totalCurve: no visible global function definition for
  'dnorm'
plotFitted : <anonymous>: no visible global function definition for
  'dnorm'
plotTheoretical: no visible global function definition for
  'nclass.Sturges'
plotTheoretical: no visible global function definition for 'dbinom'
setPriors: no visible global function definition for 'qbinom'
Undefined global functions or variables:
  abline dbinom dgamma dnorm nclass.Sturges plot pnorm points qbinom
  qgamma qnorm
Consider adding
  importFrom("grDevices", "nclass.Sturges")
  importFrom("graphics", "abline", "plot", "points")
  importFrom("stats", "dbinom", "dgamma", "dnorm", "pnorm", "qbinom",
             "qgamma", "qnorm")
to your NAMESPACE file.
plot.segRatio: no visible global function definition for 'hist'
plot.segRatio: no visible global function definition for 'par'
plot.segRatio: no visible global function definition for 'layout'
plot.simAutoCross: no visible global function definition for 'plot'
plot.simAutoMarkers: no visible global function definition for 'plot'
sim.autoCross: no visible global function definition for 'rmultinom'
sim.autoMarkers: no visible global function definition for 'rmultinom'
sim.autoMarkers: no visible global function definition for 'rbinom'
sim.autoMarkers: no visible global function definition for 'rbeta'
test.segRatio: no visible global function definition for 'chisq.test'
test.segRatio: no visible global function definition for 'pbinom'
Undefined global functions or variables:
  chisq.test hist layout par pbinom plot rbeta rbinom rmultinom
Consider adding
  importFrom("graphics", "hist", "layout", "par", "plot")
  importFrom("stats", "chisq.test", "pbinom", "rbeta", "rbinom",
             "rmultinom")
to your NAMESPACE file.
'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.
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.
popRangeSim: no visible global function definition for 'write.table'
Undefined global functions or variables:
  write.table
Consider adding
  importFrom("utils", "write.table")
to your NAMESPACE file.
Running examples in 'popRange-Ex.R' failed
The error most likely occurred in:

> ### Name: popRangeSim
> ### Title: popRangeSim
> ### Aliases: popRangeSim
> 
> ### ** Examples
>  
> ## Example: In this scenario, we are simulating a 3x3 grid of populations for 50 
> ## generations. Each population starts with 100 diploid individuals. Each individual 
> ## has a 0.01 probability of migrating away from their populations. There are 100 
> ## SNPs that all have a starting frequency of 0.5, and the program outputs the standard 
> ## "results" file, as well as a PLINK file. 
> 
> ## Commands
> 
> mat = matrix(1,nrow=3,ncol=3) 
> popRangeSim(world = mat, popSize = 100, diploid = TRUE, nGens = 50,
+               mig = 0.01, SNP_model = 0, nSNPs = 100, SNPs_starting_freq = 0.5, 
+               outfile= "outFile1", PLINK=TRUE)
Error in loadNamespace(name) : there is no package called 'reticulate'
[1] "Could not find an acceptable version of python with numpy installed. This should be able to locate python \n      anywhere on your computer, but perhaps try adding python to your PATH if you think this message is an error."
Error in popRangeSim(world = mat, popSize = 100, diploid = TRUE, nGens = 50,  : 
  
Execution halted
estMod.rinvGamma.mar29: no visible global function definition for
  'rgamma'
life.expectancy.stationary: no visible global function definition for
  'head'
life.expectancy.stationary: no visible global function definition for
  'tail'
log.lhood.mar29: no visible global function definition for 'dnorm'
log.post.mar29: no visible global function definition for 'dnorm'
popRecon.sampler: no visible global function definition for 'rnorm'
popRecon.sampler: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm head rgamma rnorm runif tail
Consider adding
  importFrom("stats", "dnorm", "rgamma", "rnorm", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Missing or unexported object: 'forecast::simulate.Arima'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
'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.
findBonds: no visible global function definition for 'runif'
rPotts1ParDecoup: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File 'PottsUtils/libs/i386/PottsUtils.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'sw.o'
File 'PottsUtils/libs/x64/PottsUtils.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'sw.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.
Error in re-building vignettes:
  ...
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in analyseMCMCs(object$fitMCMC$chains, stat = NULL, statName = "loglik",  :
  For  loglik calling coda::effectiveSize resulted in an error: Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 
  0 (non-NA) cases

Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in analyseMCMCs(object$fitMCMC$chains, stat = NULL, statName = "AIC",  :
  For  AIC calling coda::effectiveSize resulted in an error: Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 
  0 (non-NA) cases

Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in analyseMCMCs(object$fitMCMC$chains, stat = NULL, statName = "AICc",  :
  For  AICc calling coda::effectiveSize resulted in an error: Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 
  0 (non-NA) cases

Quitting from lines 419-430 (UserGuide.Rmd) 
Error: processing vignette 'UserGuide.Rmd' failed with diagnostics:
package 'RcppArmadillo' not found
Execution halted
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

powell: no visible global function definition for 'Quote'
Undefined global functions or variables:
  Quote
Consider adding
  importFrom("methods", "Quote")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File 'powell/libs/i386/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'
File 'powell/libs/x64/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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
  'plot'
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'
plotDom: no visible global function definition for 'plot'
plotNsibs: no visible global function definition for 'plot'
plotNtdt: no visible global function definition for 'plot'
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 plot pnorm points qnorm rexp rnorm
  uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Packages which this enhances but not available for checking:
  'org.EcSakai.eg.db' 'org.Pf.plasmo.db'
graphic.ppls.splines: no visible global function definition for 'par'
graphic.ppls.splines: no visible global function definition for 'plot'
graphic.ppls.splines: no visible global function definition for 'lines'
jack.ppls: no visible global function definition for 'cov'
penalized.pls: no visible binding for global variable 'var'
penalized.pls.default: no visible global function definition for 'var'
penalized.pls.kernel: no visible global function definition for 'var'
penalized.pls.select: no visible global function definition for 'var'
sim.data.ppls: no visible global function definition for 'runif'
sim.data.ppls: no visible global function definition for 'var'
sim.data.ppls: no visible global function definition for 'rnorm'
ttest.ppls: no visible global function definition for 'coef'
ttest.ppls: no visible global function definition for 'vcov'
ttest.ppls: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef cov lines par plot pt rnorm runif var vcov
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "coef", "cov", "pt", "rnorm", "runif", "var",
             "vcov")
to your NAMESPACE file.
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.
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 'plot'
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 plot sd text var
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "hist", "pairs", "par", "plot", "text")
  importFrom("stats", "IQR", "median", "sd", "var")
to your NAMESPACE file.
prais.winsten: no visible global function definition for 'model.frame'
prais.winsten: no visible global function definition for 'as.formula'
prais.winsten: no visible global function definition for 'tail'
Undefined global functions or variables:
  as.formula model.frame tail
Consider adding
  importFrom("stats", "as.formula", "model.frame")
  importFrom("utils", "tail")
to your NAMESPACE file.
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.
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.
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 hidden files and directories:
  data/.Rapp.history
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'deSolve' which was already attached by Depends.
  Please remove these calls from your code.
LVCompGames: no visible global function definition for 'runif'
LVCompGames: no visible global function definition for 'plot'
LVCompGames: no visible global function definition for 'axis'
LVCompGames: no visible global function definition for 'box'
LVCompGames: no visible global function definition for 'lines'
LVCompGames: no visible global function definition for 'points'
MetaSim: no visible global function definition for 'runif'
chesson: no visible global function definition for 'rbeta'
chesson: no visible global function definition for 'dbeta'
chesson : rhof: no visible global function definition for 'dbeta'
chesson: no visible global function definition for 'integrate'
pimmlawton: no visible global function definition for 'runif'
Undefined global functions or variables:
  axis box dbeta integrate lines plot points rbeta runif
Consider adding
  importFrom("graphics", "axis", "box", "lines", "plot", "points")
  importFrom("stats", "dbeta", "integrate", "rbeta", "runif")
to your NAMESPACE file.
bias.correct.curve: no visible global function definition for 'approx'
lines.principal.curve: no visible global function definition for
  'lines'
periodic.lowess: no visible global function definition for 'lowess'
periodic.lowess: no visible global function definition for 'approx'
plot.principal.curve: no visible global function definition for 'plot'
points.principal.curve: no visible global function definition for
  'points'
principal.curve : <anonymous>: no visible global function definition
  for 'lowess'
principal.curve : <anonymous>: no visible global function definition
  for 'smooth.spline'
principal.curve : <anonymous>: no visible global function definition
  for 'predict'
principal.curve: no visible global function definition for 'var'
principal.curve: no visible global function definition for 'plot'
principal.curve: no visible global function definition for 'lines'
Undefined global functions or variables:
  approx lines lowess plot points predict smooth.spline var
Consider adding
  importFrom("graphics", "lines", "plot", "points")
  importFrom("stats", "approx", "lowess", "predict", "smooth.spline",
             "var")
to your NAMESPACE file.
basisplot: no visible global function definition for 'plot'
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 'plot'
varperc: no visible global function definition for 'lines'
varperc: no visible global function definition for 'text'
varsimp: no visible global function definition for 'plot'
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 plot points screeplot strwidth terms
  text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot", "points",
             "strwidth", "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
dplr.data.frame: no visible global function definition for 'as.formula'
dplr.fit : do.output: no visible global function definition for 'optim'
dplr.fit : do.perturb: no visible global function definition for
  'optim'
dplr.formula: no visible global function definition for 'model.frame'
dplr.formula: no visible global function definition for 'model.matrix'
dplr.formula: no visible global function definition for 'terms'
dplr.formula: no visible global function definition for
  'model.response'
dplr.formula: no visible global function definition for 'formula'
dplr.formula : <anonymous>: no visible global function definition for
  'predict'
dplr.formula: no visible global function definition for 'predict'
logreg.w : do.output: no visible global function definition for 'optim'
logreg.w : do.perturb: no visible global function definition for
  'optim'
predict.dplr: no visible global function definition for
  'delete.response'
predict.dplr: no visible global function definition for 'model.matrix'
rerlang: no visible global function definition for 'rexp'
sampleR: no visible global function definition for 'rnorm'
scaled: no visible global function definition for 'model.frame'
scaled: no visible global function definition for 'model.matrix'
scaled: no visible global function definition for 'terms'
scaled: no visible global function definition for 'model.response'
Undefined global functions or variables:
  as.formula delete.response formula model.frame model.matrix
  model.response optim predict rexp rnorm terms
Consider adding
  importFrom("stats", "as.formula", "delete.response", "formula",
             "model.frame", "model.matrix", "model.response", "optim",
             "predict", "rexp", "rnorm", "terms")
to your NAMESPACE file.
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.
.pfda.fstep: no visible global function definition for 'dist'
.pfda.main: no visible global function definition for 'plot'
.pfda.mstep: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov dist plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cov", "dist")
to your NAMESPACE file.
File 'processx/libs/i386/processx.dll':
  Found non-API call to R: 'R_new_custom_connection'
File 'processx/libs/x64/processx.dll':
  Found non-API call to R: 'R_new_custom_connection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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'
plot.ProDenICA: no visible global function definition for 'plot'
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 plot poisson predict residuals rmultinom rnorm
  rt runif smooth.spline
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dnorm", "dt", "dunif", "fitted", "poisson",
             "predict", "residuals", "rmultinom", "rnorm", "rt", "runif",
             "smooth.spline")
to your NAMESPACE file.
getCandidates: no visible binding for global variable 'envData'
getGraph: no visible binding for global variable 'envData'
getProvidedDiseaseName: no visible binding for global variable
  'envData'
getSeed: no visible binding for global variable 'envData'
getTopDiseaseMetabolites: no visible binding for global variable
  'envData'
Undefined global functions or variables:
  envData
profBinary: no visible global function definition for 'model.frame'
profBinary: no visible global function definition for 'model.matrix'
profLinear: no visible global function definition for 'model.frame'
profLinear: no visible global function definition for 'model.matrix'
profLinear: no visible global function definition for 'model.response'
profLinear: no visible global function definition for 'model.extract'
summary.profBinary: no visible global function definition for 'terms'
summary.profBinary: no visible global function definition for 'qbeta'
summary.profLinear: no visible global function definition for 'terms'
Undefined global functions or variables:
  model.extract model.frame model.matrix model.response qbeta terms
Consider adding
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "model.response", "qbeta", "terms")
to your NAMESPACE file.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   6.4Mb
    libs      1.7Mb
.simplify : <anonymous>: no visible binding for global variable 'hist'
.simplify : <anonymous>: no visible binding for global variable 'start'
.simplify: no visible binding for global variable 'start'
.simplify: no visible binding for global variable 'end'
ggplot.profr: no visible global function definition for 'ggplot'
ggplot.profr: no visible global function definition for 'geom_rect'
ggplot.profr: no visible global function definition for 'aes'
ggplot.profr: no visible binding for global variable 'start'
ggplot.profr: no visible binding for global variable 'end'
ggplot.profr: no visible global function definition for 'geom_text'
ggplot.profr: no visible binding for global variable 'time'
ggplot.profr: no visible global function definition for
  'scale_y_continuous'
ggplot.profr: no visible global function definition for
  'scale_x_continuous'
plot.profr: no visible global function definition for 'plot'
plot.profr: no visible global function definition for 'rect'
plot.profr: no visible binding for global variable 'time'
plot.profr: no visible global function definition for 'text'
profr: no visible global function definition for 'Rprof'
Undefined global functions or variables:
  Rprof aes end geom_rect geom_text ggplot hist plot rect
  scale_x_continuous scale_y_continuous start text time
Consider adding
  importFrom("graphics", "hist", "plot", "rect", "text")
  importFrom("stats", "end", "start", "time")
  importFrom("utils", "Rprof")
to your NAMESPACE file.
Package suggested but not available for checking: 'qtbase'
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.
acceptbin: no visible global function definition for 'pbinom'
acceptbin: no visible global function definition for 'qbinom'
add4ci: no visible global function definition for 'qnorm'
addz2ci: no visible global function definition for 'qnorm'
blakerci: no visible global function definition for 'qbeta'
diffpropci.Wald.mp: no visible global function definition for 'qnorm'
diffpropci.mp: no visible global function definition for 'qnorm'
diffscoreci: no visible global function definition for 'qchisq'
exactci: no visible global function definition for 'qf'
limit: no visible global function definition for 'qchisq'
midPci: no visible global function definition for 'pbinom'
oddsratioci.mp: no visible global function definition for 'qchisq'
riskscoreci: no visible global function definition for 'qnorm'
scoreci: no visible global function definition for 'qnorm'
scoreci.mp: no visible global function definition for 'qnorm'
wald2ci: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  pbinom qbeta qbinom qchisq qf qnorm
Consider adding
  importFrom("stats", "pbinom", "qbeta", "qbinom", "qchisq", "qf",
             "qnorm")
to your NAMESPACE file.
.propensityClustering.internal: no visible global function definition
  for 'as.dist'
CPBADecomposition: no visible global function definition for 'as.dist'
propensityClustering: no visible global function definition for
  'as.dist'
Undefined global functions or variables:
  as.dist
Consider adding
  importFrom("stats", "as.dist")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
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 'plot'
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 plot predict quantile rbinom var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "plot")
  importFrom("stats", "binomial", "glm", "predict", "quantile", "rbinom",
             "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Cul: no visible global function definition for 'qf'
blockScale: no visible binding for global variable 'sd'
cochranTest: no visible global function definition for 'prcomp'
cochranTest: no visible binding for global variable 'var'
cochranTest: no visible global function definition for 'matplot'
cochranTest: no visible global function definition for 'legend'
continuumRemoval : crfun: no visible global function definition for
  'chull'
continuumRemoval : crfun: no visible global function definition for
  'approx'
continuumRemoval : crfun: no visible global function definition for
  'splinefun'
detrend: no visible binding for global variable 'sd'
duplex: no visible global function definition for 'prcomp'
e2m: no visible global function definition for 'cov'
kenStone: no visible global function definition for 'prcomp'
naes: no visible global function definition for 'prcomp'
naes: no visible global function definition for 'kmeans'
puchwein: no visible global function definition for 'prcomp'
readASD: no visible global function definition for 'read.table'
resample : resfun: no visible global function definition for 'approx'
resample : resfun: no visible global function definition for
  'splinefun'
shenkWest: no visible global function definition for 'prcomp'
spliceCorrection : extrapfun: no visible global function definition for
  'lm'
standardNormalVariate: no visible binding for global variable 'sd'
Undefined global functions or variables:
  approx chull cov kmeans legend lm matplot prcomp qf read.table sd
  splinefun var
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "approx", "cov", "kmeans", "lm", "prcomp", "qf",
             "sd", "splinefun", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
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.
estimateLSEparam: no visible global function definition for 'lm'
estimateMLEparam: no visible global function definition for 'optim'
getCCnlL: no visible global function definition for 'dnorm'
iterateScampi: no visible global function definition for 'quantile'
plot.scampi: no visible global function definition for 'hist'
plot.scampiVal: no visible global function definition for 'par'
plot.scampiVal: no visible global function definition for 'hist'
plot.scampiVal: no visible global function definition for 'abline'
plot.scampiVal: no visible global function definition for 'qqnorm'
plot.scampiVal: no visible global function definition for 'qqline'
sampleInitialVector: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline dnorm hist lm optim par qqline qqnorm quantile runif
Consider adding
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "dnorm", "lm", "optim", "qqline", "qqnorm",
             "quantile", "runif")
to your NAMESPACE file.
'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 'plot'
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 plot points rgb2hsv
Consider adding
  importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
  importFrom("graphics", "box", "contour", "lines", "par", "plot",
             "points")
to your NAMESPACE file.
plotwithprototypes: no visible global function definition for 'plot'
plotwithprototypes: no visible global function definition for
  'strwidth'
plotwithprototypes: no visible global function definition for
  'strheight'
plotwithprototypes: no visible global function definition for 'rect'
plotwithprototypes: no visible global function definition for 'text'
protoclust: no visible global function definition for 'as.dist'
protocut: no visible global function definition for 'cutree'
Undefined global functions or variables:
  as.dist cutree plot rect strheight strwidth text
Consider adding
  importFrom("graphics", "plot", "rect", "strheight", "strwidth", "text")
  importFrom("stats", "as.dist", "cutree")
to your NAMESPACE file.
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.
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.
Found the following significant warnings:
  gaussianProcesses/GaussianProcess.h:66:7: warning: 'GaussianProcess::Observations' will be initialized after [-Wreorder]
  gaussianProcesses/GaussianProcess.h:64:22: warning:   'CovarianceFunction& GaussianProcess::covFunc' [-Wreorder]
  gaussianProcesses/GaussianProcess.cpp:3:1: warning:   when initialized here [-Wreorder]
  gaussianProcesses/GaussianProcess.h:64:22: warning: 'GaussianProcess::covFunc' will be initialized after [-Wreorder]
  gaussianProcesses/GaussianProcess.cpp:6:12: warning:   base 'ForwardModel' [-Wreorder]
See 'd:/Rcompile/CRANpkg/local/3.5/psgp.Rcheck/00install.out' for details.
'library' or 'require' call to 'doParallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
learnParameters: no visible global function definition for
  'coordinates'
makePrediction: no visible global function definition for 'coordinates'
spatialPredict.psgp: no visible global function definition for
  'coordinates'
spatialPredict.psgp: no visible global function definition for
  'makeCluster'
spatialPredict.psgp: no visible global function definition for
  'registerDoParallel'
spatialPredict.psgp: no visible global function definition for
  'clusterEvalQ'
spatialPredict.psgp: no visible global function definition for
  '%dopar%'
spatialPredict.psgp: no visible global function definition for
  'foreach'
spatialPredict.psgp: no visible global function definition for
  'stopCluster'
spatialPredict.psgp: no visible global function definition for
  'SpatialPointsDataFrame'
spatialPredict.psgp: no visible global function definition for 'bbox'
spatialPredict.psgp: no visible global function definition for
  'proj4string<-'
spatialPredict.psgp: no visible global function definition for
  'proj4string'
Undefined global functions or variables:
  %dopar% SpatialPointsDataFrame bbox clusterEvalQ coordinates foreach
  makeCluster proj4string proj4string<- registerDoParallel stopCluster
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.
'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.
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.
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.
'library' or 'require' calls to packages already attached by Depends:
  'multilevel' 'nlme'
  Please remove these calls from your code.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/psycho.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        3.8Mb
    examples   2.3Mb
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.
PurBayes: no visible global function definition for 'update'
PurBayes: no visible global function definition for 'sd'
plot.PurBayes: no visible global function definition for 'plot'
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 plot quantile sd update
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "quantile", "sd", "update")
to your NAMESPACE file.
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.
.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').
pyramid: no visible global function definition for 'plot'
pyramid: no visible global function definition for 'segments'
pyramid: no visible global function definition for 'lines'
pyramid: no visible global function definition for 'text'
pyramid: no visible global function definition for 'rect'
pyramidf: no visible global function definition for 'segments'
pyramidf: no visible global function definition for 'lines'
pyramidf: no visible global function definition for 'text'
pyramidf: no visible global function definition for 'rect'
Undefined global functions or variables:
  lines plot rect segments text
Consider adding
  importFrom("graphics", "lines", "plot", "rect", "segments", "text")
to your NAMESPACE file.
Found the following significant warnings:
  PythonInR.c:150:46: warning: ISO C99 requires rest arguments to be used
  PythonInR.c:179:51: warning: ISO C99 requires rest arguments to be used
  PythonInR.c:185:38: warning: ISO C99 requires rest arguments to be used
  PythonInR.c:189:45: warning: ISO C99 requires rest arguments to be used
  PythonInR.c:273:76: warning: ISO C99 requires rest arguments to be used
  PythonInR.c:278:53: warning: ISO C99 requires rest arguments to be used
See 'd:/Rcompile/CRANpkg/local/3.5/PythonInR.Rcheck/00install.out' for details.
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 'plot'
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 plot points polygon
  printCoefmat
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new")
  importFrom("graphics", "axis", "hist", "par", "plot", "points",
             "polygon")
  importFrom("stats", "density", "p.adjust", "printCoefmat")
to your NAMESPACE file.
dmm_fn: no visible global function definition for 'dnorm'
dmm_noweights_fn: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
left.just : colClasses : <anonymous>: no visible global function
  definition for 'as'
view_data: no visible global function definition for 'data'
Undefined global functions or variables:
  as data
Consider adding
  importFrom("methods", "as")
  importFrom("utils", "data")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: 'biom'
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.
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.
Error in re-building vignettes:
  ...
The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins,
    rowRanges

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

    type

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

    aperm, apply

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'select()' returned 1:many mapping between keys and
columns
Download the knownGene table ... OK
Download the knownToLocusLink table ... 
Error: processing vignette 'QNB-Overview.Rnw' failed with diagnostics:
 chunk 7 (label = The complete processing flow) 
Error : Bad Request

Execution halted
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

Calc.Expr: no visible global function definition for 'read.csv'
Calc.Expr: no visible binding for global variable 'Type'
Calc.Expr: no visible binding for global variable 'Identifier'
Calc.Expr: no visible binding for global variable 'Fluor'
GroupPlot: no visible global function definition for 'read.csv'
GroupPlot: no visible binding for global variable 'Type'
GroupPlot: no visible global function definition for
  'aggregate.data.frame'
plot.CT: no visible global function definition for 'sd'
plot.CT: no visible global function definition for 'barplot'
plot.CT: no visible binding for global variable 'tr_gene_name'
plot.CT : errorbars: no visible global function definition for 'arrows'
plot.CT: no visible global function definition for 'box'
Undefined global functions or variables:
  Fluor Identifier Type aggregate.data.frame arrows barplot box
  read.csv sd tr_gene_name
Consider adding
  importFrom("graphics", "arrows", "barplot", "box")
  importFrom("stats", "aggregate.data.frame", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
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.
Packages in Depends field not imported from:
  'graph' 'igraph' 'pcalg' 'qtl' 'sem'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    contrib   3.7Mb
    doc       2.9Mb
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').
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'
qualint: no visible global function definition for 'plot'
qualval: no visible global function definition for 'qnorm'
qualval: no visible global function definition for 'plot'
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 plot pnorm qnorm rnorm sd tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "dbinom", "pchisq", "pnorm", "qnorm",
             "rnorm", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.1Mb
Package suggested but not available for checking: 'fastshp'
File 'QUIC/libs/i386/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'
File 'QUIC/libs/x64/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
draw_legend: no visible global function definition for 'legend'
draw_legend: no visible global function definition for 'par'
draw_nodes: no visible global function definition for 'lines'
draw_nodes: no visible global function definition for 'points'
draw_nodes: no visible global function definition for 'text'
draw_vertical_lines: no visible global function definition for 'lines'
draw_vertical_lines: no visible global function definition for 'abline'
layout_large_plot: no visible global function definition for 'par'
layout_large_plot: no visible global function definition for 'mtext'
layout_large_plot: no visible global function definition for 'axis'
layout_large_plot: no visible global function definition for 'lines'
layout_small_plot: no visible global function definition for 'par'
rquipu: no visible global function definition for 'colors'
rquipu: no visible global function definition for 'jpeg'
rquipu: no visible global function definition for 'png'
rquipu: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  abline axis colors dev.off jpeg legend lines mtext par png points
  text
Consider adding
  importFrom("grDevices", "colors", "dev.off", "jpeg", "png")
  importFrom("graphics", "abline", "axis", "legend", "lines", "mtext",
             "par", "points", "text")
to your NAMESPACE file.
File 'qVarSel/libs/i386/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'
File 'qVarSel/libs/x64/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.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.
S3 methods shown with full name in documentation object 'summary_table':
  'cbind.qwraps2_summary_table'

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.
mutualCoherence : .setOneMutualP: no visible global function definition
  for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
conf2d.default: no visible global function definition for 'polygon'
conf2d_int: no visible global function definition for 'contourLines'
Undefined global functions or variables:
  contourLines polygon
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "polygon")
to your NAMESPACE file.
'library' or 'require' call to 'rgdal' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'matrixStats' 'rgdal' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
FancyPies: no visible global function definition for 'rainbow'
FancyPies: no visible global function definition for 'plot'
FancyPies: no visible global function definition for 'polygon'
Hist2GE: no visible global function definition for 'dist'
Pies2GE: no visible global function definition for 'rainbow'
Plots2GE: no visible global function definition for 'aggregate'
Plots2GE: no visible global function definition for 'x11'
Plots2GE: no visible global function definition for 'title'
Plots2GE: no visible global function definition for 'png'
Plots2GE: no visible global function definition for 'dev.off'
PolyLines2GE: no visible global function definition for 'rainbow'
Shapes2GE: no visible global function definition for 'rainbow'
Undefined global functions or variables:
  aggregate dev.off dist plot png polygon rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow", "x11")
  importFrom("graphics", "plot", "polygon", "title")
  importFrom("stats", "aggregate", "dist")
to your NAMESPACE file.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      9.3Mb
Found the following significant warnings:
  Warning: working directory was changed to 'd:/Rcompile/CRANpkg/local/3.5', resetting
  Warning: working directory was changed to 'd:/Rcompile/CRANpkg/local/3.5/r2lh.Rcheck/tmp', resetting
Packages suggested but not available for checking: 'rcom' 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
PPT.AddBlankSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'write.table'
PPT.AddDataFrame: no visible global function definition for 'write.csv'
PPT.AddGraphicstoSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.cur'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.list'
PPT.AddGraphicstoSlide: no visible global function definition for
  'savePlot'
PPT.AddTextSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleOnlySlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleSlide: no visible global function definition for
  'comIsValidHandle'
PPT.ApplyTemplate: no visible global function definition for
  'comIsValidHandle'
PPT.Close: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'comCreateObject'
PPT.Init: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'COMCreate'
PPT.Present: no visible global function definition for
  'comIsValidHandle'
PPT.SaveAs: no visible global function definition for
  'comIsValidHandle'
PPT.getAbsolutePath : PPT.filePath: no visible global function
  definition for 'readWindowsShortcut'
Undefined global functions or variables:
  COMCreate comCreateObject comIsValidHandle dev.cur dev.list
  readWindowsShortcut savePlot write.csv write.table
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "savePlot")
  importFrom("utils", "write.csv", "write.table")
to your NAMESPACE file.
r2stl: no visible global function definition for 'persp'
Undefined global functions or variables:
  persp
Consider adding
  importFrom("graphics", "persp")
to your NAMESPACE file.
'library' or 'require' call to 'rgl' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'lattice' 'leaps' 'rgl' 's20x'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'rpvm'
'library' or 'require' call to 'rpvm' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
race : killSlaves.exit: no visible global function definition for
  '.PVM.initsend'
race : killSlaves.exit: no visible global function definition for
  '.PVM.send'
race : killSlaves.exit: no visible global function definition for
  '.PVM.exit'
race: no visible global function definition for '.PVM.mytid'
race: no visible global function definition for '.PVM.spawn'
race: no visible global function definition for '.PVM.initsend'
race: no visible global function definition for '.PVM.pkstrvec'
race: no visible global function definition for '.PVM.send'
race: no visible global function definition for '.PVM.recv'
race: no visible global function definition for '.PVM.bufinfo'
race: no visible global function definition for '.PVM.upkstrvec'
race : job.start: no visible global function definition for
  '.PVM.initsend'
race : job.start: no visible global function definition for
  '.PVM.pkint'
race : job.start: no visible global function definition for '.PVM.send'
race : job.wait: no visible global function definition for '.PVM.recv'
race : job.wait: no visible global function definition for
  '.PVM.bufinfo'
race : job.wait: no visible global function definition for
  '.PVM.upkint'
race : job.wait: no visible global function definition for
  '.PVM.upkdblvec'
race : aux2.friedman: no visible global function definition for
  'pchisq'
race : aux2.friedman: no visible global function definition for 'qt'
race : aux.friedman: no visible global function definition for
  'wilcox.test'
race : aux.ttest: no visible global function definition for 't.test'
race : aux.ttest: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  .PVM.bufinfo .PVM.exit .PVM.initsend .PVM.mytid .PVM.pkint
  .PVM.pkstrvec .PVM.recv .PVM.send .PVM.spawn .PVM.upkdblvec
  .PVM.upkint .PVM.upkstrvec p.adjust pchisq qt t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "qt", "t.test",
             "wilcox.test")
to your NAMESPACE file.
getsonde: no visible global function definition for 'read.table'
plotsonde: no visible global function definition for 'par'
plotwind: no visible global function definition for 'plot'
plotwind: no visible global function definition for 'mtext'
plotwind: no visible global function definition for 'abline'
skewt.axis: no visible global function definition for 'par'
skewt.axis: no visible global function definition for 'plot'
skewt.axis: no visible global function definition for 'axis'
skewt.axis: no visible global function definition for 'mtext'
skewt.axis: no visible global function definition for 'segments'
skewt.axis: no visible global function definition for 'text'
skewt.axis: no visible global function definition for 'lines'
skewt.lines: no visible global function definition for 'lines'
skewt.points: no visible global function definition for 'points'
station.symbol: no visible global function definition for 'sd'
station.symbol: no visible global function definition for 'par'
station.symbol: no visible global function definition for 'lines'
station.symbol: no visible global function definition for 'polygon'
station.symbol: no visible global function definition for 'text'
station.symbol: no visible global function definition for 'segments'
Undefined global functions or variables:
  abline axis lines mtext par plot points polygon read.table sd
  segments text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "plot", "points", "polygon", "segments", "text")
  importFrom("stats", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
RnDif.het: no visible global function definition for 'runif'
RnDif.hom: no visible global function definition for 'runif'
RnDifAdv.hom: no visible global function definition for 'runif'
SoilAdv.hom: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
cpc_get_rawdata: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
plot.rsm: no visible global function definition for 'par'
plot.rsm: no visible global function definition for 'abline'
plot.rsm: no visible global function definition for 'barplot'
Undefined global functions or variables:
  abline barplot par
Consider adding
  importFrom("graphics", "abline", "barplot", "par")
to your NAMESPACE file.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   2.8Mb
.disableThreads: no visible global function definition for
  'stopCluster'
.enableThreads: no visible global function definition for 'detectCores'
.enableThreads: no visible global function definition for
  'makePSOCKcluster'
.enableThreads: no visible global function definition for
  'clusterExport'
.enableThreads: no visible global function definition for 'clusterCall'
.forwardSelection: no visible binding for global variable 'var'
.forwardSelection: no visible global function definition for 'glm'
.forwardSelection: no visible global function definition for 'formula'
.forwardSelection: no visible global function definition for 'binomial'
.forwardSelection: no visible global function definition for 'lm'
.forwardSelection: no visible global function definition for 'predict'
.predict.internal: no visible global function definition for 'predict'
randomGLM: no visible binding for global variable 'cor'
randomGLM: no visible binding for global variable 'sd'
randomGLM: no visible global function definition for 'var'
thinRandomGLM: no visible global function definition for 'glm'
thinRandomGLM: no visible global function definition for 'binomial'
thinRandomGLM: no visible global function definition for 'lm'
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.
anovaF: no visible global function definition for 'anova'
anovaF: no visible global function definition for 'lm'
randInterval: no visible global function definition for 'quantile'
randInterval : <anonymous>: no visible global function definition for
  'quantile'
randPlot: no visible global function definition for 'par'
randPlot: no visible global function definition for 'hist'
randPlot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline anova hist lm par quantile
Consider adding
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "anova", "lm", "quantile")
to your NAMESPACE file.
bartels.rank.test: no visible global function definition for 'na.omit'
bartels.rank.test: no visible global function definition for 'pbeta'
bartels.rank.test: no visible global function definition for 'pnorm'
cox.stuart.test: no visible global function definition for 'pbinom'
difference.sign.test: no visible global function definition for
  'na.omit'
difference.sign.test: no visible global function definition for 'pnorm'
rank.test: no visible global function definition for 'na.omit'
rank.test: no visible global function definition for 'pnorm'
rruns: no visible global function definition for 'runif'
runs.test: no visible global function definition for 'median'
runs.test: no visible global function definition for 'na.omit'
runs.test: no visible global function definition for 'points'
runs.test: no visible global function definition for 'abline'
runs.test: no visible global function definition for 'gray'
runs.test: no visible global function definition for 'pnorm'
turning.point.test: no visible global function definition for 'embed'
turning.point.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline embed gray median na.omit pbeta pbinom pnorm points runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "points")
  importFrom("stats", "embed", "median", "na.omit", "pbeta", "pbinom",
             "pnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  congruRand.c:180:3: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:187:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:188:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:189:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/3.5/randtoolbox.Rcheck/00install.out' for details.
rank.L2R: no visible global function definition for 'kmeans'
rank.L2R: no visible global function definition for 'pnorm'
rank.LN: no visible global function definition for 'kmeans'
rank.LN: no visible global function definition for 'pnorm'
rank.gs: no visible global function definition for 'qnorm'
rank.wald: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  kmeans pnorm qnorm
Consider adding
  importFrom("stats", "kmeans", "pnorm", "qnorm")
to your NAMESPACE file.
CropSpatialPolygonsDataFrame: no visible global function definition for
  'bbox'
CropSpatialPolygonsDataFrame: no visible global function definition for
  'clipPolys'
DiagnoseFailure: no visible global function definition for 'points'
Undefined global functions or variables:
  bbox clipPolys points
Consider adding
  importFrom("graphics", "points")
to your NAMESPACE file.
'library' or 'require' call to 'BSgenome.Hsapiens.UCSC.hg19' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
freq: no visible global function definition for 'xtabs'
freq: no visible binding for global variable 'na.pass'
freq: no visible global function definition for 'melt'
freq: no visible global function definition for 'complete.cases'
freq: no visible global function definition for 'tail'
kurtosis: no visible global function definition for 'na.omit'
label: no visible global function definition for 'tail'
name: no visible global function definition for 'tail'
nvalid : <anonymous>: no visible global function definition for
  'na.omit'
rp.desc: no visible global function definition for 'melt.data.frame'
rp.desc: no visible global function definition for 'cast'
rp.desc: no visible global function definition for 'na.omit'
rp.desc : <anonymous>: no visible global function definition for 'tail'
rp.desc : <anonymous>: no visible global function definition for 'head'
rp.freq: no visible global function definition for 'xtabs'
rp.freq: no visible binding for global variable 'na.pass'
rp.freq: no visible global function definition for 'melt'
rp.freq: no visible global function definition for 'complete.cases'
rp.freq: no visible global function definition for 'tail'
rp.label: no visible global function definition for 'tail'
rp.name: no visible global function definition for 'tail'
rp.outlier : lundcrit: no visible global function definition for 'qf'
rp.outlier: no visible global function definition for 'lm'
rp.outlier: no visible global function definition for 'rstandard'
rp.valid : <anonymous>: no visible global function definition for
  'na.omit'
skewness: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  cast complete.cases head lm melt melt.data.frame na.omit na.pass qf
  rstandard tail xtabs
Consider adding
  importFrom("stats", "complete.cases", "lm", "na.omit", "na.pass", "qf",
             "rstandard", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
fnRAP: no visible global function definition for 'chisq.test'
fnRAP: no visible global function definition for 'combn'
Undefined global functions or variables:
  chisq.test combn
Consider adding
  importFrom("stats", "chisq.test")
  importFrom("utils", "combn")
to your NAMESPACE file.
Packages suggested but not available for checking: 'gurobi' 'rgurobi'
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.3Mb
plotarc: no visible global function definition for 'par'
plotarc: no visible global function definition for 'plot'
plotarc: no visible global function definition for 'lines'
plotpoly: no visible global function definition for 'par'
plotpoly: no visible global function definition for 'plot'
plotpoly: no visible global function definition for 'polygon'
Undefined global functions or variables:
  lines par plot polygon
Consider adding
  importFrom("graphics", "lines", "par", "plot", "polygon")
to your NAMESPACE file.
INT_FIX: no visible global function definition for 'rbinom'
INT_FIX: no visible global function definition for 'glm'
INT_FIX: no visible global function definition for 'as.formula'
INT_FIX: no visible global function definition for 'residuals'
INT_FIX: no visible global function definition for 'var'
INT_RAN: no visible global function definition for 'rbinom'
INT_RAN: no visible global function definition for 'as.formula'
INT_RAN: no visible global function definition for 'predict'
JOINT: no visible global function definition for 'rbinom'
JOINT: no visible global function definition for 'glm'
JOINT: no visible global function definition for 'as.formula'
JOINT: no visible global function definition for 'var'
JOINT: no visible global function definition for 'residuals'
pKuonen: no visible global function definition for 'pchisq'
pKuonen: no visible global function definition for 'uniroot'
pKuonen: no visible global function definition for 'pnorm'
rareGE: no visible global function definition for 'rbinom'
rareGE: no visible global function definition for 'as.formula'
rareGE: no visible global function definition for 'predict'
rareGE: no visible global function definition for 'glm'
rareGE: no visible global function definition for 'residuals'
rareGE: no visible global function definition for 'var'
rareGE_joint_mc: no visible global function definition for 'pchisq'
rareGE_joint_mc: no visible global function definition for 'qchisq'
wuweights: no visible global function definition for 'dbeta'
Undefined global functions or variables:
  as.formula dbeta glm pchisq pnorm predict qchisq rbinom residuals
  uniroot var
Consider adding
  importFrom("stats", "as.formula", "dbeta", "glm", "pchisq", "pnorm",
             "predict", "qchisq", "rbinom", "residuals", "uniroot",
             "var")
to your NAMESPACE file.
BiogTest.individual: no visible global function definition for 'combn'
BiogTest.individual: no visible global function definition for 'runif'
BiogTest.individual: no visible global function definition for 'rlnorm'
BiogTest.individual: no visible global function definition for
  'rnbinom'
BiogTest.sample: no visible global function definition for 'combn'
BiogTest.sample: no visible global function definition for 'runif'
BiogTest.sample: no visible global function definition for 'rlnorm'
BiogTest.sample: no visible global function definition for 'rnbinom'
BiogTest.sample: no visible global function definition for 'aggregate'
EcoTest.individual: no visible global function definition for 'xtabs'
plot.BiogTest: no visible global function definition for 'quantile'
plot.BiogTest: no visible global function definition for 'combn'
plot.EcoTest: no visible global function definition for 'quantile'
Undefined global functions or variables:
  aggregate combn quantile rlnorm rnbinom runif xtabs
Consider adding
  importFrom("stats", "aggregate", "quantile", "rlnorm", "rnbinom",
             "runif", "xtabs")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   1.8Mb
rateratio.test: no visible global function definition for
  'complete.cases'
rateratio.test: no visible global function definition for 'pbinom'
rateratio.test : p.L: no visible global function definition for 'qbeta'
rateratio.test : p.U: no visible global function definition for 'qbeta'
Undefined global functions or variables:
  complete.cases pbinom qbeta
Consider adding
  importFrom("stats", "complete.cases", "pbinom", "qbeta")
to your NAMESPACE file.
concordance: no visible global function definition for 'quantile'
concordance : Normal: no visible global function definition for 'qnorm'
concordance : Normal: no visible global function definition for 'pnorm'
concordance : MC: no visible global function definition for 'rmultinom'
concordance : MC: no visible global function definition for 'quantile'
concordance: no visible global function definition for 'qnorm'
concordance: no visible global function definition for 'pnorm'
concordance : Chisq: no visible global function definition for 'qchisq'
concordance : Chisq: no visible global function definition for 'pchisq'
concordance : Normal2: no visible global function definition for
  'qnorm'
concordance : Normal2: no visible global function definition for
  'pnorm'
concordance : MC2: no visible global function definition for
  'rmultinom'
concordance : MC2: no visible global function definition for 'quantile'
wlin.conc: no visible global function definition for 'quantile'
wlin.conc : MC: no visible global function definition for 'rmultinom'
wlin.conc : MC: no visible global function definition for 'quantile'
wquad.conc: no visible global function definition for 'quantile'
wquad.conc : MC: no visible global function definition for 'rmultinom'
wquad.conc : MC: no visible global function definition for 'quantile'
Undefined global functions or variables:
  pchisq pnorm qchisq qnorm quantile rmultinom
Consider adding
  importFrom("stats", "pchisq", "pnorm", "qchisq", "qnorm", "quantile",
             "rmultinom")
to your NAMESPACE file.
.GCD: no visible global function definition for 'as.polynomial'
.LCM: no visible global function definition for 'as.polynomial'
.is_zero_polynomial: no visible global function definition for 'coef'
.poly2expr: no visible global function definition for 'coef'
integral.rationalfun: no visible global function definition for 'coef'
integraterf.transcendent: no visible global function definition for
  'coef'
rationalfun: no visible global function definition for 'polynomial'
rationalfun.poly: no visible global function definition for
  'polynomial'
rationalfun.poly: no visible global function definition for
  'is.polynomial'
rfun: no visible global function definition for 'polynomial'
rfun.poly: no visible global function definition for 'polynomial'
rfun.poly: no visible global function definition for 'is.polynomial'
simplify: no visible global function definition for 'coef'
simplify: no visible global function definition for 'polynomial'
Undefined global functions or variables:
  as.polynomial coef is.polynomial polynomial
Consider adding
  importFrom("stats", "coef")
to your NAMESPACE file.
.avisApiBusAvanzada: no visible global function definition for
  'read.csv'
.avisRenderMapAdmin: no visible global function definition for 'points'
.avisRenderMapAdmin: no visible global function definition for 'rect'
.avisRenderMapPhysical: no visible global function definition for
  'points'
avisMap: no visible global function definition for 'par'
avisMap: no visible global function definition for 'layout'
Undefined global functions or variables:
  layout par points read.csv rect
Consider adding
  importFrom("graphics", "layout", "par", "points", "rect")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
GetHistoricTradeData: 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.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
bn2nbn: no visible binding for global variable 'bn.fit'
chain4chain: no visible binding for global variable 'head'
chain4chain: no visible binding for global variable 'tail'
estimate8arcs: no visible global function definition for 'lm'
estimate8arcs: no visible global function definition for 'coefficients'
estimate8nbn: no visible global function definition for 'lm'
estimate8nbn: no visible global function definition for 'as.formula'
estimate8nbn: no visible global function definition for 'anova'
estimate8nbn: no visible global function definition for 'coefficients'
generate8chain: no visible global function definition for 'runif'
generate8chain: no visible global function definition for 'rbinom'
generate8nbn: no visible global function definition for 'runif'
generate8nbn: no visible global function definition for 'rbinom'
nbn2bnfit: no visible global function definition for 'model2network'
nbn2bnfit: no visible global function definition for 'custom.fit'
simulate8gema: no visible global function definition for 'rnorm'
simulate8mn: no visible global function definition for 'mvrnorm'
simulate8nbn: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  anova as.formula bn.fit coefficients custom.fit head lm model2network
  mvrnorm rbinom rnorm runif tail
Consider adding
  importFrom("stats", "anova", "as.formula", "coefficients", "lm",
             "rbinom", "rnorm", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
SumTestSens: no visible global function definition for 'pnorm'
binarysens: no visible global function definition for 'dbinom'
hlsens: no visible global function definition for 'wilcox.test'
iv_sens: no visible global function definition for 'pnorm'
mcontrol: no visible global function definition for 'pnorm'
psens: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dbinom pnorm wilcox.test
Consider adding
  importFrom("stats", "dbinom", "pnorm", "wilcox.test")
to your NAMESPACE file.
':::' call which should be '::': 'tools:::file_path_as_absolute'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'tools:::file_test'
  See the note in ?`:::` about the use of this operator.
genBugsScript: no visible global function definition for 'runif'
getBugsOutput: no visible global function definition for 'read.table'
rbugs2coda: no visible global function definition for 'as.mcmc'
rbugs2coda: no visible global function definition for 'mcmc'
rbugs2coda: no visible global function definition for 'as.mcmc.list'
Undefined global functions or variables:
  as.mcmc as.mcmc.list mcmc read.table runif
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "read.table")
to your NAMESPACE file.
find_available_versions: no visible global function definition for
  'contrib.url'
find_available_versions: no visible global function definition for
  'available.packages'
install_version: no visible global function definition for
  'contrib.url'
install_version: no visible global function definition for
  'available.packages'
install_version: no visible global function definition for
  'install_url'
load_available_packages: no visible global function definition for
  'contrib.url'
validate_installed_package: no visible global function definition for
  'installed.packages'
Undefined global functions or variables:
  available.packages contrib.url install_url installed.packages
Consider adding
  importFrom("utils", "available.packages", "contrib.url",
             "installed.packages")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'RColorBrewer' 'classInt' 'maptools'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RColorBrewer' 'classInt' 'maptools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
RC.read.table: 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.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
Found the following significant warnings:
  Warning: working directory was changed to 'D:/temp/RtmpmapofS/RLIBS_278a87c885ca4/RchivalTag/example_files', resetting
  Warning: working directory was changed to 'D:/temp/RtmpmapofS/RLIBS_278a87c885ca4/RchivalTag/example_files', resetting
  Warning: working directory was changed to 'D:/temp/RtmpmapofS/RLIBS_278a87c885ca4/RchivalTag/example_files', resetting
  Warning: working directory was changed to 'D:/temp/RtmpmapofS/RLIBS_278a87c885ca4/RchivalTag/example_files', resetting
.onAttach: no visible global function definition for
  'packageDescription'
rselect.list: no visible global function definition for 'select.list'
Undefined global functions or variables:
  packageDescription select.list
Consider adding
  importFrom("utils", "packageDescription", "select.list")
to your NAMESPACE file.
climdex.data.frame: no visible global function definition for
  'as.PCICt'
Undefined global functions or variables:
  as.PCICt
get_ClinicalCodes: no visible global function definition for 'read.csv'
get_ClinicalCodes : <anonymous>: 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.
Packages in Depends field not imported from:
  'Rcpp' 'RcppEigen'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rclusterpp.package.skeleton: no visible global function definition for
  'packageDescription'
Undefined global functions or variables:
  packageDescription
Consider adding
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
cmaOptimDP: no visible global function definition for 'flush.console'
Undefined global functions or variables:
  flush.console
Consider adding
  importFrom("utils", "flush.console")
to your NAMESPACE file.
.onAttach: no visible global function definition for 'palette'
.onAttach: no visible global function definition for 'dev.off'
helpAboutBCA: no visible global function definition for 'help'
Undefined global functions or variables:
  dev.off help palette
Consider adding
  importFrom("grDevices", "dev.off", "palette")
  importFrom("utils", "help")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'biclust' 'fabia' 'iBBiG' 'superbiclust' 'BcDiag' 'rqubic' 'BicARE'
  's4vd' 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
enterTableMHTest : onOK: no visible global function definition for
  'na.omit'
startStop: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Namespace with empty importFrom: 'tcltk'
'library' or 'require' calls to packages already attached by Depends:
  'depthTools' 'tcltk'
  Please remove these calls from your code.
computeMBD : OnOutput: no visible global function definition for
  'tkbutton'
computeMBD: no visible global function definition for 'tkbutton'
computeMBD : OnPlot: no visible global function definition for
  'tkcanvas'
computeMBD : OnPlot: no visible global function definition for
  'tkbutton'
computeTmean: no visible global function definition for 'tkcanvas'
computeTmean: no visible global function definition for 'tkbutton'
computeTmean : onOK: no visible global function definition for 'par'
plotCentralCurves: no visible global function definition for 'tkcanvas'
plotCentralCurves: no visible global function definition for 'tkbutton'
plotCentralCurves : onOK: no visible global function definition for
  'par'
Undefined global functions or variables:
  par tkbutton tkcanvas
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
'library' or 'require' call to 'FrF2.catlg128' 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:
  'Rcmdr' 'multcomp'
  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:
  'Rcmdr' 'TeachingDemos' 'tseries' 'abind' 'MASS' 'xts' 'forecast'
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:
  'MASS' 'tseries'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'MASS' 'Rcmdr' 'TeachingDemos' 'abind' 'forecast' 'tseries' 'xts'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls in package code:
  'abind' 'e1071' 'qcc'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'ENmisc' 'Hmisc' 'Rcmdr' 'vcd'
  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 'getRcmdr'
.onAttach: no visible global function definition for 'closeCommander'
.onAttach: no visible global function definition for 'Commander'
mosaicMenuItem: no visible global function definition for
  'mosaicSelectDialog'
mosaicMenuItem: no visible global function definition for 'Message'
Undefined global functions or variables:
  Commander Message closeCommander getRcmdr mosaicSelectDialog
Packages in Depends field not imported from:
  'orloca' 'orloca.es'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rcmdr.new.loca.p: no visible binding for global variable 'top'
Rcmdr.new.loca.p: no visible binding for global variable 'buttonsFrame'
Rcmdr.orloca.norm: no visible binding for global variable 'top'
Rcmdr.orloca.norm : onOK: no visible binding for global variable
  'normaVariable'
Rcmdr.orloca.norm: no visible binding for global variable 'normaFrame'
Rcmdr.orloca.norm: no visible binding for global variable
  'buttonsFrame'
Rcmdr.rloca.p: no visible binding for global variable 'top'
Rcmdr.rloca.p: no visible binding for global variable 'buttonsFrame'
Rcmdr.zsum: no visible binding for global variable 'top'
Rcmdr.zsum: no visible binding for global variable 'buttonsFrame'
Rcmdr.zsummin: no visible binding for global variable 'top'
Rcmdr.zsummin : onOK: no visible binding for global variable
  'algorithmVariable'
Rcmdr.zsummin : onOK: no visible binding for global variable '.sol'
Rcmdr.zsummin: no visible binding for global variable 'algorithmFrame'
Rcmdr.zsummin: no visible binding for global variable 'buttonsFrame'
Undefined global functions or variables:
  .sol algorithmFrame algorithmVariable buttonsFrame normaFrame
  normaVariable top
BOXWP: no visible binding for global variable 'top'
BOXWP: no visible binding for global variable 'buttonsFrame'
HIST: no visible binding for global variable 'top'
HIST: no visible binding for global variable 'buttonsFrame'
QQN: no visible binding for global variable 'top'
QQN: no visible binding for global variable 'buttonsFrame'
Undefined global functions or variables:
  buttonsFrame top
Namespaces with empty importFrom:
  'stats' 'tcltk'
fncLRpROC: no visible global function definition for 'palette'
fncLRpROC : onOK : convert: no visible global function definition for
  'col2rgb'
fncLRpROC : onOK : convert: no visible global function definition for
  'rgb'
fncPairedpROC: no visible global function definition for 'palette'
fncPairedpROC : onOK : convert: no visible global function definition
  for 'col2rgb'
fncPairedpROC : onOK : convert: no visible global function definition
  for 'rgb'
fncUnpairedpROC: no visible global function definition for 'palette'
fncUnpairedpROC : onOK : convert: no visible global function definition
  for 'col2rgb'
fncUnpairedpROC : onOK : convert: no visible global function definition
  for 'rgb'
fncvpROC: no visible global function definition for 'palette'
fncvpROC : onOK : convert: no visible global function definition for
  'col2rgb'
fncvpROC : onOK : convert: no visible global function definition for
  'rgb'
Undefined global functions or variables:
  col2rgb palette rgb
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
to your NAMESPACE file.
SampleSizes: no visible global function definition for 'xtabs'
SampleSizes: no visible global function definition for 'weighted.mean'
SampleSizes: no visible global function definition for 'reshape'
stage1Sample.fn: no visible global function definition for 'runif'
stage2Sample.fn: no visible global function definition for 'runif'
strata.options : onOK: no visible global function definition for
  'packageDescription'
Undefined global functions or variables:
  packageDescription reshape runif weighted.mean xtabs
Consider adding
  importFrom("stats", "reshape", "runif", "weighted.mean", "xtabs")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
'library' or 'require' call to 'SLC' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'SLC'
  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:
  'Rcmdr' 'tcltk' 'car' 'RColorBrewer' 'colorspace' 'vcd'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' call to 'car' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RColorBrewer' 'Rcmdr' 'car' 'colorspace' 'vcd'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rcmdr.steeptestDij : onOK: no visible binding for global variable
  'replications'
Rcmdr.steeptestPij : onOK: no visible binding for global variable
  'replications'
Undefined global functions or variables:
  replications
Consider adding
  importFrom("stats", "replications")
to your NAMESPACE file.
Package suggested but not available for checking: 'ROpenOffice'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.1Mb
brewer.pal: no visible global function definition for 'rgb'
display.brewer.all: no visible global function definition for 'par'
display.brewer.all: no visible global function definition for 'plot'
display.brewer.all: no visible global function definition for 'rect'
display.brewer.all: no visible global function definition for 'text'
display.brewer.pal: no visible global function definition for 'image'
Undefined global functions or variables:
  image par plot rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "image", "par", "plot", "rect", "text")
to your NAMESPACE file.
addLine: no visible global function definition for 'abline'
ellipse: no visible global function definition for 'approx'
ellipse: no visible global function definition for 'tail'
Undefined global functions or variables:
  abline approx tail
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rcplex.Rcheck/00install.out' for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include   5.3Mb
    libs      1.6Mb
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    include  25.7Mb
    libs      1.8Mb
File which contains pragma(s) suppressing diagnostics:
  'inst/include/RcppBlazeConfig.h'
Packages in Depends field not imported from:
  'Rcpp' 'RcppClassic'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs      1.8Mb
File which contains pragma(s) suppressing important diagnostics:
  'inst/include/Eigen/src/Core/arch/SSE/Complex.h'
File which contains pragma(s) suppressing diagnostics:
  'inst/include/Eigen/src/Core/util/DisableStupidWarnings.h'
Gauss: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
This is BibTeX, Version 0.99d (MiKTeX 2.9)
The top-level auxiliary file: RcppGSL-intro.aux
I couldn't open database file Rcpp.bib
---line 151 of file RcppGSL-intro.aux
 : \bibdata{Rcpp
 :              }
I'm skipping whatever remains of this command
The style file: jss.bst
I found no database files---while reading file RcppGSL-intro.aux
Warning--I didn't find a database entry for "GSL"
Warning--I didn't find a database entry for "JSS:Rcpp"
Warning--I didn't find a database entry for "Eddelbuettel:2013:Rcpp"
Warning--I didn't find a database entry for "CRAN:Rcpp"
Warning--I didn't find a database entry for "R:Main"
Warning--I didn't find a database entry for "CRAN:RcppArmadillo"
Warning--I didn't find a database entry for "Eddelbuettel+Sanderson:2013:RcppArmadillo"
Warning--I didn't find a database entry for "Sanderson:2010:Armadillo"
Warning--I didn't find a database entry for "CRAN:RcppEigen"
Warning--I didn't find a database entry for "JSS:RcppEigen"
Warning--I didn't find a database entry for "CRAN:inline"
Warning--I didn't find a database entry for "CRAN:Rcpp:Attributes"
(There were 2 error messages)
Error: processing vignette 'RcppGSL-intro.Rmd' failed with diagnostics:
Failed to build the bibliography via bibtex
Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    include   1.8Mb
    lib       3.9Mb
    libs      2.9Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      1.7Mb
Files which contain pragma(s) suppressing diagnostics:
  'inst/include/msgpack/v1/adaptor/array_ref.hpp'
  'inst/include/msgpack/v1/adaptor/boost/optional.hpp'
  'inst/include/msgpack/v1/adaptor/map.hpp'
  'inst/include/msgpack/v1/adaptor/vector.hpp'
  'inst/include/msgpack/v1/adaptor/vector_char.hpp'
  'inst/include/msgpack/v1/adaptor/vector_unsigned_char.hpp'
  'inst/include/msgpack/v2/x3_parse.hpp'
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib       8.0Mb
    libs      1.0Mb
Files which contain pragma(s) suppressing important diagnostics:
  'src/tbb/src/test/test_combinable.cpp'
  'src/tbb/src/test/test_enumerable_thread_specific.cpp'
Files which contain pragma(s) suppressing diagnostics:
  'src/tbb/src/test/test_aligned_space.cpp'
  'src/tbb/src/test/test_atomic.cpp'
  'src/tbb/src/test/test_tagged_msg.cpp'
  'src/tbb/src/test/test_task_priority.cpp'
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs     26.1Mb
Files which contain pragma(s) suppressing diagnostics:
  'inst/include/ql/math/distributions/normaldistribution.hpp'
  'inst/include/ql/math/matrix.hpp'
  'inst/include/ql/math/optimization/levenbergmarquardt.hpp'
  'inst/include/ql/math/statistics/incrementalstatistics.hpp'
  'inst/include/ql/time/date.hpp' 'inst/include/ql/time/imm.hpp'
  'inst/include/ql/utilities/dataparsers.hpp'
  'inst/include/ql/utilities/null.hpp'
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.3Mb
    libs      2.0Mb
get_rollit_source: no visible global function definition for
  'file.edit'
Undefined global functions or variables:
  file.edit
Consider adding
  importFrom("utils", "file.edit")
to your NAMESPACE file.
installed size is 30.7Mb
  sub-directories of 1Mb or more:
    include   4.5Mb
    lib      22.1Mb
    libs      3.9Mb
Package suggested but not available for checking: 'Rcompression'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Packages in Depends field not imported from:
  'MASS' 'Matrix' 'lattice' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CUR: no visible global function definition for 'runif'
CUR: no visible global function definition for 'new'
plotLeverage,CURobj: no visible global function definition for 'plot'
plotLeverage,CURobj: no visible global function definition for 'points'
plotLeverage,CURobj: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline new plot points runif
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("methods", "new")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Drda1: no visible global function definition for 'model.matrix'
permute.rows: no visible global function definition for 'runif'
plot.rdacv: no visible global function definition for 'par'
rda.plotmat: no visible global function definition for 'par'
rda.plotmat: no visible global function definition for 'plot'
rda.plotmat: no visible global function definition for 'layout'
rda.plotmat: no visible global function definition for 'image'
rda.plotmat: no visible global function definition for 'terrain.colors'
rda.plotmat: no visible global function definition for 'axis'
rda.plotmat: no visible global function definition for 'points'
rda.plotmat: no visible global function definition for 'legend'
rda1: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  axis image layout legend model.matrix par plot points runif
  terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "image", "layout", "legend", "par",
             "plot", "points")
  importFrom("stats", "model.matrix", "runif")
to your NAMESPACE file.
get.datamarket.csv: no visible global function definition for
  'read.csv'
getUserAgent: no visible global function definition for 'sessionInfo'
Undefined global functions or variables:
  read.csv sessionInfo
Consider adding
  importFrom("utils", "read.csv", "sessionInfo")
to your NAMESPACE file.
distimage: no visible binding for global variable 'terrain.colors'
distimage: no visible global function definition for 'filled.contour'
distimage: no visible global function definition for 'title'
distimage: no visible global function definition for 'axis'
distimage: no visible global function definition for 'lines'
drawkpc: no visible global function definition for 'plot'
drawkpc: no visible global function definition for 'segments'
drawkpc: no visible global function definition for 'lines'
modelimage: no visible binding for global variable 'topo.colors'
modelimage: no visible global function definition for 'filled.contour'
modelimage: no visible global function definition for 'title'
modelimage: no visible global function definition for 'axis'
modelimage: no visible global function definition for 'lines'
sincdata: no visible global function definition for 'runif'
sincdata: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  axis filled.contour lines plot rnorm runif segments terrain.colors
  title topo.colors
Consider adding
  importFrom("grDevices", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "filled.contour", "lines", "plot",
             "segments", "title")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
sumry_categorical: no visible global function definition for 'freq'
sumry_continous: no visible global function definition for 'quantile'
Undefined global functions or variables:
  freq quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/RDieHarder.Rcheck/00install.out' for details.
Running 'testthat.R' [79s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > test_check("rdomains")
  -- 1. Error: dmoz cat (@test-dmoz-cat.R#5)  ------------------------------------
  Failed to connect to github.com port 443: Timed out
  1: get_dmoz_data() at testthat/test-dmoz-cat.R:5
  2: curl_download("https://github.com/soodoku/domain_classifier/blob/master/rdomains/data-raw/dmoz/dmoz_domain_category.zip?raw=true", 
         tmp)
  
  Shallalist Data saved to the following destination: ./ 
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Error: dmoz cat (@test-dmoz-cat.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
ip2coordinates: no visible global function definition for 'URLencode'
street2coordinates: no visible global function definition for
  'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
checkForVServer: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   2.6Mb
Files which contain pragma(s) suppressing diagnostics:
  'inst/include/re2/prog.h' 'inst/include/re2/re2.h'
  'inst/include/re2/regexp.h' 'src/dfa.cc' 'src/onepass.cc'
File 'readr/libs/i386/readr.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'
File 'readr/libs/x64/readr.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  9: structure(list(x, skip = skip, comment = comment, ...), class = c(paste0("source_", 
         type), "source"))
  10: read_connection(path)
  11: open(con, "rb")
  12: open.connection(con, "rb")
  
  == testthat results  ===========================================================
  OK: 507 SKIPPED: 2 FAILED: 2
  1. Error: read_file works via https (@test-read-file.R#52) 
  2. Error: read_file works via https on gz file (@test-read-file.R#57) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  closing unused connection 3 (https://raw.githubusercontent.com/tidyverse/readr/master/tests/testthat/eol-cr.txt) 
  Execution halted
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  9: structure(list(x, skip = skip, comment = comment, ...), class = c(paste0("source_", 
         type), "source"))
  10: read_connection(path)
  11: open(con, "rb")
  12: open.connection(con, "rb")
  
  == testthat results  ===========================================================
  OK: 507 SKIPPED: 2 FAILED: 2
  1. Error: read_file works via https (@test-read-file.R#52) 
  2. Error: read_file works via https on gz file (@test-read-file.R#57) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  closing unused connection 4 (https://raw.githubusercontent.com/tidyverse/readr/master/tests/testthat/eol-cr.txt) 
  Execution halted
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  9: FUN(X[[i]], ...)
  10: listMatchingFile(x, ignoreMissing = ignoreMissing, lastRound = lastRound)
  11: downloadRemote(i, ignoreMissing = ignoreMissing)
  12: httr::stop_for_status(r)
  
  == testthat results  ===========================================================
  OK: 124 SKIPPED: 11 FAILED: 5
  1. Failure: test encoding function on simple text files (@test-encoding.R#7) 
  2. Failure: test encoding function on simple text files (@test-encoding.R#12) 
  3. Failure: test encoding function on simple text files (@test-encoding.R#17) 
  4. Error: test remote text file (@test-readtext.R#84) 
  5. Error: test remote csv file (@test-readtext.R#98) 
  
  Error: testthat unit tests failed
  Execution halted
'library' or 'require' calls to packages already attached by Depends:
  'leaps' 'mgcv'
  Please remove these calls from your code.
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for 'abline'
bestmods: no visible global function definition for 'axis'
bestmods: no visible global function definition for 'lines'
cic: no visible global function definition for 'lsfit'
cic: no visible global function definition for 'var'
cvic: no visible global function definition for 'lsfit'
cvic: no visible global function definition for 'lm'
eic: no visible global function definition for 'lsfit'
eic: no visible global function definition for 'lm'
ic.min: no visible global function definition for 'lsfit'
scoremods: no visible global function definition for 'lsfit'
scoremods: no visible global function definition for 'var'
xy: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.
Package required but not available: 'Rmosek'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ReCiPa: no visible global function definition for 'count.fields'
ReCiPa: no visible global function definition for 'read.table'
Undefined global functions or variables:
  count.fields read.table
Consider adding
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/redcapAPI.Rcheck/00install.out' for details.
mergeNamespace_roclet: no visible global function definition for
  'new_roclet'
Undefined global functions or variables:
  new_roclet
AutoCorrelationLRtest: no visible global function definition for
  'logLik'
AutoCorrelationLRtest: no visible global function definition for
  'pchisq'
REEMtree: no visible global function definition for 'terms'
REEMtree: no visible binding for global variable 'SubsetVector'
REEMtree: no visible global function definition for 'predict'
REEMtree: no visible global function definition for 'logLik'
fitted.REEMtree: no visible global function definition for 'fitted'
plot.REEMtree: no visible global function definition for 'plot'
predict.REEMtree: no visible global function definition for 'predict'
residuals.REEMtree: no visible global function definition for
  'residuals'
Undefined global functions or variables:
  SubsetVector fitted logLik pchisq plot predict residuals terms
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "fitted", "logLik", "pchisq", "predict",
             "residuals", "terms")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'fitted.REEMtree':
  'fitted.REEMtree'

S3 methods shown with full name in documentation object 'logLik':
  'logLik.REEMtree'

S3 methods shown with full name in documentation object 'plot':
  'plot.REEMtree'

S3 methods shown with full name in documentation object 'predict':
  'predict.REEMtree'

S3 methods shown with full name in documentation object 'print':
  'print.REEMtree'

S3 methods shown with full name in documentation object 'ranef.REEMtree':
  'ranef.REEMtree'

S3 methods shown with full name in documentation object 'residuals.REEMtree':
  'residuals.REEMtree'

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.
cook.outliers: no visible global function definition for 'lm'
cook.outliers: no visible global function definition for
  'cooks.distance'
nonparRI: no visible global function definition for 'quantile'
plot.interval: no visible global function definition for 'par'
plot.interval: no visible global function definition for 'plot.new'
plot.interval: no visible global function definition for 'plot.window'
plot.interval: no visible global function definition for 'segments'
plot.interval: no visible global function definition for 'axis'
plot.interval: no visible global function definition for 'title'
plot.interval: no visible global function definition for 'legend'
plot.interval: no visible global function definition for 'box'
plot.interval: no visible global function definition for 'text'
robust: no visible global function definition for 'qt'
singleRefLimit: no visible global function definition for 'qnorm'
singleRefLimit: no visible global function definition for
  'shapiro.test'
singleRefLimit: no visible global function definition for 'ks.test'
Undefined global functions or variables:
  axis box cooks.distance ks.test legend lm par plot.new plot.window
  qnorm qt quantile segments shapiro.test text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "par", "plot.new",
             "plot.window", "segments", "text", "title")
  importFrom("stats", "cooks.distance", "ks.test", "lm", "qnorm", "qt",
             "quantile", "shapiro.test")
to your NAMESPACE file.
Running 'test-all.R' [2s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  > res<-overlapJuncs(qry,junc)
  [overlapJuncs] Input preparation.
  [overlapJuncs] Query size          :         7	Ref  size :         92
  [overlapJuncs] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  [overlapJuncs] i:  1	seqid: 1   	query set:       7	ref set:    82
  [overlapJuncs] Result assemly.
  [overlapJuncs] Finished.
  > 
  > if(! all(is.na(res$sod)==c(TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE)) )
  +     stop("[test_overlap_juncs] Wrong res$sod NA's.")
  > 
  > if(sum(res$nref) != 27)
  +     stop("[test_overlap_juncs] Wrong sum of res$nref.")
  Error: [test_overlap_juncs] Wrong sum of res$nref.
  Execution halted
HanoiTower: no visible global function definition for 'object.size'
plot.HanoiTower: no visible global function definition for 'plot'
plot.HanoiTower: no visible global function definition for 'polygon'
plot.HanoiTower: no visible global function definition for 'text'
Undefined global functions or variables:
  object.size plot polygon text
Consider adding
  importFrom("graphics", "plot", "polygon", "text")
  importFrom("utils", "object.size")
to your NAMESPACE file.
Data2wd: no visible binding for global variable 'var'
getRsq: no visible global function definition for 'var'
plot.wcr: no visible global function definition for 'plot'
plot.wcr: no visible global function definition for 'image'
plot.wcr: no visible global function definition for 'par'
plot.wnet: no visible global function definition for 'plot'
plot.wnet: no visible global function definition for 'image'
plot.wnet: no visible global function definition for 'par'
waveletGetCV: no visible binding for global variable 'median'
waveletGetCV: no visible binding for global variable 'sd'
wcr: no visible binding for global variable 'var'
wcr: no visible global function definition for 'cov'
wcr: no visible global function definition for 'lm'
wcr: no visible global function definition for 'ginv'
wcr: no visible global function definition for 'glm'
wnet: no visible binding for global variable 'var'
wnet: no visible global function definition for 'predict'
Undefined global functions or variables:
  cov ginv glm image lm median par plot predict sd var
Consider adding
  importFrom("graphics", "image", "par", "plot")
  importFrom("stats", "cov", "glm", "lm", "median", "predict", "sd",
             "var")
to your NAMESPACE file.
cluster.reg: no visible global function definition for 'rnorm'
cluster.reg: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
.area.my: no visible global function definition for 'density'
optimalGT : <anonymous>: no visible global function definition for
  'median'
optimalGT: no visible global function definition for 'png'
optimalGT: no visible global function definition for 'dev.off'
permutation: no visible global function definition for 'flush.console'
plot.wls: no visible global function definition for 'par'
plot.wls: no visible global function definition for 'plot'
plot.wls: no visible global function definition for 'text'
plot.wls: no visible global function definition for 'abline'
reGenotyper: no visible global function definition for 'flush.console'
reGenotyper: no visible binding for global variable 'var'
reGenotyper: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline density dev.off flush.console median par plot png text var
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "par", "plot", "text")
  importFrom("stats", "density", "median", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
binregtest: no visible global function definition for 'str'
binregtest: no visible binding for global variable 'str'
binregtest: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif str
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'Rcplex'
.onAttach: no visible global function definition for
  'packageDescription'
.relax.cv.elnet: no visible global function definition for 'predict'
.relax.cv.elnet: no visible binding for global variable 'weighted.mean'
.relax.cv.lognet: no visible global function definition for 'predict'
.relax.cv.lognet: no visible binding for global variable
  'weighted.mean'
.relax.cvcompute: no visible binding for global variable
  'weighted.mean'
.single.column: no visible global function definition for 'glm'
.single.column: no visible global function definition for 'coef'
cv.alpha.relaxnet: no visible global function definition for
  'mc.reset.stream'
cv.alpha.relaxnet: no visible global function definition for 'mclapply'
cv.relaxnet: no visible global function definition for 'predict'
cv.relaxnet: no visible global function definition for
  'mc.reset.stream'
cv.relaxnet: no visible global function definition for 'mclapply'
predict.cv.alpha.relaxnet: no visible global function definition for
  'predict'
predict.cv.relaxnet: no visible global function definition for
  'predict'
predict.relaxnet: no visible global function definition for 'predict'
Undefined global functions or variables:
  coef glm mc.reset.stream mclapply packageDescription predict
  weighted.mean
Consider adding
  importFrom("stats", "coef", "glm", "predict", "weighted.mean")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
'library' or 'require' call to 'lars' which was already attached by Depends.
  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.
relaxo: no visible global function definition for 'lars'
Undefined global functions or variables:
  lars
'library' or 'require' call to 'tkrplot' 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: 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
print.summary.rem: no visible global function definition for
  'printCoefmat'
print.summary.rem: no visible global function definition for 'pnorm'
print.summary.rem: no visible binding for global variable 'quantile'
print.summary.rem: no visible global function definition for 'pchisq'
print.summary.rem.dyad: no visible global function definition for
  'printCoefmat'
print.summary.rem.dyad: no visible global function definition for
  'pnorm'
print.summary.rem.dyad: no visible global function definition for
  'pchisq'
rem: no visible global function definition for 'rnorm'
rem: no visible global function definition for 'dnorm'
rem: no visible global function definition for 'runif'
rem: no visible global function definition for 'rchisq'
rem: no visible global function definition for 'cov'
rem.dyad: no visible global function definition for 'rnorm'
rem.dyad: no visible global function definition for 'optim'
rem.dyad: no visible global function definition for 'rchisq'
rem.dyad: no visible global function definition for 'quantile'
rem.dyad: no visible global function definition for 'sd'
rem.dyad: no visible global function definition for 'var'
rem.dyad.lprior: no visible global function definition for 'dnorm'
rem.dyad.lprior: no visible global function definition for 'dt'
Undefined global functions or variables:
  cov dnorm dt optim pchisq pnorm printCoefmat quantile rchisq rnorm
  runif sd var
Consider adding
  importFrom("stats", "cov", "dnorm", "dt", "optim", "pchisq", "pnorm",
             "printCoefmat", "quantile", "rchisq", "rnorm", "runif",
             "sd", "var")
to your NAMESPACE file.
CapDistSlope: no visible global function definition for 'coef'
CapDistSlope: no visible global function definition for 'lm'
EnergyEntropyDecomp: no visible global function definition for 'legend'
FernholzDecomp: no visible global function definition for 'legend'
Invest: no visible global function definition for 'par'
Invest: no visible global function definition for 'legend'
SimMarketModel: no visible global function definition for 'rnorm'
plot.capdist: no visible global function definition for 'plot'
plot.capdist: no visible global function definition for 'abline'
plot.capdist: no visible global function definition for 'lm'
plot.toymkt: no visible global function definition for 'par'
plot.toymkt: no visible global function definition for 'plot'
plot.toymkt: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline coef legend lm par plot rnorm
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "coef", "lm", "rnorm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'plyr' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'Hmisc:::label.default'
  See the note in ?`:::` about the use of this operator.
S3 methods shown with full name in documentation object 'as.data.frame.correlation':
  'as.data.frame.correlation'

S3 methods shown with full name in documentation object 'as.data.frame.freq':
  'as.data.frame.freq'

S3 methods shown with full name in documentation object 'as.data.frame.summarize':
  'as.data.frame.summarize'

S3 methods shown with full name in documentation object 'as.data.frame.summarize.by':
  'as.data.frame.summarize.by'

S3 methods shown with full name in documentation object 'as.data.frame.survival':
  'as.data.frame.survival'

S3 methods shown with full name in documentation object 'as.data.frame.tabular':
  'as.data.frame.tabular'

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.
MakeHierarchyTree: no visible global function definition for
  'as.formula'
Undefined global functions or variables:
  as.formula
Consider adding
  importFrom("stats", "as.formula")
to your NAMESPACE file.
Running examples in 'Reol-Ex.R' failed
The error most likely occurred in:

> ### Name: DownloadSearchedTaxa
> ### Title: Download Page Content From EOL
> ### Aliases: DownloadEOLpages DownloadSearchedTaxa
> 
> ### ** Examples
> 
> #Download taxa files to working directory in R
> ## Not run: DownloadEOLpages(c(1,2,3), to.file=TRUE, MyKey)
> ## Not run: 
> ##D DownloadSearchedTaxa(c("Anolis_carolinensis", 
> ##D 	"Anolis garmani"), to.file=TRUE, exact=TRUE)
> ## End(Not run)
> 
> #Save data as an R object rather than download files
> 
> MyTaxa <- c("Camelus dromedarius")
> MyEOLs <- DownloadSearchedTaxa(MyTaxa, to.file=FALSE)
Opening and ending tag mismatch: hr line 5 and body
Opening and ending tag mismatch: body line 3 and html
Premature end of data in tag html line 1
Error: 1: Opening and ending tag mismatch: hr line 5 and body
2: Opening and ending tag mismatch: body line 3 and html
3: Premature end of data in tag html line 1
Execution halted
RearrangeData: no visible global function definition for 'rainbow'
RearrangeData: no visible global function definition for 'hclust'
RearrangeData: no visible global function definition for
  'as.dendrogram'
RearrangeData: no visible global function definition for 'heatmap'
RearrangeData: no visible global function definition for 'pdf'
RearrangeData: no visible global function definition for
  'colorRampPalette'
RearrangeData: no visible global function definition for 'legend'
RearrangeData: no visible global function definition for 'dev.off'
RearrangeJoseph: no visible global function definition for
  'write.table'
RearrangeJoseph: no visible global function definition for
  'as.dendrogram'
RearrangeJoseph: no visible global function definition for
  'order.dendrogram'
colorDendClass : colLab: no visible global function definition for
  'is.leaf'
colorDendClass: no visible global function definition for 'dendrapply'
colorDendClass: no visible global function definition for 'plot'
testData1: no visible global function definition for 'runif'
testData1: no visible global function definition for 'image'
testData2: no visible global function definition for 'runif'
testData2: no visible global function definition for 'image'
Undefined global functions or variables:
  as.dendrogram colorRampPalette dendrapply dev.off hclust heatmap
  image is.leaf legend order.dendrogram pdf plot rainbow runif
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "rainbow")
  importFrom("graphics", "image", "legend", "plot")
  importFrom("stats", "as.dendrogram", "dendrapply", "hclust", "heatmap",
             "is.leaf", "order.dendrogram", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
GlobTestMissing: no visible global function definition for 'lme'
GlobTestMissing: no visible global function definition for 'anova'
TestStatSP: no visible global function definition for 'pf'
TestStatSimple: no visible global function definition for 'ginv'
TestStatSimple: no visible global function definition for 'pf'
Undefined global functions or variables:
  anova ginv lme pf
Consider adding
  importFrom("stats", "anova", "pf")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.8Mb
CA: no visible global function definition for 'readClipboard'
LL: no visible global function definition for 'readClipboard'
US: no visible global function definition for 'readClipboard'
delete: no visible global function definition for 'menu'
doc_temp: no visible global function definition for 'menu'
html5: no visible global function definition for 'na.omit'
install_pandoc: no visible global function definition for
  'download.file'
latexlist: no visible global function definition for 'readClipboard'
new_report: no visible global function definition for 'tail'
new_report: no visible global function definition for 'head'
new_report: no visible global function definition for 'menu'
presentation: no visible global function definition for 'head'
presentation: no visible global function definition for 'tail'
presentation: no visible global function definition for 'menu'
repo2github: no visible global function definition for 'download.file'
repo2github: no visible global function definition for 'unzip'
reveal.js: no visible global function definition for 'na.omit'
strWrap: no visible global function definition for 'readClipboard'
update_bib: no visible global function definition for 'tail'
update_bib: no visible global function definition for 'menu'
Undefined global functions or variables:
  download.file head menu na.omit readClipboard tail unzip
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "download.file", "head", "menu", "readClipboard",
             "tail", "unzip")
to your NAMESPACE file.
MBoxtest: no visible global function definition for 'var'
jrparams: no visible global function definition for 'prcomp'
jrparams: no visible global function definition for 'predict'
jrparams: no visible global function definition for 'qchisq'
jrparams: no visible global function definition for 'qf'
Undefined global functions or variables:
  prcomp predict qchisq qf var
Consider adding
  importFrom("stats", "prcomp", "predict", "qchisq", "qf", "var")
to your NAMESPACE file.
call.eqs: no visible global function definition for 'write.table'
read.eqs: no visible global function definition for 'read.fwf'
Undefined global functions or variables:
  read.fwf write.table
Consider adding
  importFrom("utils", "read.fwf", "write.table")
to your NAMESPACE file.
.resampleMakeFunction: no visible global function definition for 'is'
.resampleSetSeed: no visible global function definition for 'runif'
CI.bca: no visible global function definition for 'is'
CI.bca: no visible global function definition for 'qnorm'
CI.bca: no visible global function definition for 'pnorm'
CI.t: no visible global function definition for 'qt'
ExpandProbs: no visible global function definition for 'pnorm'
ExpandProbs: no visible global function definition for 'qt'
colVars : f: no visible global function definition for 'var'
colVars: no visible global function definition for 'var'
hist.resample: no visible global function definition for 'density'
hist.resample: no visible global function definition for 'lines'
hist.resample: no visible global function definition for 'points'
hist.resample: no visible global function definition for 'approx'
hist.resample: no visible global function definition for 'segments'
resample: no visible global function definition for 'is'
samp.bootknife: no visible global function definition for 'runif'
samp.bootstrap: no visible global function definition for 'runif'
Undefined global functions or variables:
  approx density is lines pnorm points qnorm qt runif segments var
Consider adding
  importFrom("graphics", "lines", "points", "segments")
  importFrom("methods", "is")
  importFrom("stats", "approx", "density", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages in Depends field not imported from:
  'gWidgets' 'gWidgetsRGtk2' 'plyr' 'reshape2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
reshapeGUI: no visible global function definition for 'gwindow'
reshapeGUI: no visible global function definition for 'gnotebook'
reshapeGUI: no visible global function definition for 'size<-'
reshapeGUI: no visible global function definition for 'ggroup'
reshapeGUI: no visible global function definition for 'gtable'
reshapeGUI: no visible global function definition for 'addSpring'
reshapeGUI: no visible global function definition for 'gbutton'
reshapeGUI: no visible global function definition for 'glabel'
reshapeGUI: no visible global function definition for 'gedit'
reshapeGUI: no visible global function definition for 'gcheckbox'
reshapeGUI: no visible global function definition for 'gdf'
reshapeGUI: no visible global function definition for 'visible<-'
reshapeGUI: no visible global function definition for
  'addHandlerClicked'
reshapeGUI : <anonymous>: no visible global function definition for
  'gmessage'
reshapeGUI : <anonymous>: no visible global function definition for
  'svalue'
reshapeGUI : <anonymous>: no visible global function definition for
  'svalue<-'
reshapeGUI : <anonymous>: no visible global function definition for
  'delete'
reshapeGUI : <anonymous>: no visible global function definition for
  'add'
reshapeGUI : <anonymous>: no visible global function definition for
  'gdf'
reshapeGUI : <anonymous>: no visible global function definition for
  'visible<-'
reshapeGUI: no visible global function definition for
  'addHandlerChanged'
updateMeltCodeBox: no visible global function definition for 'svalue<-'
Undefined global functions or variables:
  add addHandlerChanged addHandlerClicked addSpring delete gbutton
  gcheckbox gdf gedit ggroup glabel gmessage gnotebook gtable gwindow
  size<- svalue svalue<- visible<-
GUI_template : onHelp: no visible global function definition for 'help'
Undefined global functions or variables:
  help
Consider adding
  importFrom("utils", "help")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'retimes' 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.
dexgauss: no visible global function definition for 'pnorm'
loglik: no visible global function definition for 'pnorm'
mexgauss: no visible global function definition for 'sd'
rexgauss: no visible global function definition for 'rnorm'
rexgauss: no visible global function definition for 'rexp'
timefit: no visible global function definition for 'optim'
timefit: no visible global function definition for 'sd'
timefit: no visible global function definition for 'par'
timefit: no visible global function definition for 'hist'
timefit: no visible global function definition for 'density'
timefit: no visible global function definition for 'curve'
timefit: no visible global function definition for 'new'
plot,timefit: no visible global function definition for 'density'
plot,timefit: no visible global function definition for 'par'
plot,timefit: no visible global function definition for 'curve'
Undefined global functions or variables:
  curve density hist new optim par pnorm rexp rnorm sd
Consider adding
  importFrom("graphics", "curve", "hist", "par")
  importFrom("methods", "new")
  importFrom("stats", "density", "optim", "pnorm", "rexp", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to 'pso' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.reweight: no visible global function definition for 'par'
plot.reweight: no visible global function definition for 'plot'
plot.reweight: no visible global function definition for 'density'
plot.reweight: no visible global function definition for 'rug'
reweight: no visible global function definition for 'aggregate'
search.best.h: no visible global function definition for 'quantile'
Undefined global functions or variables:
  aggregate density par plot quantile rug
Consider adding
  importFrom("graphics", "par", "plot", "rug")
  importFrom("stats", "aggregate", "density", "quantile")
to your NAMESPACE file.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
FDSNGetTimeSeries: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
fs_author_ids : <anonymous>: no visible global function definition for
  'select.list'
fs_download : <anonymous>: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file select.list
Consider adding
  importFrom("utils", "download.file", "select.list")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'XML' 'xts'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
quoteFXTsData : function.fx: no visible global function definition for
  'xmlValue'
quoteFundTsData : function.fund: no visible global function definition
  for 'xmlValue'
quoteStockTsData : function.stock: no visible global function
  definition for 'xmlSize'
quoteStockTsData : function.stock: no visible global function
  definition for 'xmlValue'
quoteTsData: no visible global function definition for 'xmlRoot'
quoteTsData: no visible global function definition for 'htmlTreeParse'
quoteTsData: no visible global function definition for
  'xmlErrorCumulator'
quoteTsData: no visible global function definition for 'xmlSize'
toXts: no visible global function definition for 'as.xts'
Undefined global functions or variables:
  as.xts htmlTreeParse xmlErrorCumulator xmlRoot xmlSize xmlValue
plot.forensicbatwing: no visible global function definition for 'plot'
print.batwing: no visible global function definition for 'tail'
Undefined global functions or variables:
  plot tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
.testLTS: no visible binding for global variable 'stackloss'
Undefined global functions or variables:
  stackloss
Consider adding
  importFrom("datasets", "stackloss")
to your NAMESPACE file.
gabriel.plot: no visible global function definition for 'barplot'
gabriel.plot: no visible global function definition for 'arrows'
rgabriel: no visible binding for global variable 'sd'
rgabriel : psmm_x: no visible global function definition for 'pnorm'
rgabriel : psmm: no visible global function definition for 'integrate'
rgabriel : qsmm: no visible global function definition for 'qnorm'
rgabriel : qsmm: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  arrows barplot integrate pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "arrows", "barplot")
  importFrom("stats", "integrate", "pnorm", "qnorm", "sd", "uniroot")
to your NAMESPACE file.
Package in Depends field not imported from: 'gsl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gammaIntegral: no visible global function definition for 'integrate'
gammaIntegral : <anonymous>: no visible global function definition for
  'hyperg_1F1'
gammaMLE: no visible global function definition for 'weighted.mean'
gammaMME: no visible binding for global variable 'sd'
gammaMME: no visible binding for global variable 'var'
Undefined global functions or variables:
  hyperg_1F1 integrate sd var weighted.mean
Consider adding
  importFrom("stats", "integrate", "sd", "var", "weighted.mean")
to your NAMESPACE file.
installed size is 75.2Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      63.9Mb
    pictures   1.3Mb
    proj       5.0Mb
genoud: multiple local function definitions for 'fn1.bfgs' with
  different formal arguments
genoud: multiple local function definitions for 'gr1' with different
  formal arguments
genoud: multiple local function definitions for 'hess.fn' with
  different formal arguments
genoud_transform: multiple local function definitions for 'fn1.bfgs'
  with different formal arguments
genoud_transform: multiple local function definitions for 'gr1' with
  different formal arguments
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.8Mb
gexf.to.igraph: no visible global function definition for 'rgb'
igraph.to.gexf: no visible global function definition for 'col2rgb'
Undefined global functions or variables:
  col2rgb rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
to your NAMESPACE file.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc     3.1Mb
    fonts   1.5Mb
    libs    2.0Mb
Packages suggested but not available for checking: 'pmg' 'SVGAnnotation'
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    extra   9.3Mb
'library' or 'require' call to 'gWidgetsRGtk2' 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:
  'RGtk2' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.6Mb
    libs   5.1Mb
File 'RGtk2/libs/i386/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'
File 'RGtk2/libs/x64/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
dbConnect,H2Driver: no visible global function definition for '.jgetEx'
dbSendQuery,H2Connection-character: no visible global function
  definition for '.jfield'
Undefined global functions or variables:
  .jfield .jgetEx
.quick_fetch: no visible global function definition for 'POST'
.quick_fetch: no visible global function definition for 'add_headers'
.quick_fetch: no visible global function definition for
  'stop_for_status'
.quick_fetch: no visible global function definition for 'content'
fetch_healthdata: no visible binding for global variable 'resources'
fetch_healthdata : <anonymous>: no visible binding for global variable
  'filters'
Undefined global functions or variables:
  POST add_headers content filters resources stop_for_status
Packages in Depends field not imported from:
  'RCurl' 'XML' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ECL: no visible global function definition for 'new'
ECLDataset: no visible global function definition for 'new'
ECLDedUp: no visible global function definition for 'new'
ECLDistribute: no visible global function definition for 'new'
ECLIterate: no visible global function definition for 'new'
ECLJoin: no visible global function definition for 'new'
ECLOutput: no visible global function definition for 'new'
ECLProject: no visible global function definition for 'new'
ECLRecord: no visible global function definition for 'new'
ECLRollUp: no visible global function definition for 'new'
ECLSort: no visible global function definition for 'new'
ECLTOPN: no visible global function definition for 'new'
ECLTable: no visible global function definition for 'new'
ECLTransform: no visible global function definition for 'new'
eclDirectCall: no visible global function definition for 'postForm'
parseResults: no visible global function definition for 'xmlRoot'
parseResults: no visible global function definition for 'xmlTreeParse'
parseResults: no visible global function definition for 'getNodeSet'
parseResults: no visible global function definition for 'xmlGetAttr'
parseResults: no visible global function definition for 'xmlValue'
parseResults: no visible global function definition for 'write.table'
Undefined global functions or variables:
  getNodeSet new postForm write.table xmlGetAttr xmlRoot xmlTreeParse
  xmlValue
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Files which contain pragma(s) suppressing diagnostics:
  'src/RhpcMPI.c' 'src/worker/RhpcWorker.c'
RHT.2samp : my.HotellingT2 : my.InvCov2: no visible global function
  definition for 'cov'
RHT.2samp : get.lambda : get.para: no visible global function
  definition for 'optimize'
RHT.2samp : get.lambda : gg: no visible global function definition for
  'qchisq'
RHT.2samp : get.lambda : ggl: no visible global function definition for
  'qnorm'
RHT.2samp : <anonymous>: no visible global function definition for
  'cov'
RHT.fun : my.HotellingT : my.InvCov: no visible global function
  definition for 'cov'
RHT.fun : get.lambda : get.para: no visible global function definition
  for 'optimize'
RHT.fun : get.lambda : gg: no visible global function definition for
  'qchisq'
RHT.fun : get.lambda : ggl: no visible global function definition for
  'qnorm'
RHT.fun : <anonymous>: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov optimize qchisq qnorm
Consider adding
  importFrom("stats", "cov", "optimize", "qchisq", "qnorm")
to your NAMESPACE file.
FusedQDA : <anonymous>: no visible global function definition for 'cov'
RidgeFused: no visible binding for global variable 'cov2cor'
RidgeFusedCV : <anonymous>: no visible global function definition for
  'cov'
SSRidgeFused : <anonymous>: no visible global function definition for
  'cov'
Undefined global functions or variables:
  cov cov2cor
Consider adding
  importFrom("stats", "cov", "cov2cor")
to your NAMESPACE file.
ridit.raw: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
R2ngon: no visible global function definition for 'approx'
plotR2pre: no visible global function definition for 'plot'
plotR2pre: no visible global function definition for 'points'
plotR2pre: no visible global function definition for 'gray'
plotR2pre: no visible global function definition for 'legend'
plotR2pre: no visible global function definition for 'rainbow'
Undefined global functions or variables:
  approx gray legend plot points rainbow
Consider adding
  importFrom("grDevices", "gray", "rainbow")
  importFrom("graphics", "legend", "plot", "points")
  importFrom("stats", "approx")
to your NAMESPACE file.
plot.ijzip: no visible global function definition for 'plot'
plot.ijzip : <anonymous>: no visible global function definition for
  'plot'
plot.ijzip: no visible global function definition for 'axis'
read.ijzip: no visible global function definition for 'unzip'
Undefined global functions or variables:
  axis plot unzip
Consider adding
  importFrom("graphics", "axis", "plot")
  importFrom("utils", "unzip")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Quitting from lines 100-102 (rinatVignette.Rmd) 
Error: processing vignette 'rinatVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
indexBytes: no visible global function definition for 'object.size'
rindexBytes: no visible global function definition for 'object.size'
Undefined global functions or variables:
  object.size
Consider adding
  importFrom("utils", "object.size")
to your NAMESPACE file.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    lib    3.5Mb
    libs   4.8Mb
File 'RInside/libs/i386/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/i386/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Eindex: no visible global function definition for 'txtProgressBar'
Eindex: no visible global function definition for 'setTxtProgressBar'
Emc: no visible global function definition for 'txtProgressBar'
Emc: no visible global function definition for 'setTxtProgressBar'
Emc: no visible global function definition for 'ecdf'
Hier2L: no visible global function definition for 'var'
Null.Hp.RInSp: no visible global function definition for
  'txtProgressBar'
Null.Hp.RInSp: no visible global function definition for 'rmultinom'
Null.Hp.RInSp: no visible global function definition for
  'setTxtProgressBar'
PSicalc: no visible global function definition for 'txtProgressBar'
PSicalc: no visible global function definition for 'setTxtProgressBar'
PSicalc: no visible global function definition for 'ecdf'
WTcMC: no visible global function definition for 'ecdf'
WTdMC: no visible global function definition for 'ecdf'
import.RInSp: no visible global function definition for 'read.table'
like.Wi: no visible global function definition for 'pchisq'
like.Wi: no visible global function definition for 'qchisq'
sumMC.RInSp: no visible global function definition for 'hist'
sumMC.RInSp: no visible global function definition for 'nclass.Sturges'
sumMC.RInSp: no visible global function definition for 'legend'
sumMC.RInSp: no visible global function definition for 'segments'
sumMC.RInSp: no visible global function definition for 'quantile'
Undefined global functions or variables:
  ecdf hist legend nclass.Sturges pchisq qchisq quantile read.table
  rmultinom segments setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("grDevices", "nclass.Sturges")
  importFrom("graphics", "hist", "legend", "segments")
  importFrom("stats", "ecdf", "pchisq", "qchisq", "quantile",
             "rmultinom", "var")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
Running 'test-all.R' [18s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  No yaml delimiters found
  1: expect_true(inherits(import(shorturl), "data.frame"), label = "Import remote file") at testthat/test_remote.R:25
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: inherits(import(shorturl), "data.frame")
  5: import(shorturl)
  6: .import(file = file, ...)
  7: .import.rio_csvy(file = file, ...)
  8: csvy::read_csvy(file = file, ...)
  9: stop("No yaml delimiters found")
  
  == DONE ========================================================================
  No-one is perfect!
  Error: Test failures
  Execution halted
'library' or 'require' calls in package code:
  'doMC' 'doSNOW' 'e1071' 'fftw' 'foreach' 'jpeg' 'png' 'rggobi'
  'tkrplot'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'parallel' 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
desmat.sanitize: no visible global function definition for 'aggregate'
dispdist: no visible global function definition for 'quantile'
dispdist: no visible global function definition for 'hist'
dispdist: no visible global function definition for 'lines'
estate: no visible global function definition for 'weighted.mean'
estate: no visible global function definition for 'lm'
genperms: no visible global function definition for 'combn'
genprobexact: no visible global function definition for 'ave'
invert.ci: no visible global function definition for 'quantile'
invert.ci: no visible global function definition for 'uniroot'
omni.ate: no visible global function definition for 'hist'
omni.ate: no visible global function definition for 'lines'
omni.ate: no visible global function definition for 'quantile'
resresplot: no visible global function definition for 'lm'
resresplot: no visible global function definition for 'symbols'
resresplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline aggregate ave combn hist lines lm quantile symbols uniroot
  weighted.mean
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "symbols")
  importFrom("stats", "aggregate", "ave", "lm", "quantile", "uniroot",
             "weighted.mean")
  importFrom("utils", "combn")
to your NAMESPACE file.
Running 'test-BinomialRegression.R' [0s]
  Running 'test-BrierScore.R' [11s]
  Running 'test-CauseSpecificCoxRegression.R' [7s]
  Running 'test-FineGrayRegression.R' [3s]
  Running 'test-ate.R' [39s]
  Running 'test-boxplotScore.R' [3s]
  Running 'test-confidenceBand_vs_timereg.R' [7s]
  Running 'test-iidCox.R' [4s]
  Running 'test-phreg.R' [0s]
  Running 'test-predictCSC_vs_mstate.R' [11s]
  Running 'test-predictCox-CSC-Risk_internal.R' [10s]
  Running 'test-predictCox_vs_timereg.R' [9s]
  Running 'test-score.R' [17s]
Running the tests in 'tests/test-predictCSC_vs_mstate.R' failed.
Last 13 lines of output:
  + })
  Error: Test failed: 'predict.CSC(2a) - compare to mstate'
  * as.double(pred.RR1a$absRisk.se) not equal to pred.probtrans[, "se2"].
  72/80 mismatches (average diff: NaN)
  [9]  NaN - 0.0296 == NaN
  [10] NaN - 0.0318 == NaN
  [11] NaN - 0.0337 == NaN
  [12] NaN - 0.0355 == NaN
  [13] NaN - 0.0372 == NaN
  [14] NaN - 0.0387 == NaN
  [15] NaN - 0.0401 == NaN
  [16] NaN - 0.0414 == NaN
  [17] NaN - 0.0427 == NaN
  ...
  Execution halted
KM.plot: no visible global function definition for 'plot'
KM.plot: no visible global function definition for 'lines'
SchoenSmooth: no visible global function definition for 'lm'
llCoxReg: no visible binding for global variable 'time'
risksetAUC: no visible global function definition for 'abline'
risksetROC: no visible global function definition for 'abline'
weightedKM: no visible binding for global variable 'time'
Undefined global functions or variables:
  abline lines lm plot time
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "lm", "time")
to your NAMESPACE file.
Alg2: no visible global function definition for 'uniroot'
Alg3: no visible global function definition for 'optim'
NVCopula: no visible global function definition for 'rnorm'
NVCopula: no visible global function definition for 'rgamma'
NVCopula: no visible global function definition for 'var'
NVCopula: no visible global function definition for 'cov'
NVCopula: no visible global function definition for 'qnorm'
NVCopulaMT: no visible global function definition for 'rnorm'
NVCopulaMT: no visible global function definition for 'rgamma'
NVCopulaMT: no visible global function definition for 'var'
NVCopulaMT: no visible global function definition for 'cov'
NVCopulaMT: no visible global function definition for 'qnorm'
R2X: no visible global function definition for 'write.table'
ReturnCopula: no visible global function definition for 'qt'
ReturnCopula: no visible global function definition for 'pt'
SISCopula: no visible global function definition for 'runif'
SISCopula: no visible global function definition for 'qnorm'
SISCopula: no visible global function definition for 'rnorm'
SISCopula: no visible global function definition for 'qgamma'
SISCopula: no visible global function definition for 'var'
SISCopula: no visible global function definition for 'cov'
SISCopulaMT: no visible global function definition for 'runif'
SISCopulaMT: no visible global function definition for 'qnorm'
SISCopulaMT: no visible global function definition for 'rnorm'
SISCopulaMT: no visible global function definition for 'qgamma'
SISCopulaMT: no visible global function definition for 'var'
SISCopulaMT: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov optim pt qgamma qnorm qt rgamma rnorm runif uniroot var
  write.table
Consider adding
  importFrom("stats", "cov", "optim", "pt", "qgamma", "qnorm", "qt",
             "rgamma", "rnorm", "runif", "uniroot", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
rite : exitWiz: no visible global function definition for 'bringToTop'
rite : loadHistory: no visible global function definition for
  'savehistory'
rite : saveGist: no visible global function definition for 'browseURL'
rite : uploadToRPubs : processEntry: no visible global function
  definition for 'browseURL'
rite : runCode: no visible global function definition for 'savehistory'
rite : runCode: no visible global function definition for 'loadhistory'
rite : knittxt: no visible global function definition for 'Sweave'
rite : knittxt: no visible global function definition for 'browseURL'
rite : addHighlighting : addHighlight: no visible global function
  definition for 'packageDescription'
rite : addHighlighting : addHighlight: no visible global function
  definition for 'na.omit'
rite : about : <anonymous>: no visible global function definition for
  'browseURL'
rite : <anonymous>: no visible global function definition for
  'capture.output'
rite : <anonymous>: no visible global function definition for
  'update.packages'
rite : <anonymous>: no visible global function definition for 'help'
rite : f1: no visible global function definition for 'help'
rite : f1: no visible global function definition for 'help.search'
rite : commandCompletion: no visible global function definition for
  'apropos'
rite : findreplace : <anonymous>: no visible global function definition
  for 'browseURL'
Undefined global functions or variables:
  Sweave apropos bringToTop browseURL capture.output help help.search
  loadhistory na.omit packageDescription savehistory update.packages
Consider adding
  importFrom("grDevices", "bringToTop")
  importFrom("stats", "na.omit")
  importFrom("utils", "Sweave", "apropos", "browseURL", "capture.output",
             "help", "help.search", "loadhistory", "packageDescription",
             "savehistory", "update.packages")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'compiler' 'signal'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NumConv: no visible global function definition for 'pchip'
NumConv: no visible global function definition for 'cmpfun'
NumDeconv: no visible global function definition for 'pchip'
NumDeconv : error_function: no visible global function definition for
  'pchip'
NumDeconv: no visible global function definition for 'cmpfun'
NumDeconv: no visible global function definition for 'optim'
RivivcA: no visible global function definition for 'lm'
Undefined global functions or variables:
  cmpfun lm optim pchip
Consider adding
  importFrom("stats", "lm", "optim")
to your NAMESPACE file.
Tbsb : ksiint: no visible global function definition for 'pgamma'
Tbsb: no visible global function definition for 'pchisq'
Tbsc: no visible global function definition for 'qchisq'
riv_classical: no visible global function definition for 'cov'
riv_classical: no visible global function definition for 'pt'
riv_sest: no visible global function definition for 'pt'
riv_sest: no visible global function definition for 'mad'
riv_sest: no visible global function definition for 'mahalanobis'
riv_withDummies: no visible global function definition for 'coef'
riv_withDummies : <anonymous>: no visible global function definition
  for 'coef'
Undefined global functions or variables:
  coef cov mad mahalanobis pchisq pgamma pt qchisq
Consider adding
  importFrom("stats", "coef", "cov", "mad", "mahalanobis", "pchisq",
             "pgamma", "pt", "qchisq")
to your NAMESPACE file.
Found the following significant warnings:
  jri.h:21:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri.c:308:27: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri_glue.c:24:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/rJava.Rcheck/00install.out' for details.
Found the following possibly unsafe calls:
File 'rJava/R/import.R':
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File 'rJava/R/jinit.R':
  unlockBinding(x, .env)
  unlockBinding(x, pe)
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.5/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Undocumented S4 methods:
  generic 'dbReadTable' and siglist 'JDBCConnection,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
cubeHelix : <anonymous>: no visible global function definition for
  'rgb'
rdirichlet: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  rgamma rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "rgamma")
to your NAMESPACE file.
read.pedfile: no visible global function definition for 'download.file'
read.pedfile.info: no visible global function definition for
  'read.table'
read.pedfile.map: no visible global function definition for
  'read.table'
write.pedfile: no visible global function definition for 'is'
Undefined global functions or variables:
  download.file is read.table
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "download.file", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
getStatsData: no visible global function definition for 'xmlRoot'
getStatsData: no visible global function definition for 'xmlTreeParse'
getStatsData: no visible global function definition for 'xmlValue'
getStatsData: no visible global function definition for 'getNodeSet'
getStatsData: no visible global function definition for 'xmlSApply'
getStatsData: no visible binding for global variable 'xmlGetAttr'
getStatsData: no visible binding for global variable 'xmlValue'
getStatsData: no visible global function definition for 'new'
getStatsList: no visible global function definition for 'xmlRoot'
getStatsList: no visible global function definition for 'xmlTreeParse'
getStatsList: no visible global function definition for 'xmlValue'
getStatsList: no visible binding for global variable 'xmlGetAttr'
getStatsList : <anonymous>: no visible global function definition for
  'xmlValue'
getStatsList : <anonymous>: no visible global function definition for
  'xmlGetAttr'
print.jpstat: no visible global function definition for 'head'
Undefined global functions or variables:
  getNodeSet head new xmlGetAttr xmlRoot xmlSApply xmlTreeParse
  xmlValue
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  libjson/Source/JSONGlobals.h:43:50: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  libjson/Source/JSONGlobals.h:44:49: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  libjson/Source/JSONSharedString.h:297:17: warning: 'json_shared_string::len' will be initialized after [-Wreorder]
  libjson/Source/JSONSharedString.h:295:40: warning:   'json_shared_string::json_shared_string_internal* json_shared_string::_str' [-Wreorder]
  libjson/Source/JSONSharedString.h:180:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONSharedString.h:182:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:79:7: warning: 'JSONStream::state' will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:76:28: warning:   'void (* JSONStream::call)(void*, void*)' [-Wreorder]
  JSONStream.cpp:8:1: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:77:27: warning: 'JSONStream::err_call' will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:75:17: warning:   'json_string JSONStream::buffer' [-Wreorder]
  JSONStream.cpp:12:1: warning:   when initialized here [-Wreorder]
  JSONValidator.cpp:394:105: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  JSONValidator.cpp:397:104: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  libjson/Source/internalJSONNode.h:257:18: warning: 'internalJSONNode::_name_encoded' will be initialized after [-Wreorder]
  libjson/Source/internalJSONNode.h:256:17: warning:   'json_string internalJSONNode::_name' [-Wreorder]
  internalJSONNode.cpp:78:1: warning:   when initialized here [-Wreorder]
See 'd:/Rcompile/CRANpkg/local/3.5/RJSONIO.Rcheck/00install.out' for details.
'library' or 'require' call to 'rJava' which was already attached by Depends.
  Please remove these calls from your code.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    datasets   8.6Mb
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    exe  45.1Mb
cv.coef: no visible global function definition for 'sd'
normalize.softmax: no visible global function definition for 'plogis'
plot.rknnBeg: no visible global function definition for 'plot'
plot.rknnBel: no visible global function definition for 'plot'
plot.rknnSupport: no visible global function definition for 'dotchart'
predicted: no visible global function definition for 'influence'
predicted: no visible global function definition for 'fitted'
predicted: no visible global function definition for 'resid'
pressresid: no visible global function definition for 'influence'
pressresid: no visible global function definition for 'resid'
Undefined global functions or variables:
  dotchart fitted influence plogis plot resid sd
Consider adding
  importFrom("graphics", "dotchart", "plot")
  importFrom("stats", "fitted", "influence", "plogis", "resid", "sd")
to your NAMESPACE file.
':::' calls which should be '::':
  'stats:::dexp' 'stats:::dgamma' 'stats:::dweibull' 'stats:::pexp'
  'stats:::pgamma' 'stats:::pweibull' 'stats:::qexp' 'stats:::qgamma'
  'stats:::qweibull' 'stats:::rexp' 'stats:::rgamma' 'stats:::rweibull'
  See the note in ?`:::` about the use of this operator.
Found the following Makefile(s) without a final LF:
  src/Makevars.in
Some 'make' programs ignore lines not ending in LF.
Package in Depends field not imported from: 'msm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'EMSRb_internal' 'EM_internal' 'PD_internal'
EMSRb_internal: no visible global function definition for 'qnorm'
EM_internal: no visible global function definition for 'dnorm'
EM_internal: no visible global function definition for 'pnorm'
PD_internal: no visible global function definition for 'qtnorm'
PD_internal: no visible global function definition for 'sd'
Undefined global functions or variables:
  dnorm pnorm qnorm qtnorm sd
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "sd")
to your NAMESPACE file.
ma.filter: no visible global function definition for 'par'
ma.filter: no visible global function definition for 'lines'
ma.filter: no visible global function definition for 'abline'
qn: no visible global function definition for 'lm'
qn: no visible global function definition for 'var'
qn: no visible global function definition for 'resid'
ss.filter: no visible global function definition for 'smooth.spline'
ss.filter: no visible global function definition for 'par'
ss.filter: no visible global function definition for 'lines'
ss.filter: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline lines lm par resid smooth.spline var
Consider adding
  importFrom("graphics", "abline", "lines", "par")
  importFrom("stats", "lm", "resid", "smooth.spline", "var")
to your NAMESPACE file.
Mallows: no visible global function definition for 'runif'
Mallows: no visible global function definition for 'x11'
Mallows: no visible global function definition for 'plot'
Mallows: no visible global function definition for 'dev.off'
UpdateLambda: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  dev.off plot runif uniroot x11
Consider adding
  importFrom("grDevices", "dev.off", "x11")
  importFrom("graphics", "plot")
  importFrom("stats", "runif", "uniroot")
to your NAMESPACE file.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    rmd   5.9Mb
.onLoad: warning in dir(dll.path, pattern = this.ext, full = FALSE):
  partial argument match of 'full' to 'full.names'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[1], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[2], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: no visible global function definition for 'quantile'
diagnos.envel: no visible global function definition for 'qnorm'
diagnos.envel: no visible binding for global variable 'quantile'
hrplot: no visible global function definition for 'plot'
hrplot: no visible global function definition for 'lines'
hrplot: no visible global function definition for 'abline'
hrplot: no visible global function definition for 'text'
sim.chain: no visible global function definition for 'rnorm'
simRandWalk: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  abline lines plot qnorm quantile rnorm text
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
File 'RMC/libs/i386/RMC.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'RMC.o', 'predict.o'
  Found 'rand', possibly from 'rand' (C)
    Object: 'ap.o'
File 'RMC/libs/x64/RMC.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'RMC.o', 'predict.o'
  Found 'rand', possibly from 'rand' (C)
    Object: 'ap.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'grid' which was already attached by Depends.
  Please remove these calls from your code.
CI: no visible global function definition for 'sd'
CI: no visible global function definition for 'qt'
L: no visible global function definition for 'sd'
L: no visible global function definition for 'residuals'
Qa: no visible global function definition for 'logLik'
Qb: no visible global function definition for 'residuals'
Qc: no visible global function definition for 'residuals'
Qc: no visible global function definition for 'logLik'
STDERR: no visible global function definition for 'sd'
group.UCL: no visible global function definition for 'aggregate'
lr.glover: no visible binding for global variable 'logLik'
lr.glover: no visible binding for global variable 'update'
lr.glover : nobs0: no visible binding for global variable 'nobs'
lr.glover : nobs0 : nobs2: no visible global function definition for
  'residuals'
lr.glover : tlab: no visible global function definition for 'terms'
lr.glover : name: no visible global function definition for 'formula'
lr.glover : modelUpdate: no visible global function definition for
  'as.formula'
lr.glover: no visible global function definition for 'model.frame'
lr.glover: no visible binding for global variable 'AIC'
lr.glover: no visible binding for global variable 'BIC'
summarySE : <anonymous>: no visible global function definition for 'sd'
summarySE: no visible global function definition for 'qt'
Undefined global functions or variables:
  AIC BIC aggregate as.formula formula logLik model.frame nobs qt
  residuals sd terms update
Consider adding
  importFrom("stats", "AIC", "BIC", "aggregate", "as.formula", "formula",
             "logLik", "model.frame", "nobs", "qt", "residuals", "sd",
             "terms", "update")
to your NAMESPACE file.
Combi: no visible global function definition for 'new'
barplotMixCluster: no visible global function definition for 'is'
barplotMixCluster: no visible global function definition for 'par'
barplotMixCluster: no visible global function definition for 'lines'
barplotMixCluster: no visible global function definition for 'text'
barplotMixCluster: no visible global function definition for 'title'
barplotMixCluster: no visible global function definition for 'mtext'
histMixCluster: no visible global function definition for 'is'
histMixCluster: no visible global function definition for 'par'
histMixCluster: no visible global function definition for 'dnorm'
histMixCluster: no visible global function definition for 'lines'
mixmodEntPlot: no visible global function definition for 'par'
mixmodEntPlot: no visible global function definition for 'lines'
mixmodEntPlot: no visible global function definition for 'axis'
mixmodEntPlot: no visible global function definition for 'title'
mixmodEntPlot: no visible binding for global variable 'par'
plot,MixmodCombi: no visible global function definition for 'par'
plot,MixmodCombi: no visible global function definition for 'plot.new'
plot,MixmodCombi: no visible global function definition for 'title'
Undefined global functions or variables:
  axis dnorm is lines mtext new par plot.new text title
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot.new",
             "text", "title")
  importFrom("methods", "is", "new")
  importFrom("stats", "dnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.pLGP_qvec: no visible global function definition for 'ppois'
.qLGP_pvec: no visible global function definition for 'qpois'
.rLGP.failsafe: no visible global function definition for 'runif'
.subdmg: no visible global function definition for 'dbinom'
dnegbin: no visible global function definition for 'dnbinom'
pLGP: no visible global function definition for 'ppois'
qLGP: no visible global function definition for 'qpois'
rLGP: no visible global function definition for 'rpois'
rLGP: no visible global function definition for 'rnorm'
rLGP: no visible global function definition for 'runif'
rbinegbin: no visible global function definition for 'rnbinom'
rmanaclash: no visible global function definition for 'rbinom'
rmanaclash: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbinom dnbinom ppois qpois rbinom rnbinom rnorm rpois runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "ppois", "qpois", "rbinom",
             "rnbinom", "rnorm", "rpois", "runif")
to your NAMESPACE file.
predict.MOA_trainedmodel: no visible global function definition for
  'delete.response'
predict.MOA_trainedmodel: no visible global function definition for
  'model.frame'
trainMOA: no visible binding for global variable 'na.exclude'
Undefined global functions or variables:
  delete.response model.frame na.exclude
Consider adding
  importFrom("stats", "delete.response", "model.frame", "na.exclude")
to your NAMESPACE file.
dbGetDistinct,RMongo-character-character-character: no visible global
  function definition for 'read.table'
dbGetQueryForKeys,RMongo-character-character-character-numeric-numeric:
  no visible global function definition for 'read.csv'
Undefined global functions or variables:
  read.csv read.table
Consider adding
  importFrom("utils", "read.csv", "read.table")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rmosek.Rcheck/00install.out' for details.
CoeffYWeq: no visible global function definition for 'index'
fitdistrForPrecipitation: no visible global function definition for
  'fitdistr'
generate.CCGammaObject: no visible binding for global variable 'rnorm'
generate.CCGammaObject: no visible global function definition for
  'pnorm'
generate.YuleWalkerCoefficientBlockmatrices: no visible binding for
  global variable 'rnorm'
generate.YuleWalkerCoefficientBlockmatricesPerEachMonth: no visible
  binding for global variable 'rnorm'
generatePrecipitationAmount: no visible global function definition for
  'str'
omega_inv: no visible global function definition for 'uniroot'
qqfit: no visible binding for global variable 'qexp'
qqfit: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  ecdf fitdistr index pnorm qexp rnorm str uniroot
Consider adding
  importFrom("stats", "ecdf", "pnorm", "qexp", "rnorm", "uniroot")
  importFrom("utils", "str")
to your NAMESPACE file.
rms.pval: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
dWishartSpike: no visible global function definition for 'dnorm'
pWishartSpike: no visible global function definition for 'pnorm'
qWishartSpike: no visible global function definition for 'qnorm'
rWishartSpike: no visible global function definition for 'qnorm'
rmp: no visible global function definition for 'runif'
rtw: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm pnorm qnorm runif
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'library' or 'require' calls in package code:
  'DESeq' 'seqinr' 'topGO'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'rnaturalearthhires'
.isPath: no visible global function definition for 'tail'
.isPath: no visible global function definition for 'head'
navGraph : <anonymous>: no visible global function definition for
  'tail'
navGraph : <anonymous>: no visible global function definition for 'sd'
navGraph: no visible global function definition for 'colors'
ng_image_array_gray : <anonymous>: no visible global function
  definition for 'grey'
scagGraph: no visible global function definition for 'quantile'
closeViz,NG_Viz2DAxis: no visible global function definition for
  'dev.off'
initializeViz,NG_Viz2DAxis: no visible global function definition for
  'dev.new'
initializeViz,NG_Viz2DAxis: no visible global function definition for
  'dev.cur'
plot,NG_graph-ANY: no visible global function definition for 'box'
plot,NG_graph-ANY: no visible global function definition for 'axis'
plot,NG_graph-ANY: no visible global function definition for 'points'
plot,NG_graph-ANY: no visible global function definition for 'text'
plot,NG_graph-ANY: no visible global function definition for 'segments'
updateViz,NG_Viz2DAxis: no visible global function definition for
  'dev.set'
Undefined global functions or variables:
  axis box colors dev.cur dev.new dev.off dev.set grey head points
  quantile sd segments tail text
Consider adding
  importFrom("grDevices", "colors", "dev.cur", "dev.new", "dev.off",
             "dev.set", "grey")
  importFrom("graphics", "axis", "box", "points", "segments", "text")
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/progress/include/RProgress.h:172:27: warning: ISO C++ forbids variable length array 'bar' [-Wvla]
  d:/RCompile/CRANpkg/lib/3.5/progress/include/RProgress.h:220:26: warning: ISO C++ forbids variable length array 'spaces' [-Wvla]
See 'd:/Rcompile/CRANpkg/local/3.5/rncl.Rcheck/00install.out' for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Packages suggested but not available for checking: 'rrdf' 'Sxslt'
.collapse: no visible global function definition for 'head'
RNGinfo: no visible global function definition for 'setNames'
RNGlibs: no visible global function definition for 'tail'
RNGseq : <anonymous>: no visible global function definition for
  'nextRNGStream'
RNGseq: no visible global function definition for 'nextRNGStream'
RNGseq_seed: no visible global function definition for 'runif'
RNGseq_seed: no visible global function definition for 'nextRNGStream'
checkRNG: no visible global function definition for 'checkTrue'
nextRNG: no visible global function definition for 'runif'
.setRNG,numeric: no visible global function definition for 'runif'
Undefined global functions or variables:
  checkTrue head nextRNGStream runif setNames tail
Consider adding
  importFrom("stats", "runif", "setNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
well19937.validate: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.5Mb
Nnls.trimW : fun1: no visible global function definition for 'runif'
initM: no visible global function definition for 'runif'
rnmf: no visible global function definition for 'txtProgressBar'
rnmf: no visible global function definition for 'setTxtProgressBar'
see: no visible global function definition for 'heat.colors'
see: no visible global function definition for 'colorRampPalette'
see: no visible global function definition for 'grey'
see: no visible global function definition for 'par'
see: no visible global function definition for 'image'
see: no visible global function definition for 'mtext'
simtum: no visible global function definition for 'runif'
simtum: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  colorRampPalette grey heat.colors image mtext par rnorm runif
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "image", "mtext", "par")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'robustbase' 'sfsmisc'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.BuildPartial: no visible global function definition for 'as.formula'
.BuildPartial: no visible global function definition for 'residuals'
.PairwiseCorrelation : .Standardize : <anonymous>: no visible global
  function definition for 'na.omit'
.PairwiseCorrelation : .Standardize: no visible binding for global
  variable 'median'
.PairwiseCorrelation: no visible global function definition for
  'complete.cases'
.yw: no visible global function definition for 'toeplitz'
FastQn: no visible global function definition for 'median'
FastQn: no visible global function definition for 'mad'
fqn: no visible global function definition for 'median'
fqn: no visible global function definition for 'mad'
psdcor: no visible global function definition for 'posdefify'
psdcor: no visible global function definition for 'nearcor'
robar: no visible global function definition for 'frequency'
robcor: no visible global function definition for 'covMcd'
s_FastQn: no visible global function definition for 'median'
Undefined global functions or variables:
  as.formula complete.cases covMcd frequency mad median na.omit nearcor
  posdefify residuals toeplitz
Consider adding
  importFrom("stats", "as.formula", "complete.cases", "frequency", "mad",
             "median", "na.omit", "residuals", "toeplitz")
to your NAMESPACE file.
QD2coef.f: no visible global function definition for 'ppoints'
QD2coef.f: no visible global function definition for 'lsfit'
QD2funC.f: no visible global function definition for 'ppoints'
QD2funC.f: no visible global function definition for 'lsfit'
gminit: no visible global function definition for 'var'
lywalg: no visible global function definition for 'median'
qloggamma: no visible global function definition for 'qgamma'
qloggamma: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  lsfit median ppoints qgamma qnorm var
Consider adding
  importFrom("stats", "lsfit", "median", "ppoints", "qgamma", "qnorm",
             "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'ROptRegTS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
RobRSVD: no visible global function definition for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
Package suggested but not available for checking: 'SSOAP'
'LinkingTo' for
  'mgcv' 'robustbase'
are unused as they have no 'include' directory
Packages in Depends field not imported from:
  'Rcpp' 'RcppArmadillo' 'mgcv' 'robustbase'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GIC: no visible global function definition for 'integrate'
QM.poisson: no visible global function definition for 'ppois'
QM.poisson: no visible global function definition for 'dpois'
cplot.robustgam: no visible global function definition for 'plot'
expect.poisson: no visible global function definition for 'dpois'
expect.poisson: no visible global function definition for 'ppois'
pred.robustgam: no visible global function definition for
  'Predict.matrix'
robust.sigma: no visible global function definition for 'median'
robustgam: no visible global function definition for 's'
robustgam: no visible global function definition for
  'smooth.construct.tp.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.cr.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.ps.smooth.spec'
robustgam : w.fun: no visible global function definition for 'covMcd'
robustgam.GIC.optim: no visible global function definition for 'optim'
robustgam.crossval : w.fun: no visible global function definition for
  'covMcd'
robustgam.crossval: no visible global function definition for
  'integrate'
smooth.construct.tr.smooth.spec: no visible global function definition
  for 'quantile'
w.binomial: no visible global function definition for 'pbinom'
w.poisson: no visible global function definition for 'ppois'
Undefined global functions or variables:
  Predict.matrix covMcd dpois integrate median optim pbinom plot ppois
  quantile s smooth.construct.cr.smooth.spec
  smooth.construct.ps.smooth.spec smooth.construct.tp.smooth.spec
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dpois", "integrate", "median", "optim", "pbinom",
             "ppois", "quantile")
to your NAMESPACE file.
aggregateRanks: no visible binding for global variable 'median'
aggregateRanks: no visible global function definition for 'pnorm'
betaScores: no visible global function definition for 'pbeta'
correctBetaPvaluesExact: no visible binding for global variable 'qbeta'
thresholdBetaScore: no visible global function definition for 'pbeta'
Undefined global functions or variables:
  median pbeta pnorm qbeta
Consider adding
  importFrom("stats", "median", "pbeta", "pnorm", "qbeta")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'penalized' 'splines' 'survival' 'survivalROC'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boot.ROC: no visible global function definition for 'qnorm'
boot.ROC: no visible global function definition for 'penalized'
boot.ROC: no visible global function definition for 'coefficients'
boot.ROC: no visible global function definition for 'sd'
boot.ROC: no visible global function definition for 'optL1'
boot.ROCt: no visible global function definition for 'qnorm'
boot.ROCt: no visible global function definition for 'penalized'
boot.ROCt: no visible global function definition for 'Surv'
boot.ROCt: no visible global function definition for 'coefficients'
boot.ROCt: no visible global function definition for 'sd'
boot.ROCt: no visible global function definition for 'survivalROC'
boot.ROCt: no visible global function definition for 'optL1'
Undefined global functions or variables:
  Surv coefficients optL1 penalized qnorm sd survivalROC
Consider adding
  importFrom("stats", "coefficients", "qnorm", "sd")
to your NAMESPACE file.
'library' or 'require' call to 'ROCR' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'ROCR'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
o.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
p.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
o.rocc: no visible global function definition for 'prediction'
o.rocc: no visible global function definition for 'performance'
o.rocc: no visible global function definition for 'binom.test'
tr.rocc: no visible global function definition for 'prediction'
tr.rocc: no visible global function definition for 'performance'
Undefined global functions or variables:
  binom.test performance prediction
Consider adding
  importFrom("stats", "binom.test")
to your NAMESPACE file.
NPROCwoGS: no visible global function definition for 'quantile'
NPROCwoGS : rdirichlet: no visible global function definition for
  'rgamma'
NPROCwoGS: no visible global function definition for 'rbinom'
NPROCwoGS: no visible global function definition for 'rbeta'
NPROCwoGS: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  quantile rbeta rbinom rgamma
Consider adding
  importFrom("stats", "quantile", "rbeta", "rbinom", "rgamma")
to your NAMESPACE file.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'RODBC'
A package should be listed in only one of these fields.
'library' or 'require' call to 'RODBC' which was already attached by Depends.
  Please remove these calls from your code.
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'ROI.plugin.cplex'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/ROracle.Rcheck/00install.out' for details.
ROSE.eval: no visible global function definition for 'methods'
ROSE.eval: no visible binding for global variable 'model.frame'
ROSE.eval: no visible binding for global variable 'predict'
adj.formula: no visible global function definition for 'terms'
adj.formula: no visible global function definition for 'as.formula'
omnibus.balancing: no visible binding for global variable 'model.frame'
ou.sampl: no visible global function definition for 'rbinom'
over.sampl: no visible global function definition for 'rbinom'
plot.roc.inner: no visible global function definition for 'plot'
roc.curve: no visible global function definition for 'lines'
roc.curve: no visible global function definition for 'abline'
rose.real: no visible binding for global variable 'sd'
rose.real: no visible global function definition for 'sd'
rose.real: no visible global function definition for 'rnorm'
rose.sampl: no visible global function definition for 'rbinom'
under.sampl: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  abline as.formula lines methods model.frame plot predict rbinom rnorm
  sd terms
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "predict", "rbinom",
             "rnorm", "sd", "terms")
  importFrom("utils", "methods")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.2Mb
bestFM: no visible global function definition for 'data'
gaRoth: no visible global function definition for 'data'
ros: no visible global function definition for 'na.omit'
rosunc: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
mfix : m4m: no visible global function definition for 'median'
rrfa: no visible global function definition for 'predict'
rrfb: no visible global function definition for 'predict'
rrfc1: no visible global function definition for 'predict'
rrfc2: no visible global function definition for 'predict'
rrfc3: no visible global function definition for 'predict'
rrfc4: no visible global function definition for 'predict'
rrfc5 : regdat: no visible global function definition for 'predict'
rrfc5 : regdat: no visible global function definition for 'glm'
rrfc5: no visible global function definition for 'predict'
rrfc6: no visible global function definition for 'predict'
rrfc7: no visible global function definition for 'predict'
rrfd: no visible global function definition for 'predict'
rrfe : rdms: no visible global function definition for 'rbinom'
rrfe: no visible global function definition for 'predict'
Undefined global functions or variables:
  glm median predict rbinom
Consider adding
  importFrom("stats", "glm", "median", "predict", "rbinom")
to your NAMESPACE file.
.computeValueReduct: no visible global function definition for 'combn'
.findAllReductsFromCore: no visible global function definition for
  'combn'
.findFirstReductsFromCore: no visible global function definition for
  'combn'
.findSmallestReductFamilyFromCore: no visible global function
  definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'cbind.fill':
  'cbind.fill'

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.
royston.test: no visible global function definition for 'shapiro.test'
royston.test: no visible global function definition for 'cor'
royston.test: no visible global function definition for 'qnorm'
royston.test: no visible global function definition for 'pnorm'
royston.test: no visible global function definition for 'cov'
royston.test: no visible global function definition for 'mahalanobis'
royston.test: no visible global function definition for 'qqplot'
royston.test: no visible global function definition for 'qchisq'
royston.test: no visible global function definition for 'ppoints'
royston.test: no visible global function definition for 'abline'
royston.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline cor cov mahalanobis pchisq pnorm ppoints qchisq qnorm qqplot
  shapiro.test
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "cor", "cov", "mahalanobis", "pchisq", "pnorm",
             "ppoints", "qchisq", "qnorm", "qqplot", "shapiro.test")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'RandomFields' 'akima' 'denstrip' 'geoR' 'lattice' 'maps'
  'mgcv' 'rgl' 'sm' 'tkrplot'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
Package in Depends field not imported from: 'hash'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
P: no visible global function definition for 'has.key'
get_rand_int: no visible global function definition for 'runif'
last: no visible global function definition for 'tail'
rand_partitions: no visible global function definition for 'hash'
Undefined global functions or variables:
  has.key hash runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
evalMedian: no visible global function definition for 'xtabs'
evalMode: no visible global function definition for 'xtabs'
rpartScore: no visible global function definition for 'model.extract'
rpartScore: no visible global function definition for 'var'
rpartScore: no visible binding for global variable 'var'
splitAbs: no visible global function definition for 'xtabs'
Undefined global functions or variables:
  model.extract var xtabs
Consider adding
  importFrom("stats", "model.extract", "var", "xtabs")
to your NAMESPACE file.
'library' or 'require' call to 'RODBC' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
rpart.rules.push: no visible global function definition for 'sqlSave'
rpart.rules.table : <anonymous>: no visible global function definition
  for 'setNames'
rpart.subrules.table : <anonymous>: no visible global function
  definition for 'setNames'
Undefined global functions or variables:
  setNames sqlSave
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'survival'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'MASS' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GenerateData: no visible global function definition for 'mvrnorm'
GetVarImp : FitPenalizedModel: no visible global function definition
  for 'clogit'
Undefined global functions or variables:
  clogit mvrnorm
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.8Mb
S3 methods shown with full name in documentation object 'rbind.feat':
  'rbind.feat'

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.
Unexported objects imported by ':::' calls:
  'rpostgis:::dbBuildTableQuery' 'rpostgis:::dbConnCheck'
  'rpostgis:::dbExistsTable' 'rpostgis:::dbTableNameFix'
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  Warning: working directory was changed to 'D:/temp/RtmpUXEZp5/RLIBS_10afc6f7e3f0b/RPPanalyzer/extdata', resetting
  Warning: working directory was changed to 'D:/temp/RtmpUXEZp5/RLIBS_10afc6f7e3f0b/RPPanalyzer/extdata', resetting
  Warning: working directory was changed to 'D:/temp/RtmpUXEZp5/RLIBS_10afc6f7e3f0b/RPPanalyzer/extdata', resetting
  Warning: working directory was changed to 'D:/temp/RtmpUXEZp5/RLIBS_10afc6f7e3f0b/RPPanalyzer/extdata', resetting
  Warning: working directory was changed to 'D:/temp/RtmpUXEZp5/RLIBS_10afc6f7e3f0b/RPPanalyzer/extdata', resetting
but_last: no visible global function definition for 'head'
first: no visible global function definition for 'head'
last: no visible global function definition for 'tail'
preview_frames: no visible global function definition for 'str'
print.EprimeFrame: no visible global function definition for 'str'
print.FrameList: no visible global function definition for 'str'
Undefined global functions or variables:
  head str tail
Consider adding
  importFrom("utils", "head", "str", "tail")
to your NAMESPACE file.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.4Mb
rpygeo.geoprocessor: warning in system(py.call, invisible = TRUE,
  minimize = TRUE, wait = wait): partial argument match of 'minimize'
  to 'minimized'
Package which this enhances but not available for checking: 'rjpod'
Found the following significant warnings:
  Warning: working directory was changed to 'D:/temp/RtmpATWzql', resetting
  Warning: working directory was changed to 'D:/temp/RtmpATWzql', resetting
  Warning: working directory was changed to 'D:/temp/RtmpATWzql', resetting
rrBlupM6: no visible global function definition for 'optimize'
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'glasso' 'matrixcalc' 'mvoutlier' 'pcaPP'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
rrest: no visible binding for global variable 'glasso'
rrest: no visible global function definition for 'pcout'
rrest: no visible global function definition for 'var'
rrest: no visible global function definition for 'mahalanobis'
rrlda : centerObservations: no visible global function definition for
  'l1median_NLM'
rrlda : df.L2glasso: no visible global function definition for
  'duplication.matrix'
rrlda : alt.df.L2glasso: no visible global function definition for
  'lower.triangle'
Undefined global functions or variables:
  duplication.matrix glasso l1median_NLM lower.triangle mahalanobis
  pcout var
Consider adding
  importFrom("stats", "mahalanobis", "var")
to your NAMESPACE file.
'library' or 'require' call to 'robustbase' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.computekappa: no visible global function definition for 'pnorm'
.computekappa: no visible global function definition for 'dnorm'
.initmethod : <anonymous>: no visible global function definition for
  'median'
.initmethod: no visible global function definition for 'model.matrix'
.mspe: no visible global function definition for 'rnorm'
.mspe : <anonymous>: no visible global function definition for 'rnorm'
makedata: no visible global function definition for 'rnorm'
makedata : addraneff: no visible global function definition for 'rnorm'
plot.meanssaemodel: no visible global function definition for 'par'
plot.meanssaemodel: no visible global function definition for 'plot'
plot.meanssaemodel: no visible global function definition for 'lines'
plot.meanssaemodel: no visible global function definition for 'axis'
plot.meanssaemodel: no visible global function definition for 'grid'
plot.meanssaemodel: no visible global function definition for 'box'
plot.meanssaemodel: no visible global function definition for 'legend'
plot.meanssaemodel: no visible global function definition for 'arrows'
saemodel: no visible global function definition for 'model.frame'
saemodel: no visible global function definition for 'model.response'
saemodel: no visible global function definition for 'model.matrix'
summary.fitsaemodel: no visible global function definition for 'pt'
summary.fitsaemodel: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  arrows axis box dnorm grid legend lines median model.frame
  model.matrix model.response par plot pnorm printCoefmat pt rnorm
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "grid", "legend",
             "lines", "par", "plot")
  importFrom("stats", "dnorm", "median", "model.frame", "model.matrix",
             "model.response", "pnorm", "printCoefmat", "pt", "rnorm")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/RSAP.Rcheck/00install.out' for details.
Files named as vignettes but with no recognized vignette engine:
   'vignettes/Untitled.Rnw'
(Is a VignetteBuilder field missing?)
stripslash: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
f_cal_chk_f: no visible global function definition for 'qf'
f_main: no visible binding for global variable 'median'
f_main: no visible binding for global variable 'sd'
f_main: no visible global function definition for 'write.table'
f_main_p: no visible global function definition for 'write.table'
f_main_p: no visible global function definition for 'runif'
get_random_filename: no visible global function definition for 'runif'
rSCA.correlation: no visible global function definition for
  'read.table'
rSCA.correlation: no visible global function definition for 'read.csv'
rSCA.correlation: no visible global function definition for 'cor'
rSCA.inference: no visible global function definition for 'read.table'
rSCA.inference: no visible global function definition for 'read.csv'
rSCA.inference: no visible global function definition for 'na.omit'
rSCA.missing: no visible global function definition for 'read.table'
rSCA.missing: no visible global function definition for 'read.csv'
rSCA.modeling: no visible global function definition for 'read.table'
rSCA.modeling: no visible global function definition for 'read.csv'
rSCA.modeling: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  cor median na.omit qf read.csv read.table runif sd write.table
Consider adding
  importFrom("stats", "cor", "median", "na.omit", "qf", "runif", "sd")
  importFrom("utils", "read.csv", "read.table", "write.table")
to your NAMESPACE file.
convexhull: no visible global function definition for 'chull'
convexhull: no visible global function definition for 'rnorm'
drawcompletegraph: no visible global function definition for 'plot'
drawcompletegraph: no visible global function definition for 'segments'
getbag: no visible global function definition for 'plot'
getbag: no visible global function definition for 'chull'
getbag: no visible global function definition for 'polygon'
getbag: no visible global function definition for 'points'
inflate: no visible global function definition for 'rnorm'
rsmed: no visible global function definition for 'runif'
rsplot: no visible global function definition for 'plot'
rsplot: no visible global function definition for 'chull'
rsplot: no visible global function definition for 'polygon'
rsplot: no visible global function definition for 'points'
rsrings: no visible global function definition for 'plot'
rsrings: no visible global function definition for 'chull'
rsrings: no visible global function definition for 'polygon'
rsrings: no visible global function definition for 'points'
rstinterval: no visible global function definition for 'plot'
rstinterval: no visible global function definition for 'runif'
rstinterval: no visible global function definition for 'rnorm'
rstinterval: no visible global function definition for 'chull'
rstinterval: no visible global function definition for 'polygon'
Undefined global functions or variables:
  chull plot points polygon rnorm runif segments
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "plot", "points", "polygon", "segments")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
rsem: no visible global function definition for 'write.table'
rsem.Ascov: no visible global function definition for 'qchisq'
rsem.Ascov: no visible global function definition for 'pchisq'
rsem.emmusig: no visible global function definition for 'na.omit'
rsem.emmusig: no visible global function definition for 'qchisq'
rsem.emmusig: no visible global function definition for 'pchisq'
rsem.fit: no visible global function definition for 'pchisq'
rsem.fit: no visible global function definition for 'pf'
rsem.print : print.estimate: no visible global function definition for
  'pnorm'
rsem.weight: no visible global function definition for 'qchisq'
rsem.weight: no visible global function definition for 'pchisq'
semdiag.call.eqs: no visible global function definition for
  'write.table'
semdiag.read.eqs: no visible global function definition for 'read.fwf'
Undefined global functions or variables:
  na.omit pchisq pf pnorm qchisq read.fwf write.table
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pf", "pnorm", "qchisq")
  importFrom("utils", "read.fwf", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/Rserve.Rcheck/00install.out' for details.
Rserve: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/Rserve/libs/i386/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/3.5/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
addNoisyCopies: no visible global function definition for 'rnorm'
eta: no visible global function definition for 'var'
gaussClassifier: no visible global function definition for 'runif'
getSigma: no visible global function definition for 'sd'
getSigma: no visible binding for global variable 'sd'
sfaClassify: no visible global function definition for 'rainbow'
sfaClassify: no visible global function definition for 'par'
sfaClassify: no visible global function definition for 'plot'
sfaClassify: no visible global function definition for 'points'
sfaClassify: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines par plot points rainbow rnorm runif sd var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("stats", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'biwt' 'cairoDevice' 'fBasics' 'gplots' 'gWidgets' 'gWidgetsRGtk2'
  'minerva' 'parmigene' 'stringr' 'snowfall'
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:
  'grDevices' 'snowfall'
  Please remove these calls from your code.
'library' or 'require' call to 'ctc' 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:
  'biwt' 'cairoDevice' 'fBasics' 'gWidgets' 'gWidgetsRGtk2' 'gplots'
  'minerva' 'parmigene' 'snowfall' 'stringr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
filterSD: no visible binding for global variable 'sd'
filterSD: no visible global function definition for 'quantile'
fit_lasso: no visible global function definition for 'coef'
fit_prlasso: no visible global function definition for 'coef'
rsig: no visible binding for global variable 'mclapply'
rsig.all: no visible binding for global variable 'mclapply'
rsig.all : <anonymous>: no visible global function definition for
  'flush.console'
rsig.all : <anonymous>: no visible global function definition for
  'predict'
Undefined global functions or variables:
  coef flush.console mclapply predict quantile sd
Consider adding
  importFrom("stats", "coef", "predict", "quantile", "sd")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Running examples in 'RSMET-Ex.R' failed
The error most likely occurred in:

> ### Name: meteofranceSynop
> ### Title: SYNOP Weather Data in France
> ### Aliases: meteofranceSynop
> 
> ### ** Examples
> 
>  
> 
> library(ggmap)
Loading required package: ggplot2
> data(meteofranceSynop)
> 
> 
> 
> 
> data=meteofranceSynop[meteofranceSynop$timestamp==meteofranceSynop$timestamp[250],]
> 
> 
> 
> map <- get_map(location ="France", zoom = 6)
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=France&zoom=6&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=France&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "France"
Error in data.frame(ll.lat = ll[1], ll.lon = ll[2], ur.lat = ur[1], ur.lon = ur[2]) : 
  arguments imply differing number of rows: 0, 1
Calls: get_map -> get_googlemap -> data.frame
Execution halted
negbin.pow : negbin.disp: no visible global function definition for
  'rpois'
negbin.pow : negbin.disp: no visible global function definition for
  'rnbinom'
negbin.pow : inner.fcn: no visible global function definition for
  'na.omit'
negbin.pow : inner.fcn: no visible global function definition for
  'quantile'
negbin.pow: no visible global function definition for 'txtProgressBar'
negbin.pow: no visible global function definition for
  'setTxtProgressBar'
poiss.pow : inner.fcn: no visible global function definition for
  'rpois'
poiss.pow : inner.fcn: no visible global function definition for
  'quantile'
poiss.pow: no visible global function definition for 'txtProgressBar'
poiss.pow: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  na.omit quantile rnbinom rpois setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "quantile", "rnbinom", "rpois")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  17.2Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
rbing.O2: no visible global function definition for 'runif'
rbing.O2: no visible global function definition for 'rbeta'
rbing.O2: no visible global function definition for 'rbinom'
rbing.Op: no visible global function definition for 'rnorm'
rbing.Op: no visible global function definition for 'rbinom'
rbing.Op: no visible global function definition for 'runif'
rbmf.O2: no visible global function definition for 'runif'
rmf.matrix: no visible global function definition for 'runif'
rmf.vector: no visible global function definition for 'rnorm'
rmf.vector: no visible global function definition for 'rbinom'
rustiefel: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rbeta rbinom rnorm runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rnorm", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: 'plyr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
RStorm: no visible global function definition for 'alply'
Undefined global functions or variables:
  alply
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R Under development (unstable) (2017-12-30 r73992)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6002) Service Pack 2

Matrix products: default

locale:
[1] LC_COLLATE=C                 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=C                LC_NUMERIC=C                
[5] LC_TIME=C                   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RSVGTipsDevice_1.0-7

loaded via a namespace (and not attached):
[1] compiler_3.5.0
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: Shapes and Points, Tooltips are Title + 1 Line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    Lib  11.6Mb
Math.Sym: no visible binding for global variable 'transtab'
jythonStart: no visible global function definition for '.jinit'
jythonStart: no visible global function definition for '.jnew'
jythonStart: no visible binding for global variable '.Jython'
sympy: no visible binding for global variable '.Jython'
sympy: no visible global function definition for '.jstrVal'
sympyStart: no visible binding for global variable '.Jython'
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab
barplot.rtconnect: no visible global function definition for 'rainbow'
barplot.rtconnect: no visible global function definition for 'text'
plot.rtconnect: no visible global function definition for 'par'
plot.rtconnect: no visible global function definition for 'plot'
plot.rtconnect: no visible global function definition for 'axis.Date'
rtconnect: no visible global function definition for 'read.table'
Undefined global functions or variables:
  axis.Date par plot rainbow read.table text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis.Date", "par", "plot", "text")
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
classify_model: no visible global function definition for 'predict'
cross_validate: no visible global function definition for 'predict'
read_data: no visible global function definition for 'read.csv'
read_data: no visible global function definition for 'read.delim'
Undefined global functions or variables:
  predict read.csv read.delim
Consider adding
  importFrom("stats", "predict")
  importFrom("utils", "read.csv", "read.delim")
to your NAMESPACE file.
plotGLCM: no visible global function definition for 'plot'
plotGLCM: no visible global function definition for 'points'
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
.forest.plot: no visible global function definition for 'par'
.forest.plot: no visible global function definition for 'plot'
.forest.plot: no visible global function definition for 'abline'
.forest.plot: no visible global function definition for 'arrows'
.forest.plot: no visible global function definition for 'points'
.forest.plot.scale: no visible global function definition for 'par'
.forest.plot.scale: no visible global function definition for 'plot'
.forest.plot.scale: no visible global function definition for 'axTicks'
.forest.plot.scale : <anonymous>: no visible global function definition
  for 'lines'
.forest.plot.scale: no visible global function definition for 'lines'
.forest.plot.scale: no visible global function definition for 'text'
.rtf.plot: no visible global function definition for 'png'
.rtf.plot: no visible global function definition for 'dev.off'
.rtf.trellis.object: no visible global function definition for 'png'
.rtf.trellis.object: no visible global function definition for
  'dev.off'
addSessionInfo.RTF: no visible global function definition for
  'sessionInfo'
Undefined global functions or variables:
  abline arrows axTicks dev.off lines par plot png points sessionInfo
  text
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "arrows", "axTicks", "lines", "par",
             "plot", "points", "text")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       1.8Mb
    projects   2.3Mb
File 'rtop/libs/i386/rtop.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'vred.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'vred.o'
File 'rtop/libs/x64/rtop.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'vred.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'vred.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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   2.1Mb
Packages in Depends field not imported from:
  'Runuran' 'cairoDevice' 'gWidgets' 'gWidgetsRGtk2' 'rvgtest'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'utils:::.getHelpFile'
  See the note in ?`:::` about the use of this operator.
Running examples in 'RunuranGUI-Ex.R' failed
The error most likely occurred in:

> ### Name: unuran.gui
> ### Title: A GUI for the UNU.RAN random variate generators.
> ### Aliases: unuran.gui
> ### Keywords: distribution datagen
> 
> ### ** Examples
> 
> ## start GUI to Runuran random number generator
> unuran.gui()
Error in unclass(x) : cannot unclass an external pointer
Calls: unuran.gui ... .delete -> .delete -> .delete -> ==.RGtkObject -> identical
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
HapMendlianCheck: no visible global function definition for
  'write.table'
rvPDT.test.sub: no visible global function definition for 'pnorm'
whap.prehap: no visible global function definition for 'write.table'
whap.prehap: no visible global function definition for 'read.table'
Undefined global functions or variables:
  pnorm read.table write.table
Consider adding
  importFrom("stats", "pnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
'library' or 'require' call to 'pixmap' which was already attached by Depends.
  Please remove these calls from your code.
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  'par'
rvideopoker : showBack: no visible global function definition for
  'title'
rvideopoker : showCardsInitially: no visible global function definition
  for 'title'
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Package suggested but not available for checking: 'gpuR'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    include   5.3Mb
S3 methods shown with full name in documentation object 'cbind.rv':
  'cbind.rv' 'rbind.rv'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
lc_TDT: no visible global function definition for 'pchisq'
rvTDT: no visible global function definition for 'dbeta'
Undefined global functions or variables:
  dbeta pchisq
Consider adding
  importFrom("stats", "dbeta", "pchisq")
to your NAMESPACE file.
LASSO: no visible global function definition for 'lm'
LASSO: no visible global function definition for 'anova'
LASSO: no visible global function definition for 'glm'
LASSO: no visible global function definition for 'pchisq'
LASSO : <anonymous>: no visible global function definition for
  'extractAIC'
PCR : <anonymous>: no visible global function definition for 'cor'
PLS : <anonymous>: no visible global function definition for 'cor'
RR : RRscore: no visible binding for global variable 'sd'
SPLS: no visible global function definition for 'lm'
SPLS: no visible global function definition for 'anova'
SPLS : <anonymous>: no visible global function definition for
  'extractAIC'
VTWOD : getScores: no visible global function definition for 'sd'
VTWOD : getScores: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  anova cor extractAIC glm lm pchisq pnorm sd
Consider adding
  importFrom("stats", "anova", "cor", "extractAIC", "glm", "lm",
             "pchisq", "pnorm", "sd")
to your NAMESPACE file.
check_ISO_code: no visible binding for global variable 'NoAm_country'
check_ISO_code: no visible binding for global variable 'SoAm_country'
check_ISO_code: no visible binding for global variable 'Oceana_country'
check_ISO_code: no visible binding for global variable 'Africa_country'
check_ISO_code: no visible binding for global variable 'Asia_country'
check_ISO_code: no visible binding for global variable 'Eur_country'
climate_map: no visible binding for global variable 'data'
date_correct: no visible global function definition for 'tail'
Undefined global functions or variables:
  Africa_country Asia_country Eur_country NoAm_country Oceana_country
  SoAm_country data tail
Consider adding
  importFrom("utils", "data", "tail")
to your NAMESPACE file.
RWBP.default: no visible global function definition for 'na.omit'
RWBP.default: no visible global function definition for 'kmeans'
RWBP.formula: no visible global function definition for 'model.extract'
plot.RWBP: no visible global function definition for 'plot'
predict.RWBP: no visible global function definition for 'head'
Undefined global functions or variables:
  head kmeans model.extract na.omit plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "kmeans", "model.extract", "na.omit")
  importFrom("utils", "head")
to your NAMESPACE file.
weblogo: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    java  10.6Mb
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
getcolors: no visible global function definition for 'rainbow'
lines.rief: no visible global function definition for 'lines.default'
lines.riif: no visible global function definition for 'lines.default'
lines.rirf: no visible global function definition for 'lines.default'
plot.ifile: no visible global function definition for 'plot'
plot.rief: no visible global function definition for 'plot.default'
plot.rief: no visible global function definition for 'lines'
plot.riif: no visible global function definition for 'plot.default'
plot.riif: no visible global function definition for 'lines'
plot.rirf: no visible global function definition for 'plot.default'
plot.rirf: no visible global function definition for 'lines'
plot.rtef: no visible global function definition for 'plot.default'
plot.rtif: no visible global function definition for 'plot.default'
plot.rtrf: no visible global function definition for 'plot.default'
read.ifile: no visible global function definition for 'read.table'
read.pfile: no visible global function definition for 'read.table'
write.wdat: no visible global function definition for 'write.table'
Undefined global functions or variables:
  lines lines.default plot plot.default rainbow read.table write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "lines.default", "plot",
             "plot.default")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
.dwt: no visible global function definition for 'median'
.udwt: no visible global function definition for 'median'
plotSignalTransformation: no visible global function definition for
  'plot'
plotSignalTransformation: no visible global function definition for
  'box'
plotSignalTransformation: no visible global function definition for
  'axis'
plotSignalTransformation: no visible global function definition for
  'lines'
plotSignalTransformation: no visible global function definition for
  'legend'
Undefined global functions or variables:
  axis box legend lines median plot
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot")
  importFrom("stats", "median")
to your NAMESPACE file.
Analyze: no visible global function definition for 'runif'
Analyze: no visible global function definition for 'mcmc'
Analyze: no visible global function definition for 'varnames<-'
AnalyzeWithExitPoll: no visible global function definition for 'runif'
AnalyzeWithExitPoll: no visible global function definition for 'mcmc'
AnalyzeWithExitPoll: no visible global function definition for
  'varnames<-'
Tune: no visible global function definition for 'runif'
TuneWithExitPoll: no visible global function definition for 'runif'
form.mcmc.object: no visible global function definition for
  'varnames<-'
gendata.ep : rdirichlet: no visible global function definition for
  'rgamma'
gendata.ep : rwish: no visible global function definition for 'rchisq'
gendata.ep : rwish: no visible global function definition for 'rnorm'
gendata.ep: no visible global function definition for 'rpois'
gendata.ep: no visible global function definition for 'runif'
gendata.ep: no visible global function definition for 'rmultinom'
gendata.ep: no visible global function definition for 'cov2cor'
gq.summary: no visible global function definition for 'mcmc.list'
gq.summary: no visible global function definition for 'mcmc'
gq_diagnostics: no visible global function definition for 'mcmc.list'
gq_diagnostics: no visible global function definition for 'mcmc'
gq_diagnostics: no visible global function definition for 'gelman.diag'
gq_diagnostics: no visible global function definition for 'geweke.diag'
gq_diagnostics: no visible global function definition for 'heidel.diag'
gq_diagnostics: no visible global function definition for
  'autocorr.diag'
Undefined global functions or variables:
  autocorr.diag cov2cor gelman.diag geweke.diag heidel.diag mcmc
  mcmc.list rchisq rgamma rmultinom rnorm rpois runif varnames<-
Consider adding
  importFrom("stats", "cov2cor", "rchisq", "rgamma", "rmultinom",
             "rnorm", "rpois", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: 'SnakeCharmR'
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/Ryacas.Rcheck/00install.out' for details.
'library' or 'require' call to 'vcd' 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:
  'foreign' 'ggplot2' 'grid' 'psych'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'foreign:::adQuote'
  See the note in ?`:::` about the use of this operator.
.onAttach: no visible global function definition for 'winMenuAdd'
.onAttach: no visible global function definition for 'winMenuAddItem'
calc.hist.breaks: no visible global function definition for
  'nclass.Sturges'
calc.hist.breaks: no visible global function definition for 'nclass.FD'
calc.hist.breaks: no visible global function definition for
  'nclass.scott'
check.class: no visible global function definition for 'as.formula'
gtkColorSelectionForPlotGetColor: no visible global function definition
  for 'rgb'
gtkColorSelectionWidgetNew: no visible global function definition for
  'colors'
gtkFileChooserDialogFilteredActivate: no visible binding for global
  variable 'theme_grey'
localize: no visible global function definition for 'localeToCharset'
summary.CrossTable : twoDimTable: no visible global function definition
  for 'addmargins'
summary.CrossTable: no visible global function definition for
  'assocstats'
write.spss: no visible global function definition for 'write.table'
write.stata: no visible global function definition for 'write.table'
Undefined global functions or variables:
  addmargins as.formula assocstats colors localeToCharset nclass.FD
  nclass.Sturges nclass.scott rgb theme_grey winMenuAdd winMenuAddItem
  write.table
Consider adding
  importFrom("grDevices", "colors", "nclass.FD", "nclass.Sturges",
             "nclass.scott", "rgb")
  importFrom("stats", "addmargins", "as.formula")
  importFrom("utils", "localeToCharset", "winMenuAdd", "winMenuAddItem",
             "write.table")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    sample_data   3.2Mb
calculate.summary: no visible global function definition for 'sd'
detect.saccades: no visible global function definition for 'median'
diagnostic.plot: no visible global function definition for 'dev.new'
diagnostic.plot: no visible global function definition for 'par'
diagnostic.plot: no visible global function definition for 'recordPlot'
diagnostic.plot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.new dev.off median par recordPlot sd
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "recordPlot")
  importFrom("graphics", "par")
  importFrom("stats", "median", "sd")
to your NAMESPACE file.
eblupDyn: no visible global function definition for 'model.frame'
eblupDyn: no visible global function definition for 'model.matrix'
eblupDyn: no visible global function definition for 'pnorm'
eblupRY: no visible global function definition for 'model.frame'
eblupRY: no visible global function definition for 'model.matrix'
eblupRY: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  model.frame model.matrix pnorm
Consider adding
  importFrom("stats", "model.frame", "model.matrix", "pnorm")
to your NAMESPACE file.
SAENET.nnet: no visible global function definition for 'as.formula'
SAENET.nnet: no visible global function definition for 'rnorm'
SAENET.train: no visible global function definition for 'predict'
Undefined global functions or variables:
  as.formula predict rnorm
Consider adding
  importFrom("stats", "as.formula", "predict", "rnorm")
to your NAMESPACE file.
fit.saery.AR1: no visible global function definition for 'qnorm'
fit.saery.MA1: no visible global function definition for 'qnorm'
fit.saery.indep: no visible global function definition for 'qnorm'
mse.saery.boot.AR1.typeI: no visible global function definition for
  'rnorm'
mse.saery.boot.AR1.typeI: no visible global function definition for
  'write.table'
mse.saery.boot.AR1.typeII: no visible global function definition for
  'rnorm'
mse.saery.boot.AR1.typeII: no visible global function definition for
  'write.table'
mse.saery.boot.MA1.typeI: no visible global function definition for
  'rnorm'
mse.saery.boot.MA1.typeI: no visible global function definition for
  'write.table'
mse.saery.boot.MA1.typeII: no visible global function definition for
  'rnorm'
mse.saery.boot.MA1.typeII: no visible global function definition for
  'write.table'
plot.saery: no visible global function definition for 'devAskNewPage'
plot.saery: no visible global function definition for 'par'
plot.saery: no visible global function definition for 'plot'
plot.saery: no visible global function definition for 'abline'
plot.saery: no visible global function definition for 'title'
plot.saery: no visible global function definition for 'axis'
plot.saery: no visible global function definition for 'lines'
plot.saery: no visible global function definition for 'legend'
pvalue: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline axis devAskNewPage legend lines par plot pnorm qnorm rnorm
  title write.table
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "pnorm", "qnorm", "rnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package in Depends field not imported from: 'lpSolveAPI'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glm: no visible binding for global variable 'gaussian'
glm: no visible global function definition for 'glm.control'
glm: no visible global function definition for 'model.response'
glm: no visible global function definition for 'is.empty.model'
glm: no visible global function definition for 'model.matrix'
glm: no visible global function definition for 'model.weights'
glm: no visible global function definition for 'model.offset'
glm: no visible global function definition for 'model.extract'
glm: no visible global function definition for 'glm.fit'
glm: no visible global function definition for '.getXlevels'
separator: no visible global function definition for 'make.lp'
separator: no visible global function definition for 'set.column'
separator: no visible global function definition for 'set.rhs'
separator: no visible global function definition for 'set.constr.type'
separator: no visible global function definition for 'set.objfn'
separator: no visible global function definition for 'set.bounds'
separator: no visible global function definition for 'lp.control'
separator: no visible global function definition for 'get.variables'
separator: no visible global function definition for 'set.basis'
separator: no visible global function definition for
  'get.dual.solution'
Undefined global functions or variables:
  .getXlevels gaussian get.dual.solution get.variables glm.control
  glm.fit is.empty.model lp.control make.lp model.extract model.matrix
  model.offset model.response model.weights set.basis set.bounds
  set.column set.constr.type set.objfn set.rhs
Consider adding
  importFrom("stats", ".getXlevels", "gaussian", "glm.control",
             "glm.fit", "is.empty.model", "model.extract",
             "model.matrix", "model.offset", "model.response",
             "model.weights")
to your NAMESPACE file.
plot.safidesign: no visible global function definition for 'par'
plot.safidesign: no visible global function definition for 'matplot'
plot.safidesign: no visible global function definition for 'axis'
plot.safimodel : plot.coef: no visible global function definition for
  'colorRampPalette'
plot.safimodel : plot.coef: no visible global function definition for
  'barplot'
plot.safimodel : plot.coef: no visible global function definition for
  'axis'
plot.safimodel : plot.coef: no visible global function definition for
  'abline'
plot.safimodel : plot.coef: no visible global function definition for
  'box'
plot.safimodel: no visible global function definition for 'par'
safiModel: no visible global function definition for 'lm'
Undefined global functions or variables:
  abline axis barplot box colorRampPalette lm matplot par
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "axis", "barplot", "box", "matplot",
             "par")
  importFrom("stats", "lm")
to your NAMESPACE file.
Running examples in 'SAGA-Ex.R' failed
The error most likely occurred in:

> ### Name: plot
> ### Title: provides a custom plot of a genarch object
> ### Aliases: plot.genarch
> 
> ### ** Examples
> 
> data(PH)
> results <- AnalyzeCrossesMM(PH)
The following composite effects cannot be estimated with the line 
means available because they estimate identical quantities to 
lower order effects: 
CaAd

The composite genetic effects that will be tested are: 
 Aa, Ad, Ca, Mea, Med, AaAa, AaAd, AdAd, CaAa 

Generating Models....
 50
 100
 150
 200
 250
26 models were removed due to high covariances 
or linear relationships between predictor variables.  
The remaining 229 models have been evaluated.


AICc weights were used to select the minimum number of models whose weights sum 
to greater than 95% this model set includes 12 model(s)
> plot(results)
Error in if (maxval < 0) maxval <- 0 : 
  missing value where TRUE/FALSE needed
Calls: plot -> plot.genarch
Execution halted
Package suggested but not available for checking: 'synchronicity'
propdiff.acc: no visible global function definition for 'rbeta'
propdiff.acc: no visible global function definition for 'rbinom'
propdiff.acc: no visible global function definition for 'pbeta'
propdiff.alc: no visible global function definition for 'rbeta'
propdiff.alc: no visible global function definition for 'rbinom'
propdiff.alc: no visible global function definition for 'qbeta'
propdiff.freq: no visible global function definition for 'qnorm'
propdiff.mblacc: no visible global function definition for 'rbeta'
propdiff.mblacc: no visible global function definition for 'rbinom'
propdiff.mblacc: no visible global function definition for 'pbeta'
propdiff.mblalc: no visible global function definition for 'rbeta'
propdiff.mblalc: no visible global function definition for 'rbinom'
propdiff.mblalc: no visible global function definition for 'qbeta'
propdiff.mblmodwoc: no visible global function definition for 'qchisq'
propdiff.mblmodwoc: no visible global function definition for 'pbeta'
propdiff.mblwoc: no visible global function definition for 'pbeta'
propdiff.modwoc: no visible global function definition for 'qchisq'
propdiff.modwoc: no visible global function definition for 'pbeta'
propdiff.woc: no visible global function definition for 'pbeta'
Undefined global functions or variables:
  pbeta qbeta qchisq qnorm rbeta rbinom
Consider adding
  importFrom("stats", "pbeta", "qbeta", "qchisq", "qnorm", "rbeta",
             "rbinom")
to your NAMESPACE file.
plot.samEL: no visible global function definition for 'matplot'
plot.samHL: no visible global function definition for 'matplot'
plot.samLL: no visible global function definition for 'matplot'
plot.samQL: no visible global function definition for 'matplot'
predict.samEL: no visible global function definition for 'ns'
predict.samHL: no visible global function definition for 'ns'
predict.samLL: no visible global function definition for 'ns'
predict.samQL: no visible global function definition for 'ns'
samEL: no visible global function definition for 'ns'
samHL: no visible global function definition for 'ns'
samHL: no visible binding for global variable 'median'
samLL: no visible global function definition for 'ns'
samQL: no visible global function definition for 'ns'
Undefined global functions or variables:
  matplot median ns
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "median")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'impute' 'matrixStats'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'impute' 'matrixStats'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
S3 methods shown with full name in documentation object 'samr-internal':
  'plot.SAMoutput' 'print.SAMoutput'

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.
GraphBinaryForestPlot: no visible global function definition for
  'abline'
GraphBinaryForestPlot: no visible global function definition for 'text'
GraphContinuousForestPlot: no visible global function definition for
  'abline'
GraphContinuousForestPlot: no visible global function definition for
  'text'
ImputeBinaryEvents: no visible global function definition for 'rbinom'
ImputeSMD: no visible global function definition for 'rnorm'
funnelplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline rbinom rnorm text
Consider adding
  importFrom("graphics", "abline", "text")
  importFrom("stats", "rbinom", "rnorm")
to your NAMESPACE file.
generate.sample.core: no visible global function definition for
  'predict'
mdh: no visible global function definition for 'model.frame'
mdh: no visible binding for global variable 'na.fail'
mdh: no visible global function definition for '.getXlevels'
mdh: no visible global function definition for 'quantile'
mdh: no visible global function definition for 'hist'
predict.mdh: no visible global function definition for 'model.frame'
samur: no visible global function definition for 'predict'
Undefined global functions or variables:
  .getXlevels hist model.frame na.fail predict quantile
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", ".getXlevels", "model.frame", "na.fail", "predict",
             "quantile")
to your NAMESPACE file.
download.sas7bdat.sources : <anonymous>: no visible global function
  definition for 'download.file'
generate.sas7bdat.source: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
parse.SAScii: no visible binding for global variable 'end'
parse.SAScii: no visible binding for global variable 'start'
read.SAScii: no visible global function definition for 'download.file'
read.SAScii: no visible global function definition for 'unzip'
read.SAScii: no visible global function definition for 'read.fwf'
read.SAScii: no visible global function definition for 'capture.output'
Undefined global functions or variables:
  capture.output download.file end read.fwf start unzip
Consider adding
  importFrom("stats", "end", "start")
  importFrom("utils", "capture.output", "download.file", "read.fwf",
             "unzip")
to your NAMESPACE file.
SASPECT: no visible global function definition for 'dbinom'
my.SOnePro: missing arguments not allowed in calls to 'c'
my.ttest: no visible global function definition for 'var'
Undefined global functions or variables:
  dbinom var
Consider adding
  importFrom("stats", "dbinom", "var")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/SASxport.Rcheck/00install.out' for details.
loads: no visible global function definition for 'untar'
saves: no visible global function definition for 'tar'
Undefined global functions or variables:
  tar untar
Consider adding
  importFrom("utils", "tar", "untar")
to your NAMESPACE file.
clogistCalc: no visible global function definition for 'model.matrix'
clogistCalc: no visible global function definition for 'glm.fit'
clogistCalc: no visible global function definition for 'binomial'
clogistInfo : all.not.equal: no visible global function definition for
  'var'
geeUOmega: no visible global function definition for 'model.extract'
geeUOmega: no visible global function definition for 'model.matrix'
geeUOmega: no visible binding for global variable 'contrasts'
mgee: no visible binding for global variable 'gaussian'
sawsCalc: no visible global function definition for 'pf'
sawsCalc: no visible global function definition for 'qt'
Undefined global functions or variables:
  binomial contrasts gaussian glm.fit model.extract model.matrix pf qt
  var
Consider adding
  importFrom("stats", "binomial", "contrasts", "gaussian", "glm.fit",
             "model.extract", "model.matrix", "pf", "qt", "var")
to your NAMESPACE file.
File which contains pragma(s) suppressing important diagnostics:
  'src/Eigen/src/Core/arch/SSE/Complex.h'
File which contains pragma(s) suppressing diagnostics:
  'src/Eigen/src/Core/util/DisableStupidWarnings.h'
K: no visible global function definition for 'dnorm'
sBF: no visible global function definition for 'density'
sBF: no visible global function definition for 'txtProgressBar'
sBF: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  density dnorm setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "density", "dnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
plot.psgc: no visible global function definition for 'par'
plot.psgc: no visible global function definition for 'barplot'
plot.psgc: no visible global function definition for 'hist'
plotci.sA: no visible global function definition for 'par'
plotci.sA: no visible global function definition for 'plot'
plotci.sA: no visible global function definition for 'points'
plotci.sA: no visible global function definition for 'segments'
plotci.sA: no visible global function definition for 'abline'
plotci.sA: no visible global function definition for 'axis'
qM.sM: no visible binding for global variable 'quantile'
rwish: no visible global function definition for 'rnorm'
sbgcop.mcmc: no visible global function definition for 'qnorm'
sbgcop.mcmc: no visible global function definition for 'rnorm'
sbgcop.mcmc: no visible global function definition for 'cov'
sbgcop.mcmc: no visible global function definition for 'runif'
sbgcop.mcmc: no visible global function definition for 'pnorm'
sbgcop.mcmc: no visible global function definition for 'quantile'
summary.psgc: no visible global function definition for 'acf'
Undefined global functions or variables:
  abline acf axis barplot cov hist par plot pnorm points qnorm quantile
  rnorm runif segments
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "hist", "par",
             "plot", "points", "segments")
  importFrom("stats", "acf", "cov", "pnorm", "qnorm", "quantile",
             "rnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  d:/Compiler/gcc-4.9.3/local330/include/gmp-x64.h:140:23: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/Compiler/gcc-4.9.3/local330/include/gmp-x64.h:141:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/sbrl.Rcheck/00install.out' for details.
fitSBSA: no visible binding for global variable 'var'
fitSBSA: no visible global function definition for 'var'
fitSBSA: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
ChooseBest: no visible global function definition for 'head'
GetScores: no visible global function definition for 'write.table'
ReportTable: no visible binding for global variable 'sd'
ReportTable: no visible global function definition for 'write.table'
Undefined global functions or variables:
  head sd write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "head", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'lars'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
lse: no visible global function definition for 'lm'
predict.scalreg: no visible global function definition for 'fitted'
slassoEst: no visible global function definition for 'qnorm'
slassoEst: no visible global function definition for 'lars'
slassoEst: no visible global function definition for 'predict.lars'
Undefined global functions or variables:
  fitted lars lm predict.lars qnorm
Consider adding
  importFrom("stats", "fitted", "lm", "qnorm")
to your NAMESPACE file.
Found the following significant warnings:
  BGPscan.h:63:10: warning: 'BGPscan::m_beta_alt' will be initialized after [-Wreorder]
  BGPscan.h:49:15: warning:   'arma::uword BGPscan::m_inc_idx' [-Wreorder]
  BGPscan.h:96:8: warning:   when initialized here [-Wreorder]
  USTscan.h:28:15: warning: 'USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_counts' will be initialized after [-Wreorder]
  USTscan.h:23:15: warning:   'arma::uword USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_num_locs' [-Wreorder]
  USTscan.h:62:8: warning:   when initialized here [-Wreorder]
  USTscan.h:30:15: warning: 'USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_zone_lengths' will be initialized after [-Wreorder]
  USTscan.h:26:15: warning:   'bool USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_store_everything' [-Wreorder]
See 'd:/Rcompile/CRANpkg/local/3.5/scanstatistics.Rcheck/00install.out' for details.
plot.scair: no visible global function definition for 'par'
plot.scair: no visible global function definition for 'plot'
plot.scair: no visible global function definition for 'points'
plot.scar: no visible global function definition for 'par'
plot.scar: no visible global function definition for 'plot'
plot.scar: no visible global function definition for 'points'
predict.scair: no visible global function definition for 'approx'
predict.scar: no visible global function definition for 'approx'
scair: no visible global function definition for 'gaussian'
scair: no visible global function definition for 'runif'
scair: no visible global function definition for 'rnorm'
scar: no visible global function definition for 'gaussian'
scar: no visible global function definition for 'glm.fit'
scar: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx gaussian glm.fit par plot points rnorm runif
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "approx", "gaussian", "glm.fit", "rnorm", "runif")
to your NAMESPACE file.
prime.factor: no visible global function definition for 'data'
prime.factor: no visible binding for global variable 'primlist'
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
futuresplot: no visible global function definition for 'rainbow'
plot.schwartz2f.fit: no visible global function definition for
  'colorRampPalette'
plot.schwartz2f.fit: no visible global function definition for
  'rainbow'
plot,schwartz2f.fit-missing: no visible global function definition for
  'colorRampPalette'
plot,schwartz2f.fit-missing: no visible global function definition for
  'rainbow'
Undefined global functions or variables:
  colorRampPalette rainbow
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
to your NAMESPACE file.
'library' or 'require' call to 'QUIC' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
scio.cv: no visible global function definition for 'cov'
scio.refit: no visible global function definition for 'QUIC'
Undefined global functions or variables:
  QUIC cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
score.GGUM: no visible global function definition for 'dnorm'
score.GGUM: no visible global function definition for 'hist'
score.GGUM: no visible global function definition for 'write.table'
Undefined global functions or variables:
  dnorm hist write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
CreatePssm: no visible binding for global variable 'training'
Undefined global functions or variables:
  training
bdecomp : <anonymous>: no visible global function definition for 'var'
betafam: no visible global function definition for 'integrate'
calcscore.formula: no visible global function definition for
  'model.response'
plotscore: no visible binding for global variable 'plot'
plotscore: no visible global function definition for 'lines'
Undefined global functions or variables:
  integrate lines model.response plot var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "integrate", "model.response", "var")
to your NAMESPACE file.
plot.SK: no visible global function definition for 'plot'
plot.SK: no visible global function definition for 'segments'
plot.SK: no visible global function definition for 'axis'
plot.SK: no visible global function definition for 'mtext'
Undefined global functions or variables:
  axis mtext plot segments
Consider adding
  importFrom("graphics", "axis", "mtext", "plot", "segments")
to your NAMESPACE file.
Newsboy: no visible global function definition for 'qnorm'
Newsboy: no visible global function definition for 'dnorm'
Newsboy: no visible global function definition for 'pnorm'
SCperf: no visible global function definition for 'ARMAtoMA'
SCperf: no visible global function definition for 'qnorm'
SSL: no visible global function definition for 'qnorm'
SSL: no visible global function definition for 'ARMAtoMA'
Undefined global functions or variables:
  ARMAtoMA dnorm pnorm qnorm
Consider adding
  importFrom("stats", "ARMAtoMA", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'RCurl' 'XML'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RCurl' 'XML'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
scrape: no visible global function definition for 'getURLAsynchronous'
scrape: no visible global function definition for 'runif'
scrape: no visible global function definition for 'capture.output'
scrape: no visible binding for global variable 'xmlParse'
scrape: no visible binding for global variable 'htmlParse'
Undefined global functions or variables:
  capture.output getURLAsynchronous htmlParse runif xmlParse
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'oligoClasses'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Files which contain pragma(s) suppressing diagnostics:
  'src/scrm/macros.h' 'src/scrm/model.h'
lahiri.design: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
estimateTimeToComputeTargetDefinition: no visible global function
  definition for 'flush.console'
estimateTimeToComputeTargetDefinition: no visible global function
  definition for 'combn'
initialize,sdcTargetDefinitionClass: no visible global function
  definition for 'flush.console'
initialize,sdcTargetDefinitionClass: no visible global function
  definition for 'combn'
initialize,sdcTargetDefinitionClass: no visible global function
  definition for 'quantile'
initialize,sdcTargetMatrixClass: no visible global function definition
  for 'flush.console'
Undefined global functions or variables:
  combn flush.console quantile
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "combn", "flush.console")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: sp
sdm 1.0-41 (2017-07-26)
rgdal: version: 1.2-16, (SVN revision 701)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.0, released 2017/04/28
 Path to GDAL shared files: D:/temp/Rtmp2J8d24/RLIBS_211a8153e7219/rgdal/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: D:/temp/Rtmp2J8d24/RLIBS_211a8153e7219/rgdal/proj
 Linking to sp version: 1.2-6 
Loading required package: dismo
Loading required package: mgcv
Quitting from lines 45-52 (quick_sdm.Rmd) 
Error: processing vignette 'quick_sdm.Rmd' failed with diagnostics:
fitFunction cannot be identified!
Execution halted
'library' or 'require' calls in package code:
  'raster' 'sp'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
sealasso: no visible global function definition for 'lars'
weight.calc: no visible global function definition for 'lars'
Undefined global functions or variables:
  lars
adx: no visible global function definition for 'abline'
adx: no visible global function definition for 'legend'
dx: no visible global function definition for 'abline'
dx: no visible global function definition for 'legend'
maxd: no visible global function definition for 'abline'
maxd: no visible global function definition for 'legend'
pc: no visible global function definition for 'rainbow'
pc: no visible global function definition for 'plot'
pc: no visible global function definition for 'abline'
pc: no visible global function definition for 'legend'
pc: no visible global function definition for 'points'
pcu: no visible global function definition for 'rainbow'
pcu: no visible global function definition for 'plot'
pcu: no visible global function definition for 'abline'
pcu: no visible global function definition for 'legend'
pcu: no visible global function definition for 'points'
rmsd: no visible global function definition for 'abline'
rmsd: no visible global function definition for 'legend'
rsd: no visible global function definition for 'abline'
rsd: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend plot points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "plot", "points")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'NADA' 'lubridate' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package in Depends field not imported from: 'JM'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SEchart: no visible global function definition for 'plot'
SEchart: no visible global function definition for 'rect'
SEchart: no visible global function definition for 'par'
SEchart: no visible global function definition for 'grid'
SEchart: no visible global function definition for 'axis'
SEchart: no visible global function definition for 'text'
SEchart: no visible global function definition for 'lines'
SEchart: no visible global function definition for 'heat.colors'
SEchart: no visible global function definition for 'topo.colors'
SEchart: no visible global function definition for 'cm.colors'
SEchart: no visible global function definition for 'terrain.colors'
SEchart: no visible global function definition for 'gray.colors'
SEchart: no visible global function definition for 'rainbow'
SEchart: no visible global function definition for 'points'
SEchart: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis cm.colors gray.colors grid heat.colors legend lines par plot
  points rainbow rect terrain.colors text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "gray.colors", "heat.colors",
             "rainbow", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "plot", "points", "rect", "text")
to your NAMESPACE file.
fdc2s: no visible global function definition for 'lm'
fdc3s: no visible global function definition for 'lm'
fds2s: no visible global function definition for 'lm'
fds3s: no visible global function definition for 'lm'
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
.read.SeerStatTXT: no visible global function definition for
  'read.table'
.write.SeerStatTXT: 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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
'library' or 'require' calls in package code:
  'rgdal' 'spdep' 'spgrass6'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.use.spgrass6: no visible global function definition for 'listw2mat'
.use.spgrass6: no visible global function definition for 'sn2listw'
conprof: no visible global function definition for 'axis'
conprof: no visible global function definition for 'lines'
isp: no visible global function definition for 'combn'
points.SegLocal: no visible global function definition for 'points'
Undefined global functions or variables:
  axis combn lines listw2mat points sn2listw
Consider adding
  importFrom("graphics", "axis", "lines", "points")
  importFrom("utils", "combn")
to your NAMESPACE file.
get.infectiousness: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.xml_missing', '[.xml_nodeset', '[[.xml_missing', 'xml_attr<-.xml_missing', 'xml_attr<-.xml_node', 'xml_attr<-.xml_nodeset', 'xml_attrs<-.xml_missing', 'xml_attrs<-.xml_node', 'xml_attrs<-.xml_nodeset', 'xml_name<-.xml_missing', 'xml_name<-.xml_node', 'xml_name<-.xml_nodeset', 'xml_text<-.xml_missing', 'xml_text<-.xml_node', 'xml_text<-.xml_nodeset', 'as.character.xml_document', 'as.character.xml_missing', 'as.character.xml_node', 'as.character.xml_nodeset', 'as_list.xml_missing', 'as_list.xml_node', 'as_list.xml_nodeset', 'as_xml_document.character', 'as_xml_document.connection', 'as_xml_document.list', 'as_xml_document.raw', 'as_xml_document.response', 'as_xml_document.xml_document', 'as_xml_document.xml_node', 'as_xml_document.xml_nodeset', 'format.xml_node', 'is.na.xml_missing', 'is.na.xml_node', 'is.na.xml_nodeset', 'nodeset_apply.xml_document', 'nodeset_apply.xml_missing', 'nodeset_apply.xml_node', 'nodeset_apply.xml_nodeset', 'print.xml_document', 'print.xml_missing [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/selectr.Rcheck/00install.out' for details.
get_statistics_from_file: no visible global function definition for
  'read.csv'
glm_anova: no visible global function definition for 'aov'
glm_anova: no visible global function definition for 'glm'
glm_anova: no visible global function definition for 'gaussian'
glm_anova: no visible global function definition for 'anova'
glm_anova: no visible global function definition for 'quasipoisson'
glm_anova: no visible global function definition for 'sd'
glm_anova: no visible global function definition for 'p.adjust'
ttest_cohens_d: no visible global function definition for 't.test'
ttest_cohens_d: no visible global function definition for 'sd'
Undefined global functions or variables:
  anova aov gaussian glm p.adjust quasipoisson read.csv sd t.test
Consider adding
  importFrom("stats", "anova", "aov", "gaussian", "glm", "p.adjust",
             "quasipoisson", "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
getbinPost: no visible binding for global variable 'dbeta'
getbinPost: no visible binding for global variable 'pbeta'
getbinPost : fu: no visible global function definition for 'dbinom'
getbinPost : fu: no visible global function definition for 'predict'
getbinPost: no visible global function definition for 'integrate'
getbinPost: no visible global function definition for 'splinefun'
int.funct: no visible global function definition for 'integrate'
int.funct2: no visible global function definition for 'integrate'
min.abs: no visible global function definition for 'uniroot'
plot.SEL: no visible global function definition for 'plot'
print.SEL: no visible global function definition for 'integrate'
print.summary.SEL : foo1: no visible global function definition for
  'predict'
print.summary.SEL : foo2: no visible global function definition for
  'predict'
print.summary.SEL: no visible global function definition for
  'integrate'
quantSEL: no visible global function definition for 'predict'
quantSEL: no visible global function definition for 'splinefun'
rvSEL: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbeta dbinom integrate pbeta plot predict runif splinefun uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
Package in Depends field not imported from: 'sem'
  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:
  'datautils' 'irlba'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
computeKernel: no visible binding for global variable 'sd'
computeKernel: no visible global function definition for 'dist'
computeKernel: no visible global function definition for 'quantile'
computeProjectionFromKernel : <anonymous>: no visible global function
  definition for 'irlba'
distortions: no visible binding for global variable 'sd'
distortions: no visible global function definition for 'dist'
Undefined global functions or variables:
  dist irlba quantile sd
Consider adding
  importFrom("stats", "dist", "quantile", "sd")
to your NAMESPACE file.
ChiSquaredLRTest: no visible global function definition for 'na.omit'
ChiSquaredLRTest: no visible global function definition for 'cov'
ChiSquaredLRTest: no visible global function definition for 'dmvnorm'
ChiSquaredLRTest: no visible global function definition for 'pchisq'
NormalTheoryLRTest: no visible global function definition for 'na.omit'
NormalTheoryLRTest: no visible global function definition for 'cov'
NormalTheoryLRTest: no visible global function definition for 'dmvnorm'
NormalTheoryLRTest: no visible global function definition for 'sd'
NormalTheoryLRTest: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  cov dmvnorm na.omit pchisq pnorm sd
Consider adding
  importFrom("stats", "cov", "na.omit", "pchisq", "pnorm", "sd")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'XML' 'boot' 'sem'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  'boot:::const' 'stats:::AIC.logLik' 'stats:::BIC.logLik'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'addPath.plsm' 'endogenous' 'predecessors' 'qSquared' 'reorder'
  'resempls' 'residuals.sempls'
efficiencies.semsfa: no visible global function definition for 'dnorm'
efficiencies.semsfa: no visible global function definition for 'pnorm'
fan: no visible global function definition for 'pnorm'
plot.semsfa: no visible global function definition for 'hist'
plot.semsfa: no visible global function definition for 'plot'
plot.semsfa: no visible global function definition for 'density'
semsfa: no visible global function definition for 'residuals'
semsfa: no visible global function definition for 'loess'
semsfa: no visible global function definition for 'optimize'
semsfa: no visible global function definition for 'pnorm'
semsfa: no visible binding for global variable 'sd'
summary.semsfa: no visible global function definition for 'pt'
summary.semsfa: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  density dnorm hist loess optimize plot pnorm printCoefmat pt
  residuals sd
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "density", "dnorm", "loess", "optimize", "pnorm",
             "printCoefmat", "pt", "residuals", "sd")
to your NAMESPACE file.
.plot_attachment: no visible global function definition for 'dev.off'
.update_list: no visible global function definition for 'modifyList'
mime_part.data.frame: no visible global function definition for
  'write.table'
mime_part.ggplot: no visible binding for global variable 'pdf'
mime_part.matrix: no visible global function definition for
  'write.table'
mime_part.trellis: no visible binding for global variable 'pdf'
Undefined global functions or variables:
  dev.off modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
to your NAMESPACE file.
'library' or 'require' call to 'rtiff' which was already attached by Depends.
  Please remove these calls from your code.
gconv: no visible global function definition for 'convolve'
sens.analysis.aberrant.rank: no visible global function definition for
  'pnorm'
sens.analysis.mh: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  convolve pnorm
Consider adding
  importFrom("stats", "convolve", "pnorm")
to your NAMESPACE file.
mscorev: no visible global function definition for 'quantile'
senmwCI : funcCI: no visible global function definition for 'qnorm'
senmwCI : funcCI2: no visible global function definition for 'qnorm'
separable1k: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm quantile
Consider adding
  importFrom("stats", "pnorm", "qnorm", "quantile")
to your NAMESPACE file.
plot.sensitivity.2.0d: no visible global function definition for 'gray'
sensitivitySGD: no visible global function definition for 'tail'
sensitivitySGL: no visible global function definition for 'tail'
Undefined global functions or variables:
  gray tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("utils", "tail")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'cbind.Simulations':
  'cbind.Simulations'

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.
separationplot: no visible global function definition for 'dev.new'
separationplot: no visible global function definition for 'pdf'
separationplot: no visible global function definition for 'par'
separationplot: no visible global function definition for 'plot'
separationplot: no visible global function definition for 'title'
separationplot: no visible global function definition for 'segments'
separationplot: no visible global function definition for 'rect'
separationplot: no visible global function definition for 'points'
separationplot: no visible global function definition for 'lines'
separationplot: no visible global function definition for
  'colorRampPalette'
separationplot: no visible global function definition for 'layout'
separationplot: no visible global function definition for 'plot.new'
separationplot: no visible global function definition for 'legend'
separationplot: no visible global function definition for 'dev.off'
separationplot: no visible global function definition for 'locator'
sp.categorical: no visible global function definition for 'dev.new'
sp.categorical: no visible global function definition for 'pdf'
sp.categorical: no visible global function definition for 'par'
sp.categorical: no visible global function definition for 'layout'
sp.categorical: no visible global function definition for 'plot'
sp.categorical: no visible global function definition for 'text'
sp.categorical: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  colorRampPalette dev.new dev.off layout legend lines locator par pdf
  plot plot.new points rect segments text title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
             "pdf")
  importFrom("graphics", "layout", "legend", "lines", "locator", "par",
             "plot", "plot.new", "points", "rect", "segments", "text",
             "title")
to your NAMESPACE file.
GammaDist: no visible binding for global variable 'rgamma'
VEpowerPP: no visible global function definition for 'qnorm'
applyStopRules: no visible global function definition for 'qnorm'
finalLogRankTest: no visible global function definition for 'qnorm'
finalLogRankTest: no visible global function definition for 'pchisq'
generateDropout: no visible global function definition for 'rexp'
generateEnrollment: no visible global function definition for 'rpois'
generateEnrollment: no visible global function definition for 'runif'
generateInfection: no visible global function definition for 'rexp'
generateInfection : <anonymous>: no visible global function definition
  for 'rexp'
getAlphaPerTest: no visible global function definition for 'uniroot'
getHarmBound: no visible global function definition for 'dbinom'
getHarmBound: no visible global function definition for 'write.csv'
getTreatmentAssignment : <anonymous>: no visible global function
  definition for 'runif'
getTreatmentAssignment: no visible global function definition for
  'runif'
simTrial: no visible global function definition for 'runif'
sumTrialOneTrtArm: no visible global function definition for 'quantile'
testVE: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  dbinom pchisq qnorm quantile rexp rgamma rpois runif uniroot
  write.csv
Consider adding
  importFrom("stats", "dbinom", "pchisq", "qnorm", "quantile", "rexp",
             "rgamma", "rpois", "runif", "uniroot")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    libs   2.9Mb
plotenz : addmark: no visible global function definition for 'par'
plotenz : addmark: no visible global function definition for 'plot'
plotenz : addmark: no visible global function definition for 'text'
plotenz : addmark: no visible global function definition for 'segments'
plotenz : addband: no visible global function definition for 'segments'
plotenz : addband: no visible global function definition for 'text'
plotenz: no visible global function definition for 'layout'
plotenz: no visible global function definition for 'text'
plotenz: no visible global function definition for 'dev.new'
Undefined global functions or variables:
  dev.new layout par plot segments text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "layout", "par", "plot", "segments", "text")
to your NAMESPACE file.
Running examples in 'SequenceAnalysis-Ex.R' failed
The error most likely occurred in:

> ### Name: SequenceAnalysis.Complement
> ### Title: SequenceAnalysis.Complement
> ### Aliases: SequenceAnalysis.Complement
> 
> ### ** Examples
> 
> SequenceAnalysis.Complement("actagtcacgatcag")
       Complement 
"TGATCAGTGCTAGTC" 
> SequenceAnalysis.Complement(UniprotKB="O15131")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Complement 
     "N/A" 
> SequenceAnalysis.Complement(UniprotKB="O15131",CDS=TRUE)
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in Nucleotide_Sequence[[3]] : subscript out of bounds
Calls: SequenceAnalysis.Complement
Execution halted
capture: no visible binding for global variable 'resultText'
restore.session: no visible binding for global variable
  '.save.session.packages'
restore.session: no visible binding for global variable
  '.save.session.search'
save.session: no visible global function definition for 'dev.list'
save.session: no visible binding for '<<-' assignment to
  '.save.session.search'
save.session: no visible binding for '<<-' assignment to
  '.save.session.packages'
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
setpath: no visible global function definition for 'cov'
setpath: no visible global function definition for 'median'
setpath: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cov median pchisq
Consider adding
  importFrom("stats", "cov", "median", "pchisq")
to your NAMESPACE file.
random.number.test: no visible global function definition for 'runif'
random.number.test: no visible global function definition for 'rnorm'
setRNG: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
'library' or 'require' call to 'graphics' which was already attached by Depends.
  Please remove these calls from your code.
severity: no visible global function definition for 'qnorm'
severity: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
L_exp: no visible global function definition for 'pnorm'
L_hNV: no visible global function definition for 'pnorm'
L_trunc: no visible global function definition for 'pnorm'
L_trunc_mufest: no visible global function definition for 'pnorm'
dgp: no visible global function definition for 'runif'
dgp: no visible global function definition for 'rnorm'
eff.sfa: no visible global function definition for 'predict'
fitted.sfa: no visible global function definition for 'predict'
predict.sfa: no visible global function definition for 'coef'
print.sfa: no visible global function definition for 'coef'
residuals.sfa: no visible global function definition for 'fitted'
sfa: no visible global function definition for 'model.frame'
sfa: no visible global function definition for 'model.response'
sfa.fit: no visible global function definition for 'lm'
sfa.fit: no visible global function definition for 'resid'
sfa.fit: no visible global function definition for 'var'
sfa.fit: no visible global function definition for 'optim'
summary.sfa: no visible global function definition for 'logLik'
summary.sfa: no visible global function definition for 'pchisq'
te.eff.sfa: no visible global function definition for 'residuals'
te.eff.sfa: no visible global function definition for 'pnorm'
u.sfa: no visible global function definition for 'residuals'
u.sfa: no visible global function definition for 'dnorm'
u.sfa: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  coef dnorm fitted lm logLik model.frame model.response optim pchisq
  pnorm predict resid residuals rnorm runif var
Consider adding
  importFrom("stats", "coef", "dnorm", "fitted", "lm", "logLik",
             "model.frame", "model.response", "optim", "pchisq", "pnorm",
             "predict", "resid", "residuals", "rnorm", "runif", "var")
to your NAMESPACE file.
installed size is 87.2Mb
  sub-directories of 1Mb or more:
    doc     10.1Mb
    gdal     3.9Mb
    libs    64.6Mb
    proj     5.0Mb
    sqlite   1.5Mb
Found the following significant warnings:
  data/data_set.h:79:25: warning: 'data_set::xpMat_' will be initialized after [-Wreorder]
  data/data_set.h:64:7: warning:   'arma::mat data_set::Y' [-Wreorder]
  data/data_set.h:23:3: warning:   when initialized here [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:30:10: warning: 'onedim_learn_rate::scale_' will be initialized after [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:27:10: warning:   'double onedim_learn_rate::gamma_' [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:18:3: warning:   when initialized here [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:51:10: warning: 'ddim_learn_rate::eta_' will be initialized after [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:48:10: warning:   'double ddim_learn_rate::a_' [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:24:3: warning:   when initialized here [-Wreorder]
See 'd:/Rcompile/CRANpkg/local/3.5/sgd.Rcheck/00install.out' for details.
coxCrossVal: no visible binding for global variable 'sd'
error.bars: no visible global function definition for 'segments'
linCrossVal: no visible binding for global variable 'sd'
logitCrossVal: no visible binding for global variable 'sd'
plot.cv.SGL: no visible global function definition for 'points'
Undefined global functions or variables:
  points sd segments
Consider adding
  importFrom("graphics", "points", "segments")
  importFrom("stats", "sd")
to your NAMESPACE file.
.computePStar: no visible global function definition for 'uniroot'
plotBoundary: no visible global function definition for
  'scale_y_continuous'
Undefined global functions or variables:
  scale_y_continuous uniroot
Consider adding
  importFrom("stats", "uniroot")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Matrix' 'fields'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
distLaplacian: no visible global function definition for 'sparseMatrix'
gmdDeflation: no visible global function definition for 'rnorm'
laplacian: no visible global function definition for 'sparseMatrix'
Undefined global functions or variables:
  rnorm sparseMatrix
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
amse: no visible global function definition for 'na.omit'
arb: no visible global function definition for 'na.omit'
rdatagen: no visible global function definition for 'qnorm'
rdatagen: no visible global function definition for 'pbinom'
rdatagen: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  na.omit pbinom pnorm qnorm
Consider adding
  importFrom("stats", "na.omit", "pbinom", "pnorm", "qnorm")
to your NAMESPACE file.
UQnormalize.count: no visible binding for global variable 'quantile'
plotNScores: no visible global function definition for 'par'
plotNScores: no visible global function definition for 'hist'
plotNScores: no visible global function definition for 'title'
plotScores: no visible global function definition for 'par'
plotScores: no visible global function definition for 'hist'
plotScores: no visible global function definition for 'title'
sgRSEA: no visible binding for global variable 'sd'
sgRSEA: no visible global function definition for 'p.adjust'
sgRSEA.mean: no visible binding for global variable 'sd'
sgRSEA.mean: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  hist p.adjust par quantile sd title
Consider adding
  importFrom("graphics", "hist", "par", "title")
  importFrom("stats", "p.adjust", "quantile", "sd")
to your NAMESPACE file.
'library' or 'require' call to 'foreign' which was already attached by Depends.
  Please remove these calls from your code.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    www   9.5Mb
popify: no visible global function definition for 'runif'
tipify: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    www   6.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    semantic   5.7Mb
get_selected_names: no visible global function definition for 'tail'
get_selected_names: no visible global function definition for 'head'
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
shrink.estim: no visible global function definition for 'cov'
shrink.estim: no visible global function definition for 'cor'
shrink.estim: no visible global function definition for 'cov2cor'
targetCor: no visible global function definition for 'cor.test'
targetCor: no visible global function definition for 'cor'
targetCor: no visible global function definition for 'sd'
targetCor: no visible global function definition for 'cov'
targetD: no visible binding for global variable 'var'
targetF: no visible global function definition for 'cov'
targetF: no visible global function definition for 'cor'
targetG: no visible global function definition for 'cor'
targetG: no visible global function definition for 'sd'
targetG: no visible global function definition for 'cov'
targetGpos: no visible global function definition for 'cor'
targetGpos: no visible global function definition for 'sd'
targetGpos: no visible global function definition for 'cov'
targetGstar: no visible global function definition for 'cor'
targetGstar: no visible global function definition for 'sd'
targetGstar: no visible global function definition for 'cov'
Undefined global functions or variables:
  cor cor.test cov cov2cor sd var
Consider adding
  importFrom("stats", "cor", "cor.test", "cov", "cov2cor", "sd", "var")
to your NAMESPACE file.
.params: no visible binding for global variable 'URLencode'
.params: no visible global function definition for 'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'hdrcde' 'coda' 'MASS' 'bayesm' 'mnormt' 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'MASS' 'bayesm' 'coda' 'hdrcde' 'mnormt' 'spatstat'
  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:
  'ade4' 'corpcor'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
filter.PCA.default: no visible global function definition for
  'princomp'
filter.mRMR.default: no visible global function definition for
  'discretize'
gaussian.default: no visible global function definition for 'cov'
gaussian.default: no visible global function definition for
  'cov.shrink'
plot.verify.cv: no visible global function definition for 'plot'
plot.verify.cv: no visible global function definition for 'points'
plot.verify.ho: no visible global function definition for 'plot'
plot.verify.ho: no visible global function definition for 'points'
plot.verify.loo: no visible global function definition for 'plot'
plot.verify.loo: no visible global function definition for 'points'
predict.dpa1: no visible global function definition for 'cor'
predict.filter.PCA: no visible global function definition for 'predict'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'is.struct'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'var'
simulator.Simple1: no visible global function definition for 'rnorm'
verify.ho.default: no visible global function definition for 'predict'
verify.loo.default: no visible global function definition for 'predict'
Undefined global functions or variables:
  cor cov cov.shrink discretize is.struct plot points predict princomp
  rnorm var
Consider adding
  importFrom("graphics", "plot", "points")
  importFrom("stats", "cor", "cov", "predict", "princomp", "rnorm",
             "var")
to your NAMESPACE file.
dSepAdji: no visible global function definition for 'as'
dag2cpdagAdj: no visible global function definition for 'as'
randomDAG: no visible global function definition for 'rbinom'
structIntervDist: no visible global function definition for 'as'
Undefined global functions or variables:
  as rbinom
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rbinom")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
plot.std: no visible global function definition for 'rainbow'
plot.std: no visible global function definition for 'legend'
read.std: no visible global function definition for 'read.table'
std: no visible global function definition for 'na.exclude'
Undefined global functions or variables:
  legend na.exclude rainbow read.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend")
  importFrom("stats", "na.exclude")
  importFrom("utils", "read.table")
to your NAMESPACE file.
.cluster: no visible global function definition for 'kmeans'
.plot.sigclust: no visible global function definition for 'par'
.plot.sigclust: no visible global function definition for 'density'
.plot.sigclust: no visible global function definition for 'runif'
.plot.sigclust: no visible global function definition for 'dnorm'
.plot.sigclust: no visible global function definition for 'lines'
.plot.sigclust: no visible global function definition for 'points'
.plot.sigclust: no visible global function definition for 'title'
.plot.sigclust: no visible global function definition for 'text'
.plot.sigclust: no visible global function definition for 'qnorm'
.plot.sigclust: no visible global function definition for 'abline'
.plot.sigclust: no visible global function definition for 'quantile'
.plot.sigclust: no visible global function definition for 'legend'
.simnull: no visible global function definition for 'rnorm'
.vareigen: no visible global function definition for 'mad'
.vareigen: no visible global function definition for 'cov'
sigclust: no visible global function definition for 'sd'
sigclust: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline cov density dnorm kmeans legend lines mad par pnorm points
  qnorm quantile rnorm runif sd text title
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "points",
             "text", "title")
  importFrom("stats", "cov", "density", "dnorm", "kmeans", "mad",
             "pnorm", "qnorm", "quantile", "rnorm", "runif", "sd")
to your NAMESPACE file.
Sight.Est: no visible global function definition for 'glm'
Sight.Est: no visible global function definition for 'binomial'
Sight.Est: no visible global function definition for 'coef'
Sight.Est: no visible global function definition for 'terms'
Sight.Est: no visible binding for global variable 'binomial'
covtheta: no visible global function definition for 'cov'
print.sightest: no visible global function definition for 'qnorm'
summary.sightest: no visible global function definition for 'qnorm'
vardiff: no visible global function definition for 'vcov'
vardiff: no visible global function definition for 'coef'
vardiff: no visible global function definition for 'terms'
varlog.lam: no visible global function definition for 'vcov'
varlog.lam: no visible global function definition for 'coef'
varlog.lam: no visible global function definition for 'terms'
Undefined global functions or variables:
  binomial coef cov glm qnorm terms vcov
Consider adding
  importFrom("stats", "binomial", "coef", "cov", "glm", "qnorm", "terms",
             "vcov")
to your NAMESPACE file.
plot.intersect: no visible global function definition for 'points'
plot.intersect: no visible global function definition for 'plot'
plot.receiver: no visible global function definition for 'points'
plot.receiver: no visible global function definition for 'plot'
plot.receiver: no visible global function definition for 'segments'
plot.transmitter: no visible global function definition for 'points'
plot.transmitter: no visible global function definition for 'plot'
plot.transmitter: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot points segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
to your NAMESPACE file.
signmedian.test: no visible global function definition for 'median'
signmedian.test: no visible global function definition for 'binom.test'
signmedian.test: no visible global function definition for 'pbinom'
signmedian.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  binom.test median pbinom pnorm
Consider adding
  importFrom("stats", "binom.test", "median", "pbinom", "pnorm")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'gdata' 'splines'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.SII: no visible global function definition for 'plot'
plot.SII: no visible global function definition for 'lines'
plot.SII: no visible global function definition for 'abline'
plot.SII: no visible global function definition for 'legend'
sii : approx.l: no visible global function definition for 'approx'
sii.excel: no visible global function definition for 'predict'
sii.excel : approx.l: no visible global function definition for
  'approx'
Undefined global functions or variables:
  abline approx legend lines plot predict
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
linearextrapolation: no visible global function definition for 'coef'
linearextrapolation: no visible global function definition for 'lm'
plotsimexaft: no visible global function definition for 'plot'
plotsimexaft: no visible global function definition for 'lm'
plotsimexaft: no visible global function definition for 'predict'
plotsimexaft: no visible global function definition for 'lines'
plotsimexaft: no visible global function definition for 'points'
plotsimexaft: no visible global function definition for 'legend'
print.simexaft: no visible global function definition for 'coef'
quadraticextrapolation: no visible global function definition for
  'coef'
quadraticextrapolation: no visible global function definition for 'lm'
simexaft: no visible global function definition for 'terms'
simexaft: no visible global function definition for 'rnorm'
simexaft: no visible binding for global variable 'var'
simexaft: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  coef legend lines lm plot pnorm points predict rnorm terms var
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "coef", "lm", "pnorm", "predict", "rnorm", "terms",
             "var")
to your NAMESPACE file.
getFormula: no visible global function definition for 'as.formula'
internalSimXyplot : f: no visible global function definition for
  'median'
runSimulation: no visible global function definition for 'runif'
setup: no visible global function definition for 'runif'
clusterSetup,ANY-data.frame-SampleControl: no visible binding for
  global variable 'cnam'
clusterSetup,ANY-data.frame-TwoStageControl: no visible binding for
  global variable 'cnam'
initialize,DCARContControl: no visible binding for global variable
  'rnorm'
initialize,DataControl: no visible binding for global variable 'rnorm'
Undefined global functions or variables:
  as.formula cnam median rnorm runif
Consider adding
  importFrom("stats", "as.formula", "median", "rnorm", "runif")
to your NAMESPACE file.
cumallcausehr: no visible global function definition for 'integrate'
plotbe: no visible global function definition for 'plot'
plotbe: no visible global function definition for 'lines'
plotbe: no visible global function definition for 'legend'
plotcph: no visible global function definition for 'confint'
plotcph: no visible global function definition for 'plot'
plotcph: no visible global function definition for 'abline'
plotcph: no visible global function definition for 'axis'
plotcph: no visible global function definition for 'polygon'
plotcph: no visible global function definition for 'lines'
plotnae: no visible global function definition for 'plot'
simCR: no visible global function definition for 'rnorm'
simEBMT: no visible global function definition for 'model.matrix'
simexit: no visible global function definition for 'runif'
simexitinner: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  abline axis confint integrate legend lines model.matrix plot polygon
  rnorm runif uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "plot",
             "polygon")
  importFrom("stats", "confint", "integrate", "model.matrix", "rnorm",
             "runif", "uniroot")
to your NAMESPACE file.
'library' or 'require' call to 'boot' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'boot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'simpleboot/R/zzz.R':
  .onLoad calls:
    require(boot)

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

lo.boot.resample: warning in sample(1:nrow(orig.data), rep = TRUE, prob
  = weights): partial argument match of 'rep' to 'replace'
lo.boot.resample: warning in sample(res, rep = TRUE, prob = weights):
  partial argument match of 'rep' to 'replace'
S3 methods shown with full name in documentation object 'pairs.boot':
  'pairs.boot'

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.
randInitializeWeights: 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:
  expression.h:80:10: warning: 'ev3::Operand::exponent' will be initialized after [-Wreorder]
  expression.h:58:7: warning:   'int ev3::Operand::dependency' [-Wreorder]
  expression.cpp:271:1: warning:   when initialized here [-Wreorder]
  expression.cpp:276:1: warning:   when initialized here [-Wreorder]
  expression.cpp:281:1: warning:   when initialized here [-Wreorder]
  expression.cpp:286:1: warning:   when initialized here [-Wreorder]
  expression.h:83:11: warning: 'ev3::Operand::depexponent' will be initialized after [-Wreorder]
  expression.cpp:317:1: warning:   when initialized here [-Wreorder]
See 'd:/Rcompile/CRANpkg/local/3.5/simplr.Rcheck/00install.out' for details.
Package in Depends field not imported from: 'mclust'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Simpsons: no visible global function definition for 'Mclust'
Simpsons: no visible global function definition for 'lm'
Simpsons: no visible global function definition for 'plot'
Simpsons: no visible global function definition for 'abline'
Simpsons: no visible global function definition for 'par'
Simpsons: no visible global function definition for 'legend'
Simpsons: no visible global function definition for 'txtProgressBar'
Simpsons: no visible global function definition for 'setTxtProgressBar'
Simpsons: no visible global function definition for 'quantile'
plot.Simpson: no visible global function definition for 'plot'
plot.Simpson: no visible global function definition for 'lm'
plot.Simpson: no visible global function definition for 'abline'
plot.Simpson: no visible global function definition for 'par'
plot.Simpson: no visible global function definition for 'legend'
Undefined global functions or variables:
  Mclust abline legend lm par plot quantile setTxtProgressBar
  txtProgressBar
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "lm", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
simrel: no visible global function definition for 'runif'
simrel: no visible global function definition for 'rnorm'
simrelplot: no visible global function definition for 'par'
simrelplot: no visible global function definition for 'layout'
simrelplot: no visible global function definition for 'devAskNewPage'
simrelplot: no visible global function definition for 'dev.hold'
simrelplot: no visible global function definition for 'plot'
simrelplot: no visible global function definition for 'abline'
simrelplot: no visible global function definition for 'dev.flush'
simrelplot: no visible global function definition for 'points'
simrelplot: no visible global function definition for 'axis'
simrelplot: no visible global function definition for 'mtext'
simrelplot: no visible global function definition for 'box'
simrelplot: no visible global function definition for 'cov'
Undefined global functions or variables:
  abline axis box cov dev.flush dev.hold devAskNewPage layout mtext par
  plot points rnorm runif
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "box", "layout", "mtext",
             "par", "plot", "points")
  importFrom("stats", "cov", "rnorm", "runif")
to your NAMESPACE file.
Found the following hidden files and directories:
  vignettes/.Rhistory
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'abind' 'svUnit'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
simSummary: no visible global function definition for 'abind'
simSummary_unitTests: no visible global function definition for
  'clearLog'
simSummary_unitTests: no visible global function definition for
  'runTest'
simSummary_unitTests: no visible global function definition for
  'svSuite'
simSummary_unitTests: no visible global function definition for 'Log'
simSummary_unitTests: no visible global function definition for 'stats'
simSummary_unitTests: no visible global function definition for
  'metadata'
simSummary_unitTests: no visible global function definition for
  'errorLog'
Undefined global functions or variables:
  Log abind clearLog errorLog metadata runTest stats svSuite
evalGrids: no visible global function definition for 'sessionInfo'
meanAndNormCI: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd sessionInfo
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
plot.CorrAn : SAPplot: no visible global function definition for 'plot'
plot.CorrAn : SAPtitle: no visible global function definition for
  'title'
plot.CorrAn : SAPtitle: no visible global function definition for
  'mtext'
plot.CorrAn : SAPplotpuntos: no visible global function definition for
  'points'
plot.CorrAn : SAPplotpuntos: no visible global function definition for
  'text'
plot.CorrAn: no visible global function definition for 'dev.new'
plot.SimAn : SAPplot: no visible global function definition for 'plot'
plot.SimAn : SAPtitle: no visible global function definition for
  'title'
plot.SimAn : SAPtitle: no visible global function definition for
  'mtext'
plot.SimAn : SAPplotpuntos: no visible global function definition for
  'points'
plot.SimAn : SAPplotpuntos: no visible global function definition for
  'text'
plot.SimAn: no visible global function definition for 'dev.new'
plot.SimAn: no visible global function definition for 'points'
plot.SimAn: no visible global function definition for 'text'
plot.SimAn: no visible global function definition for 'par'
plot.SimAn: no visible global function definition for 'plot'
plot.SimAn: no visible global function definition for 'title'
plot.SimAn: no visible global function definition for 'axis'
plot.SimAn: no visible global function definition for 'arrows'
Undefined global functions or variables:
  arrows axis dev.new mtext par plot points text title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "arrows", "axis", "mtext", "par", "plot",
             "points", "text", "title")
to your NAMESPACE file.
Running examples in 'sisus-Ex.R' failed
The error most likely occurred in:

> ### Name: sisus.run
> ### Title: driver program for SISUS
> ### Aliases: sisus.run
> 
> ### ** Examples
> 
> # set working directory for many output files with setwd()
> # see http://statacumen.com/sisus for workbook
> filename = "http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls";
> sisus.run(filename)
trying URL 'http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls'
Warning in download.file(xls, tf, mode = "wb") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in download.file(xls, tf, mode = "wb") : 
  cannot open URL 'http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls'
Calls: sisus.run ... as.matrix -> <Anonymous> -> xls2sep -> download.file
Error in file.exists(tfn) : invalid 'file' argument
Calls: sisus.run ... get.data -> as.matrix -> <Anonymous> -> file.exists
Execution halted
cvskda: no visible global function definition for 'detectCores'
cvskda: no visible global function definition for 'makeCluster'
cvskda: no visible global function definition for 'clusterApplyLB'
cvskda: no visible global function definition for 'mclapply'
cvskda: no visible global function definition for 'stopCluster'
Undefined global functions or variables:
  clusterApplyLB detectCores makeCluster mclapply stopCluster
dskt: no visible global function definition for 'dt'
pskt: no visible global function definition for 'pt'
qskt: no visible global function definition for 'qt'
rskt: no visible global function definition for 'runif'
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'kmndirs'
Unavailable namespace imported from by a ':::' call: 'kmndirs'
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tthread/tinythread.h:632:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tbb_stddef.h:463:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/atomic.h:29:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:42:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:43:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:75:21: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:102:10: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:80:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:127:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/skm.Rcheck/00install.out' for details.
plot.sla: no visible global function definition for 'title'
plot.sla: no visible global function definition for 'abline'
print.sla: no visible global function definition for 'coef'
sla.default: no visible global function definition for 'lm'
sla.default: no visible global function definition for 'anova'
Undefined global functions or variables:
  abline anova coef lm title
Consider adding
  importFrom("graphics", "abline", "title")
  importFrom("stats", "anova", "coef", "lm")
to your NAMESPACE file.
slcestimates: no visible global function definition for 'par'
slcestimates: no visible global function definition for 'plot'
slcestimates: no visible global function definition for 'abline'
slcestimates: no visible global function definition for 'lines'
slcestimates: no visible global function definition for 'axis'
slcestimates: no visible global function definition for 'points'
slcestimates: no visible global function definition for 'title'
Undefined global functions or variables:
  abline axis lines par plot points title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "points", "title")
to your NAMESPACE file.
cvsmac: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
File 'smco/R/smco.R':
  .onAttach calls:
    cat(paste("This is smco package", version, "\n"))

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

smco: no visible global function definition for 'runif'
smco: no visible global function definition for 'rnorm'
smco: no visible global function definition for 'qnorm'
smco: no visible global function definition for 'pnorm'
smco: no visible global function definition for 'optim'
Undefined global functions or variables:
  optim pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "optim", "pnorm", "qnorm", "rnorm", "runif")
to your NAMESPACE file.
SMCP : fun: no visible global function definition for 'cor'
manipulate : fun: no visible global function definition for 'sd'
sp: no visible binding for global variable 'sd'
Undefined global functions or variables:
  cor sd
Consider adding
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
File 'SMC/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("##\n", "## Sequential Monte Carlo Package (SMC)\n",     "##\n", "## Functionality: sequential Monte Carlo (SMC) or sequential importance\n",     "## sampling (SIS) or hidden Markov models (HMM), particle filter (PF)\n",     "## and auxiliary particle filter (APF)\n", "##\n", "## Use: \"help(package = SMC)\" at the R prompt for more info\n",     "##\n", "## Copyright (C) 2006-", this.year, " Gopi Goswami\n",     "##\n", "##    Created by: Gopi Goswami <goswami@stat.harvard.edu>\n",     "## Maintained by: Gopi Goswami <grgoswami@gmail.com>\n",     "##\n")

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

.MHUpdateFuncGen.PF : MHUpdateFunc: no visible global function
  definition for 'runif'
MarkovSwitchingFuncGenerator : generateNextStreamsFunc: no visible
  global function definition for 'runif'
MarkovSwitchingFuncGenerator: no visible global function definition for
  'rnorm'
MarkovSwitchingFuncGenerator: no visible global function definition for
  'runif'
MarkovSwitchingFuncGenerator : logObsDensFunc: no visible global
  function definition for 'dnorm'
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for 'dnorm'
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for 'runif'
Undefined global functions or variables:
  dnorm rnorm runif
Consider adding
  importFrom("stats", "dnorm", "rnorm", "runif")
to your NAMESPACE file.
em: no visible global function definition for 'coxph'
em: no visible global function definition for 'optim'
plotpredictsmcure: no visible global function definition for 'plot'
plotpredictsmcure: no visible global function definition for 'matplot'
plotpredictsmcure: no visible global function definition for 'lines'
smcure: no visible binding for global variable 'na.omit'
smcure: no visible global function definition for 'model.frame'
smcure: no visible global function definition for 'model.extract'
smcure: no visible global function definition for 'model.matrix'
smcure: no visible global function definition for 'coxph'
smcure: no visible global function definition for 'survreg'
smcure: no visible binding for global variable 'var'
smcure: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  coxph lines matplot model.extract model.frame model.matrix na.omit
  optim plot pnorm survreg var
Consider adding
  importFrom("graphics", "lines", "matplot", "plot")
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "na.omit", "optim", "pnorm", "var")
to your NAMESPACE file.
branching.resample: no visible global function definition for 'rbinom'
cov.weights: no visible global function definition for 'var'
inverse.cdf.weights: no visible global function definition for 'runif'
multinomial.resample: no visible global function definition for 'runif'
stratified.resample: no visible global function definition for 'runif'
systematic.resample: no visible global function definition for 'runif'
Undefined global functions or variables:
  rbinom runif var
Consider adding
  importFrom("stats", "rbinom", "runif", "var")
to your NAMESPACE file.
'library' or 'require' call to 'proxy' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'proxy' 'tm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
normalize: no visible binding for global variable 'sd'
simDic: no visible global function definition for 'simil'
simDoc: no visible global function definition for 'simil'
Undefined global functions or variables:
  sd simil
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Grad.sph: no visible global function definition for 'dist'
IMDS: no visible global function definition for 'cmdscale'
IMDS: no visible global function definition for 'as.dist'
IMDS: no visible global function definition for 'runif'
IMDS: no visible global function definition for 'optim'
idistSph: no visible global function definition for 'dist'
obj.sph: no visible global function definition for 'dist'
plot.imds: no visible binding for global variable 'lines'
plot.imds: no visible global function definition for 'plot'
plot.imds: no visible global function definition for 'text'
plot.imds: no visible global function definition for 'rect'
Undefined global functions or variables:
  as.dist cmdscale dist lines optim plot rect runif text
Consider adding
  importFrom("graphics", "lines", "plot", "rect", "text")
  importFrom("stats", "as.dist", "cmdscale", "dist", "optim", "runif")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'lattice' 'splines'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'lattice' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
getRoughnessMatrix: no visible global function definition for 'ns'
plotSmeDiagnostic: no visible global function definition for 'layout'
plotSmeDiagnostic: no visible global function definition for 'plot'
plotSmeModel: no visible global function definition for 'plot'
plotSmeModel: no visible global function definition for 'lines'
plotSmeModel: no visible global function definition for 'col2rgb'
plotSmeModel: no visible global function definition for 'polygon'
plotSmeModel: no visible global function definition for 'rgb'
plotSmeRaw: no visible global function definition for 'xyplot'
plotSmeRaw : <anonymous>: no visible global function definition for
  'panel.xyplot'
plotSmeRaw : <anonymous>: no visible global function definition for
  'panel.lines'
sme.default: no visible global function definition for 'ns'
sme.list: no visible binding for global variable 'ns'
sme.list : <anonymous>: no visible global function definition for 'ns'
vcov.sme: no visible global function definition for 'ns'
Undefined global functions or variables:
  col2rgb layout lines ns panel.lines panel.xyplot plot polygon rgb
  xyplot
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "layout", "lines", "plot", "polygon")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'ggplot2' 'reshape'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'corpcor' 'ggplot2' 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls in package code:
  'MASS' 'survival'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
lines.SmithWilsonYieldCurve: no visible global function definition for
  'lines'
plot.SmithWilsonYieldCurve: no visible global function definition for
  'plot'
points.SmithWilsonYieldCurve: no visible global function definition for
  'points'
Undefined global functions or variables:
  lines plot points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
Fourier2d: no visible global function definition for 'fft'
kernel2dsmooth: no visible global function definition for 'fft'
Undefined global functions or variables:
  fft
Consider adding
  importFrom("stats", "fft")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: items 'package:smotefamily' were removed from the search path
'library' or 'require' calls in package code:
  'akima' 'misc3d' 'rgl' 'rpanel' 'tkrplot'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dNMR: no visible global function definition for 'pnorm'
dNMR: no visible global function definition for 'dnorm'
pNMR: no visible global function definition for 'pnorm'
pNMR: no visible global function definition for 'dnorm'
rMR: no visible global function definition for 'rnorm'
rMR: no visible global function definition for 'rchisq'
Undefined global functions or variables:
  dnorm pnorm rchisq rnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm", "rchisq", "rnorm")
to your NAMESPACE file.
SMVar.paired : <anonymous>: no visible global function definition for
  'var'
SMVar.paired: no visible global function definition for 'var'
SMVar.paired: no visible global function definition for 'pt'
SMVar.paired: no visible global function definition for 'p.adjust'
SMVar.paired: no visible global function definition for 'write.table'
SMVar.unpaired : <anonymous>: no visible global function definition for
  'var'
SMVar.unpaired: no visible global function definition for 'var'
SMVar.unpaired: no visible global function definition for 'pt'
SMVar.unpaired: no visible global function definition for 'p.adjust'
SMVar.unpaired: no visible global function definition for 'write.table'
Undefined global functions or variables:
  p.adjust pt var write.table
Consider adding
  importFrom("stats", "p.adjust", "pt", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
sclust: no visible global function definition for 'var'
snipEM: no visible global function definition for 'cov'
stEM: no visible global function definition for 'cov'
stEM: no visible global function definition for 'quantile'
Undefined global functions or variables:
  cov quantile var
Consider adding
  importFrom("stats", "cov", "quantile", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'snow'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
KS.test: no visible global function definition for 'quantile'
KS.test : Fgaus: no visible global function definition for 'pnorm'
KS.test: no visible global function definition for 'setNames'
cs.test: no visible global function definition for 'pbinom'
cs.test: no visible global function definition for 'pnorm'
cs.test: no visible global function definition for 'setNames'
kde: no visible global function definition for 'quantile'
kde : Fgaus: no visible global function definition for 'pnorm'
kde: no visible global function definition for 'par'
kre: no visible global function definition for 'quantile'
kre: no visible global function definition for 'lines'
ns.test: no visible global function definition for 'complete.cases'
ns.test: no visible global function definition for 'qnorm'
ns.test: no visible global function definition for 'pnorm'
ns.test: no visible global function definition for 'pchisq'
ns.test: no visible global function definition for 'setNames'
ns.test: no visible global function definition for 'qt'
quant.test: no visible global function definition for 'complete.cases'
quant.test: no visible global function definition for 'pbinom'
quant.test: no visible global function definition for 'pnorm'
quant.test: no visible global function definition for 'setNames'
quant.test: no visible global function definition for 'quantile'
quant.test: no visible global function definition for 'phyper'
runs.test: no visible global function definition for 'median'
runs.test: no visible global function definition for 'setNames'
runs.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  complete.cases lines median par pbinom pchisq phyper pnorm qnorm qt
  quantile setNames
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "complete.cases", "median", "pbinom", "pchisq",
             "phyper", "pnorm", "qnorm", "qt", "quantile", "setNames")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'mvtnorm' 'combinat'
A package should be listed in only one of these fields.
chisq.test.a: no visible global function definition for 'chisq.test'
maxsel: no visible global function definition for 'complete.cases'
maxsel.asymp.test: no visible global function definition for
  'complete.cases'
Undefined global functions or variables:
  chisq.test complete.cases
Consider adding
  importFrom("stats", "chisq.test", "complete.cases")
to your NAMESPACE file.
MDSplot: no visible global function definition for 'par'
MDSplot: no visible global function definition for 'rainbow'
MDSplot: no visible global function definition for 'plot'
MDSplot: no visible global function definition for 'pairs'
classCenter : <anonymous>: no visible binding for global variable
  'median'
grow.snpRF: no visible global function definition for 'update'
na.roughfix.data.frame : roughfix: no visible global function
  definition for 'median'
na.roughfix.default: no visible global function definition for 'median'
outlier.default: no visible global function definition for 'median'
outlier.default: no visible global function definition for 'mad'
plot.margin: no visible global function definition for
  'installed.packages'
plot.margin: no visible global function definition for 'rainbow'
plot.margin: no visible global function definition for 'plot.default'
plot.snpRF: no visible global function definition for 'matplot'
tuneSnpRF: no visible global function definition for 'axis'
varImpPlot: no visible global function definition for 'par'
varImpPlot: no visible global function definition for 'dotchart'
varImpPlot: no visible global function definition for 'mtext'
Undefined global functions or variables:
  axis dotchart installed.packages mad matplot median mtext pairs par
  plot plot.default rainbow update
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "dotchart", "matplot", "mtext", "pairs",
             "par", "plot", "plot.default")
  importFrom("stats", "mad", "median", "update")
  importFrom("utils", "installed.packages")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Biostrings' 'GenomicRanges' 'IRanges' 'Rsamtools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in 'SocialMediaMineR-Ex.R' failed
The error most likely occurred in:

> ### Name: SocialMediaMineR
> ### Title: A Social Media Search and Analytic Tool
> ### Aliases: SocialMediaMineR-package SocialMediaMineR
> ### Keywords: IO
> 
> ### ** Examples
> 
> get_socialmedia("http://www.nytimes.com/")
trying URL 'https://curl.haxx.se/ca/cacert.pem'
Warning in download.file(url = "https://curl.haxx.se/ca/cacert.pem", destfile = "cacert.perm") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in download.file(url = "https://curl.haxx.se/ca/cacert.pem", destfile = "cacert.perm") : 
  cannot open URL 'https://curl.haxx.se/ca/cacert.pem'
Calls: get_socialmedia -> download.file
Execution halted
calculate.areas: no visible global function definition for 'runif'
calculate.gradedareas: no visible global function definition for
  'rnorm'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'SoDA' 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.
Missing or unexported object: 'base::WHAT'
Packages in Depends field not imported from:
  'MASS' 'magic' 'ppls' 'psych'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
get.hnx.B.initialW: no visible global function definition for
  'normalize.vector'
get.hnx.B.initialW: no visible global function definition for 'adiag'
hclust.wrap: no visible global function definition for 'hclust'
hclust.wrap: no visible global function definition for 'dist'
hclust.wrap: no visible global function definition for 'cutree'
my.normdata.gen: no visible global function definition for 'mvrnorm'
my.normdata.gen: no visible global function definition for 'rnorm'
odc.clust: no visible binding for global variable 'kmeans'
odc.cv: no visible global function definition for 'ginv'
odc.optimallambda2: no visible global function definition for 'tr'
odc.optimallambda2: no visible global function definition for 'ginv'
odc.optimallambda2: no visible binding for global variable 'sd'
sodc.clust: no visible binding for global variable 'kmeans'
Undefined global functions or variables:
  adiag cutree dist ginv hclust kmeans mvrnorm normalize.vector rnorm
  sd tr
Consider adding
  importFrom("stats", "cutree", "dist", "hclust", "kmeans", "rnorm",
             "sd")
to your NAMESPACE file.
hsvScale: no visible global function definition for 'hsv'
plotConcentric: no visible global function definition for 'plot'
plotConcentric: no visible global function definition for 'points'
plotConcentric: no visible global function definition for 'legend'
plotPoints: no visible global function definition for 'plot'
plotStress: no visible global function definition for 'plot'
plotStress: no visible global function definition for 'polygon'
plotStress: no visible global function definition for 'points'
Undefined global functions or variables:
  hsv legend plot points polygon
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "legend", "plot", "points", "polygon")
to your NAMESPACE file.
HardKMeansDemo: no visible global function definition for
  'graphics.off'
HardKMeansDemo: no visible global function definition for 'plot'
HardKMeansDemo: no visible global function definition for 'points'
initializeMeansMatrix: no visible global function definition for
  'runif'
initializeMeansMatrix: no visible global function definition for 'dist'
normalizeMatrix: no visible global function definition for 'sd'
plotRoughKMeans: no visible global function definition for
  'graphics.off'
plotRoughKMeans: no visible global function definition for 'plot'
plotRoughKMeans: no visible global function definition for 'points'
Undefined global functions or variables:
  dist graphics.off plot points runif sd
Consider adding
  importFrom("grDevices", "graphics.off")
  importFrom("graphics", "plot", "points")
  importFrom("stats", "dist", "runif", "sd")
to your NAMESPACE file.
Ssimpute.als: no visible global function definition for 'rnorm'
Ssvd.als: no visible global function definition for 'rnorm'
cs.default: no visible binding for global variable 'weighted.mean'
simpute.als: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm weighted.mean
Consider adding
  importFrom("stats", "rnorm", "weighted.mean")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'aqp' 'lattice' 'methods' 'munsell' 'splancs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls in package code:
  'chemometrics' 'spatstat'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.soma: no visible global function definition for 'plot'
soma: no visible global function definition for 'runif'
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
bm: no visible global function definition for 'rnorm'
bm: no visible global function definition for 'ts'
fbm: no visible global function definition for 'fft'
fbm: no visible global function definition for 'rnorm'
fbm: no visible global function definition for 'ts'
gbm: no visible global function definition for 'rnorm'
gbm: no visible global function definition for 'ts'
Undefined global functions or variables:
  fft rnorm ts
Consider adding
  importFrom("stats", "fft", "rnorm", "ts")
to your NAMESPACE file.
getAlpha: no visible global function definition for 'pbinom'
kfweOrd: no visible global function definition for 'qnbinom'
Undefined global functions or variables:
  pbinom qnbinom
Consider adding
  importFrom("stats", "pbinom", "qnbinom")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'someMTP' 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' call to 'hexbin' which was already attached by Depends.
  Please remove these calls from your code.
hexbinpie: no visible global function definition for 'quantile'
hexbinpie: no visible global function definition for 'polygon'
hexbinpie: no visible global function definition for 'text'
makehexbinplot: no visible global function definition for 'rainbow'
makehexbinplot: no visible global function definition for 'col2rgb'
makehexbinplot: no visible global function definition for 'edit'
makehexbinplot: no visible global function definition for 'dev.new'
makehexbinplot: no visible global function definition for 'plot.new'
makehexbinplot: no visible global function definition for 'plot.window'
makehexbinplot: no visible global function definition for 'box'
makehexbinplot: no visible global function definition for 'axis'
makehexbinplot: no visible global function definition for 'legend'
som.plot: no visible global function definition for 'read.table'
Undefined global functions or variables:
  axis box col2rgb dev.new edit legend plot.new plot.window polygon
  quantile rainbow read.table text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rainbow")
  importFrom("graphics", "axis", "box", "legend", "plot.new",
             "plot.window", "polygon", "text")
  importFrom("stats", "quantile")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
dfrag: no visible global function definition for 'qgeom'
dfrag: no visible global function definition for 'plogis'
dfrag: no visible global function definition for 'dgeom'
estAbund: no visible global function definition for 'xtabs'
mmN : <anonymous>: no visible global function definition for 'uniroot'
pfrag: no visible global function definition for 'qgeom'
phi.deriv.default: no visible global function definition for
  'model.matrix'
phi.deriv.default: no visible binding for global variable 'sd'
phi.update.default: no visible global function definition for 'glm'
phi.update.default: no visible binding for global variable
  'quasipoisson'
phi.update.default: no visible global function definition for 'predict'
phi.update.lframe: no visible global function definition for 'glm'
phi.update.lframe: no visible binding for global variable
  'quasipoisson'
phi.update.lframe: no visible global function definition for 'predict'
pr.y.given.x : <anonymous>: no visible global function definition for
  'dpois'
pr.y.given.x : <anonymous> : <anonymous>: no visible global function
  definition for 'dpois'
pr.y.given.x : <anonymous>: no visible global function definition for
  'convolve'
qfrag: no visible global function definition for 'qgeom'
rfrag: no visible global function definition for 'qgeom'
simSonic: no visible global function definition for 'rpois'
Undefined global functions or variables:
  convolve dgeom dpois glm model.matrix plogis predict qgeom
  quasipoisson rpois sd uniroot xtabs
Consider adding
  importFrom("stats", "convolve", "dgeom", "dpois", "glm",
             "model.matrix", "plogis", "predict", "qgeom",
             "quasipoisson", "rpois", "sd", "uniroot", "xtabs")
to your NAMESPACE file.
plot.soo_function: no visible global function definition for
  'terrain.colors'
plot.soo_function: no visible binding for global variable 'image'
plot.soo_function: no visible binding for global variable 'contour'
plot3d: no visible global function definition for 'persp3d'
plot3d: no visible global function definition for 'terrain.colors'
random_parameters.soo_function: no visible global function definition
  for 'runif'
random_rotation_matrix: no visible global function definition for
  'runif'
Undefined global functions or variables:
  contour image persp3d runif terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "contour", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
simdata_contaminated : <anonymous>: no visible global function
  definition for 'rbinom'
simdata_uniform : multivariate_uniform : <anonymous>: no visible global
  function definition for 'runif'
which_min: no visible global function definition for 'head'
which_min: no visible global function definition for 'tail'
Undefined global functions or variables:
  head rbinom runif tail
Consider adding
  importFrom("stats", "rbinom", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
convert_municipality_names: no visible global function definition for
  'read.csv'
regression_plot: no visible binding for global variable 'loess'
regression_plot: no visible global function definition for
  'colorRampPalette'
regression_plot: no visible global function definition for
  'loess.control'
regression_plot: no visible global function definition for 'predict'
regression_plot : <anonymous>: no visible global function definition
  for 'quantile'
regression_plot : <anonymous>: no visible global function definition
  for 'pnorm'
regression_plot: no visible global function definition for
  'flush.console'
regression_plot: no visible global function definition for 'density'
Undefined global functions or variables:
  colorRampPalette density flush.console loess loess.control pnorm
  predict quantile read.csv
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "density", "loess", "loess.control", "pnorm",
             "predict", "quantile")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
'library' or 'require' call to 'rgdal' 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.
analyzeSP23Design: no visible global function definition for 'plot'
exploreSP23Design: no visible global function definition for
  'txtProgressBar'
exploreSP23Design: no visible global function definition for
  'setTxtProgressBar'
generateClinicalTrialData : <anonymous>: no visible global function
  definition for 'runif'
generateClinicalTrialData: no visible global function definition for
  'rbinom'
generateClinicalTrialData: no visible global function definition for
  'rexp'
mHP.b : crossingProbDiff: no visible global function definition for
  'pnorm'
mHP.b : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.b: no visible global function definition for 'qnorm'
mHP.b: no visible global function definition for 'uniroot'
mHP.c : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.c: no visible global function definition for 'uniroot'
mHP.c: no visible global function definition for 'qnorm'
performInterimLook: no visible global function definition for 'optim'
performInterimLook: no visible global function definition for
  'constrOptim'
performInterimLook: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  Miwa constrOptim optim plot pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
SPA: no visible global function definition for 'var'
Score.Test.Interact: no visible global function definition for 'pchisq'
Score.Test.Overall: no visible global function definition for 'var'
Score.Test.Overall: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq var
Consider adding
  importFrom("stats", "pchisq", "var")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'glasso' 'limSolve'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glasso.miss: no visible global function definition for 'cov'
glasso.miss: no visible global function definition for 'glasso'
glasso.miss: no visible global function definition for 'Solve'
space.miss: no visible global function definition for 'Solve'
Undefined global functions or variables:
  Solve cov glasso
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
'library' or 'require' call to 'Matrix' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Matrix' 'igraph' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GenPar: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Rcpp' 'colorspace' 'picante'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error in re-building vignettes:
  ...

    decompose, spectrum

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

    union

Loading required package: sp
loading reproducible     0.1.3
loading quickPlot        0.1.2
loading SpaDES.core      0.1.0
loading SpaDES.tools     0.1.0
loading SpaDES.addins    0.1.0

Default paths for SpaDES directories set to:
  cachePath:  D:\temp\RtmpeYkqYl/SpaDES/cache
  inputPath:  D:\temp\RtmpeYkqYl/SpaDES/inputs
  modulePath: D:\temp\RtmpeYkqYl/SpaDES/modules
  outputPath: D:\temp\RtmpeYkqYl/SpaDES/outputs
These can be changed using 'setPaths()'. See '?setPaths'.
Quitting from lines 48-61 (iii-cache.Rmd) 
Error: processing vignette 'iii-cache.Rmd' failed with diagnostics:
Some packages required for the simulation are not installed:
    tkrplot
Execution halted
Running 'test-all.R' [12s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 457 SKIPPED: 13 FAILED: 21
  1. Error: adj.R: torus does not work as expected (@test-adj.R#124) 
  2. Error: D:/temp/Rtmpgbouif/R.INSTALL306fc572d4c3d/SpaDES.tools/man/cir.Rd 
  3. Error: D:/temp/Rtmpgbouif/R.INSTALL306fc572d4c3d/SpaDES.tools/man/distances.Rd 
  4. Error: D:/temp/Rtmpgbouif/R.INSTALL306fc572d4c3d/SpaDES.tools/man/initiateAgents.Rd 
  5. Error: D:/temp/Rtmpgbouif/R.INSTALL306fc572d4c3d/SpaDES.tools/man/randomPolygons.Rd 
  6. Error: D:/temp/Rtmpgbouif/R.INSTALL306fc572d4c3d/SpaDES.tools/man/specnumperpatch-probs.Rd 
  7. Error: D:/temp/Rtmpgbouif/R.INSTALL306fc572d4c3d/SpaDES.tools/man/splitRaster.Rd 
  8. Error: D:/temp/Rtmpgbouif/R.INSTALL306fc572d4c3d/SpaDES.tools/man/spokes.Rd 
  9. Error: D:/temp/Rtmpgbouif/R.INSTALL306fc572d4c3d/SpaDES.tools/man/spread.Rd 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
hausman: no visible global function definition for 'pchisq'
span.formula: no visible global function definition for 'model.frame'
span.formula: no visible global function definition for 'model.matrix'
span.formula: no visible global function definition for
  'model.response'
spbe: no visible global function definition for 'cor'
spbe: no visible global function definition for 'pt'
spfe: no visible global function definition for 'cor'
spfe: no visible global function definition for 'pt'
sprandom: no visible global function definition for 'cor'
sprandom: no visible global function definition for 'pt'
summary.span: no visible global function definition for 'printCoefmat'
Undefined global functions or variables:
  cor model.frame model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "pchisq", "printCoefmat", "pt")
to your NAMESPACE file.
plot.spa: no visible global function definition for 'plot'
plot.spa: no visible global function definition for 'lines'
plot.spa: no visible global function definition for 'points'
plot.spa: no visible global function definition for 'gray'
plot.spa: no visible global function definition for 'box'
predict.spa: no visible global function definition for 'fitted'
predict.spa: no visible global function definition for 'coef'
spa.gcv: no visible global function definition for 'density'
spa.gcv: no visible global function definition for 'quantile'
spa.sim: no visible global function definition for 'runif'
spa.sim: no visible global function definition for 'rnorm'
spa.sim: no visible global function definition for 'rbinom'
update.spa: no visible global function definition for 'quantile'
Undefined global functions or variables:
  box coef density fitted gray lines plot points quantile rbinom rnorm
  runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "box", "lines", "plot", "points")
  importFrom("stats", "coef", "density", "fitted", "quantile", "rbinom",
             "rnorm", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RCurl' 'XML'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPARQL : <anonymous>: no visible global function definition for
  'URLencode'
SPARQL: no visible binding for global variable 'getURL'
SPARQL: no visible global function definition for 'URLencode'
SPARQL: no visible binding for global variable 'xmlParse'
SPARQL: no visible global function definition for 'getNodeSet'
SPARQL: no visible global function definition for 'xpathApply'
SPARQL: no visible binding for global variable 'postForm'
get_attr: no visible global function definition for 'getNodeSet'
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for 'getNodeSet'
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for 'xmlDoc'
get_value: no visible global function definition for 'xmlDoc'
get_value: no visible global function definition for 'xpathSApply'
get_value: no visible binding for global variable 'xmlValue'
get_value: no visible global function definition for 'xpathApply'
get_value: no visible binding for global variable 'xmlGetAttr'
readCSVstring: no visible global function definition for 'read.csv'
readTSVstring: no visible global function definition for 'read.delim'
Undefined global functions or variables:
  URLencode getNodeSet getURL postForm read.csv read.delim xmlDoc
  xmlGetAttr xmlParse xmlValue xpathApply xpathSApply
Consider adding
  importFrom("utils", "URLencode", "read.csv", "read.delim")
to your NAMESPACE file.
f.I2.cont: no visible global function definition for 'combn'
f.I2.dich: no visible global function definition for 'combn'
f.pstar.cont: no visible global function definition for 'combn'
f.pstar.dich: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
image.matrixBC: no visible global function definition for 'dev.new'
image.matrixBC: no visible global function definition for 'image'
image.matrixBC: no visible global function definition for 'heat.colors'
image.matrixBC: no visible global function definition for 'axis'
image.matrixBC: no visible global function definition for 'title'
image.sparseBC: no visible global function definition for 'dev.new'
image.sparseBC: no visible global function definition for 'image'
image.sparseBC: no visible global function definition for 'heat.colors'
image.sparseBC: no visible global function definition for 'axis'
image.sparseBC: no visible global function definition for 'tail'
image.sparseBC: no visible global function definition for 'title'
matrixBC: no visible global function definition for 'kmeans'
sparseBC: no visible global function definition for 'kmeans'
sparseBC.choosekr: no visible global function definition for 'kmeans'
sparseBC.choosekr: no visible binding for global variable 'sd'
Undefined global functions or variables:
  axis dev.new heat.colors image kmeans sd tail title
Consider adding
  importFrom("grDevices", "dev.new", "heat.colors")
  importFrom("graphics", "axis", "image", "title")
  importFrom("stats", "kmeans", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
Unexported object imported by a ':::' call: 'igraph:::as_graphnel'
  See the note in ?`:::` about the use of this operator.
Clarketest: no visible global function definition for 'pbinom'
Clarketest: no visible global function definition for 'qbinom'
DIC: no visible global function definition for 'model.matrix'
LogLike: no visible global function definition for 'model.matrix'
Vuongtest: no visible global function definition for 'var'
Vuongtest: no visible global function definition for 'qnorm'
Vuongtest: no visible global function definition for 'pnorm'
est.sc: no visible global function definition for 'model.matrix'
gpind: no visible global function definition for 'rgamma'
nbind: no visible global function definition for 'rgamma'
poiind: no visible global function definition for 'rgamma'
zigpind: no visible global function definition for 'rbinom'
zigpind: no visible global function definition for 'rgamma'
zipind: no visible global function definition for 'rbinom'
zipind: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  model.matrix pbinom pnorm qbinom qnorm rbinom rgamma var
Consider adding
  importFrom("stats", "model.matrix", "pbinom", "pnorm", "qbinom",
             "qnorm", "rbinom", "rgamma", "var")
to your NAMESPACE file.
gev.impute: no visible global function definition for 'rnorm'
gev.init: no visible global function definition for 'rbinom'
gev.init: no visible global function definition for 'var'
gev.init: no visible global function definition for 'optimize'
gev.logscore: no visible global function definition for 'density'
gev.logscore: no visible global function definition for 'splinefun'
gev.update.M: no visible global function definition for 'runif'
gev.update.hyper: no visible global function definition for 'rgamma'
gev.update.lambda: no visible global function definition for 'rnorm'
gev.update.lambda: no visible global function definition for 'dgamma'
gev.update.lambda: no visible global function definition for 'dnorm'
gev.update.lambda: no visible global function definition for 'runif'
gev.update.tau.kappa: no visible global function definition for 'rnorm'
gev.update.tau.kappa: no visible global function definition for 'dnorm'
gev.update.tau.kappa: no visible global function definition for 'runif'
gev.update.tau.mu: no visible global function definition for 'rnorm'
gev.update.tau.mu: no visible global function definition for 'dnorm'
gev.update.tau.mu: no visible global function definition for 'runif'
gev.update.tau.xi: no visible global function definition for 'rnorm'
gev.update.tau.xi: no visible global function definition for 'dnorm'
gev.update.tau.xi: no visible global function definition for 'runif'
gev.update.theta: no visible global function definition for 'rnorm'
gp.like.lambda: no visible global function definition for 'dgamma'
Undefined global functions or variables:
  density dgamma dnorm optimize rbinom rgamma rnorm runif splinefun var
Consider adding
  importFrom("stats", "density", "dgamma", "dnorm", "optimize", "rbinom",
             "rgamma", "rnorm", "runif", "splinefun", "var")
to your NAMESPACE file.
codisp: no visible global function definition for 'complete.cases'
cor.spatial: no visible global function definition for 'complete.cases'
modified.ttest: no visible global function definition for
  'complete.cases'
modified.ttest: no visible global function definition for 'cor'
plot.codisp: no visible global function definition for 'plot'
plot.codisp: no visible global function definition for 'title'
Undefined global functions or variables:
  complete.cases cor plot title
Consider adding
  importFrom("graphics", "plot", "title")
  importFrom("stats", "complete.cases", "cor")
to your NAMESPACE file.
I2BR: no visible global function definition for 'pnorm'
I2SmD2: no visible global function definition for 'pnorm'
IBR: no visible global function definition for 'pnorm'
ISmD2: no visible global function definition for 'pnorm'
MestimatorBR: no visible global function definition for 'optim'
MestimatorSmith: no visible global function definition for 'optim'
psidotBR: no visible global function definition for 'dnorm'
psidotBR: no visible global function definition for 'pnorm'
psidotSmD2: no visible global function definition for 'dnorm'
psidotSmD2: no visible global function definition for 'pnorm'
tailBRInt: no visible global function definition for 'pnorm'
tailSmithInt: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm optim pnorm
Consider adding
  importFrom("stats", "dnorm", "optim", "pnorm")
to your NAMESPACE file.
bbox_to_SpatialPolygons: no visible global function definition for
  'CRS'
bbox_to_SpatialPolygons: no visible global function definition for
  'Polygon'
bbox_to_SpatialPolygons: no visible global function definition for
  'Polygons'
bbox_to_SpatialPolygons: no visible global function definition for
  'SpatialPolygons'
list.raster.files: no visible global function definition for 'CRS'
list.raster.files: no visible global function definition for
  'spTransform'
list.raster.files: no visible global function definition for
  'SpatialPolygonsDataFrame'
list.raster.files: no visible global function definition for 'spChFIDs'
predict_rasterEngine : predict.rasterEngine_function: no visible global
  function definition for 'complete.cases'
projectRaster_rigorous : chunk_function: no visible global function
  definition for 'spTransform'
projectRaster_rigorous : chunk_function: no visible global function
  definition for 'CRS'
spatial_sync_raster: no visible global function definition for 'bbox'
spatial_sync_vector: no visible global function definition for
  'spTransform'
spatial_sync_vector: no visible global function definition for 'CRS'
Undefined global functions or variables:
  CRS Polygon Polygons SpatialPolygons SpatialPolygonsDataFrame bbox
  complete.cases spChFIDs spTransform
Consider adding
  importFrom("stats", "complete.cases")
to your NAMESPACE file.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tthread/tinythread.h:632:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tbb_stddef.h:463:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/atomic.h:29:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:42:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:43:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:75:21: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:102:10: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:80:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:127:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/SpatMCA.Rcheck/00install.out' for details.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tthread/tinythread.h:632:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tbb_stddef.h:463:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/atomic.h:29:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:42:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:43:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:75:21: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:102:10: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:80:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:127:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/SpatPCA.Rcheck/00install.out' for details.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    R      4.9Mb
    doc    4.7Mb
    help   5.0Mb
    libs   1.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.1Mb
GenerateCliquesCovariance: 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: 'spDataLarge'
bartlett: no visible global function definition for 'pchisq'
local.rbfdot: no visible binding for global variable 'sd'
local.rbfdot: no visible global function definition for 'dist'
local.rbfdot : <anonymous>: no visible global function definition for
  'median'
speccalt: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  dist kmeans median pchisq sd
Consider adding
  importFrom("stats", "dist", "kmeans", "median", "pchisq", "sd")
to your NAMESPACE file.
ChaoBunge: no visible global function definition for 'qnorm'
ChaoLee1992: no visible global function definition for 'qnorm'
Pmix: no visible global function definition for 'dpois'
PmixSCon: no visible global function definition for 'dbeta'
bootPCG: no visible global function definition for 'flush.console'
bootPCG: no visible global function definition for 'quantile'
bootPnpmle: no visible global function definition for 'flush.console'
bootPnpmle: no visible global function definition for 'quantile'
bootUnpmle: no visible global function definition for 'flush.console'
bootUnpmle: no visible global function definition for 'quantile'
chao1984: no visible global function definition for 'qnorm'
jackknife: no visible global function definition for 'dbinom'
jackknife: no visible global function definition for 'qnorm'
pcg: no visible global function definition for 'flush.console'
unpmle: no visible global function definition for 'flush.console'
untrunPmix: no visible global function definition for 'dpois'
Undefined global functions or variables:
  dbeta dbinom dpois flush.console qnorm quantile
Consider adding
  importFrom("stats", "dbeta", "dbinom", "dpois", "qnorm", "quantile")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
randomCorrelations: no visible global function definition for 'cor'
specGlm : <anonymous>: no visible global function definition for 'coef'
specLm : <anonymous>: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef cor
Consider adding
  importFrom("stats", "coef", "cor")
to your NAMESPACE file.
Packages required but not available: 'xcms' 'MAIT'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'leaps' which was already attached by Depends.
  Please remove these calls from your code.
modSearch: no visible global function definition for 'glm'
modSearch: no visible binding for global variable 'binomial'
modSearch: no visible global function definition for 'na.omit'
modSearch: no visible global function definition for 'as.formula'
speff: no visible binding for global variable 'na.pass'
speff: no visible global function definition for 'model.matrix'
speff: no visible global function definition for 'terms'
speff: no visible global function definition for 'model.response'
speff: no visible global function definition for 'as.formula'
speff: no visible global function definition for 'predict'
speff: no visible global function definition for 'na.omit'
speff: no visible global function definition for 'glm'
speff: no visible binding for global variable 'na.omit'
speffSurv: no visible global function definition for 'model.matrix'
speffSurv: no visible global function definition for 'terms'
speffSurv: no visible global function definition for 'model.response'
speffSurv: no visible global function definition for 'as.formula'
speffSurv: no visible global function definition for 'uniroot'
summary.speff: no visible global function definition for 'qnorm'
summary.speff: no visible global function definition for 'pnorm'
summary.speffSurv: no visible global function definition for 'qnorm'
summary.speffSurv: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  as.formula binomial glm model.matrix model.response na.omit na.pass
  pnorm predict qnorm terms uniroot
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "model.matrix",
             "model.response", "na.omit", "na.pass", "pnorm", "predict",
             "qnorm", "terms", "uniroot")
to your NAMESPACE file.
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
spe: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: 'rgl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pointsphere: no visible global function definition for 'runif'
rgl.sphMW: no visible global function definition for 'plot3d'
rgl.sphcirc: no visible global function definition for 'rotate3d'
rgl.sphcirc: no visible global function definition for 'lines3d'
rgl.sphgrid: no visible global function definition for 'open3d'
rgl.sphgrid: no visible global function definition for 'plot3d'
rgl.sphgrid: no visible global function definition for 'lines3d'
rgl.sphgrid: no visible global function definition for 'text3d'
rgl.sphpoints: no visible global function definition for 'points3d'
rgl.sphsun: no visible global function definition for 'plot3d'
rgl.sphtext: no visible global function definition for 'text3d'
Undefined global functions or variables:
  lines3d open3d plot3d points3d rotate3d runif text3d
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'lars' 'parallel' 'randomForest'
  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 'quadprog' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'quadprog'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPIn: no visible global function definition for 'density'
SPIn: no visible global function definition for 'quantile'
SPIn: no visible global function definition for 'solve.QP'
bootSPIn: no visible global function definition for 'runif'
plot.SPIn: no visible global function definition for 'hist'
plot.SPIn: no visible global function definition for 'lines'
plot.SPIn: no visible global function definition for 'text'
plot.SPIn: no visible global function definition for 'quantile'
plot.SPIn: no visible global function definition for 'legend'
Undefined global functions or variables:
  density hist legend lines quantile runif solve.QP text
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "text")
  importFrom("stats", "density", "quantile", "runif")
to your NAMESPACE file.
spi: no visible global function definition for 'read.table'
spi: no visible global function definition for 'ecdf'
spi: no visible global function definition for 'qnorm'
spi: no visible global function definition for 'colorRampPalette'
spi: no visible global function definition for 'filled.contour'
spi: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis colorRampPalette ecdf filled.contour qnorm read.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "filled.contour")
  importFrom("stats", "ecdf", "qnorm")
  importFrom("utils", "read.table")
to your NAMESPACE file.
NoSep: no visible global function definition for 'setNames'
Reshape: no visible global function definition for 'setNames'
Reshape: no visible global function definition for 'reshape'
read.concat: no visible global function definition for 'count.fields'
read.concat: no visible global function definition for 'read.table'
Undefined global functions or variables:
  count.fields read.table reshape setNames
Consider adding
  importFrom("stats", "reshape", "setNames")
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
R2.global: no visible global function definition for 'var'
calculer.var.exp: no visible global function definition for 'var'
creer.noeud: no visible global function definition for 'var'
ponderer.classe: no visible global function definition for 'var'
ponderer.classe: no visible global function definition for 'cov'
spodt: no visible global function definition for 'model.frame'
spodt.tree: no visible global function definition for 'plot.new'
spodt.tree: no visible global function definition for 'par'
spodt.tree: no visible global function definition for 'plot.window'
spodt.tree: no visible global function definition for 'text'
spodt.tree: no visible global function definition for 'segments'
test.spodt: no visible global function definition for 'model.frame'
test.spodt: no visible global function definition for 'hist'
test.spodt: no visible global function definition for 'abline'
tracer.noeud: no visible global function definition for 'text'
tracer.noeud: no visible global function definition for 'segments'
Undefined global functions or variables:
  abline cov hist model.frame par plot.new plot.window segments text
  var
Consider adding
  importFrom("graphics", "abline", "hist", "par", "plot.new",
             "plot.window", "segments", "text")
  importFrom("stats", "cov", "model.frame", "var")
to your NAMESPACE file.
Ell.Theta: no visible global function definition for 'ell.theta'
confid.int.theta: no visible global function definition for 'qchisq'
confid.int.theta : sim.c: no visible global function definition for
  'runif'
confid.int.theta: no visible global function definition for 'quantile'
dd.est: no visible global function definition for 'ecdf'
ks.sporm : Simul: no visible global function definition for 'runif'
ks.stat: no visible global function definition for 'ecdf'
plotor: no visible global function definition for 'ecdf'
plotor: no visible global function definition for 'plot'
test.theta: no visible global function definition for 'ecdf'
test.theta : sim: no visible global function definition for 'runif'
Undefined global functions or variables:
  ecdf ell.theta plot qchisq quantile runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "ecdf", "qchisq", "quantile", "runif")
to your NAMESPACE file.
fetch_NBAPlayerStatistics: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.7Mb
plot.SPRT: no visible global function definition for 'par'
plot.SPRT: no visible global function definition for 'plot'
plot.SPRT: no visible global function definition for 'abline'
print.SPRT: no visible global function definition for 'head'
Undefined global functions or variables:
  abline head par plot
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("utils", "head")
to your NAMESPACE file.
fssa20: no visible global function definition for 'runif'
fssa2d: no visible global function definition for 'runif'
fssa30: no visible global function definition for 'runif'
fssa3d: no visible global function definition for 'runif'
ssa20: no visible global function definition for 'runif'
ssa2d: no visible global function definition for 'runif'
ssa30: no visible global function definition for 'runif'
ssa3d: no visible global function definition for 'runif'
ssi20: no visible global function definition for 'runif'
ssi2d: no visible global function definition for 'runif'
ssi30: no visible global function definition for 'runif'
ssi3d: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   1.9Mb
plotThin: no visible global function definition for 'par'
plotThin: no visible global function definition for 'dev.interactive'
plotThin: no visible global function definition for 'plot'
plotThin: no visible global function definition for 'hist'
thin: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  dev.interactive hist par plot write.csv
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "hist", "par", "plot")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
.GameSPT: no visible global function definition for 'runif'
.GameSPT: no visible global function definition for 'points'
.GameST: no visible global function definition for 'runif'
.GameST: no visible global function definition for 'points'
.arc: no visible global function definition for 'lines'
.ptpedal: no visible global function definition for 'polygon'
.sptpedal2: no visible global function definition for 'segments'
.sptpedal3: no visible global function definition for 'polygon'
.sptpedal4: no visible global function definition for 'polygon'
chaos.spt: no visible global function definition for 'plot'
chaos.spt: no visible global function definition for 'polygon'
chaos.spt: no visible global function definition for 'runif'
chaos.spt: no visible global function definition for 'points'
chaos.st: no visible global function definition for 'plot'
chaos.st: no visible global function definition for 'polygon'
chaos.st: no visible global function definition for 'runif'
chaos.st: no visible global function definition for 'points'
plot.spt: no visible global function definition for 'plot'
plot.spt: no visible global function definition for 'polygon'
plot.st: no visible global function definition for 'plot'
plot.st: no visible global function definition for 'polygon'
Undefined global functions or variables:
  lines plot points polygon runif segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "polygon",
             "segments")
  importFrom("stats", "runif")
to your NAMESPACE file.
CMCSimulation: no visible global function definition for 'rexp'
CMCSimulation: no visible global function definition for 'plot'
CMCSimulation: no visible global function definition for 'axis'
booking_clerkMC: no visible global function definition for 'runif'
booking_clerkMC: no visible global function definition for 'rexp'
fixedpoint_show: no visible global function definition for 'plot'
fixedpoint_show: no visible global function definition for 'lines'
mean.trapTransect: no visible global function definition for
  'weighted.mean'
newtonraphson_show: no visible global function definition for 'plot'
newtonraphson_show: no visible global function definition for 'lines'
print.transectHolder: no visible global function definition for 'str'
print.trapTransect: no visible global function definition for 'str'
sd.transectHolder: no visible global function definition for 'sd'
simulate.transectHolder: no visible global function definition for
  'runif'
Undefined global functions or variables:
  axis lines plot rexp runif sd str weighted.mean
Consider adding
  importFrom("graphics", "axis", "lines", "plot")
  importFrom("stats", "rexp", "runif", "sd", "weighted.mean")
  importFrom("utils", "str")
to your NAMESPACE file.
sGda : <anonymous>: no visible global function definition for 'cov'
sortgene: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  cov model.matrix
Consider adding
  importFrom("stats", "cov", "model.matrix")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'RJDBC' 'RMySQL' 'RODBC' 'RPostgreSQL' 'RSQLite' 'tcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cacheQuery: no visible global function definition for 'read.csv'
cacheQuery: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  read.csv write.csv
Consider adding
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
SQN: no visible binding for global variable 'median'
SQN: no visible global function definition for 'quantile'
SQN.demo.data: no visible global function definition for 'rnorm'
mix.qn: no visible global function definition for 'ecdf'
mix.qn: no visible global function definition for 'quantile'
Undefined global functions or variables:
  ecdf median quantile rnorm
Consider adding
  importFrom("stats", "ecdf", "median", "quantile", "rnorm")
to your NAMESPACE file.
plot.srafit: no visible global function definition for 'layout'
plot.srafit: no visible global function definition for 'par'
sraData : vartruncGauss : ff: no visible global function definition for
  'dnorm'
sraData : vartruncGauss : ff: no visible global function definition for
  'pnorm'
sraData : vartruncGauss: no visible global function definition for
  'uniroot'
sraPlotMean: no visible global function definition for 'axis'
sraPlotMean: no visible global function definition for 'points'
sraPlotMean: no visible global function definition for 'lines'
sraPlotMeanResid: no visible global function definition for 'axis'
sraPlotMeanResid: no visible global function definition for 'abline'
sraPlotMeanResid: no visible global function definition for 'points'
sraPlotVar: no visible global function definition for 'axis'
sraPlotVar: no visible global function definition for 'points'
sraPlotVar: no visible global function definition for 'lines'
sraPlotVarResid: no visible global function definition for 'axis'
sraPlotVarResid: no visible global function definition for 'abline'
sraPlotVarResid: no visible global function definition for 'points'
sraPlotlegend: no visible global function definition for 'legend'
sraStartingvalues : sraStartingvalues.mu0: no visible global function
  definition for 'rnorm'
sraStartingvalues : sraStartingvalues.logvarA0: no visible global
  function definition for 'rnorm'
sraStartingvalues : sraStartingvalues.logvarE0: no visible global
  function definition for 'rnorm'
sraStartingvalues: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  abline axis dnorm layout legend lines par pnorm points rnorm uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "layout", "legend", "lines",
             "par", "points")
  importFrom("stats", "dnorm", "pnorm", "rnorm", "uniroot")
to your NAMESPACE file.
Found the following hidden files and directories:
  .Rapp.history
  inst/script/.Rapp.history
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
File 'sROC/R/onload.R':
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

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

AUC : TrapezInt: no visible global function definition for 'approx'
AUC : SimpsonInt: no visible global function definition for 'approx'
CI.CDF: no visible global function definition for 'qnorm'
bw.CDF: no visible global function definition for 'sd'
bw.CDF: no visible global function definition for 'IQR'
bw.CDF.pi: no visible global function definition for 'sd'
bw.CDF.pi: no visible global function definition for 'bw.nrd0'
bw.CDF.pi: no visible global function definition for 'bw.nrd'
bw.CDF.pi: no visible global function definition for 'bw.ucv'
bw.CDF.pi: no visible global function definition for 'bw.bcv'
bw.CDF.pi: no visible global function definition for 'bw.SJ'
bw.CDF.pi: no visible global function definition for 'IQR'
plot.CDF: no visible global function definition for 'plot.default'
plot.CDF: no visible global function definition for 'lines'
plot.CDF: no visible global function definition for 'polygon'
plot.ROC: no visible global function definition for 'plot.default'
plot.ROC: no visible global function definition for 'abline'
Undefined global functions or variables:
  IQR abline approx bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv lines
  plot.default polygon qnorm sd
Consider adding
  importFrom("graphics", "abline", "lines", "plot.default", "polygon")
  importFrom("stats", "IQR", "approx", "bw.SJ", "bw.bcv", "bw.nrd",
             "bw.nrd0", "bw.ucv", "qnorm", "sd")
to your NAMESPACE file.
ssd : correction_method_D: no visible global function definition for
  'rnorm'
ssd : generate_bootstrap: no visible global function definition for
  'rmultinom'
ssd : bootstrap_method: no visible global function definition for
  'median'
ssd : bootstrap_method: no visible global function definition for
  'quantile'
ssd : unbalanced_generate_bootstrap: no visible global function
  definition for 'rmultinom'
ssd : unbalanced_bootstrap_method: no visible global function
  definition for 'median'
ssd : unbalanced_bootstrap_method: no visible global function
  definition for 'quantile'
ssd: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  median qchisq quantile rmultinom rnorm
Consider adding
  importFrom("stats", "median", "qchisq", "quantile", "rmultinom",
             "rnorm")
to your NAMESPACE file.
L_hNV: no visible global function definition for 'pnorm'
L_hNV_rho: no visible global function definition for 'pnorm'
eff.ssfa: no visible global function definition for 'pnorm'
plot_fitted: no visible global function definition for 'lines'
plot_moran: no visible global function definition for 'residuals'
print.summary.ssfa: no visible global function definition for
  'printCoefmat'
ssfa: no visible global function definition for 'model.frame'
ssfa: no visible global function definition for 'model.response'
ssfa.fit: no visible global function definition for 'lm'
ssfa.fit: no visible global function definition for 'var'
ssfa.fit: no visible global function definition for 'logLik'
summary.ssfa: no visible global function definition for 'pnorm'
summary.ssfa: no visible global function definition for 'logLik'
summary.ssfa: no visible global function definition for 'pchisq'
summary.ssfa: no visible binding for global variable 'df'
u.ssfa: no visible global function definition for 'dnorm'
u.ssfa: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  df dnorm lines lm logLik model.frame model.response pchisq pnorm
  printCoefmat residuals var
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "df", "dnorm", "lm", "logLik", "model.frame",
             "model.response", "pchisq", "pnorm", "printCoefmat",
             "residuals", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'survey'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.model: no visible global function definition for 'hadamard'
Undefined global functions or variables:
  hadamard
sslCoTrain: no visible global function definition for 'predict'
sslSelfTrain: 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 significant warnings:
  Warning: working directory was changed to 'D:/temp/Rtmpe8Fime', resetting
Found the following significant warnings:
  Warning: working directory was changed to 'D:/temp/Rtmp0uYpuN', resetting
map.world: no visible global function definition for 'par'
map.world: no visible global function definition for 'plot.new'
map.world: no visible global function definition for 'plot.window'
map.world: no visible global function definition for 'lines'
map.world: no visible global function definition for 'title'
map.world: no visible global function definition for 'axis'
map.world: no visible global function definition for 'box'
plot.smooth.sspline: no visible global function definition for
  'predict'
plot.smooth.sspline: no visible global function definition for
  'filled.contour'
plot.smooth.sspline: no visible binding for global variable
  'terrain.colors'
plot.smooth.sspline: no visible global function definition for 'title'
plot.smooth.sspline: no visible global function definition for 'axis'
station: no visible binding for global variable 'WTdiff'
station: no visible global function definition for 'points'
Undefined global functions or variables:
  WTdiff axis box filled.contour lines par plot.new plot.window points
  predict terrain.colors title
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "box", "filled.contour", "lines", "par",
             "plot.new", "plot.window", "points", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
calcgroup : probtotrating: no visible global function definition for
  'convolve'
enterratdata: no visible global function definition for 'edit'
gplot.SSrat: no visible global function definition for 'par'
gplot.SSrat: no visible global function definition for 'plot'
gplot.SSrat: no visible global function definition for 'legend'
Undefined global functions or variables:
  convolve edit legend par plot
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "convolve")
  importFrom("utils", "edit")
to your NAMESPACE file.
SS.ID: no visible global function definition for 'var'
SS.sim.chol: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm var
Consider adding
  importFrom("stats", "rnorm", "var")
to your NAMESPACE file.
error.est : <anonymous>: no visible global function definition for
  'median'
holm.robust: no visible global function definition for 'pnorm'
holm.robust: no visible global function definition for 'median'
holm.robust: no visible global function definition for 'mad'
huberize: no visible global function definition for 'quantile'
ssvd.initial: no visible global function definition for 'mad'
ssvd.iter.thresh: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad median pnorm quantile
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "quantile")
to your NAMESPACE file.
.ls.objects: no visible binding for global variable 'object.size'
Undefined global functions or variables:
  object.size
Consider adding
  importFrom("utils", "object.size")
to your NAMESPACE file.
.expandLevels: no visible global function definition for 'na.omit'
.ffStack: no visible global function definition for 'na.omit'
.ffffStack: no visible global function definition for 'na.omit'
Stack : <anonymous>: no visible global function definition for
  'na.omit'
ffStack,ffdf-data.frame: no visible global function definition for
  'na.omit'
ffStack,ffdf-ffdf: no visible global function definition for 'na.omit'
ffStack,ffdf-list: 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.
genericPlot: no visible global function definition for 'dev.new'
genericPlot: no visible global function definition for 'par'
genericPlot: no visible global function definition for 'rainbow'
genericPlot: no visible global function definition for 'plot'
genericPlot: no visible global function definition for 'lines'
genericPlot: no visible global function definition for 'legend'
genericPlot: no visible global function definition for 'dev.copy2pdf'
genericPlot: no visible global function definition for 'dev.copy2eps'
genericPlot: no visible global function definition for 'dev.print'
genericPlot: no visible binding for global variable 'png'
genericPlot: no visible binding for global variable 'tiff'
plotStrains: no visible global function definition for 'rainbow'
plotStrains: no visible global function definition for 'dev.new'
plotStrains: no visible global function definition for 'par'
plotStrains: no visible global function definition for 'plot'
plotStrains: no visible global function definition for 'lines'
plotStrains: no visible global function definition for 'legend'
plotStrains: no visible global function definition for 'dev.copy2pdf'
plotStrains: no visible global function definition for 'dev.copy2eps'
plotStrains: no visible global function definition for 'dev.print'
plotStrains: no visible binding for global variable 'png'
plotStrains: no visible binding for global variable 'tiff'
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par plot png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'np' 'sp'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'np' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for 'npudensbw'
stkde: no visible global function definition for 'npudens'
stkde: no visible global function definition for 'quantile'
stkde: no visible global function definition for 'heat.colors'
stkde: no visible global function definition for 'par'
stkde: no visible global function definition for 'image'
stkde: no visible global function definition for 'contour'
stkde.base: no visible global function definition for 'npudensbw'
stkde.base: no visible global function definition for 'npudens'
stkde.sig: no visible global function definition for 'SpatialPoints'
stkde.sig: no visible global function definition for 'spsample'
stkde.sig: no visible global function definition for 'bbox'
stkde.sig: no visible global function definition for 'quantile'
stkde.sig: no visible global function definition for 'heat.colors'
stkde.sig: no visible global function definition for 'par'
stkde.sig: no visible global function definition for 'image'
stkde.sig: no visible global function definition for 'contour'
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
find.names: no visible global function definition for 'na.omit'
generate.names: no visible global function definition for 'na.omit'
standardize.countrynames: no visible global function definition for
  'data'
standardize.names: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    include   8.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   5.0Mb
'library' or 'require' call to 'codetools' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'codetools' 'gss'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following hidden files and directories:
  inst/.Renviron.d
  inst/.Rprofile.d
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
actvspred: no visible global function definition for 'quantile'
actvspred: no visible global function definition for 'aggregate'
actvspred: no visible global function definition for 'par'
actvspred: no visible global function definition for 'plot'
actvspred: no visible global function definition for 'lines'
auc: no visible global function definition for 'par'
auc: no visible global function definition for 'plot'
decile: no visible global function definition for 'quantile'
dqcontinuous : numoutliers: no visible global function definition for
  'quantile'
dqcontinuous : <anonymous>: no visible global function definition for
  'sd'
dqcontinuous : <anonymous>: no visible global function definition for
  'quantile'
gini: no visible global function definition for 'par'
gini: no visible global function definition for 'plot'
gini: no visible global function definition for 'abline'
iv: no visible global function definition for 'quantile'
iv: no visible global function definition for 'aggregate'
ks: no visible global function definition for 'aggregate'
ks: no visible global function definition for 'par'
ks: no visible global function definition for 'plot'
ks: no visible global function definition for 'lines'
outliers: no visible global function definition for 'quantile'
outliers: no visible global function definition for 'na.omit'
pentile: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline aggregate lines na.omit par plot quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot")
  importFrom("stats", "aggregate", "na.omit", "quantile", "sd")
to your NAMESPACE file.
inspect: no visible global function definition for 'par'
inspect: no visible global function definition for 'abline'
inspect: no visible global function definition for 'lines'
inspect: no visible global function definition for 'points'
plotfit: no visible global function definition for 'dev.off'
plotfit: no visible global function definition for 'par'
plotfit: no visible global function definition for 'lines'
plotfit: no visible global function definition for 'points'
plotfit: no visible global function definition for 'legend'
plothill: no visible global function definition for 'par'
plothill: no visible global function definition for 'abline'
plothill: no visible global function definition for 'points'
plotmultifit: no visible global function definition for 'par'
plotmultifit: no visible global function definition for 'lines'
plotmultifit: no visible global function definition for 'points'
plotmultifit: no visible global function definition for 'pexp'
plotmultifit: no visible global function definition for 'plnorm'
plotmultifit: no visible global function definition for 'ppois'
plotmultifit: no visible global function definition for 'legend'
plotols: no visible global function definition for 'dev.off'
plotols: no visible global function definition for 'lm'
plotols: no visible global function definition for 'par'
plotols: no visible global function definition for 'abline'
plotols: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline dev.off legend lines lm par pexp plnorm points ppois
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "points")
  importFrom("stats", "lm", "pexp", "plnorm", "ppois")
to your NAMESPACE file.
getStp: no visible global function definition for 'lm'
plot.steeptest: no visible global function definition for 'plot'
plot.steeptest: no visible global function definition for 'axis'
plot.steeptest: no visible global function definition for 'box'
plot.steeptest: no visible global function definition for 'lm'
plot.steeptest: no visible global function definition for 'abline'
plot.steeptest: no visible global function definition for 'legend'
plot.steeptest: no visible global function definition for
  'as.graphicsAnnot'
steeptest: no visible global function definition for 'lm'
summary.steeptest: no visible global function definition for 'var'
summary.steeptest: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline as.graphicsAnnot axis box legend lm plot quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend", "plot")
  importFrom("stats", "lm", "quantile", "var")
to your NAMESPACE file.
Stem.Bootstrap: no visible global function definition for 'runif'
filtering: no visible global function definition for 'is.ts'
filtering: no visible global function definition for 'ts'
filtering: no visible global function definition for 'start'
filtering: no visible global function definition for 'end'
filtering: no visible global function definition for 'frequency'
kalman: no visible global function definition for 'ts'
smoothing: no visible global function definition for 'is.ts'
smoothing: no visible global function definition for 'ts'
smoothing: no visible global function definition for 'start'
smoothing: no visible global function definition for 'end'
smoothing: no visible global function definition for 'frequency'
Undefined global functions or variables:
  end frequency is.ts runif start ts
Consider adding
  importFrom("stats", "end", "frequency", "is.ts", "runif", "start",
             "ts")
to your NAMESPACE file.
cv.step.plr: no visible global function definition for 'binomial'
cv.step.plr: no visible global function definition for 'predict'
cv.step.plr: no visible binding for global variable 'var'
plr: no visible global function definition for 'binomial'
predict.stepplr: no visible global function definition for 'predict'
summary.plr: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  binomial pnorm predict var
Consider adding
  importFrom("stats", "binomial", "pnorm", "predict", "var")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plr-internal':
  'anova.stepplr' 'print.plr' 'print.stepplr' 'summary.plr'
  'summary.stepplr'

S3 methods shown with full name in documentation object 'predict.plr':
  'predict.plr'

S3 methods shown with full name in documentation object 'predict.stepplr':
  'predict.stepplr'

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.
File 'stepPlr/libs/i386/stepPlr.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: 'cg_descent.o'
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
    Object: 'cg_descent.o'
File 'stepPlr/libs/x64/stepPlr.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: 'cg_descent.o'
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
    Object: 'cg_descent.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
d1spectrum: no visible global function definition for 'fft'
d2spectrum: no visible global function definition for 'fft'
plot.d1nat: no visible global function definition for 'plot'
plot.d1nat: no visible global function definition for 'lines'
plot.d1nat: no visible global function definition for 'legend'
plot.d1nat: no visible global function definition for 'title'
plot.d1spec: no visible global function definition for 'plot'
plot.d1spec: no visible global function definition for 'lines'
plot.d1spec: no visible global function definition for 'legend'
plot.d1spec: no visible global function definition for 'title'
plot.d2spec: no visible global function definition for 'plot'
plot.d2spec: no visible global function definition for 'lines'
plot.d2spec: no visible global function definition for 'legend'
plot.d2spec: no visible global function definition for 'title'
plot.pvalign: no visible global function definition for 'plot'
plot.pvalign: no visible global function definition for 'lines'
plot.pvalign: no visible global function definition for 'legend'
plot.pvalign: no visible global function definition for 'title'
print.d1nat: no visible global function definition for 'plot'
print.d1spec: no visible global function definition for 'plot'
print.d2spec: no visible global function definition for 'plot'
print.pvalign: no visible global function definition for 'plot'
utild1bin: no visible global function definition for 'median'
utild1bin: no visible global function definition for 'sd'
utild1clean: no visible global function definition for 'sd'
utild1filt: no visible global function definition for 'convolve'
Undefined global functions or variables:
  convolve fft legend lines median plot sd title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "title")
  importFrom("stats", "convolve", "fft", "median", "sd")
to your NAMESPACE file.
na.stinterp.default: no visible global function definition for 'time'
na.stinterp.default: no visible global function definition for
  'na.omit'
Undefined global functions or variables:
  na.omit time
Consider adding
  importFrom("stats", "na.omit", "time")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: working directory was changed to 'D:/temp/RtmpUzyEuO', resetting
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tthread/tinythread.h:632:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/StMoSim.Rcheck/00install.out' for details.
myQQNorm: no visible global function definition for 'mad'
myQQNorm: no visible global function definition for 'qnorm'
myQQNorm: no visible global function definition for 'plot'
myQQNorm: no visible global function definition for 'matlines'
myQQNorm: no visible global function definition for 'points'
myQQNorm: no visible global function definition for 'qqline'
myQQNorm: no visible global function definition for 'box'
qqnormSim,lm: no visible global function definition for 'resid'
Undefined global functions or variables:
  box mad matlines plot points qnorm qqline resid
Consider adding
  importFrom("graphics", "box", "matlines", "plot", "points")
  importFrom("stats", "mad", "qnorm", "qqline", "resid")
to your NAMESPACE file.
sharpe: no visible global function definition for 'sd'
sortino: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Namespace with empty importFrom: 'tcltk2'
DetailOpLines: no visible global function definition for
  'tkProgressBar'
DetailOpLines: no visible global function definition for
  'setTkProgressBar'
MultiTrainWithInventory: no visible global function definition for
  'tkProgressBar'
MultiTrainWithInventory: no visible global function definition for
  'setTkProgressBar'
SimHistory: no visible global function definition for 'tkProgressBar'
SimHistory: no visible global function definition for
  'setTkProgressBar'
Undefined global functions or variables:
  setTkProgressBar tkProgressBar
Error in re-building vignettes:
  ...
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "VignetteforSTPGA.ltx" --max-iterations=20 -I "D:/RCompile/recent/R/share/texmf/tex/latex" -I "D:/RCompile/recent/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed

LaTeX errors:
! LaTeX Error: File `dirtytalk.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

Execution halted
Packages in Depends field not imported from:
  'cubature' 'deldir' 'splancs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
StratPhyloCongruence: no visible global function definition for 'runif'
StratPhyloCongruence: no visible global function definition for
  'txtProgressBar'
StratPhyloCongruence: no visible global function definition for
  'setTxtProgressBar'
StratPhyloCongruence: no visible global function definition for 'pnorm'
StratPhyloCongruence: no visible global function definition for 'sd'
geoscalePhylo: no visible global function definition for 'data'
geoscalePhylo: no visible global function definition for 'par'
geoscalePhylo: no visible global function definition for 'text'
geoscalePhylo: no visible global function definition for 'segments'
geoscalePhylo: no visible global function definition for 'rect'
geoscalePhylo: no visible global function definition for 'rgb'
Undefined global functions or variables:
  data par pnorm rect rgb runif sd segments setTxtProgressBar text
  txtProgressBar
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "rect", "segments", "text")
  importFrom("stats", "pnorm", "runif", "sd")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
HRatio: no visible global function definition for 'qnorm'
icweib: no visible global function definition for 'model.frame'
icweib: no visible binding for global variable 'na.pass'
icweib: no visible global function definition for 'complete.cases'
icweib: no visible global function definition for 'model.matrix'
icweib: no visible global function definition for 'optim'
icweib: no visible global function definition for 'pchisq'
icweib: no visible global function definition for 'pnorm'
plot.icweib : getstat: no visible global function definition for
  'qnorm'
plot.icweib: no visible global function definition for 'plot'
plot.icweib: no visible global function definition for 'lines'
plot.icweib: no visible global function definition for 'legend'
print.icweib: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  complete.cases legend lines model.frame model.matrix na.pass optim
  pchisq plot pnorm qnorm
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "complete.cases", "model.frame", "model.matrix",
             "na.pass", "optim", "pchisq", "pnorm", "qnorm")
to your NAMESPACE file.
'library' or 'require' call to 'ROAuth' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  icu55/i18n/winnmfmt.h:152:11: warning: 'icu_55::Win32NumberFormat::fFractionDigitsSet' will be initialized after [-Wreorder]
  icu55/i18n/winnmfmt.h:151:17: warning:   'icu_55::FormatInfo* icu_55::Win32NumberFormat::fFormatInfo' [-Wreorder]
  icu55/i18n/winnmfmt.cpp:138:1: warning:   when initialized here [-Wreorder]
See 'd:/Rcompile/CRANpkg/local/3.5/stringi.Rcheck/00install.out' for details.
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
File which contains pragma(s) suppressing important diagnostics:
  'src/icu55/i18n/decNumber.c'
breakpoints.formula: no visible global function definition for
  '%dopar%'
breakpoints.formula: no visible binding for global variable 'i'
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
sctest.default: no visible global function definition for 'tail'
Undefined global functions or variables:
  %dopar% i tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
PlotHypTree: no visible global function definition for 'browseURL'
treePValues: no visible global function definition for 'lm'
treePValues: no visible global function definition for 'pf'
plot,GBH-ANY: no visible binding for global variable 'sorted.hyp'
plot,GBH-ANY: no visible binding for global variable 'pval'
plot,GBH-ANY: no visible binding for global variable 'group'
plot,GBH-ANY: no visible binding for global variable 'type'
Undefined global functions or variables:
  browseURL group lm pf pval sorted.hyp type
Consider adding
  importFrom("stats", "lm", "pf")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'stsm.class' 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.
stsm.model: no visible global function definition for 'is.ts'
stsm.model: no visible global function definition for 'var'
stsm.model: no visible global function definition for 'frequency'
stsm.model: no visible global function definition for 'na.omit'
stsm.model: no visible global function definition for 'fft'
stsm.model: no visible global function definition for 'new'
stsm.sgf: no visible global function definition for 'frequency'
char2numeric,stsm: no visible global function definition for
  'frequency'
set.cpar,stsm: no visible global function definition for 'validObject'
set.nopars,stsm: no visible global function definition for
  'validObject'
set.pars,stsm: no visible global function definition for 'validObject'
transPars,stsm: no visible global function definition for 'var'
Undefined global functions or variables:
  fft frequency is.ts na.omit new validObject var
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "fft", "frequency", "is.ts", "na.omit", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
SubLasso: no visible global function definition for 'predict'
SubLasso: no visible global function definition for 'coef'
SubLasso: no visible global function definition for 'dev.new'
SubLasso: no visible global function definition for 'cor'
SubLasso: no visible global function definition for 'boxplot'
predict.sublasso: no visible global function definition for 'predict'
Undefined global functions or variables:
  boxplot coef cor dev.new predict
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "boxplot")
  importFrom("stats", "coef", "cor", "predict")
to your NAMESPACE file.
identifyGraph: no visible global function definition for 'phyper'
mytriangle: no visible global function definition for 'symbols'
plotGraph: no visible global function definition for 'par'
plotGraph: no visible global function definition for 'plot'
updateOrgEnvir: no visible global function definition for 'read.table'
Undefined global functions or variables:
  par phyper plot read.table symbols
Consider adding
  importFrom("graphics", "par", "plot", "symbols")
  importFrom("stats", "phyper")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following significant warnings:
  RMcrt.h:80:13: warning: 'extendedleaps::rmdata::gdt' will be initialized after [-Wreorder]
  RMcrt.h:76:10: warning:   'bool extendedleaps::rmdata::unreliable' [-Wreorder]
  RMcrt.cpp:19:1: warning:   when initialized here [-Wreorder]
  RVcrt.h:101:18: warning: 'extendedleaps::rvdata::e' will be initialized after [-Wreorder]
  RVcrt.h:99:10: warning:   'bool extendedleaps::rvdata::unreliable' [-Wreorder]
  RVcrt.cpp:36:1: warning:   when initialized here [-Wreorder]
See 'd:/Rcompile/CRANpkg/local/3.5/subselect.Rcheck/00install.out' for details.
predict.subsemble: no visible global function definition for 'predict'
predict.subsemble: no visible binding for global variable 'family'
subsemble: no visible global function definition for 'gaussian'
subsemble: no visible global function definition for 'detectCores'
subsemble : .make_Z_l: no visible global function definition for
  'parSapply'
subsemble : .make_Z_l: no visible global function definition for
  'makeCluster'
subsemble : .make_Z_l: no visible global function definition for
  'stopCluster'
subsemble: no visible global function definition for 'parSapply'
subsemble: no visible global function definition for 'makeCluster'
subsemble: no visible global function definition for 'stopCluster'
subsemble: no visible global function definition for 'predict'
Undefined global functions or variables:
  detectCores family gaussian makeCluster parSapply predict stopCluster
Consider adding
  importFrom("stats", "family", "gaussian", "predict")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'ROCR' 'penalized'
  Please remove these calls from your code.
ELF: no visible global function definition for 'pt'
ELF: no visible global function definition for 'qnorm'
ELF: no visible global function definition for 'lm'
ELF: no visible global function definition for 'lowess'
ELF: no visible global function definition for 'dnorm'
ELF: no visible global function definition for 'approx'
subtype: no visible global function definition for 'runif'
subtype: no visible global function definition for 'hclust'
subtype: no visible global function definition for 'dist'
subtype: no visible global function definition for 'cutree'
subtype: no visible global function definition for 'pt'
subtype: no visible global function definition for 'heatmap'
test_subtype_only: no visible global function definition for 'pt'
test_subtype_only: no visible global function definition for 'survdiff'
test_subtype_only: no visible global function definition for 'survfit'
test_subtype_only: no visible global function definition for 'title'
ufun: no visible global function definition for 'dnorm'
ufun: no visible global function definition for 'lowess'
Undefined global functions or variables:
  approx cutree dist dnorm hclust heatmap lm lowess pt qnorm runif
  survdiff survfit title
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "approx", "cutree", "dist", "dnorm", "hclust",
             "heatmap", "lm", "lowess", "pt", "qnorm", "runif")
to your NAMESPACE file.
playSudoku : replot: no visible global function definition for 'par'
playSudoku : replot: no visible global function definition for 'plot'
playSudoku : replot: no visible global function definition for
  'segments'
playSudoku : replot: no visible global function definition for 'text'
playSudoku: no visible global function definition for 'tktoplevel'
playSudoku: no visible global function definition for 'tkwm.title'
playSudoku: no visible global function definition for 'tkrplot'
playSudoku: no visible global function definition for 'tktext'
playSudoku: no visible global function definition for 'tkscrollbar'
playSudoku : <anonymous>: no visible global function definition for
  'tkyview'
playSudoku: no visible global function definition for 'tkconfigure'
playSudoku : <anonymous>: no visible global function definition for
  'tkset'
playSudoku: no visible global function definition for 'tkpack'
playSudoku: no visible global function definition for 'tcl'
playSudoku: no visible global function definition for 'tkcget'
playSudoku : showz: no visible global function definition for
  'tkrreplot'
playSudoku : type: no visible global function definition for 'tkinsert'
playSudoku : type: no visible global function definition for 'tksee'
playSudoku : kb: no visible global function definition for 'tkdestroy'
playSudoku: no visible global function definition for
  'getGraphicsEvent'
playSudoku: no visible global function definition for 'tkbind'
playSudoku: no visible global function definition for 'tkwait.window'
Undefined global functions or variables:
  getGraphicsEvent par plot segments tcl text tkbind tkcget tkconfigure
  tkdestroy tkinsert tkpack tkrplot tkrreplot tkscrollbar tksee tkset
  tktext tktoplevel tkwait.window tkwm.title tkyview
Consider adding
  importFrom("grDevices", "getGraphicsEvent")
  importFrom("graphics", "par", "plot", "segments", "text")
to your NAMESPACE file.
SUE.fitted.values: no visible global function definition for
  'model.frame'
SUE.lm: no visible global function definition for 'model.frame'
SUE.lm: no visible global function definition for 'lm'
SUE.lm: no visible global function definition for 'anova'
SUE.plot: no visible global function definition for 'plot'
SUE.residuals: no visible global function definition for 'model.frame'
parameters : para2: no visible global function definition for 'uniroot'
parameters: no visible global function definition for 'optimize'
parameters: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  anova lm model.frame optimize plot uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
MCMCCV: no visible global function definition for 'rnorm'
MLCVGauss: no visible global function definition for 'runif'
MLCVGauss: no visible global function definition for 'optim'
SimSunderData: no visible global function definition for 'runif'
SimSunderData: no visible global function definition for 'dist'
SimSunderData: no visible global function definition for 'rnorm'
SimSunderData: no visible global function definition for 'qgamma'
SimSunderData: no visible global function definition for 'pnorm'
SimSunderData: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  dist optim pnorm qgamma rmultinom rnorm runif
Consider adding
  importFrom("stats", "dist", "optim", "pnorm", "qgamma", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
sunter: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
supcluster : itgamma: no visible global function definition for
  'rgamma'
supcluster : itgamma: no visible global function definition for
  'dgamma'
supcluster : itgamma: no visible global function definition for 'runif'
supcluster : itbeta: no visible global function definition for 'rnorm'
supcluster : itbeta: no visible global function definition for 'runif'
supcluster : itj: no visible global function definition for 'dmultinom'
supcluster: no visible global function definition for 'kmeans'
tab1: no visible global function definition for 'image'
tab1: no visible global function definition for 'gray'
tab1: no visible global function definition for 'var'
Undefined global functions or variables:
  dgamma dmultinom gray image kmeans rgamma rnorm runif var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "dgamma", "dmultinom", "kmeans", "rgamma", "rnorm",
             "runif", "var")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'gputools'
HCLtree: no visible global function definition for 'hclust'
HCLtree: no visible global function definition for 'as.dist'
plotProfilesAcrossAllSamples: no visible global function definition for
  'matplot'
plotProfilesAcrossAllSamples: no visible global function definition for
  'matlines'
plotProfilesAcrossAllSamples: no visible global function definition for
  'axis'
plotProfilesAcrossAllSamples: no visible global function definition for
  'box'
plotProfilesWithinBicluster: no visible global function definition for
  'matplot'
plotProfilesWithinBicluster: no visible global function definition for
  'title'
plotProfilesWithinBicluster: no visible global function definition for
  'axis'
plotProfilesWithinBicluster: no visible global function definition for
  'par'
plotProfilesWithinBicluster: no visible global function definition for
  'box'
plotProfilesWithinBicluster: no visible global function definition for
  'matlines'
plotProfilesWithinBicluster: no visible global function definition for
  'legend'
Undefined global functions or variables:
  as.dist axis box hclust legend matlines matplot par title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "matlines", "matplot",
             "par", "title")
  importFrom("stats", "as.dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'boa' 'coda'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
superdiag: no visible global function definition for 'as.mcmc.list'
superdiag: no visible global function definition for 'as.mcmc'
superdiag: no visible global function definition for 'runif'
superdiag: no visible global function definition for 'geweke.diag'
superdiag: no visible global function definition for 'heidel.diag'
superdiag: no visible global function definition for 'raftery.diag'
superdiag: no visible global function definition for 'gelman.diag'
Undefined global functions or variables:
  as.mcmc as.mcmc.list gelman.diag geweke.diag heidel.diag raftery.diag
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
TrainSuperMDS: no visible global function definition for 'rnorm'
TrainSuperMDSOnce: no visible global function definition for 'cmdscale'
TrainSuperMDSOnce: no visible global function definition for 'quantile'
distmat: no visible global function definition for 'dist'
Undefined global functions or variables:
  cmdscale dist quantile rnorm
Consider adding
  importFrom("stats", "cmdscale", "dist", "quantile", "rnorm")
to your NAMESPACE file.
Files named as vignettes but with no recognized vignette engine:
   'vignettes/copulas-concordance.tex'
   'vignettes/surrosurv.tex'
(Is a VignetteBuilder field missing?)
Est.Var.CCH.trueweights: no visible binding for global variable 'var'
getEstimatesSP: no visible global function definition for 'quantile'
getEstimatesSP: no visible global function definition for 'resid'
prepareDataNP: no visible global function definition for
  'complete.cases'
prepareDataSP: no visible global function definition for
  'complete.cases'
processRawOutput: no visible global function definition for 'qnorm'
survAM.estimate: no visible global function definition for 'median'
survAM.estimate: no visible binding for global variable 'sd'
Undefined global functions or variables:
  complete.cases median qnorm quantile resid sd var
Consider adding
  importFrom("stats", "complete.cases", "median", "qnorm", "quantile",
             "resid", "sd", "var")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for 'plot'
plot.survAUC: no visible global function definition for 'lines'
plot.survErr: no visible global function definition for 'plot'
plot.survErr: no visible global function definition for 'lines'
schemper: no visible global function definition for 'predict'
schemper: no visible global function definition for 'survfit'
schemper: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx lines plot predict survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
Est.PH: no visible global function definition for 'coxph'
Inf.Cval: no visible global function definition for 'rexp'
Inf.Cval: no visible global function definition for 'var'
Inf.Cval.Delta: no visible global function definition for 'rexp'
Inf.Cval.Delta: no visible global function definition for 'var'
cvC: no visible global function definition for 'coxph'
cvC: no visible global function definition for 'weighted.mean'
Undefined global functions or variables:
  coxph rexp var weighted.mean
Consider adding
  importFrom("stats", "rexp", "var", "weighted.mean")
to your NAMESPACE file.
Files named as vignettes but with no recognized vignette engine:
   'vignettes/survClip.Rnw'
(Is a VignetteBuilder field missing?)
pearson: no visible global function definition for 'cor'
plot.survcorr: no visible global function definition for 'pnorm'
plot.survcorr: no visible global function definition for 'par'
plot.survcorr: no visible global function definition for 'plot'
plot.survcorr: no visible global function definition for 'points'
survcorr: no visible global function definition for 'model.frame'
survcorr: no visible global function definition for 'qnorm'
survcorr: no visible global function definition for 'runif'
survcorr: no visible global function definition for 'pnorm'
survcorr: no visible global function definition for 'var'
survcorr: no visible global function definition for 'qt'
Undefined global functions or variables:
  cor model.frame par plot pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   1.7Mb
'library' or 'require' call to 'survival' which was already attached by Depends.
  Please remove these calls from your code.
Survgini: 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:
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:128:36: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:152:9: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/survHE.Rcheck/00install.out' for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Packages in Depends field not imported from:
  'survC1' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.HR.FUN: no visible global function definition for 'coxph'
Est.HR.FUN: no visible global function definition for 'basehaz'
Est.HR.FUN: no visible global function definition for 'approx'
Ghat.FUN: no visible global function definition for 'survfit'
IDI.INF: no visible global function definition for 'kmcens'
IDI.INF: no visible global function definition for 'quantile'
IDI.INF.GRAPH: no visible global function definition for 'plot'
IDI.INF.GRAPH: no visible global function definition for 'lines'
IDI.INF.GRAPH: no visible global function definition for 'abline'
IDI.INF.GRAPH: no visible global function definition for 'points'
IDI.INF.GRAPH: no visible global function definition for 'title'
PTB.IDI.FUN: no visible global function definition for 'rexp'
shade: no visible global function definition for 'polygon'
Undefined global functions or variables:
  abline approx basehaz coxph kmcens lines plot points polygon quantile
  rexp survfit title
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points", "polygon",
             "title")
  importFrom("stats", "approx", "quantile", "rexp")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.6Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
betaEst: no visible global function definition for 'is'
fullKernel: no visible global function definition for 'is'
halfKernel: no visible global function definition for 'is'
kernelAuto: no visible global function definition for 'quantile'
kernelAuto: no visible global function definition for 'lm'
kernelAuto: no visible global function definition for 'pnorm'
kernelFixed: no visible global function definition for 'pnorm'
lastValue: no visible global function definition for 'pnorm'
nearValue: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  is lm pnorm quantile
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "lm", "pnorm", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
fitModel: no visible global function definition for 'var'
fitModel: no visible global function definition for 'cov'
svpls: no visible global function definition for 'pt'
Undefined global functions or variables:
  cov pt var
Consider adding
  importFrom("stats", "cov", "pt", "var")
to your NAMESPACE file.
dlgMessage.tcltkGUI: no visible global function definition for 'alarm'
dlgMessage.tcltkGUI: no visible global function definition for
  'bringToTop'
Undefined global functions or variables:
  alarm bringToTop
Consider adding
  importFrom("grDevices", "bringToTop")
  importFrom("utils", "alarm")
to your NAMESPACE file.
svd3dplot: no visible global function definition for 'wireframe'
svd3dplot: no visible global function definition for 'levelplot'
Undefined global functions or variables:
  levelplot wireframe
startHttpServer : <anonymous> : Rjsonp: no visible global function
  definition for 'localeToCharset'
Undefined global functions or variables:
  localeToCharset
Consider adding
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
.onAttach : svBrowser: no visible global function definition for
  'browseURL'
.onAttach: no visible global function definition for 'loadhistory'
Undefined global functions or variables:
  browseURL loadhistory
Consider adding
  importFrom("utils", "browseURL", "loadhistory")
to your NAMESPACE file.
completion : finalize : <anonymous>: no visible global function
  definition for 'existsFunction'
listMethods: no visible global function definition for 'findFunction'
tempvar: no visible global function definition for 'runif'
Undefined global functions or variables:
  existsFunction findFunction runif
Consider adding
  importFrom("methods", "existsFunction", "findFunction")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in 'svMisc-Ex.R' failed
The error most likely occurred in:

> ### Name: toRjson
> ### Title: Convert R object to and from RJSON specification
> ### Aliases: toRjson evalRjson listToJson
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## A complex R object
> Robj <- structure(list(
+ 	a = as.double(c(1:5, 6)),
+ 	LETTERS,
+ 	c = c(c1 = 4.5, c2 = 7.8, c3 = Inf, c4 = -Inf, NA, c6 = NaN),
+ 	c(TRUE, FALSE, NA),
+ 	e = factor(c("a", "b", "a")),
+ 	f = "this is a \"string\"\nwith\tspecial chars",
+ 	g = matrix(rnorm(4), ncol = 2),
+ 	`h&'$@` = data.frame(x = 1:3, y = rnorm(3),
+ 		fact = factor(c("b", "a", "b"))),
+ 	i = Sys.Date(),
+     j = list(1:5, y = "another item")),
+     comment = "My comment\n\"",
+     anAttrib = 1:10,
+     anotherAttrib = list(TRUE, y = 1:4))
> 
> ## Convert to simplest RJSON, without attributes
> Rjson1 <- toRjson(Robj)
> Rjson1
[1] list(c(1., 2., 3., 4., 5., 6.), c("A", "B", "C", "D", "E", "F",                              
[2] "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S",                             
[3] "T", "U", "V", "W", "X", "Y", "Z"), c(4.5, 7.8, Inf, -Inf, NA,                               
[4] NaN), c(TRUE, FALSE, NA), c("a", "b", "a"), "this is a \\"string\\"\\nwith\\tspecial chars", 
[5]     c(-0.626453810742332, 0.183643324222082, -0.835628612410047,                             
[6]     1.59528080213779), list(seq(1, 3), c(0.329507771815361, -0.820468384118015,              
[7]     0.487429052428485), c("b", "a", "b")), "2018-01-05", list(                               
[8]         seq(1, 5), "another item"))                                                          
> evalRjson(Rjson1)
Error in .getClassesFromCache(Class) : 
  class should be either a character-string name or a class definition
Calls: evalRjson ... new -> getClass -> getClassDef -> .getClassesFromCache
Execution halted
Package in Depends field not imported from: 'kernlab'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'svmpath/libs/i386/svmpath.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'mi02lib.o', 'mi05funs.o', 'mi10unix.o', 'mi11sys.o',
      'mi12solv.o', 'mi20amat.o', 'mi25bfac.o', 'mi26bfac.o',
      'mi27lu.o', 'mi30spec.o', 'mi35mps.o', 'mi36mps.o', 'mi40bfil.o',
      'mi50lp.o', 'mi60srch.o', 'mi65rmod.o', 'mi70nobj.o',
      'mi80ncon.o', 'mi81ncon.o'
File 'svmpath/libs/x64/svmpath.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'mi02lib.o', 'mi05funs.o', 'mi10unix.o', 'mi11sys.o',
      'mi12solv.o', 'mi20amat.o', 'mi25bfac.o', 'mi26bfac.o',
      'mi27lu.o', 'mi30spec.o', 'mi35mps.o', 'mi36mps.o', 'mi40bfil.o',
      'mi50lp.o', 'mi60srch.o', 'mi65rmod.o', 'mi70nobj.o',
      'mi80ncon.o', 'mi81ncon.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
processSocket: no visible global function definition for 'URLdecode'
Undefined global functions or variables:
  URLdecode
Consider adding
  importFrom("utils", "URLdecode")
to your NAMESPACE file.
completeCol: no visible global function definition for 'colors'
completeCol: no visible global function definition for 'col2rgb'
completeCol: no visible global function definition for 'palette'
Undefined global functions or variables:
  col2rgb colors palette
Consider adding
  importFrom("grDevices", "col2rgb", "colors", "palette")
to your NAMESPACE file.
.formatResult : capture.str: no visible global function definition for
  'str'
createLog: no visible global function definition for 'sessionInfo'
protocol_junit.svSuiteData: no visible global function definition for
  'xmlNode'
protocol_junit.svSuiteData: no visible global function definition for
  'addChildren'
protocol_junit.svSuiteData: no visible global function definition for
  'saveXML'
protocol_junit.svTestData: no visible global function definition for
  'xmlNode'
protocol_junit.svTestData: no visible global function definition for
  'addChildren'
Undefined global functions or variables:
  addChildren saveXML sessionInfo str xmlNode
Consider adding
  importFrom("utils", "sessionInfo", "str")
to your NAMESPACE file.
svycox.calibrate: no visible global function definition for 'quantile'
svycox.calibrate: no visible binding for global variable 'median'
svycox.calibrate: no visible global function definition for
  'as.formula'
svycox.calibrate: no visible global function definition for 'plot'
svycox.calibrate: no visible global function definition for 'arrows'
svycox.calibrate: no visible global function definition for 'abline'
svycox.nomogram: no visible global function definition for 'predict'
svycox.nomogram: no visible global function definition for 'as.formula'
svycox.validate : internal.validate.func: no visible global function
  definition for 'as.formula'
svycox.validate : internal.validate.func: no visible global function
  definition for 'formula'
Undefined global functions or variables:
  abline arrows as.formula formula median plot predict quantile
Consider adding
  importFrom("graphics", "abline", "arrows", "plot")
  importFrom("stats", "as.formula", "formula", "median", "predict",
             "quantile")
to your NAMESPACE file.
additional_comp: no visible global function definition for 'aggregate'
additional_compPV : <anonymous>: no visible global function definition
  for 'aggregate'
cor.aux.func : <anonymous>: no visible global function definition for
  'cov.wt'
eta.func : <anonymous>: no visible global function definition for 'lm'
eta.func : <anonymous>: no visible global function definition for
  'anova'
glm.dummy.no.std: no visible global function definition for
  'as.formula'
pv_by: no visible binding for global variable 'var'
pv_perc: no visible binding for global variable 'var'
pv_quantile: no visible binding for global variable 'var'
svyPVcor: no visible global function definition for 'update'
svyPVcor: no visible global function definition for 'var'
svyPVeta: no visible global function definition for 'update'
svyPVeta: no visible global function definition for 'var'
svyPVglm: no visible global function definition for 'gaussian'
svyPVglm: no visible binding for global variable 'as.formula'
svyPVglm: no visible binding for global variable 'var'
svyPVglm: no visible global function definition for 'pt'
svyPVttest: no visible binding for global variable 'as.formula'
svyPVttest: no visible global function definition for 'var'
svyPVttest: no visible global function definition for 'pt'
svyPVttest: no visible binding for global variable 'var'
t.test.aux: no visible global function definition for 'as.formula'
t.test.aux: no visible global function definition for 'complete.cases'
Undefined global functions or variables:
  aggregate anova as.formula complete.cases cov.wt gaussian lm pt
  update var
Consider adding
  importFrom("stats", "aggregate", "anova", "as.formula",
             "complete.cases", "cov.wt", "gaussian", "lm", "pt",
             "update", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable 'iset' in DATA statement at (1)
  Warning: GNU Extension: Variable 'iset' at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
See 'd:/Rcompile/CRANpkg/local/3.5/SWATmodel.Rcheck/00install.out' for details.
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
readSWAT: no visible global function definition for 'read.fortran'
runSWAT2005: no visible global function definition for 'read.fortran'
runSWAT2009: no visible global function definition for 'read.fortran'
runSWAT2012: no visible global function definition for 'read.fortran'
Undefined global functions or variables:
  read.fortran
Consider adding
  importFrom("utils", "read.fortran")
to your NAMESPACE file.
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  The following object is masked from 'package:testthat':
  
      skip
  
  > 
  > test_check("swirlify")
  -- 1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R
  all(correct_output %in% readLines(file.path(path, "test.log"))) isn't true.
  
  == testthat results  ===========================================================
  OK: 6 SKIPPED: 1 FAILED: 1
  1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Packages in Depends field not imported from:
  'MASS' 'fda' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fj_pl: no visible global function definition for 'getbasismatrix'
fj_pl: no visible global function definition for 'create.bspline.basis'
fj_pl: no visible global function definition for 'getbasispenalty'
forward_backward.quantities : <anonymous>: no visible global function
  definition for 'dnorm'
function_cases1AND2: no visible global function definition for 'dnorm'
function_cases3AND4: no visible global function definition for 'dnorm'
pij_iid: no visible global function definition for 'dnorm'
pilj: no visible global function definition for 'dnorm'
updateLambda: no visible global function definition for 'optimize'
Undefined global functions or variables:
  create.bspline.basis dnorm getbasismatrix getbasispenalty optimize
Consider adding
  importFrom("stats", "dnorm", "optimize")
to your NAMESPACE file.
calc_MW: no visible global function definition for 'read.table'
cfba_moment: no visible global function definition for 'median'
cfba_moment: no visible global function definition for 'write.csv'
cfba_moment_mr: no visible global function definition for 'median'
cfba_moment_mr: no visible global function definition for 'write.csv'
cfba_moment_pw: no visible global function definition for 'median'
cfba_moment_pw: no visible global function definition for 'write.csv'
readmodel: no visible global function definition for 'as'
Undefined global functions or variables:
  as median read.table write.csv
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "median")
  importFrom("utils", "read.table", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
FECorr: no visible global function definition for 'is'
FECorr: no visible global function definition for 'write.csv'
FECorr: no visible global function definition for 'aggregate'
FECorr: no visible global function definition for 'lm'
FECorr: no visible global function definition for 'nlm'
eFBA_gene: no visible global function definition for 'is'
eFBA_gene: no visible global function definition for 'as'
eFBA_rxn : adjustTol: no visible global function definition for 'is'
eFBA_rxn: no visible global function definition for 'is'
eFBA_rxn: no visible global function definition for 'as'
findFluxGeneExpr: no visible global function definition for 'as'
findMDCFlux: no visible global function definition for 'is'
findMDCFlux: no visible global function definition for 'as'
gene2Rule: no visible global function definition for 'is'
Undefined global functions or variables:
  aggregate as is lm nlm write.csv
Consider adding
  importFrom("methods", "as", "is")
  importFrom("stats", "aggregate", "lm", "nlm")
  importFrom("utils", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/sybilSBML.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Packages suggested but not available for checking:
  'sylly.de' 'sylly.en' 'sylly.es'
symbol: no visible global function definition for 'plot.new'
symbol: no visible global function definition for 'plot.window'
symbol: no visible global function definition for 'axis'
symbol: no visible global function definition for 'box'
symbol: no visible global function definition for 'title'
symbol: no visible global function definition for 'rainbow'
symbol: no visible global function definition for 'hsv'
symbol: no visible global function definition for 'rect'
symbol: no visible global function definition for 'polygon'
symbol: no visible global function definition for 'lines'
symbol: no visible global function definition for 'text'
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window polygon rainbow rect text
  title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "polygon", "rect", "text", "title")
to your NAMESPACE file.
integrate.polynomial : f: no visible global function definition for
  'dmvnorm'
Undefined global functions or variables:
  dmvnorm
Package in Depends field not imported from: 'fields'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cwt_fw: no visible global function definition for 'fft'
cwt_iw: no visible global function definition for 'fft'
est_riskshrink_thresh: no visible global function definition for
  'median'
Undefined global functions or variables:
  fft median
Consider adding
  importFrom("stats", "fft", "median")
to your NAMESPACE file.
ProgressBAR: no visible global function definition for 'txtProgressBar'
ProgressBAR: no visible global function definition for
  'setTxtProgressBar'
cor.matrix: no visible global function definition for 'cor'
cor.matrix.partial: no visible global function definition for 'cor'
optimal: no visible global function definition for 'combn'
optimal: no visible global function definition for 'cor'
Undefined global functions or variables:
  combn cor setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "cor")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RCurl' 'RJSONIO'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls to packages already attached by Depends:
  'tcltk' 'tkrplot'
  Please remove these calls from your code.
Namespaces with empty importFrom:
  'Rcpp' 'methods'
mainNetFunction: no visible global function definition for 'png'
mainNetFunction: no visible global function definition for 'plot'
mainNetFunction: no visible global function definition for 'lines'
mainNetFunction: no visible global function definition for 'legend'
mainNetFunction: no visible global function definition for 'dev.off'
plotPR: no visible global function definition for 'plot'
plotROC: no visible global function definition for 'plot'
plotROC: no visible global function definition for 'lines'
simulatedData: no visible global function definition for 'rpois'
simulatedData : <anonymous>: no visible global function definition for
  'rpois'
simulatedData : rlognormpois: no visible global function definition for
  'rnorm'
simulatedData : rlognormpois: no visible global function definition for
  'rpois'
Undefined global functions or variables:
  dev.off legend lines plot png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'LowRankQP' 'rgenoud'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for 'LowRankQP'
gaps.plot: no visible global function definition for 'abline'
path.plot: no visible global function definition for 'lines'
path.plot: no visible global function definition for 'abline'
path.plot: no visible global function definition for 'legend'
synth: no visible binding for global variable 'sd'
synth: no visible binding for global variable 'var'
synth: no visible global function definition for 'LowRankQP'
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: 'unix'
.checkDimAndTest: no visible global function definition for
  'chisq.test'
.checkDimAndTest: no visible global function definition for
  'fisher.test'
plotTable1Heatmap: no visible global function definition for 'par'
plotTable1Heatmap: no visible global function definition for 'image'
plotTable1Heatmap: no visible global function definition for 'abline'
plotTable1Heatmap: no visible global function definition for 'axis'
plotTable1Heatmap: no visible global function definition for 'text'
plotTable1Heatmap: no visible global function definition for 'legend'
plotTable1Heatmap: no visible global function definition for 'box'
Undefined global functions or variables:
  abline axis box chisq.test fisher.test image legend par text
Consider adding
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "text")
  importFrom("stats", "chisq.test", "fisher.test")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'rbind.tableList':
  'rbind.tableList'

S3 methods shown with full name in documentation object 'rbind.tableMatrix':
  'rbind.tableMatrix'

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.
'library' or 'require' call to 'grid' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'perturb' 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: 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cellgram: no visible global function definition for 'grid.rect'
cellgram: no visible global function definition for 'gpar'
cellgram: no visible global function definition for 'grid.segments'
cellgram: no visible global function definition for 'grid.circle'
cellgram: no visible global function definition for 'grid.polygon'
cellgram: no visible global function definition for 'grid.text'
cellgram: no visible global function definition for 'unit'
compare: no visible global function definition for 'sd'
tableplot.colldiag: no visible global function definition for
  'colldiag'
tableplot.colldiag: no visible global function definition for 'xtabs'
tableplot.default: no visible global function definition for
  'grid.newpage'
tableplot.default: no visible global function definition for
  'grid.layout'
tableplot.default: no visible global function definition for 'unit'
tableplot.default: no visible global function definition for
  'pushViewport'
tableplot.default: no visible global function definition for 'viewport'
tableplot.default: no visible global function definition for
  'grid.text'
tableplot.default: no visible global function definition for
  'upViewport'
tableplot.default: no visible global function definition for 'gpar'
tableplot.default: no visible global function definition for
  'grid.rect'
tableplot.default: no visible global function definition for
  'popViewport'
Undefined global functions or variables:
  colldiag gpar grid.circle grid.layout grid.newpage grid.polygon
  grid.rect grid.segments grid.text popViewport pushViewport sd unit
  upViewport viewport xtabs
Consider adding
  importFrom("stats", "sd", "xtabs")
to your NAMESPACE file.
TCRsink: no visible global function definition for 'head'
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
itabplot : <anonymous>: no visible global function definition for
  'capture.output'
itabplot: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL capture.output
Consider adding
  importFrom("utils", "browseURL", "capture.output")
to your NAMESPACE file.
plot.tabu: no visible global function definition for 'image'
plot.tabu: no visible global function definition for 'gray'
plot.tabu: no visible global function definition for 'par'
plot.tabu: no visible global function definition for 'layout'
plot.tabu: no visible global function definition for 'plot'
Undefined global functions or variables:
  gray image layout par plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image", "layout", "par", "plot")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/tadaatoolbox.Rcheck/00install.out' for details.
NANOVA.test: no visible global function definition for 'ecdf'
NANOVA.test2: no visible global function definition for 'ecdf'
NANOVA.test3: no visible global function definition for 'ecdf'
fdr.table: no visible global function definition for 'median'
fdr.table: no visible global function definition for 'quantile'
gene.classifier1: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  ecdf median quantile write.table
Consider adding
  importFrom("stats", "ecdf", "median", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'gdata' 'ggplot2' 'grid' 'lattice' 'xtable'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
AnalyzeLVZ: no visible global function definition for 'approx'
ConvP2Vdepthinv: no visible global function definition for 'approx'
DistSummary: no visible global function definition for 'heat.colors'
Earthplot: no visible global function definition for 'heat.colors'
Earthplot: no visible global function definition for 'par'
Earthplot: no visible global function definition for 'plot'
Earthplot: no visible global function definition for 'approx'
Earthplot: no visible global function definition for 'image'
Earthplot: no visible binding for global variable 'lines'
FindRoots: no visible global function definition for 'uniroot'
InterpModel: no visible global function definition for 'approx'
LinInterp: no visible global function definition for 'approx'
PolarPlot: no visible binding for global variable 'plot'
Rayfan: no visible binding for global variable 'lines'
polaraxis: no visible global function definition for 'text'
Undefined global functions or variables:
  approx heat.colors image lines par plot text uniroot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "lines", "par", "plot", "text")
  importFrom("stats", "approx", "uniroot")
to your NAMESPACE file.
end.TawnyPortfolio: no visible global function definition for 'end'
start.TawnyPortfolio: no visible global function definition for 'start'
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
BootTree: no visible global function definition for 'hclust'
BootTree: no visible global function definition for 'dist'
BootTree: no visible global function definition for 'as.dist'
BootTree: no visible global function definition for 'cor'
BootTree: no visible binding for global variable 'var'
Pgpd: no visible global function definition for 'optim'
Pgpd : <anonymous>: no visible global function definition for 'optim'
Pgpd: no visible global function definition for 'var'
Pgpd: no visible global function definition for 'rnorm'
Pgpd: no visible global function definition for 'quantile'
Pvalue: no visible global function definition for 'rnorm'
SigTree: no visible global function definition for 'data'
TreeStat: no visible global function definition for 'hclust'
TreeStat: no visible global function definition for 'as.dist'
TreeStat: no visible global function definition for 'dist'
TreeStat: no visible global function definition for 'cor'
plot.best: no visible global function definition for 'hclust'
plot.best: no visible global function definition for 'as.dist'
plot.best: no visible global function definition for 'dist'
plot.best: no visible global function definition for 'cor'
plot.best: no visible global function definition for 'plot'
treetext: no visible global function definition for 'par'
treetext: no visible global function definition for 'text'
Undefined global functions or variables:
  as.dist cor data dist hclust optim par plot quantile rnorm text var
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "optim",
             "quantile", "rnorm", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
Package suggested but not available for checking: 'radiomics'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
    libs   1.5Mb
S3 methods shown with full name in documentation object 'top.fun':
  'slice.fun'

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.
cluster_cutoff_at_first_empty_bin: no visible global function
  definition for 'hist'
mapper1D: no visible global function definition for 'dist'
mapper1D: no visible global function definition for 'as.dist'
mapper1D: no visible global function definition for 'hclust'
mapper1D: no visible global function definition for 'cutree'
mapper2D: no visible global function definition for 'dist'
mapper2D: no visible global function definition for 'as.dist'
mapper2D: no visible global function definition for 'hclust'
mapper2D: no visible global function definition for 'cutree'
Undefined global functions or variables:
  as.dist cutree dist hclust hist
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cutree", "dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RSEIS' 'pracma' 'signal'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
tdt.quad: no visible global function definition for 'runif'
tdt.rr: no visible global function definition for 'pf'
tdt.rr: no visible global function definition for 'qbeta'
Undefined global functions or variables:
  pf qbeta runif
Consider adding
  importFrom("stats", "pf", "qbeta", "runif")
to your NAMESPACE file.
E.2SI: no visible binding for global variable 'var'
E.2SI: no visible global function definition for 'var'
E.BE: no visible global function definition for 'var'
E.Beta: no visible global function definition for 'var'
E.PO: no visible global function definition for 'var'
E.PPS: no visible global function definition for 'var'
E.SI: no visible global function definition for 'var'
E.STPPS: no visible global function definition for 'var'
E.STSI: no visible global function definition for 'var'
E.STpiPS: no visible global function definition for 'var'
E.SY: no visible global function definition for 'var'
E.WR: no visible global function definition for 'var'
E.piPS: no visible global function definition for 'var'
GREG.SI: no visible global function definition for 'var'
S.BE: no visible global function definition for 'runif'
S.PO: no visible global function definition for 'runif'
S.PPS: no visible global function definition for 'runif'
S.SI: no visible global function definition for 'runif'
S.STPPS: no visible global function definition for 'runif'
S.WR: no visible global function definition for 'rbinom'
S.piPS: no visible global function definition for 'runif'
p.WR: no visible global function definition for 'dmultinom'
Undefined global functions or variables:
  dmultinom rbinom runif var
Consider adding
  importFrom("stats", "dmultinom", "rbinom", "runif", "var")
to your NAMESPACE file.
TeachNet: no visible global function definition for 'predict'
createWeights1: no visible global function definition for 'rnorm'
createWeights2: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  predict rnorm
Consider adding
  importFrom("stats", "predict", "rnorm")
to your NAMESPACE file.
aniplotevents: no visible global function definition for 'plot'
aniplotevents: no visible global function definition for 'lines'
cbfs: no visible global function definition for 'rnorm'
cbfs: no visible global function definition for 'runif'
cbfs_red: no visible global function definition for 'arima.sim'
cbfs_red: no visible global function definition for 'runif'
eventCluster: no visible global function definition for 'princomp'
eventCluster: no visible global function definition for 'kmeans'
measures: no visible global function definition for 'sd'
measures: no visible global function definition for 'var'
measures: no visible global function definition for 'PP.test'
noiseTests: no visible global function definition for 'Box.test'
noiseTests: no visible global function definition for 'PP.test'
noiseTests: no visible global function definition for 'ar'
plotevents: no visible global function definition for 'plot'
plotevents: no visible global function definition for 'lines'
ur.za.fast : roll: no visible global function definition for 'coef'
ur.za.fast : roll: no visible global function definition for 'lm'
Undefined global functions or variables:
  Box.test PP.test ar arima.sim coef kmeans lines lm plot princomp
  rnorm runif sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "Box.test", "PP.test", "ar", "arima.sim", "coef",
             "kmeans", "lm", "princomp", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
S3 methods shown with full name in documentation object 'mean.tensor':
  'mean.tensor'

S3 methods shown with full name in documentation object 'solve.tensor':
  'solve.tensor'

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.
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for global variable 'ID'
TER.deesc.1.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B: no visible binding for global variable 'ID'
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A3.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A2.f: no visible binding for global variable 'ID'
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : B1.f: no visible binding for global variable 'ID'
TER.deesc.A.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B: no visible binding for global variable 'ID'
Undefined global functions or variables:
  ID
Depends: includes the non-default packages:
  'grid' 'quadprog' 'maps' 'maptools' 'mapdata' 'dichromat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'dichromat' 'grid' 'mapdata' 'maps' 'maptools' 'quadprog'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs      13.1Mb
    tessdata  20.9Mb
File which contains pragma(s) suppressing diagnostics:
  'inst/include/testthat/vendor/catch.h'
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.5Mb
    libs   2.1Mb
phyper_right: no visible global function definition for 'dhyper'
progression: no visible global function definition for 'density'
progression: no visible global function definition for 'plot'
progression: no visible global function definition for 'points'
progression: no visible global function definition for 'legend'
progression: no visible global function definition for 'text'
specificities.distribution.plot: no visible global function definition
  for 'dhyper'
specificities.distribution.plot: no visible global function definition
  for 'plot'
specificities.distribution.plot: no visible global function definition
  for 'Axis'
specificities.distribution.plot: no visible global function definition
  for 'arrows'
specificities.distribution.plot: no visible global function definition
  for 'text'
specificities.distribution.plot: no visible global function definition
  for 'title'
specificities.probabilities.vector: no visible global function
  definition for 'phyper'
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper plot points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "plot", "points",
             "text", "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
.dea_create_model: no visible global function definition for
  'getSrcFilename'
.wMean: no visible global function definition for 'weighted.mean'
Undefined global functions or variables:
  getSrcFilename weighted.mean
Consider adding
  importFrom("stats", "weighted.mean")
  importFrom("utils", "getSrcFilename")
to your NAMESPACE file.
transfer: no visible global function definition for 'rgamma'
transfer: no visible global function definition for 'rnorm'
transfer: no visible global function definition for 'rnbinom'
transfer: no visible global function definition for 'rpois'
transfer: no visible global function definition for 'rbinom'
transfer: no visible global function definition for 'runif'
plot,transfer: no visible global function definition for 'barplot'
plot,transfer: no visible global function definition for 'axis'
plot,transfer: no visible global function definition for 'par'
plot,transfer: no visible global function definition for 'hist'
Undefined global functions or variables:
  axis barplot hist par rbinom rgamma rnbinom rnorm rpois runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "rbinom", "rgamma", "rnbinom", "rnorm", "rpois",
             "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Matrix.h:27:18: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/TFMPvalue.Rcheck/00install.out' for details.
ParseTrueFX: no visible global function definition for 'read.csv'
TrueFXRef: no visible global function definition for 'download.file'
TrueFXRef: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL download.file read.csv
Consider adding
  importFrom("utils", "browseURL", "download.file", "read.csv")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    3.8Mb
Thinknum: no visible global function definition for 'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
coef_traceplot: no visible global function definition for 'rainbow'
coef_traceplot: no visible global function definition for 'plot'
coef_traceplot: no visible global function definition for 'abline'
coef_traceplot : <anonymous>: no visible global function definition for
  'lines'
coef_traceplot: no visible global function definition for 'text'
ee.GEE.aux : <anonymous>: no visible global function definition for
  'combn'
Undefined global functions or variables:
  abline combn lines plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
summary.tsls: no visible global function definition for 'printCoefmat'
threesls: no visible global function definition for 'cor'
threesls: no visible global function definition for 'pt'
tsls.formula: no visible global function definition for 'model.matrix'
tsls.formula: no visible global function definition for
  'model.response'
Undefined global functions or variables:
  cor model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response",
             "printCoefmat", "pt")
to your NAMESPACE file.
.LoadTickDataHK: no visible global function definition for 'read.csv'
.LoadTickDataSHSZ: no visible global function definition for 'read.csv'
DrawDown: no visible global function definition for 'na.omit'
PerformanceReport: no visible global function definition for
  'aggregate'
PerformanceReport: no visible global function definition for 'sd'
Undefined global functions or variables:
  aggregate na.omit read.csv sd
Consider adding
  importFrom("stats", "aggregate", "na.omit", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
newTiddler: no visible global function definition for 'new'
twImage: no visible global function definition for 'new'
twLink: no visible global function definition for 'new'
twList: no visible global function definition for 'new'
twTable: no visible global function definition for 'new'
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running 'testthat.R' [61s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     })
  9: expr_type_of(.x)
  10: typeof(x)
  11: duplicate(quo)
  
  == testthat results  ===========================================================
  OK: 149 SKIPPED: 2 FAILED: 5
  1. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_key_stats.R#15) 
  2. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_key_stats.R#17) 
  3. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_key_stats.R#19) 
  4. Error: Test error on invalid data inputs. (@test_tq_mutate.R#142) 
  5. Error: Test error on invalid data inputs. (@test_tq_transmute.R#121) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    level type   token
    <int> <chr>  <chr>
  1     0 number 1    
  -- 1. Failure: sheet names are returned correctly (@test-xlsx_sheet_names.R#4)  
  xlsx_sheet_names("./examples.xlsx")[1:2] not equal to c("Sheet1", "1~`!@#$%^&()_-+={}|;\"'<,>.£¹÷¦°").
  1/2 mismatches
  x[2]: "1~`!@#$%^&()_-+={}|;\"'<,>.Â£Â¹Ã·Â¦Â°"
  y[2]: "1~`!@#$%^&()_-+={}|;\"'<,>.£¹÷¦°"
  
  == testthat results  ===========================================================
  OK: 327 SKIPPED: 0 FAILED: 1
  1. Failure: sheet names are returned correctly (@test-xlsx_sheet_names.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
plot.tight.clust: no visible global function definition for 'hclust'
plot.tight.clust: no visible global function definition for 'dist'
plot.tight.clust: no visible global function definition for 'image'
plot.tight.clust: no visible global function definition for
  'colorRampPalette'
plot.tight.clust: no visible global function definition for 'axis'
plot.tight.clust: no visible global function definition for 'lines'
tight.clust : find.candidates : kmeans.classify: no visible global
  function definition for 'kmeans'
write.tight.clust: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  axis colorRampPalette dist hclust image kmeans lines write.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "image", "lines")
  importFrom("stats", "dist", "hclust", "kmeans")
  importFrom("utils", "write.table")
to your NAMESPACE file.
.viterbiTrainingEmission,contHMM-list-list: no visible global function
  definition for 'var'
sampleObs,tDist-numeric: no visible global function definition for 'rt'
Undefined global functions or variables:
  rt var
Consider adding
  importFrom("stats", "rt", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: working directory was changed to 'D:/temp/RtmpKomcEu', resetting
  Warning: working directory was changed to 'D:/temp/RtmpKomcEu', resetting
'library' or 'require' call to 'shiny' 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: 'ggplot2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
timeline: no visible global function definition for 'ggplot'
timeline: no visible global function definition for 'geom_segment'
timeline: no visible global function definition for 'aes_string'
timeline: no visible global function definition for 'geom_rect'
timeline: no visible global function definition for 'geom_text'
timeline: no visible global function definition for 'theme'
timeline: no visible global function definition for 'element_blank'
timeline: no visible global function definition for 'xlab'
timeline: no visible global function definition for 'ylab'
timeline: no visible global function definition for 'xlim'
timeline: no visible global function definition for
  'scale_y_continuous'
timeline: no visible global function definition for 'geom_point'
timeline: no visible global function definition for 'scale_color_grey'
timeline: no visible global function definition for 'geom_hline'
Undefined global functions or variables:
  aes_string element_blank geom_hline geom_point geom_rect geom_segment
  geom_text ggplot scale_color_grey scale_y_continuous theme xlab xlim
  ylab
density.tm: no visible global function definition for 'density'
mu.mle: no visible global function definition for 'optimize'
pophistory.tm: no visible binding for global variable 'quantile'
quantile.tm: no visible global function definition for 'quantile'
sample.pop: no visible global function definition for 'runif'
summary.tm: no visible global function definition for 'quantile'
Undefined global functions or variables:
  density optimize quantile runif
Consider adding
  importFrom("stats", "density", "optimize", "quantile", "runif")
to your NAMESPACE file.
generatelatencies: no visible binding for global variable 'allNames'
generatetimedeltas: no visible global function definition for 'head'
generatetimedeltas: no visible global function definition for 'tail'
generatevertexedgelist : <anonymous>: no visible global function
  definition for 'head'
generatevertexedgelist : <anonymous>: no visible global function
  definition for 'tail'
plotnetworkslices: no visible global function definition for 'par'
plotnetworkslices: no visible global function definition for 'text'
plottanet: no visible global function definition for 'plot'
plottonet: no visible global function definition for 'plot'
shortesttimepath : <anonymous>: no visible global function definition
  for 'tail'
Undefined global functions or variables:
  allNames head par plot tail text
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("methods", "allNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls in package code:
  'ggplot2' 'plyr'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Matrix' 'lubridate' 'timeDate'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
is.Bizday: no visible global function definition for 'isWeekday'
plotCalendarHeatmap: no visible global function definition for 'ddply'
plotCalendarHeatmap: no visible global function definition for '.'
plotCalendarHeatmap: no visible binding for global variable 'year'
plotCalendarHeatmap: no visible binding for global variable 'month'
plotCalendarHeatmap: no visible binding for global variable 'week'
plotCalendarHeatmap: no visible global function definition for 'ggplot'
plotCalendarHeatmap: no visible global function definition for 'aes'
plotCalendarHeatmap: no visible binding for global variable 'monthweek'
plotCalendarHeatmap: no visible binding for global variable 'weekday'
plotCalendarHeatmap: no visible global function definition for
  'geom_tile'
plotCalendarHeatmap: no visible global function definition for
  'facet_grid'
plotCalendarHeatmap: no visible global function definition for
  'scale_fill_gradientn'
projectDate: no visible global function definition for 'holidayNYSE'
projectDate: no visible global function definition for
  'sparse.model.matrix'
Undefined global functions or variables:
  . aes ddply facet_grid geom_tile ggplot holidayNYSE isWeekday month
  monthweek scale_fill_gradientn sparse.model.matrix week weekday year
boot_autocov: no visible global function definition for 'is.ts'
boot_autocov: no visible global function definition for 'tsboot'
boot_autocov: no visible global function definition for 'quantile'
boot_autocov: no visible global function definition for 'par'
boot_autocov: no visible global function definition for 'frequency'
boot_autocov: no visible global function definition for 'polygon'
boot_autocov: no visible global function definition for 'lines'
boot_autocov: no visible global function definition for 'abline'
boot_autocov: no visible global function definition for 'acf'
boot_spec: no visible global function definition for 'is.ts'
boot_spec: no visible global function definition for 'tsboot'
boot_spec: no visible global function definition for 'spec.pgram'
boot_spec: no visible global function definition for 'quantile'
boot_spec: no visible global function definition for 'polygon'
boot_spec: no visible global function definition for 'lines'
redraw: no visible global function definition for 'spec.pgram'
statistic: no visible global function definition for 'acf'
Undefined global functions or variables:
  abline acf frequency is.ts lines par polygon quantile spec.pgram
  tsboot
Consider adding
  importFrom("graphics", "abline", "lines", "par", "polygon")
  importFrom("stats", "acf", "frequency", "is.ts", "quantile",
             "spec.pgram")
to your NAMESPACE file.
createHstore.ts: no visible global function definition for 'time'
exploreDb : <anonymous>: no visible global function definition for
  'plot'
exportTsList : <anonymous>: no visible global function definition for
  'time'
exportTsList: no visible global function definition for 'write.csv2'
importTsList: no visible global function definition for 'read.csv2'
importTsList : <anonymous>: no visible global function definition for
  'as.ts'
plot.tslist: no visible global function definition for 'plot'
plot.tslist : <anonymous>: no visible global function definition for
  'time'
plot.tslist: no visible global function definition for 'par'
plot.tslist: no visible global function definition for 'legend'
readTimeSeries : <anonymous>: no visible global function definition for
  'ts'
resolveOverlap: no visible global function definition for 'is.ts'
resolveOverlap: no visible global function definition for 'frequency'
resolveOverlap: no visible global function definition for 'time'
resolveOverlap: no visible global function definition for 'ts'
storeTimeSeries: no visible binding for global variable 'frequency'
zooLikeDateConvert: no visible global function definition for 'time'
zooLikeDateConvert: no visible global function definition for
  'frequency'
zooLikeDateConvert: no visible global function definition for 'cycle'
Undefined global functions or variables:
  as.ts cycle frequency is.ts legend par plot read.csv2 time ts
  write.csv2
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "as.ts", "cycle", "frequency", "is.ts", "time",
             "ts")
  importFrom("utils", "read.csv2", "write.csv2")
to your NAMESPACE file.
author.search: no visible binding for global variable 'na.omit'
reference.list: 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.
drawGraph: no visible global function definition for 'pdf'
drawGraph: no visible global function definition for 'par'
drawGraph: no visible global function definition for 'plot'
drawGraph: no visible global function definition for 'segments'
drawGraph: no visible global function definition for 'lines'
drawGraph: no visible global function definition for 'text'
drawGraph: no visible global function definition for 'dev.off'
drugRank: no visible global function definition for 'aggregate'
floating2: no visible global function definition for 'cor'
timma: no visible global function definition for 'median'
timma: no visible global function definition for 'write.table'
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'ExPosition' 'InPosition' 'TExPosition' 'prettyGraphs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    rmarkdown   1.3Mb
tipom.car: no visible global function definition for 'abline'
tipom.car: no visible global function definition for 'axis'
tipom.heat: no visible global function definition for 'image'
tipom.heat: no visible global function definition for 'gray'
tipom.lw: no visible global function definition for 'plot'
tipom.lw: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis gray image plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'boot' 'lattice' 'splines' 'tcltk'
  Please remove these calls from your code.
ls.tree: no visible global function definition for 'lm'
ls.tree: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef lm
Consider adding
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'rgl' 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.my.tkdev: no visible global function definition for 'win.metafile'
tkpersp : draw: no visible global function definition for 'par'
tkpersp : draw: no visible global function definition for 'persp'
Undefined global functions or variables:
  par persp win.metafile
Consider adding
  importFrom("grDevices", "win.metafile")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
FLXmclust.Density: no visible global function definition for 'dmvnorm'
FLXmclust.Estimate: no visible global function definition for 'flexmix'
FLXmclust.Estimate: no visible global function definition for
  'FLXmclust'
coefmclust: no visible global function definition for 'parameters'
flexmix.Density: no visible global function definition for
  'model.matrix'
flexmix.Density: no visible global function definition for
  'model.response'
flexmix.Density: no visible global function definition for
  'model.frame'
flexmix.Density: no visible global function definition for 'dnorm'
flexmix.Density: no visible global function definition for 'dpois'
flexmix.Density: no visible global function definition for 'dbinom'
flexmix.Estimate: no visible global function definition for 'flexmix'
flexmix.Estimate: no visible global function definition for 'FLXglm'
tleplot,TLE-data.frame: no visible global function definition for
  'legend'
Undefined global functions or variables:
  FLXglm FLXmclust dbinom dmvnorm dnorm dpois flexmix legend
  model.frame model.matrix model.response parameters
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "dbinom", "dnorm", "dpois", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' which was already attached by Depends.
  Please remove these calls from your code.
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.
EMN: no visible global function definition for 'dmvnorm'
EMN: no visible global function definition for 'pmvnorm'
EMT: no visible global function definition for 'GenzBretz'
EMT: no visible global function definition for 'dmvt'
EMT: no visible global function definition for 'pmvt'
MomemNT: no visible global function definition for 'pnorm'
MomemNT: no visible global function definition for 'dnorm'
MomemNT: no visible global function definition for 'pmvnorm'
MomemNT: no visible global function definition for 'dmvnorm'
TT.moment: no visible global function definition for 'GenzBretz'
TT.moment: no visible global function definition for 'pmvt'
TT.moment: no visible global function definition for 'dt'
TT.moment: no visible global function definition for 'pt'
TT.moment: no visible global function definition for 'dmvt'
cdfNI: no visible global function definition for 'pnorm'
cdfNI: no visible global function definition for 'pt'
inits: no visible global function definition for 'lm'
Undefined global functions or variables:
  GenzBretz dmvnorm dmvt dnorm dt lm pmvnorm pmvt pnorm pt
Consider adding
  importFrom("stats", "dnorm", "dt", "lm", "pnorm", "pt")
to your NAMESPACE file.
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
search_collection: no visible global function definition for
  'URLencode'
search_company: no visible global function definition for 'URLencode'
search_keyword: no visible global function definition for 'URLencode'
search_list: no visible global function definition for 'URLencode'
search_movie: no visible global function definition for 'URLencode'
search_multi: no visible global function definition for 'URLencode'
search_person: no visible global function definition for 'URLencode'
search_tv: no visible global function definition for 'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols,  :
  not using pch[2..] since pch[1L] has multiple chars
Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols,  :
  not using pch[2..] since pch[1L] has multiple chars
Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols,  :
  not using pch[2..] since pch[1L] has multiple chars
trying URL 'http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=txt'
Warning in download.file("http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=txt",  :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Quitting from lines 1170-1178 (tmod.rmd) 
Error: processing vignette 'tmod.rmd' failed with diagnostics:
cannot open URL 'http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=txt'
Execution halted
extractContentDOM: no visible global function definition for
  'capture.output'
extractHTMLStrip: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'Rcampdf' 'Rpoppler' 'tm.lexicon.GeneralInquirer'
Package unavailable to check Rd xrefs: 'Rpoppler'
Package suggested but not available for checking: 'corpus.JSS.papers'
flowlength: no visible global function definition for 'is'
river: no visible global function definition for 'is'
sinkfill: no visible global function definition for 'is'
subcatch: no visible global function definition for 'is'
topidx: 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').
Tosls.formula: no visible global function definition for 'model.matrix'
Tosls.formula: no visible global function definition for
  'model.response'
summary: no visible global function definition for 'coef'
summary: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'Cairo' 'RGtk2' 'colorspace' 'gWidgets' 'tourr'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'TeachingDemos' 'ash'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Cairo' 'RGtk2' 'colorspace' 'gWidgets' 'tourr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'rmongodb'
ConfA: no visible global function definition for 'qf'
EstM2Sn: no visible global function definition for 'nlm'
EstM2Sn: no visible global function definition for 'qnorm'
TV.model: no visible global function definition for 'dev.new'
TV.model: no visible global function definition for 'points'
betaBino: no visible global function definition for 'pbinom'
doseD: no visible global function definition for 'lm'
doseD: no visible global function definition for 'dev.new'
doseD: no visible global function definition for 'par'
doseD: no visible global function definition for 'plot'
doseD: no visible global function definition for 'axTicks'
doseD: no visible global function definition for 'axis'
doseD: no visible global function definition for 'lines'
doseD: no visible global function definition for 'abline'
doseD: no visible global function definition for 'legend'
setD: no visible global function definition for 'dev.new'
setD: no visible global function definition for 'par'
setD: no visible global function definition for 'pbinom'
setD: no visible global function definition for 'abline'
setD: no visible global function definition for 'axis'
setD: no visible global function definition for 'rect'
setD: no visible global function definition for 'lines'
setD: no visible global function definition for 'text'
setD: no visible global function definition for 'axTicks'
setD: no visible global function definition for 'legend'
spoD : spoD_A: no visible global function definition for 'chisq.test'
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  plot points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "plot", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
align1d : obj: no visible global function definition for 'dist'
align2d : obj: no visible global function definition for 'dist'
align2d : pen: no visible global function definition for 'dist'
align2d: no visible global function definition for 'dist'
sumt: no visible global function definition for 'optim'
tpe1d: no visible global function definition for 'hclust'
tpe2d: no visible global function definition for 'hclust'
tpe2d: no visible global function definition for 'cmdscale'
Undefined global functions or variables:
  cmdscale dist hclust optim
Consider adding
  importFrom("stats", "cmdscale", "dist", "hclust", "optim")
to your NAMESPACE file.
Package in Depends field not imported from: 'lgtdl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ci.plot: no visible global function definition for 'gaussian'
ci.plot: no visible global function definition for 'qnorm'
ci.plot: no visible global function definition for 'plot'
ci.plot: no visible global function definition for 'lines'
cst.fit.ff: no visible global function definition for 'pnorm'
cstfit.1: no visible global function definition for 'var'
gof.test.boots.pf: no visible binding for global variable 'sd'
gof.test.int.1.ff: no visible global function definition for 'quantile'
gof.test.int.1.ff: no visible global function definition for 'var'
gof.test.int.ff: no visible global function definition for 'pnorm'
gofTest: no visible binding for global variable 'sd'
plotGof: no visible global function definition for 'plot'
plotGof : <anonymous>: no visible global function definition for
  'lines'
plotGof: no visible global function definition for 'lines'
sig.test.int.1.ff: no visible global function definition for 'quantile'
sig.test.int.1.ff: no visible global function definition for 'var'
sig.test.int.ff: no visible global function definition for 'pnorm'
test.boots.1: no visible binding for global variable 'sd'
tpr: no visible global function definition for 'poisson'
tpr: no visible global function definition for 'glm.fit'
tpr: no visible global function definition for 'coef'
tpr: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx coef gaussian glm.fit lines plot pnorm poisson qnorm quantile
  sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "coef", "gaussian", "glm.fit", "pnorm",
             "poisson", "qnorm", "quantile", "sd", "var")
to your NAMESPACE file.
File 'tpr/libs/i386/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'
File 'tpr/libs/x64/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.7Mb
DeadReckoning: no visible global function definition for 'filter'
DeadReckoning: no visible global function definition for 'approx'
DeadReckoning: no visible global function definition for 'lm'
Mapper: no visible global function definition for 'colorRampPalette'
Mapper: no visible global function definition for 'terrain.colors'
Mapper: no visible global function definition for 'points'
Mapper: no visible global function definition for 'axis'
Standardize: no visible global function definition for 'lm'
Undefined global functions or variables:
  approx axis colorRampPalette filter lm points terrain.colors
Consider adding
  importFrom("grDevices", "colorRampPalette", "terrain.colors")
  importFrom("graphics", "axis", "points")
  importFrom("stats", "approx", "filter", "lm")
to your NAMESPACE file.
microsoftTranslate: no visible global function definition for
  'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
rtrapezoid: 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:
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:128:36: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:152:9: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/treatSens.Rcheck/00install.out' for details.
Build_JTree: no visible global function definition for 'flush.console'
Run_JTree: no visible global function definition for 'cov2cor'
Undefined global functions or variables:
  cov2cor flush.console
Consider adding
  importFrom("stats", "cov2cor")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
LikAge: no visible global function definition for 'read.table'
bd.ME.optim: no visible global function definition for 'optim'
bd.ME.optim.rho: no visible global function definition for 'optim'
bd.ME.optim.rho.all: no visible global function definition for 'optim'
bd.MEyule.optim: no visible global function definition for 'optimize'
bd.MEyule.optim: no visible global function definition for 'optim'
bd.age.optim.matlab: no visible global function definition for
  'read.table'
bd.groups.conf: no visible global function definition for 'uniroot'
bd.shifts.plot: no visible global function definition for 'plot'
bd.shifts.plot: no visible global function definition for 'lines'
bdsky.stt.optim: no visible global function definition for 'optim'
create.mat: no visible global function definition for 'write.table'
Undefined global functions or variables:
  lines optim optimize plot read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
plot.treeperm: no visible global function definition for 'hist'
plot.treeperm: no visible global function definition for 'points'
plot.treeperm: no visible global function definition for 'text'
treeperm.formula: no visible global function definition for
  'model.frame'
treeperm.formula: no visible global function definition for
  'model.response'
Undefined global functions or variables:
  hist model.frame model.response points text
Consider adding
  importFrom("graphics", "hist", "points", "text")
  importFrom("stats", "model.frame", "model.response")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   1.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Found the following significant warnings:
  Warning: working directory was changed to 'D:/temp/RtmpymQMjo/RLIBS_32d084b425321/trib/exdata/tribometer', resetting
  Warning: working directory was changed to 'D:/temp/RtmpymQMjo/RLIBS_32d084b425321/trib/exdata/tribometer', resetting
  Warning: working directory was changed to 'D:/temp/RtmpymQMjo/RLIBS_32d084b425321/trib/exdata/profile', resetting
  Warning: working directory was changed to 'D:/temp/RtmpymQMjo/RLIBS_32d084b425321/trib/exdata/profile', resetting
plot.trifield: no visible global function definition for 'topo.colors'
plot.trifield: no visible global function definition for 'plot'
plot.trifield: no visible global function definition for 'image'
plot.trifield: no visible global function definition for 'contour'
plot.trifield: no visible global function definition for 'text'
ternary.legend: no visible global function definition for 'arrows'
ternary.legend: no visible global function definition for 'text'
triaxes: no visible global function definition for 'lines'
tribox: no visible global function definition for 'polygon'
Undefined global functions or variables:
  arrows contour image lines plot polygon text topo.colors
Consider adding
  importFrom("grDevices", "topo.colors")
  importFrom("graphics", "arrows", "contour", "image", "lines", "plot",
             "polygon", "text")
to your NAMESPACE file.
'library' or 'require' call to 'fpc' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.tkm: no visible global function definition for 'plotcluster'
plot.tkm: no visible global function definition for 'plot'
plot.tkm: no visible global function definition for 'points'
plot.tkm: no visible global function definition for 'lines'
plot.tkm: no visible global function definition for 'discrcoord'
Undefined global functions or variables:
  discrcoord lines plot plotcluster points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
cinbag: no visible global function definition for 'var'
trimTrees: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'gtools' 'mgcv'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'gtools' 'mgcv' 'msm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HtoGp: no visible global function definition for 'odd'
HtoGp: no visible global function definition for 'even'
plot.pirls.gam: no visible global function definition for 'par'
plot.pirls.gam: no visible global function definition for 'plot'
plot.pirls.gam: no visible global function definition for 'title'
plot.pirls.gam: no visible global function definition for 'lines'
plot.pirls.gam: no visible global function definition for 'rug'
plot.pirls.gam: no visible global function definition for 'mtext'
test.trioGxE: no visible global function definition for 'write.table'
trioGxE: no visible global function definition for 'quantile'
trioGxE: no visible global function definition for 'qtnorm'
trioplot: no visible global function definition for 'quantile'
trioplot: no visible global function definition for 'formula'
trioplot: no visible global function definition for 'gam'
trioplot: no visible global function definition for 'binomial'
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par plot qtnorm quantile
  rug title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "plot", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
DrawMargin: no visible global function definition for 'qnorm'
DrawProbability: no visible global function definition for 'pnorm'
Factor: no visible global function definition for 'new'
Gaussian: no visible global function definition for 'new'
LikelihoodFactor: no visible global function definition for 'new'
Parameters: no visible global function definition for 'new'
Player: no visible global function definition for 'new'
PriorFactor: no visible global function definition for 'new'
SumFactor: no visible global function definition for 'new'
TruncateFactor: no visible global function definition for 'new'
Variable: no visible global function definition for 'new'
Vdraw: no visible global function definition for 'dnorm'
Vdraw: no visible global function definition for 'pnorm'
Vwin: no visible global function definition for 'dnorm'
Vwin: no visible global function definition for 'pnorm'
Wdraw: no visible global function definition for 'dnorm'
Wdraw: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm new pnorm qnorm
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cdens: no visible global function definition for 'head'
dplot: no visible global function definition for 'knots'
dplot: no visible global function definition for 'median'
dplot: no visible global function definition for 'par'
dplot: no visible global function definition for 'plot.stepfun'
dplot: no visible global function definition for 'abline'
edf: no visible global function definition for 'approxfun'
mctest : rdist: no visible global function definition for 'runif'
mctest : S: no visible global function definition for 'optim'
qplot: no visible global function definition for 'plot'
qplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline approxfun head knots median optim par plot plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'leaps' 'locfit' 'mgcv'
  Please remove these calls from your code.
':::' calls which should be '::':
  'stats:::ARMAacf' 'stats:::acf' 'stats:::arima'
  See the note in ?`:::` about the use of this operator.
dmvnb: no visible global function definition for 'dbinom'
drvts: no visible global function definition for 'dnorm'
drvts: no visible global function definition for 'dbinom'
dsvts: no visible global function definition for 'dnorm'
rescale: no visible global function definition for 'qlogis'
rescale: no visible global function definition for 'plogis'
tslogl: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dbinom dnorm plogis qlogis
Consider adding
  importFrom("stats", "dbinom", "dnorm", "plogis", "qlogis")
to your NAMESPACE file.
tfDetails: no visible global function definition for 'start'
tfDetails: no visible global function definition for 'end'
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
Qhat: no visible global function definition for 'pnorm'
plrt: no visible global function definition for 'uniroot'
plrt: no visible global function definition for 'optimize'
simulatedata: no visible global function definition for 'rnorm'
tsc.test: no visible global function definition for 'shapiro.test'
tsc.test: no visible global function definition for 'p.adjust'
tsc.test: no visible global function definition for 'glm'
tsc.test : f: no visible global function definition for 'pnorm'
tsc.test: no visible global function definition for 'uniroot'
tsc.test: no visible global function definition for 'optimize'
variance: no visible global function definition for 'density'
variance: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  density ecdf glm optimize p.adjust pnorm rnorm shapiro.test uniroot
Consider adding
  importFrom("stats", "density", "ecdf", "glm", "optimize", "p.adjust",
             "pnorm", "rnorm", "shapiro.test", "uniroot")
to your NAMESPACE file.
Package suggested but not available for checking: 'FinTS'
Package in Depends field not imported from: 'deSolve'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
vintageMap: no visible global function definition for 'read.table'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'as.ts'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'zoo'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'frequency'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'as.ts'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'zoo'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'frequency'
Undefined global functions or variables:
  as.ts frequency read.table zoo
Consider adding
  importFrom("stats", "as.ts", "frequency")
  importFrom("utils", "read.table")
to your NAMESPACE file.
DstandardizedLoadings.TSFmodel: no visible global function definition
  for 'cov'
FAfitStats.TSFmodel: no visible global function definition for 'cov'
FAfitStats.default: no visible global function definition for 'cor'
FAfitStats.default: no visible global function definition for
  'factanal'
FAfitStats.default: no visible global function definition for 'pchisq'
FAmodelFitStats: no visible global function definition for 'pchisq'
checkResiduals.TSFmodel: no visible global function definition for
  'cov'
distribution.factorsEstEval: no visible global function definition for
  'par'
distribution.factorsEstEval: no visible binding for global variable
  'par'
distribution.factorsEstEval: no visible global function definition for
  'density'
distribution.factorsEstEval: no visible global function definition for
  'matplot'
distribution.factorsEstEval: no visible global function definition for
  'title'
summary.TSFmodel: no visible global function definition for 'start'
summary.TSFmodel: no visible global function definition for 'end'
Undefined global functions or variables:
  cor cov density end factanal matplot par pchisq start title
Consider adding
  importFrom("graphics", "matplot", "par", "title")
  importFrom("stats", "cor", "cov", "density", "end", "factanal",
             "pchisq", "start")
to your NAMESPACE file.
Func.SAX: no visible global function definition for 'sd'
Func.SAX: no visible global function definition for 'qnorm'
Func.matrix: no visible global function definition for 'qnorm'
Func.motif: no visible global function definition for 'sd'
Func.motif: no visible global function definition for 'na.omit'
Func.motif: no visible global function definition for 'combn'
Func.motif.multivariate: no visible global function definition for
  'txtProgressBar'
Func.motif.multivariate: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  combn na.omit qnorm sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "qnorm", "sd")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
dLag : dlag.f: no visible global function definition for
  'complete.cases'
distmat: no visible global function definition for 'dist'
fitCity: no visible global function definition for 'glm.control'
fitCity: no visible global function definition for 'terms'
ldmvnorm: no visible global function definition for 'mahalanobis'
lspline: no visible global function definition for 'quantile'
plot.tsdecomp: no visible global function definition for 'par'
plot.tsdecomp: no visible global function definition for 'plot'
setupFormula: no visible global function definition for 'as.formula'
spatialgibbs: no visible global function definition for 'rnorm'
spatialgibbs: no visible global function definition for 'rgamma'
spatialgibbs: no visible global function definition for 'runif'
tsdecomp: no visible global function definition for 'fft'
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par plot
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for 'index.search'
TransSphere : ttin: no visible global function definition for 't.test'
TransSphere: no visible global function definition for 'sd'
TransSphere: no visible global function definition for 'quantile'
TransSphere: no visible global function definition for 'pt'
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > 
  > library("TSP")
  > test_check("TSP")
  -- 1. Failure: (unknown) (@test-solve_TSP.R#56)  -------------------------------
  all(sapply(tours1, attr, "tour_length") == 0) isn't true.
  
  == testthat results  ===========================================================
  OK: 21 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test-solve_TSP.R#56) 
  
  Error: testthat unit tests failed
  Execution halted
TT.GS : TT.GS.sp: no visible global function definition for 'qt'
TT.GS : TT.GS.sp: no visible global function definition for 'runif'
TT.GS : TT.GS.sp: no visible global function definition for 'pt'
TT.moment: no visible global function definition for 'dt'
TT.moment: no visible global function definition for 'pt'
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
ttScreening: no visible global function definition for 'gaussian'
ttScreening: no visible global function definition for 'glm.control'
ttScreening: no visible global function definition for 'model.response'
ttScreening: no visible global function definition for 'is.empty.model'
ttScreening: no visible global function definition for 'model.matrix'
ttScreening: no visible global function definition for 'na.omit'
ttScreening: no visible global function definition for 'terms'
ttScreening: no visible global function definition for 'capture.output'
ttScreening: no visible global function definition for 'glm'
ttScreening: no visible binding for global variable 'gaussian'
ttScreening: no visible global function definition for 'pt'
ttScreening: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  capture.output gaussian glm glm.control is.empty.model model.matrix
  model.response na.omit p.adjust pt terms
Consider adding
  importFrom("stats", "gaussian", "glm", "glm.control", "is.empty.model",
             "model.matrix", "model.response", "na.omit", "p.adjust",
             "pt", "terms")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
.saveDevice: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off
Consider adding
  importFrom("grDevices", "dev.off")
to your NAMESPACE file.
ttwa: no visible global function definition for 'aggregate'
ttwa: no visible global function definition for 'txtProgressBar'
ttwa: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  aggregate setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
':::' calls which should be '::':
  'knitr:::is_html_output' 'knitr:::is_latex_output'
  See the note in ?`:::` about the use of this operator.
http.connection: no visible global function definition for 'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'gsl' 'igraph' 'snowfall'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
accelerate: no visible global function definition for 'modifyList'
boxplot.turbosim: no visible global function definition for 'par'
boxplot.turbosim: no visible global function definition for 'axis'
boxplot.turbosim: no visible global function definition for 'mtext'
dataprof.turbosim: no visible global function definition for 'quantile'
dataprof.turbosim: no visible global function definition for 'par'
dataprof.turbosim: no visible global function definition for 'plot'
dataprof.turbosim: no visible global function definition for 'lines'
dataprof.turbosim: no visible global function definition for 'segments'
dataprof.turbosim: no visible global function definition for 'legend'
line.search: no visible global function definition for 'optimize'
pairs.turbosim: no visible global function definition for 'par'
pairs.turbosim: no visible global function definition for 'plot'
pairs.turbosim: no visible global function definition for 'legend'
pairs.turbosim: no visible global function definition for 'axis'
pairs.turbosim: no visible global function definition for 'title'
pairs.turbosim: no visible global function definition for 'coef'
pairs.turbosim: no visible global function definition for 'abline'
pairs.turbosim: no visible global function definition for 'text'
plot.turbo: no visible global function definition for 'plot'
plot.turbo: no visible global function definition for 'lines'
plot.turbo: no visible global function definition for 'legend'
turboSim: no visible binding for global variable 'par'
turboem: no visible global function definition for 'modifyList'
Undefined global functions or variables:
  abline axis coef legend lines modifyList mtext optimize par plot
  quantile segments text title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "mtext",
             "par", "plot", "segments", "text", "title")
  importFrom("stats", "coef", "optimize", "quantile")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
turf: no visible global function definition for 'read.table'
turf: no visible global function definition for 'flush.console'
turf.combos: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn flush.console read.table
Consider adding
  importFrom("utils", "combn", "flush.console", "read.table")
to your NAMESPACE file.
TwoCop: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
condnorm: no visible global function definition for 'pnorm'
condnorm: no visible global function definition for 'dnorm'
find.p.joint: no visible global function definition for 'integrate'
find.p.joint.alt: no visible global function definition for 'integrate'
termsInt: no visible global function definition for 'pnorm'
termsInt.alt: no visible global function definition for 'pnorm'
twoStageNull: no visible global function definition for 'qnorm'
twoStageNull: no visible global function definition for 'optimize'
twoStagePower: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm integrate optimize pnorm qnorm
Consider adding
  importFrom("stats", "dnorm", "integrate", "optimize", "pnorm", "qnorm")
to your NAMESPACE file.
txtacf: no visible binding for global variable 'na.fail'
txtacf: no visible global function definition for 'acf'
txtboxplot : <anonymous>: no visible global function definition for
  'boxplot.stats'
txtboxplot: no visible global function definition for 'boxplot.stats'
txtdensity: no visible global function definition for 'density'
Undefined global functions or variables:
  acf boxplot.stats density na.fail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "acf", "density", "na.fail")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: working directory was changed to 'D:/temp/RtmpWwWboD/treePos/2018_01_10/run', resetting
Crm: no visible global function definition for 'integrate'
Crm : <anonymous>: no visible global function definition for
  'integrate'
Crm: no visible global function definition for 'optimize'
ail1: no visible global function definition for 'uniroot'
ail2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ail2: no visible global function definition for 'uniroot'
aip : fu : <anonymous>: no visible global function definition for
  'integrate'
aip: no visible global function definition for 'uniroot'
ait1: no visible global function definition for 'uniroot'
ait2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ait2: no visible global function definition for 'uniroot'
sim3p3: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'palette'
simCrm: no visible global function definition for 'gray'
simCrm: no visible global function definition for 'plot'
simCrm: no visible global function definition for 'abline'
simCrm: no visible global function definition for 'lines'
ssim3p3: no visible global function definition for 'txtProgressBar'
ssim3p3: no visible global function definition for 'setTxtProgressBar'
ssimCrm: no visible global function definition for 'txtProgressBar'
ssimCrm: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  abline gray integrate lines optimize palette plot rbinom
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
rmd2pdf: no visible global function definition for 'tail'
rnw2pdf: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc         2.2Mb
    dummydata   1.4Mb
    libs        4.1Mb
ubRacing : predCandidate: no visible global function definition for
  'predict'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'pchisq'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'qt'
ubRacing : aux.friedman.edit: no visible global function definition for
  'wilcox.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  't.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  'p.adjust'
ubRacing : idFolds: no visible global function definition for
  'quantile'
ubRacing: no visible binding for global variable 'sd'
ubSmoteExs: no visible global function definition for 'runif'
Undefined global functions or variables:
  p.adjust pchisq predict qt quantile runif sd t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "predict", "qt", "quantile",
             "runif", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.
med: no visible global function definition for 'quantile'
uh: no visible global function definition for 'mad'
uh.bu: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad quantile
Consider adding
  importFrom("stats", "mad", "quantile")
to your NAMESPACE file.
permute.rows: no visible global function definition for 'runif'
uniCox: no visible global function definition for 'quantile'
uniCoxCV: no visible global function definition for 'quantile'
uniCoxCV: no visible global function definition for 'coxph'
uniCoxCV: no visible binding for global variable 'var'
Undefined global functions or variables:
  coxph quantile runif var
Consider adding
  importFrom("stats", "quantile", "runif", "var")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'predict.uniCox':
  'predict.uniCox'

S3 methods shown with full name in documentation object 'uniCox-internal':
  'print.uniCoxCVFit' 'print.uniCoxFit'

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.
dudewicz.unif.test: no visible global function definition for 'runif'
frosini.unif.test: no visible global function definition for 'runif'
hegazy.unif.test: no visible global function definition for 'runif'
kolmogorov.unif.test: no visible global function definition for 'runif'
kuiper.unif.test: no visible global function definition for 'runif'
neyman.unif.test: no visible global function definition for 'runif'
quesenberry.unif.test: no visible global function definition for
  'runif'
sarkadi.unif.test: no visible global function definition for 'runif'
sherman.unif.test: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
cumcount: no visible global function definition for 'setNames'
uniqtag: no visible global function definition for 'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
plot.upclassfit: no visible global function definition for 'frame'
plot.upclassfit: no visible global function definition for 'par'
plot.upclassfit: no visible global function definition for 'axis'
plot.upclassfit: no visible global function definition for 'matplot'
plot.upclassfit: no visible global function definition for 'legend'
plot.upclassfit: no visible global function definition for 'title'
Undefined global functions or variables:
  axis frame legend matplot par title
Consider adding
  importFrom("graphics", "axis", "frame", "legend", "matplot", "par",
             "title")
to your NAMESPACE file.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > test_check("urltools")
  -- 1. Failure: Check decoding and encoding are equivalent (@test_encoding.R#23) 
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Hinrichtung_auf_dem_AltstÃ¤dter_Ring.JPG/120px-Hinrichtung_auf_dem_AltstÃ
  x[1]: ¤dter_Ring.JPG"
  y[1]: "Hinrichtung_auf_dem_Altstädter_Ring.JPG/120px-Hinrichtung_auf_dem_Altstäd
  y[1]: ter_Ring.JPG"
  
  == testthat results  ===========================================================
  OK: 157 SKIPPED: 0 FAILED: 1
  1. Failure: Check decoding and encoding are equivalent (@test_encoding.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > test_check("urltools")
  -- 1. Failure: Check decoding and encoding are equivalent (@test_encoding.R#23) 
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Hinrichtung_auf_dem_AltstÃ¤dter_Ring.JPG/120px-Hinrichtung_auf_dem_AltstÃ
  x[1]: ¤dter_Ring.JPG"
  y[1]: "Hinrichtung_auf_dem_Altstädter_Ring.JPG/120px-Hinrichtung_auf_dem_Altstäd
  y[1]: ter_Ring.JPG"
  
  == testthat results  ===========================================================
  OK: 157 SKIPPED: 0 FAILED: 1
  1. Failure: Check decoding and encoding are equivalent (@test_encoding.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: 'USAboundariesData'
readSEER: no visible global function definition for 'read.fwf'
Undefined global functions or variables:
  read.fwf
Consider adding
  importFrom("utils", "read.fwf")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'UScensus2000cdp/R/zzz.R':
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000cdp\").\n")
    cat("Type help(package=\"UScensus2000cdp\") to get started.\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'UScensus2000tract/R/zzz.R':
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000tract\").\n")
    cat("Type help(package=\"UScensus2000tract\") to get started.\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
'library' or 'require' call to 'rgdal' 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:
  'foreign' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
File 'uuid/libs/i386/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'
File 'uuid/libs/x64/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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'
uwham.boot: no visible binding for global variable 'var'
Undefined global functions or variables:
  axis lines plot.new plot.window rect var
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
  importFrom("stats", "var")
to your NAMESPACE file.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
Packages suggested but not available for checking: 'vaers' 'vaersND'
Files named as vignettes but with no recognized vignette engine:
   'vignettes/News.Rmd'
(Is a VignetteBuilder field missing?)
Mammen: no visible global function definition for 'runif'
PR2: no visible global function definition for 'ar.burg'
PR2: no visible global function definition for 'pt'
PR2: no visible global function definition for 'pf'
PR3: no visible global function definition for 'ar.burg'
PR3: no visible global function definition for 'pt'
PR3: no visible global function definition for 'pf'
VAR.FOR: no visible global function definition for 'qnorm'
VAR.ForeB: no visible global function definition for 'runif'
VAR.LRtest: no visible global function definition for 'pchisq'
VAR.LRtest: no visible global function definition for 'pf'
VAR.PI: no visible global function definition for 'quantile'
VAR.Waldtest: no visible global function definition for 'pf'
VAR.irf: no visible global function definition for 'par'
VAR.irf: no visible global function definition for 'plot'
VAR.irf: no visible global function definition for 'abline'
VAR1.sim: no visible global function definition for 'rnorm'
resamp: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline ar.burg par pchisq pf plot pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'strucchange'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
black_scholes: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
burdenPlot: no visible global function definition for 'density'
burdenPlot: no visible global function definition for 'axis'
burdenPlot: no visible global function definition for 'points'
burdenPlot: no visible global function definition for 'lines'
burdenPlot: no visible global function definition for 'abline'
burdenPlot: no visible global function definition for 'text'
burdenPlot: no visible global function definition for 'sd'
burdenPlot: no visible global function definition for 'segments'
vbdm: no visible global function definition for 'var'
vbdm: no visible global function definition for 'pchisq'
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for 'var'
vbdmR: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
compute_KL : rtnorm: no visible global function definition for 'runif'
compute_KL : rtnorm: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'qnorm'
compute_KL: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'pnorm'
compute_KL: no visible global function definition for 'var'
compute_KL: no visible global function definition for 'rbinom'
compute_KL: no visible global function definition for 'rnorm'
compute_KL: no visible global function definition for 'sd'
vbsr: no visible global function definition for 'qchisq'
vbsr: no visible global function definition for 'var'
vbsr: no visible global function definition for 'pchisq'
vbsr: no visible global function definition for 'sd'
vbsr: no visible binding for global variable 'sd'
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
cv.vda.le.default: no visible global function definition for 'predict'
cv.vda.r.default: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Compare2FDS: no visible global function definition for 'runif'
Compare2FDS: no visible global function definition for 'lm'
Compare2FDS: no visible global function definition for 'model.matrix'
Compare2FDS: no visible global function definition for 'plot'
Compare2FDS: no visible global function definition for 'abline'
Compare2FDS: no visible global function definition for 'lines'
Compare2FDS: no visible global function definition for 'text'
Compare2Vdg: no visible global function definition for 'par'
Compare2Vdg: no visible global function definition for 'plot'
Compare2Vdg: no visible global function definition for 'lines'
Compare2Vdg: no visible global function definition for 'legend'
FDSPlot: no visible global function definition for 'runif'
FDSPlot: no visible global function definition for 'lm'
FDSPlot: no visible global function definition for 'model.matrix'
FDSPlot: no visible global function definition for 'plot'
FDSPlot: no visible global function definition for 'abline'
Vdgraph: no visible global function definition for 'par'
Vdgraph: no visible global function definition for 'plot'
Vdgraph: no visible global function definition for 'lines'
Vdgraph: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend lines lm model.matrix par plot runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
calculateParameters,AffineTransformation: no visible global function
  definition for 'lm'
calculateParameters,AffineTransformation: no visible global function
  definition for 'coef'
calculateParameters,SimilarityTransformation: no visible global
  function definition for 'lm'
calculateParameters,SimilarityTransformation: no visible global
  function definition for 'coef'
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for 'points'
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for 'legend'
Undefined global functions or variables:
  coef legend lm points
Consider adding
  importFrom("graphics", "legend", "points")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
vsetdiff : <anonymous>: no visible global function definition for
  'head'
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
DrawDensity3D: no visible global function definition for 'colorRamp'
DrawDensity3D: no visible global function definition for 'rgb'
ReadFromFile3D: no visible global function definition for 'read.table'
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in 'vegalite-Ex.R' failed
The error most likely occurred in:

> ### Name: from_spec
> ### Title: Take a JSON Vega-Lite Spec and render as an htmlwidget
> ### Aliases: from_spec
> 
> ### ** Examples
> 
> from_spec("http://rud.is/dl/embedded.json")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(con, "r") : cannot open the connection
Calls: from_spec -> readLines -> file
Execution halted
File 'vegan/libs/i386/vegan.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'cepin.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'cepin.o'
File 'vegan/libs/x64/vegan.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'cepin.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'cepin.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.
'library' or 'require' call to 'stats' which was already attached by Depends.
  Please remove these calls from your code.
Undocumented S4 methods:
  generic 'merge_taxa' and siglist 'vegtable,numeric,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
plot.VennDiagram : <anonymous>: no visible global function definition
  for 'hcl'
plot.VennDiagram: no visible global function definition for 'plot.new'
plot.VennDiagram: no visible global function definition for
  'plot.window'
plot.VennDiagram: no visible global function definition for 'col2rgb'
plot.VennDiagram: no visible global function definition for 'rgb'
plot.VennDiagram: no visible global function definition for 'polygon'
plot.VennDiagram: no visible global function definition for 'text'
plot.VennDiagram: no visible global function definition for 'title'
Undefined global functions or variables:
  col2rgb hcl plot.new plot.window polygon rgb text title
Consider adding
  importFrom("grDevices", "col2rgb", "hcl", "rgb")
  importFrom("graphics", "plot.new", "plot.window", "polygon", "text",
             "title")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   2.6Mb
    libs   1.3Mb
vif: no visible global function definition for 'sd'
vif: no visible global function definition for 'lm'
vif: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  lm pnorm sd
Consider adding
  importFrom("stats", "lm", "pnorm", "sd")
to your NAMESPACE file.
hyperpara: no visible binding for global variable 'var'
hyperpara: no visible global function definition for 'hist'
Undefined global functions or variables:
  hist var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "var")
to your NAMESPACE file.
panel.meansdplot : meansdplot.stats: no visible global function
  definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Package in Depends field not imported from: 'sm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
vioplot: no visible global function definition for 'quantile'
vioplot: no visible global function definition for 'median'
vioplot: no visible global function definition for 'plot.new'
vioplot: no visible global function definition for 'plot.window'
vioplot: no visible global function definition for 'axis'
vioplot: no visible global function definition for 'box'
vioplot: no visible global function definition for 'polygon'
vioplot: no visible global function definition for 'lines'
vioplot: no visible global function definition for 'rect'
vioplot: no visible global function definition for 'points'
Undefined global functions or variables:
  axis box lines median plot.new plot.window points polygon quantile
  rect
Consider adding
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "points", "polygon", "rect")
  importFrom("stats", "median", "quantile")
to your NAMESPACE file.
viopoints.default: no visible global function definition for 'par'
viopoints.default: no visible global function definition for 'plot.new'
viopoints.default: no visible global function definition for
  'plot.window'
viopoints.default: no visible global function definition for 'axis'
viopoints.default: no visible global function definition for 'arrows'
viopoints.default: no visible global function definition for
  'getFromNamespace'
viopoints.default: no visible global function definition for 'title'
viopoints.default: no visible global function definition for 'box'
Undefined global functions or variables:
  arrows axis box getFromNamespace par plot.new plot.window title
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "par", "plot.new",
             "plot.window", "title")
  importFrom("utils", "getFromNamespace")
to your NAMESPACE file.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc           4.7Mb
    htmlwidgets   3.6Mb
Decile.Plot: no visible global function definition for 'barplot'
Decile.Plot: no visible global function definition for 'axis'
Sliding.Window: no visible global function definition for 'plot'
Sliding.Window: no visible global function definition for 'lines'
Sliding.Window: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis barplot legend lines plot
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "plot")
to your NAMESPACE file.
RCplot: no visible global function definition for 'residuals'
RCplot: no visible global function definition for 'predict'
RCplot: no visible global function definition for 'par'
RCplot: no visible global function definition for 'plot.new'
RCplot: no visible global function definition for 'plot.window'
RCplot: no visible global function definition for 'strwidth'
RCplot: no visible global function definition for 'plot'
RCplot: no visible global function definition for 'abline'
RCplot: no visible global function definition for 'text'
RCplot: no visible global function definition for 'mtext'
fitted.vlmc: no visible global function definition for 'predict'
print.vlmc: no visible global function definition for 'AIC'
residuals.vlmc: no visible global function definition for 'predict'
simulate.vlmc: no visible global function definition for 'runif'
summary.vlmc: no visible global function definition for 'predict'
vlmc: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  AIC abline mtext par plot plot.new plot.window predict qchisq
  residuals runif strwidth text
Consider adding
  importFrom("graphics", "abline", "mtext", "par", "plot", "plot.new",
             "plot.window", "strwidth", "text")
  importFrom("stats", "AIC", "predict", "qchisq", "residuals", "runif")
to your NAMESPACE file.
voss1d: no visible global function definition for 'approx'
voss1d: no visible global function definition for 'rnorm'
voss1g: no visible global function definition for 'dchisq'
voss1g: no visible global function definition for 'approx'
voss1g: no visible global function definition for 'rnorm'
voss2d: no visible global function definition for 'rnorm'
voss2g: no visible global function definition for 'dchisq'
voss2g: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  approx dchisq rnorm
Consider adding
  importFrom("stats", "approx", "dchisq", "rnorm")
to your NAMESPACE file.
add.spread.vowelplot: no visible global function definition for
  'points'
add.spread.vowelplot: no visible binding for global variable 'mtext'
add.spread.vowelplot: no visible global function definition for 'lines'
add.spread.vowelplot: no visible global function definition for
  'prcomp'
add.spread.vowelplot: no visible global function definition for
  'arrows'
add.spread.vowelplot: no visible global function definition for
  'legend'
add.spread.vowelplot: no visible global function definition for 'text'
add.vowelplot: no visible global function definition for 'points'
add.vowelplot: no visible binding for global variable 'mtext'
add.vowelplot: no visible global function definition for 'arrows'
add.vowelplot: no visible global function definition for 'text'
compute.medians: no visible global function definition for 'median'
compute.sds: no visible global function definition for 'sd'
load.vowels: no visible global function definition for 'read.table'
norm.lobanov: no visible global function definition for 'sd'
vowelplot: no visible global function definition for 'plot'
vowelplot: no visible global function definition for 'legend'
vowelplot: no visible global function definition for 'arrows'
vowelplot: no visible global function definition for 'text'
Undefined global functions or variables:
  arrows legend lines median mtext plot points prcomp read.table sd
  text
Consider adding
  importFrom("graphics", "arrows", "legend", "lines", "mtext", "plot",
             "points", "text")
  importFrom("stats", "median", "prcomp", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to 'raster' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
level: no visible global function definition for 'quantile'
obj.rec: no visible global function definition for 'txtProgressBar'
obj.rec: no visible global function definition for 'setTxtProgressBar'
project: no visible global function definition for 'aggregate'
raster.proj: no visible global function definition for 'quantile'
raster.proj: no visible global function definition for 'rasterFromXYZ'
raster.proj: no visible global function definition for 'plot.new'
raster.proj: no visible global function definition for 'plot'
raster.proj: no visible global function definition for 'legend'
sub.obj: no visible global function definition for 'aggregate'
sub.obj: no visible global function definition for 'txtProgressBar'
sub.obj: no visible global function definition for 'setTxtProgressBar'
surface: no visible global function definition for 'quantile'
Undefined global functions or variables:
  aggregate legend plot plot.new quantile rasterFromXYZ
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "plot", "plot.new")
  importFrom("stats", "aggregate", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'library' or 'require' call to 'misc3d' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.vscc: no visible global function definition for 'rainbow'
plot.vscc: no visible global function definition for 'pairs'
Undefined global functions or variables:
  pairs rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "pairs")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'lattice' 'latticeExtra' 'stringdist'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ald: no visible global function definition for 'detectCores'
ald: no visible global function definition for 'mclapply'
coltheart.N: no visible global function definition for 'detectCores'
coltheart.N: no visible global function definition for 'mclapply'
hamming.distance: no visible global function definition for
  'stringdist'
ldknn: no visible global function definition for 'detectCores'
ldknn: no visible global function definition for 'mclapply'
ldknn.odds: no visible global function definition for 'glm'
ldknn.odds: no visible binding for global variable 'binomial'
ldknn.odds: no visible global function definition for 'coefficients'
levenshtein.damerau.distance: no visible global function definition for
  'stringdist'
levenshtein.distance: no visible global function definition for
  'stringdist'
plot.ldknn.run: no visible global function definition for 'histogram'
plot.ldknn.run: no visible global function definition for
  'theEconomist.theme'
plot.ldknn.run: no visible global function definition for 'xyplot'
plot.ldknn.run: no visible global function definition for 'as.layer'
Undefined global functions or variables:
  as.layer binomial coefficients detectCores glm histogram mclapply
  stringdist theEconomist.theme xyplot
Consider adding
  importFrom("stats", "binomial", "coefficients", "glm")
to your NAMESPACE file.
Package in Depends field not imported from: 'Rcpp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'waffect/libs/i386/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'
File 'waffect/libs/x64/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.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.
summary.whc: no visible global function definition for 'printCoefmat'
wahc.fit: no visible global function definition for 'pt'
wahc.fit: no visible global function definition for 'cor'
whc: no visible global function definition for 'model.frame'
whc: no visible global function definition for 'model.matrix'
whc: no visible global function definition for 'model.response'
Undefined global functions or variables:
  cor model.frame model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "printCoefmat", "pt")
to your NAMESPACE file.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.3Mb
Found the following significant warnings:
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
  Warning: working directory was changed to 'D:/temp/RtmpayzQGm', resetting
plot.wb: no visible global function definition for 'plot'
plot.wb: no visible global function definition for 'lines'
power.sum: no visible global function definition for 'plot'
power.sum: no visible global function definition for 'lines'
test.data: no visible global function definition for 'var'
test.data: no visible global function definition for 'rnorm'
test.data: no visible global function definition for 'plot'
test.data: no visible global function definition for 'lines'
wave.band: no visible binding for global variable 'var'
wave.band: no visible global function definition for 'pnorm'
wave.band: no visible global function definition for 'qnorm'
wave.band: no visible global function definition for 'plot'
wave.band: no visible global function definition for 'lines'
wb.johnson.lims: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  lines plot pnorm qnorm rnorm var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "pnorm", "qnorm", "rnorm", "var")
to your NAMESPACE file.
changepoints.sbs: no visible global function definition for 'mad'
changepoints.wbs: no visible global function definition for 'var'
changepoints.wbs: no visible global function definition for 'quantile'
plot.sbs: no visible global function definition for 'ts.plot'
plot.sbs: no visible global function definition for 'lines'
plot.sbs: no visible global function definition for 'title'
random.intervals: no visible global function definition for 'runif'
sbs.default: no visible global function definition for 'var'
wbs.default: no visible global function definition for 'var'
Undefined global functions or variables:
  lines mad quantile runif title ts.plot var
Consider adding
  importFrom("graphics", "lines", "title")
  importFrom("stats", "mad", "quantile", "runif", "ts.plot", "var")
to your NAMESPACE file.
onesamplemeantest: no visible global function definition for 'pnorm'
twosamplemeantest: no visible global function definition for 'pnorm'
wcq: no visible global function definition for 'var'
wcq: no visible global function definition for 'pnorm'
wcq.fdrc: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  p.adjust pnorm var
Consider adding
  importFrom("stats", "p.adjust", "pnorm", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'RJSONIO'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
WDI: no visible binding for global variable 'WDI_data'
WDIcache: no visible global function definition for 'fromJSON'
WDIsearch: no visible binding for global variable 'WDI_data'
Undefined global functions or variables:
  WDI_data fromJSON
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 26 SKIPPED: 0 FAILED: 18
  1. Error: canCallChrome (@test-chrome.R#3) 
  2. Error: pickUpErrorFromReturnCode (@test-chrome.R#43) 
  3. Error: pickUpErrorFromPortInUse (@test-chrome.R#62) 
  4. Error: canCallGecko (@test-gecko.R#4) 
  5. Error: pickUpErrorFromReturnCode (@test-gecko.R#44) 
  6. Error: pickUpErrorFromPortInUse (@test-gecko.R#63) 
  7. Error: canCallIEDriver (@test-iedriver.R#4) 
  8. Error: pickUpErrorFromReturnCode (@test-iedriver.R#46) 
  9. Error: pickUpErrorFromPortInUse (@test-iedriver.R#68) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    client   9.1Mb
    doc      1.0Mb
File 'webvis/R/zzz.R':
  .onLoad calls:
    print("Welcome to the webvis pacakge.")

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

[1] "Welcome to the webvis pacakge."
render.webvis: no visible global function definition for 'browseURL'
unfold.webvis : <anonymous>: no visible global function definition for
  'runif'
Undefined global functions or variables:
  browseURL runif
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plot.webvis':
  'plot.webvis'

S3 methods shown with full name in documentation object '"+.webvis"':
  '+.webvis'

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.
Weighted.Box.test: no visible global function definition for 'acf'
Weighted.Box.test: no visible binding for global variable 'na.pass'
Weighted.Box.test: no visible global function definition for 'pgamma'
Weighted.Box.test: no visible global function definition for 'pchisq'
Weighted.LM.test: no visible global function definition for 'acf'
Weighted.LM.test: no visible binding for global variable 'na.pass'
Weighted.LM.test: no visible global function definition for 'pgamma'
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
Package suggested but not available for checking: 'sbw'
print.palette: no visible global function definition for 'par'
print.palette: no visible global function definition for 'image'
print.palette: no visible global function definition for 'rect'
print.palette: no visible global function definition for 'rgb'
print.palette: no visible global function definition for 'text'
wes_palette: no visible global function definition for
  'colorRampPalette'
Undefined global functions or variables:
  colorRampPalette image par rect rgb text
Consider adding
  importFrom("grDevices", "colorRampPalette", "rgb")
  importFrom("graphics", "image", "par", "rect", "text")
to your NAMESPACE file.
Package in Depends field not imported from: 'snpStats'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Z.value: no visible global function definition for 'sd'
Z.value: no visible global function definition for 'pnorm'
pairtest: no visible global function definition for 'is'
pairtest: no visible global function definition for 'new'
pairtest: no visible global function definition for 'rbind2'
pairtest: no visible global function definition for 'p.value'
pairtest: no visible global function definition for 'single.snp.tests'
scoretest: no visible global function definition for 'pchisq'
varplot : <anonymous>: no visible global function definition for 'var'
varplot: no visible global function definition for 'plot'
varplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline is new p.value pchisq plot pnorm rbind2 sd single.snp.tests
  var
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "is", "new", "rbind2")
  importFrom("stats", "pchisq", "pnorm", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to 'markdown' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dlog.norm: no visible global function definition for 'rnorm'
fun.load.hals.a: no visible global function definition for 'sfExport'
fun.load.hals.a: no visible global function definition for 'sfLibrary'
fun.load.hals.fill: no visible global function definition for
  'sfExport'
fun.load.hals.fill: no visible global function definition for
  'sfLibrary'
fun.load.widals.a: no visible global function definition for 'sfExport'
fun.load.widals.a: no visible global function definition for
  'sfLibrary'
fun.load.widals.fill: no visible global function definition for
  'sfExport'
fun.load.widals.fill: no visible global function definition for
  'sfLibrary'
unif.mh: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif sfExport sfLibrary
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'genefilter' 'parallel'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for
  'packageDescription'
.relax.cvcompute: no visible binding for global variable
  'weighted.mean'
.relax.widenet.cv.elnet: no visible global function definition for
  'predict'
.relax.widenet.cv.elnet: no visible binding for global variable
  'weighted.mean'
.relax.widenet.cv.lognet: no visible global function definition for
  'predict'
.relax.widenet.cv.lognet: no visible binding for global variable
  'weighted.mean'
.widenet.cv.elnet: no visible global function definition for 'predict'
.widenet.cv.elnet: no visible binding for global variable
  'weighted.mean'
.widenet.cv.lognet: no visible global function definition for 'predict'
.widenet.cv.lognet: no visible binding for global variable
  'weighted.mean'
predict.widenet: no visible global function definition for 'predict'
screen.cor : <anonymous>: no visible global function definition for
  'var'
screen.cor : <anonymous>: no visible global function definition for
  'cor.test'
screen.ttest: no visible global function definition for 'colttests'
widenet: no visible global function definition for 'mc.reset.stream'
widenet: no visible global function definition for 'mclapply'
widenet: no visible global function definition for 'predict'
Undefined global functions or variables:
  colttests cor.test mc.reset.stream mclapply packageDescription
  predict var weighted.mean
Consider adding
  importFrom("stats", "cor.test", "predict", "var", "weighted.mean")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Bundesliga.Mannschaft: no visible global function definition for 'data'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible global function definition for 'data'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible global function definition for 'data'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
sens.spec: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
wilcox.selection.split: no visible global function definition for
  'pnorm'
wilcox.test2: no visible global function definition for 'wilcox.test'
Undefined global functions or variables:
  pnorm wilcox.test
Consider adding
  importFrom("stats", "pnorm", "wilcox.test")
to your NAMESPACE file.
Cs: no visible global function definition for 'wilcox.test'
Don: no visible global function definition for 'points'
Don: no visible global function definition for 'chisq.test'
Lixn: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  chisq.test pchisq points wilcox.test
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "chisq.test", "pchisq", "wilcox.test")
to your NAMESPACE file.
plotTrait: no visible global function definition for 'plot'
plotTrait: no visible global function definition for 'points'
plotTrait: no visible global function definition for 'legend'
test.windex: no visible global function definition for 'hist'
test.windex: no visible global function definition for 'abline'
test.windex: no visible global function definition for 'legend'
windex: no visible global function definition for 'sd'
windex: no visible global function definition for 'var'
windex: no visible global function definition for 'dist'
windex: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline dist hist legend plot points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "plot", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
.__A__.1 : <anonymous>: no visible binding for global variable '.hwnd'
Undefined global functions or variables:
  .hwnd
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
dbayes: no visible global function definition for 'mahalanobis'
dbayes: no visible global function definition for 'var'
wmd: no visible global function definition for 'cor'
wmd: no visible global function definition for 'var'
Undefined global functions or variables:
  cor mahalanobis var
Consider adding
  importFrom("stats", "cor", "mahalanobis", "var")
to your NAMESPACE file.
fit,Leader: no visible global function definition for 'lm'
plotfit,Leader: no visible global function definition for 'par'
plotfit,Leader: no visible global function definition for 'plot'
Undefined global functions or variables:
  lm par plot
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
File 'wnominate/libs/i386/wnominate.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'wnominate.o'
File 'wnominate/libs/x64/wnominate.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'wnominate.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.
prepareData: no visible global function definition for 'tokenize'
Undefined global functions or variables:
  tokenize
'library' or 'require' call to 'tm' 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:
  'plyr' 'reshape2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
wordmatch: no visible global function definition for 'llply'
wordmatch : <anonymous>: no visible global function definition for
  'llply'
wordmatch: no visible global function definition for 'melt'
wordmatch: no visible global function definition for 'count'
Undefined global functions or variables:
  count llply melt
pickList : <anonymous>: 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.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
simul.wsvm: no visible binding for global variable 'mixture.example'
wsvm.boost: no visible global function definition for 'plot'
Undefined global functions or variables:
  mixture.example plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
quadplot: no visible global function definition for 'median'
xgobi: no visible global function definition for 'write.table'
Undefined global functions or variables:
  median write.table
Consider adding
  importFrom("stats", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
XHWE: no visible global function definition for 'read.table'
result: no visible global function definition for 'pchisq'
result: no visible global function definition for 'rbinom'
result: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
.xssfcolor: no visible global function definition for 'col2rgb'
Undefined global functions or variables:
  col2rgb
Consider adding
  importFrom("grDevices", "col2rgb")
to your NAMESPACE file.
R5.value.default: no visible binding for global variable 'data.table'
R5.value.default: no visible global function definition for
  'as.data.table'
R5.value.parse: no visible binding for global variable 'data.table'
R5.value.parse: no visible global function definition for
  'is.data.table'
R5.value.parse: no visible global function definition for
  'as.data.table'
stampme: no visible global function definition for 'flush.console'
stampmsg: no visible global function definition for 'flush.console'
write.data.table: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
File 'xml2/libs/i386/xml2.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'
File 'xml2/libs/x64/xml2.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running examples in 'xml2-Ex.R' failed
The error most likely occurred in:

> ### Name: read_xml
> ### Title: Read HTML or XML.
> ### Aliases: read_xml read_html read_xml.character read_xml.raw
> ###   read_xml.connection
> 
> ### ** Examples
> 
> # Literal xml/html is useful for small examples
> read_xml("<foo><bar /></foo>")
{xml_document}
<foo>
[1] <bar/>
> read_html("<html><title>Hi<title></html>")
{xml_document}
<html>
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8 ...
> read_html("<html><title>Hi")
{xml_document}
<html>
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8 ...
> 
> # From a local path
> read_html(system.file("extdata", "r-project.html", package = "xml2"))
{xml_document}
<html lang="en">
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8 ...
[2] <body>\n    <div class="container page">\n      <div class="row">\n       ...
> 
> # From a url
> cd <- read_xml("http://www.xmlfiles.com/examples/cd_catalog.xml")
Error in doc_parse_raw(x, encoding = encoding, base_url = base_url, as_html = as_html,  : 
  Specification mandate value for attribute async [41]
Calls: read_xml ... read_xml.connection -> read_xml.raw -> doc_parse_raw -> .Call
Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  y[1]: "# ç\u008f¾è¡ã\u0081®å­¦æ ¡ææ³ã\u0081§ã\u0081¯ã\u0081è±èªã\u0081«ã\
  y[1]: u0081ããã\u0081ã\u0081ªãç®çèªã\u008dãè£èªã\u008d"
  
  -- 2. Failure: UTF-8 is OK (@test.R#78)  ---------------------------------------
  length(op) not equal to 1.
  1/1 mismatches
  [1] 0 - 1 == -1
  
  == testthat results  ===========================================================
  OK: 14 SKIPPED: 0 FAILED: 2
  1. Failure: UTF-8 is OK (@test.R#66) 
  2. Failure: UTF-8 is OK (@test.R#78) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    examples      4.5Mb
    libs          4.2Mb
newXMLDoc: no visible binding for global variable 'doc'
source: no visible binding for global variable 'use_file'
xmlFlatListTree : f: no visible binding for global variable 'nodeNames'
xmlFlatListTree : f: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'parentCount'
xmlFlatListTree : addNode: no visible binding for global variable
  'parentCount'
xmlFlatListTree : <anonymous>: no visible binding for global variable
  'e'
xmlFlatTree : <anonymous>: no visible binding for global variable 'e'
[[,XMLCodeFile: possible error in updateIds(doc, save = x): unused
  argument (save = x)
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount use_file
LPGM: no visible global function definition for 'flush.console'
PGM: no visible global function definition for 'flush.console'
PGM.path.neighborhood: no visible global function definition for
  'runif'
PGMSim: no visible global function definition for 'rpois'
PGMSim: no visible global function definition for 'par'
WPGMSim: no visible global function definition for 'rpois'
XMRF.Sim: no visible global function definition for 'cov2cor'
XMRF.Sim: no visible global function definition for 'rbinom'
XMRF.Sim: no visible global function definition for 'rnorm'
glm.generic: no visible global function definition for 'flush.console'
mymult: no visible global function definition for 'rmultinom'
plot.GMS: no visible global function definition for 'pdf'
plot.GMS: no visible global function definition for 'dev.off'
plotNet: no visible global function definition for 'pdf'
plotNet: no visible global function definition for 'dev.off'
print.GMS: no visible global function definition for 'str'
processSeq: no visible binding for global variable 'quantile'
processSeq: no visible binding for global variable 'var'
processSeq: no visible global function definition for 'ks.test'
rmpois : <anonymous>: no visible global function definition for 'rpois'
Undefined global functions or variables:
  cov2cor dev.off flush.console ks.test par pdf quantile rbinom
  rmultinom rnorm rpois runif str var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "cov2cor", "ks.test", "quantile", "rbinom",
             "rmultinom", "rnorm", "rpois", "runif", "var")
  importFrom("utils", "flush.console", "str")
to your NAMESPACE file.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
big.read.table: no visible global function definition for 'read.table'
big.read.table: no visible global function definition for 'object.size'
sparkline: no visible global function definition for 'is.ts'
sparkline: no visible global function definition for 'time'
sparkline: no visible global function definition for 'boxplot'
Undefined global functions or variables:
  boxplot is.ts object.size read.table time
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "is.ts", "time")
  importFrom("utils", "object.size", "read.table")
to your NAMESPACE file.
bootstrapswapcurve: no visible global function definition for 'ts'
fitted: no visible global function definition for 'ts'
forwardrates: no visible global function definition for 'ts'
residuals: no visible global function definition for 'ts'
tZC_NS: no visible global function definition for 'cmpfun'
tZC_NS_extra: no visible global function definition for 'cmpfun'
tZC_SV: no visible global function definition for 'cmpfun'
tZC_SV_extra: no visible global function definition for 'cmpfun'
ycextra: no visible global function definition for 'new'
ycinter: no visible global function definition for 'new'
ycplot: no visible global function definition for 'par'
ycplot: no visible global function definition for 'points'
ycplot: no visible global function definition for 'abline'
ycplot: no visible global function definition for 'hist'
ycplot: no visible global function definition for 'lines'
ycplot: no visible global function definition for 'density'
ycplot: no visible global function definition for 'qqnorm'
ycplot: no visible global function definition for 'qqline'
ycsummary: no visible global function definition for 'shapiro.test'
ycsummary: no visible global function definition for 'pf'
Undefined global functions or variables:
  abline cmpfun density hist lines new par pf points qqline qqnorm
  shapiro.test ts
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "points")
  importFrom("methods", "new")
  importFrom("stats", "density", "pf", "qqline", "qqnorm",
             "shapiro.test", "ts")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.NS.estimator: no visible global function definition for 'lm'
.NS.estimator: no visible global function definition for 'coef'
.NS.estimator: no visible global function definition for 'na.omit'
.NS.estimator: no visible global function definition for 'resid'
.NSS.estimator: no visible global function definition for 'lm'
.NSS.estimator: no visible global function definition for 'coef'
.NSS.estimator: no visible global function definition for 'na.omit'
.NSS.estimator: no visible global function definition for 'resid'
NSrates: no visible global function definition for 'time'
Nelson.Siegel: no visible global function definition for 'optimize'
Srates: no visible global function definition for 'time'
Svensson: no visible global function definition for 'median'
Svensson: no visible global function definition for 'optimize'
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
kmeansN: no visible global function definition for 'kmeans'
kmeansN: no visible global function definition for 'aggregate'
kmeansN2: no visible global function definition for 'aggregate'
kmeansN2: no visible binding for global variable 'sd'
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'deSolve' 'triangle'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'zdat'
S3 methods shown with full name in documentation object 'merge':
  'cbind.zoocat'

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.
ztable.glm: no visible global function definition for 'confint'
ztable.glm: no visible global function definition for 'coef'
ztable.nls: no visible global function definition for 'formula'
Undefined global functions or variables:
  coef confint formula
Consider adding
  importFrom("stats", "coef", "confint", "formula")
to your NAMESPACE file.
confint.zyp: no visible global function definition for 'qnorm'
confint.zyp: no visible global function definition for 'var'
zyp.sen: no visible global function definition for 'terms'
zyp.sen: no visible global function definition for 'median'
zyp.trend.csv: no visible global function definition for 'read.csv'
zyp.trend.csv: no visible global function definition for 'write.csv'
zyp.yuepilon: no visible global function definition for 'acf'
zyp.yuepilon: no visible binding for global variable 'na.pass'
zyp.yuepilon: no visible global function definition for 'confint'
zyp.yuepilon: no visible global function definition for 'lm'
zyp.zhang: no visible global function definition for 'acf'
zyp.zhang: no visible binding for global variable 'na.pass'
zyp.zhang: no visible global function definition for 'confint'
zyp.zhang: no visible global function definition for 'lm'
Undefined global functions or variables:
  acf confint lm median na.pass qnorm read.csv terms var write.csv
Consider adding
  importFrom("stats", "acf", "confint", "lm", "median", "na.pass",
             "qnorm", "terms", "var")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘ggplot2’

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

Packages suggested but not available for checking:
  ‘ggplot2’ ‘HH’ ‘vcd’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘circlize’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggthemes’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘scales’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: exp2
> ### Title: Data from Experiment 2 in Gauvrit, Singmann, Soler-Toscano &
> ###   Zenil
> ### Aliases: exp2
> ### Keywords: dataset
> 
> ### ** Examples
> 
> 
> # load data
> data(exp2)
> 
> exp2$K <- acss(exp2$string, 6)[,"K.6"]
> 
> m_log <- glm(response ~ K, exp2, family = binomial)
> summary(m_log)

Call:
glm(formula = response ~ K, family = binomial, data = exp2)

Deviance Residuals: 
    Min       1Q   Median       3Q      Max  
-2.2092  -0.6848   0.3150   0.7615   2.6336  

Coefficients:
            Estimate Std. Error z value Pr(>|z|)    
(Intercept) -69.8169     9.9890  -6.989 2.76e-12 ***
K             1.9004     0.2709   7.015 2.30e-12 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for binomial family taken to be 1)

    Null deviance: 276.94  on 199  degrees of freedom
Residual deviance: 183.37  on 198  degrees of freedom
AIC: 187.37

Number of Fisher Scoring iterations: 5

> 
> # odds ratio of K:
> exp(coef(m_log)[2])
       K 
6.688694 
> 
> # calculate threshold of 0.5
> (threshold <- -coef(m_log)[1]/coef(m_log)[2])
(Intercept) 
   36.73763 
> 
> require(effects)
Loading required package: effects
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘effects’
> require(lattice)
Loading required package: lattice
> plot(Effect("K", m_log), rescale.axis = FALSE, ylim = c(0, 1))
Error in Effect("K", m_log) : could not find function "Effect"
Calls: plot
Execution halted
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘plotly’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gsDesign’
Package suggested but not available for checking: ‘adephylo’
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘pegas’ ‘hierfstat’ ‘poppr’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘effects’ ‘forecast’
Packages required but not available: ‘emmeans’ ‘lmerTest’

Package suggested but not available for checking: ‘ggplot2’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aftgee
> ### Title: Accelerated Failure Time with Generalize Estimating Equation
> ### Aliases: aftgee summary.aftgee
> ### Keywords: aftgee
> 
> ### ** Examples
> 
> library(survival)
> library(copula)
Error in library(copula) : there is no package called ‘copula’
Execution halted
Packages suggested but not available for checking:
  ‘corrgram’ ‘effects’ ‘equivalence’ ‘FrF2’ ‘ggplot2’ ‘HH’ ‘nullabor’
  ‘qicharts’ ‘vcd’
Error in re-building vignettes:
  ...

Attaching package: 'gge'

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

    RedGrayBlue

Quitting from lines 44-53 (agridat_examples.Rmd) 
Error: processing vignette ‘agridat_examples.Rmd’ failed with diagnostics:
there is no package called 'HH'
Execution halted
Packages required but not available: ‘lmerTest’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘data.tree’ ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘ggseas’
Running examples in ‘aire.zmvm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: idw360
> ### Title: Inverse Distance Weighting with Directional Data
> ### Aliases: idw360
> 
> ### ** Examples
> 
> library("sp")
> library("ggplot2")
Error in library("ggplot2") : there is no package called ‘ggplot2’
Execution halted
Packages suggested but not available for checking: ‘ggmcmc’ ‘hydroPSO’
Error in re-building vignettes:
  ...
Quitting from lines 14-20 (V02.1_param_optim.Rmd) 
Error: processing vignette ‘V02.1_param_optim.Rmd’ failed with diagnostics:
there is no package called 'hydroPSO'
Execution halted
Package suggested but not available for checking: ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 43-46 (alfred.Rmd) 
Error: processing vignette ‘alfred.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘mpoly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘alphahull’
Packages suggested but not available for checking:
  ‘tidyquant’ ‘tidyverse’ ‘timetk’
Package required but not available: ‘effects’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 45-55 (ameco_dataset.Rmd) 
Error: processing vignette ‘ameco_dataset.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘colorspace’

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

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

Package suggested but not available for checking: ‘ggmap’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘caret’ ‘ggplot2’

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

Package suggested but not available for checking: ‘rbokeh’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘plotKML’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read.multiple.apache.access.log
> ### Title: Reads multiple files of apache web server.
> ### Aliases: read.multiple.apache.access.log
> 
> ### ** Examples
> 
> path <- system.file("examples", package="ApacheLogProcessor")
> path <- paste(path, "/", sep="")
> 
> #read multiple gziped logs with the prefix m_access_log_combined_
> dfLog <- read.multiple.apache.access.log(path, "m_access_log_combined_")
[1] "Starting the log processing. This may take a long time..."
[1] "Processing file  m_access_log_combined_1.log.gz"
[1] "Unziping  m_access_log_combined_1.log.gz"
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/ApacheLogProcessor/examples/m_access_log_combined_1.log': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: read.multiple.apache.access.log -> write -> cat -> file
Execution halted
Packages suggested but not available for checking: ‘afex’ ‘ez’
Running examples in ‘apa-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anova_apa
> ### Title: Report ANOVA in APA style
> ### Aliases: anova_apa
> 
> ### ** Examples
> 
> # Using the ez package
> library(ez)
Error in library(ez) : there is no package called ‘ez’
Execution halted
Packages suggested but not available for checking: ‘vcdExtra’ ‘pROC’
Error in re-building vignettes:
  ...
Quitting from lines 5-6 (./ch/glow.Rnw) 
Quitting from lines 8-8 (./ch/glow.Rnw) 
Error: processing vignette ‘aplore3-examples.Rnw’ failed with diagnostics:
there is no package called 'vcdExtra'
Execution halted
Package suggested but not available for checking: ‘caret’
Running examples in ‘AppliedPredictiveModeling-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: concrete
> ### Title: Compressive Strength of Concrete from Yeh (1998)
> ### Aliases: concrete mixtures
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(concrete)
> 
> library(caret)
Error in library(caret) : there is no package called ‘caret’
Execution halted
Packages required but not available: ‘rms’ ‘shrink’

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

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

Packages suggested but not available for checking:
  ‘colorspace’ ‘soilDB’ ‘sharpshootR’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggthemes’ ‘ggplot2’ ‘ggalt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘vcd’ ‘ggplot2’
Package required but not available: ‘TDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggplot2)
  Error in library(ggplot2) : there is no package called 'ggplot2'
  Execution halted
Package suggested but not available for checking: ‘pROC’
Running ‘testthat.R’ [14s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(arsenal)
  > 
  > test_check("arsenal")
  ── 1. Error: 08/01/2017: Beth Atkinson's subset problem (@test_modelsum.R#243)  
  there is no package called 'pROC'
  1: expect_identical(capture.output(summary(modelsum(form, data = mockstudy, subset = idx, 
         adjust = ~arm, family = "binomial"), text = TRUE)), capture.output(summary(modelsum(form, 
         data = mockstudy, subset = sex == "Male", adjust = ~arm, family = "binomial"), 
         text = TRUE))) at testthat/test_modelsum.R:243
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.output(summary(modelsum(form, data = mockstudy, subset = idx, adjust = ~arm, 
         family = "binomial"), text = TRUE))
  5: evalVis(expr)
  6: withVisible(eval(expr, pf))
  7: eval(expr, pf)
  8: eval(expr, pf)
  9: summary(modelsum(form, data = mockstudy, subset = idx, adjust = ~arm, family = "binomial"), 
         text = TRUE)
  10: modelsum(form, data = mockstudy, subset = idx, adjust = ~arm, family = "binomial")
  11: pROC::roc
  12: getExportedValue(pkg, name)
  13: asNamespace(ns)
  14: getNamespace(ns)
  15: tryCatch(loadNamespace(name), error = function(e) stop(e))
  16: tryCatchList(expr, classes, parentenv, handlers)
  17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  18: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 149 SKIPPED: 10 FAILED: 1
  1. Error: 08/01/2017: Beth Atkinson's subset problem (@test_modelsum.R#243) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: knitr
Loading required package: broom
Loading required package: gam
Loading required package: splines
Loading required package: foreach
Loaded gam 1.14-4

Loading required package: MASS
Loading required package: pROC
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'pROC'
Loading required package: rpart
Quitting from lines 180-204 (modelsum.Rmd) 
Error: processing vignette ‘modelsum.Rmd’ failed with diagnostics:
there is no package called 'pROC'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘lmerTest’
Running ‘testthat.R’ [18s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("ARTool")
  Loading required package: ARTool
  Failed with error:  'there is no package called 'lmerTest''
  ── 1. Error: artlm returns models whose data can be recovered by lsmeans (@test.
  non-numeric argument to mathematical function
  1: expect_equal(round(summary(pairs(lsmeans(artlm(m, "Moisture"), "Moisture")))$t, 5), 
         c(-5.60684, -8.19773, -3.68392, -2.59089, 1.92292, 4.51381)) at testthat/test.artlm.R:35
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 110 SKIPPED: 0 FAILED: 1
  1. Error: artlm returns models whose data can be recovered by lsmeans (@test.artlm.R#35) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

The 'lsmeans' package is being deprecated.
Users are encouraged to switch to 'emmeans'.
See help('transition') for more information, including how
to convert 'lsmeans' objects and scripts to work with 'emmeans'.
Loading required package: car

Attaching package: 'car'

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

    recode

Quitting from lines 44-50 (art-contrasts.Rmd) 
Error: processing vignette ‘art-contrasts.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘arulesViz’
Packages required but not available:
  ‘vcd’ ‘seriation’ ‘colorspace’ ‘plotly’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arvi
> ### Title: Atmospherically Resistant Vegetation Index
> ### Aliases: arvi
> 
> ### ** Examples
> 
> library (raster)
Loading required package: sp
> library (rgdal)
rgdal: version: 1.2-16, (SVN revision 701)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: /usr/share/gdal/2.2
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-6 
> # Finding the path of the sample satellite image directory.
> # User may define paths directly like "/home/ur_folder" or "C:/ur_folder"
> path <- system.file ("TM_sample", package = "ASIP")
> shapefil <- paste0 (path, "/test.shp")
> arvi (directory = path, crop = "y", ext2crop = shapefil)
OGR data source with driver: ESRI Shapefile 
Source: "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/ASIP/TM_sample/test.shp", layer: "test"
with 1 features
It has 1 fields
Integer64 fields read as strings:  id 
Error in .local(.Object, ...) : Dataset copy failed
Calls: arvi ... <Anonymous> -> new -> initialize -> initialize -> .local -> .Call
Execution halted
Packages required but not available: ‘ggplot2’ ‘llama’ ‘mlr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dae’ ‘ggplot2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘Hmisc’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compute.ALD
> ### Title: Compute ALD.
> ### Aliases: compute.ALD
> 
> ### ** Examples
> 
> library(asymLD)
> 
> # An example using haplotype frequencies from Wilson(2010)
> data(hla.freqs)
> hla.a_b <- hla.freqs[hla.freqs$locus1=="A" & hla.freqs$locus2=="B",]
> compute.ALD(hla.a_b)
   ALD.x.y is asymmetric LD for locus x conditioned on locus y

  locus1 locus2       F.1    F.1.2        F.2     F.2.1   ALD.1.2   ALD.2.1
1      A      B 0.1021811 0.340332 0.04876543 0.1903394 0.5150291 0.3857872
> hla.freqs$locus <- paste(hla.freqs$locus1, hla.freqs$locus2, sep="-")
> compute.ALD(hla.freqs[hla.freqs$locus=="C-B",])
   ALD.x.y is asymmetric LD for locus x conditioned on locus y

  locus1 locus2        F.1     F.1.2        F.2     F.2.1   ALD.1.2   ALD.2.1
1      C      B 0.08637241 0.7350216 0.05040254 0.4520268 0.8425979 0.6503396
> # Note: additonal columns on the input dataframe (e.g., "locus" above) are allowed, but
> # ignored by the function.
> 
> # An example using genotype data from the haplo.stats package
> require(haplo.stats)
Loading required package: haplo.stats
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘haplo.stats’
> data(hla.demo)
Warning in data(hla.demo) : data set ‘hla.demo’ not found
> geno <- hla.demo[,5:8]  #DPB-DPA
Error: object 'hla.demo' not found
Execution halted
Package required but not available: ‘smacof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘scales’ ‘circlize’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: save_connection
> ### Title: Write connection parameters to configuration file.
> ### Aliases: save_connection
> 
> ### ** Examples
> 
> # Write the current values of the connection parameters to the configuration file
> save_connection()
Warning in writeLines(l, fileConn) :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/atsd/connection.config': Read-only file system
Error in writeLines(l, fileConn) : cannot open the connection
Calls: save_connection -> writeLines
Execution halted
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘forecast’ ‘caret’
Running examples in ‘aurelius-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: extract_params.Arima
> ### Title: extract_params.Arima
> ### Aliases: extract_params.Arima
> 
> ### ** Examples
> 
> model <- stats::arima(presidents, c(3, 0, 0))
> extracted_model <- extract_params(model)
> 
> model <- forecast::Arima(USAccDeaths, order=c(2,2,2), seasonal=c(0,2,2))
Error in loadNamespace(name) : there is no package called ‘forecast’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘plotly’ ‘ggfortify’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 233-254 (full-example.Rmd) 
Error: processing vignette ‘full-example.Rmd’ failed with diagnostics:
there is no package called 'caret'
Execution halted
Packages required but not available: ‘RDAVIDWebService’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘pcalg’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘scales’
Error in re-building vignettes:
  ...
Quitting from lines 24-28 (use-ballr.Rmd) 
Error: processing vignette ‘use-ballr.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggExtra’

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

Package suggested but not available for checking: ‘BayesX’

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

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

Package suggested but not available for checking: ‘ggplot2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘GGally’
Error in re-building vignettes:
  ...
Warning in bas.lm(eval(object$call$formula), data = eval(object$call$data),  :
  We recommend using the implementation using the Jeffreys-Zellner-Siow prior (prior='JZS') which uses numerical integration rahter than the Laplace approximation
Quitting from lines 269-273 (BAS-vignette.Rmd) 
Error: processing vignette ‘BAS-vignette.Rmd’ failed with diagnostics:
there is no package called 'GGally'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 50-56 (BatchGetSymbols-vignette.Rmd) 
Error: processing vignette 'BatchGetSymbols-vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘heatmaply’ ‘plotly’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘rstan’ ‘rstanarm’ ‘scales’ ‘shinystan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘R2BayesX’
Package required but not available: ‘geiger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rms’ ‘ggplot2’ ‘Hmisc’
Package suggested but not available for checking: ‘geiger’
Running examples in ‘BBMV-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Sim_FPK
> ### Title: Simulation of the BBM+V process.
> ### Aliases: Sim_FPK
> 
> ### ** Examples
> 
> # Simulate data: tree + continuous trait
> library(geiger)
Error in library(geiger) : there is no package called ‘geiger’
Execution halted
Package suggested but not available for checking: ‘Hmisc’
Packages required but not available: ‘RcmdrMisc’ ‘Rcmdr’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anomedOnlybic
> ### Title: The anomedOnlybic function
> ### Aliases: anomedOnlybic
> ### Keywords: anomedOnlybic
> 
> ### ** Examples
> 
> data(breastc)
> library(biclust)
Error in library(biclust) : there is no package called ‘biclust’
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘INLA’
Error in re-building vignettes:
  ...
Warning in gzfile(file, "wb") :
  cannot open compressed file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Bchron/data/intcal09.rda’, probable reason ‘Read-only file system’
Quitting from lines 279-283 (Bchron.Rmd) 
Error: processing vignette ‘Bchron.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking: ‘bcmaps.rdata’ ‘ggplot2’
Packages required but not available: ‘treemap’ ‘ggplot2’

Package suggested but not available for checking: ‘rinat’

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

Packages suggested but not available for checking:
  ‘beadarrayExampleData’ ‘lumi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘scales’ ‘munsell’ ‘colorspace’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 51-55 (benthos.Rmd) 
Error: processing vignette ‘benthos.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘colorspace’
Package required but not available: ‘LambertW’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘plotly’ ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘FrF2’
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("bib2df")
  > test_check("bib2df")
  ── 1. Failure: bib2df() throws error messages (@tests.R#53)  ───────────────────
  `bib2df("https://www.ottlngr.de/data/x.bib")` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 15 SKIPPED: 0 FAILED: 1
  1. Failure: bib2df() throws error messages (@tests.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 87-97 (bib2df.Rmd) 
Error: processing vignette ‘bib2df.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘viridis’ ‘dendextend’ ‘randomcoloR’ ‘biclust’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘factoextra’ ‘ggplot2’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bi.format
> ### Title: Add number of vertices and edges to the input file
> ### Aliases: bi.format
> 
> ### ** Examples
> 
> bi.format(system.file("extdata", "example2.el", package = "biclique"))
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/biclique/extdata/example2.el': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: bi.format -> cat -> file
Execution halted
Package required but not available: ‘pcalg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘Hmisc’ ‘intsvy’
Package required but not available: ‘haplo.stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘cowplot’ ‘ggplot2’

Package suggested but not available for checking: ‘viridis’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: binom.bayes
> ### Title: Binomial confidence intervals using Bayesian inference
> ### Aliases: binom.bayes binom.bayes.densityplot
> ### Keywords: univar htest models
> 
> ### ** Examples
> 
> # Example using highest probability density.
> hpd <- binom.bayes(
+   x = 0:10, n = 10, type = "highest", conf.level = 0.8, tol = 1e-9)
> print(hpd)
   method  x  n shape1 shape2       mean       lower     upper sig
1   bayes  0 10    0.5   10.5 0.04545455 0.000000000 0.0769566 0.2
2   bayes  1 10    1.5    9.5 0.13636364 0.003771457 0.2145408 0.2
3   bayes  2 10    2.5    8.5 0.22727273 0.053633312 0.3494770 0.2
4   bayes  3 10    3.5    7.5 0.31818182 0.127646004 0.4728042 0.2
5   bayes  4 10    4.5    6.5 0.40909091 0.214091147 0.5858428 0.2
6   bayes  5 10    5.5    5.5 0.50000000 0.309892028 0.6901080 0.2
7   bayes  6 10    6.5    4.5 0.59090909 0.414157185 0.7859089 0.2
8   bayes  7 10    7.5    3.5 0.68181818 0.527195809 0.8723540 0.2
9   bayes  8 10    8.5    2.5 0.77272727 0.650522982 0.9463667 0.2
10  bayes  9 10    9.5    1.5 0.86363636 0.785459228 0.9962285 0.2
11  bayes 10 10   10.5    0.5 0.95454545 0.923043403 1.0000000 0.2
> binom.bayes.densityplot(hpd)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
Error: require(ggplot2) is not TRUE
Execution halted
Package required but not available: ‘Rcmdr’

Package suggested but not available for checking: ‘effects’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 263-268 (biogas_quick_start.Rnw) 
Error: processing vignette ‘biogas_quick_start.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘biogram-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.criterion_distribution
> ### Title: Plot criterion distribution
> ### Aliases: plot.criterion_distribution
> 
> ### ** Examples
> 
> target_feature <- create_feature_target(10, 375, 15, 600) 
> example_result <- distr_crit(target = target_feature[,1], 
+                              feature = target_feature[,2])
> plot(example_result)
> 
> # a ggplot2 plot
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: slam
Quitting from lines 16-40 (overview.Rmd) 
Error: processing vignette ‘overview.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘pROC’

Packages suggested but not available for checking:
  ‘Hmisc’ ‘ecospat’ ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘bioinactivation’ ‘ggplot2’ ‘MEIGOR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/biorxivr.Rcheck/vign_test/biorxivr") :
  Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/index.Rmd’
(Is a VignetteBuilder field missing?)
Quitting from lines 17-20 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
failed to load external entity "http://www.biorxiv.org/search/Ecology?page=0"
Execution halted
Packages suggested but not available for checking: ‘tidyverse’ ‘ggplot2’
Packages required but not available: ‘plsRcox’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Parsed with column specification:
cols(
  .default = col_character()
)
See spec(...) for full column specifications.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 61-79 (BIS.Rmd) 
Error: processing vignette ‘BIS.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘ggExtra’
Error in re-building vignettes:
  ...
Quitting from lines 72-75 (Intro.Rmd) 
Error: processing vignette ‘Intro.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘rstan’
Packages required but not available: ‘caret’ ‘ggplot2’ ‘pROC’

Package suggested but not available for checking: ‘bigrf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘nbpMatching’
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘tidyverse’ ‘leaflet’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘geiger’ ‘TreeSim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rstan’ ‘ggplot2’

Package suggested but not available for checking: ‘qgraph’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘threejs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘d3heatmap’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 13-32 (bodenmiller.Rmd) 
Error: processing vignette ‘bodenmiller.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘ggthemes’
Package required but not available: ‘qvalue’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘IsingFit’ ‘qgraph’ ‘mgm’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘phyloseq’
Error in re-building vignettes:
  ...
Quitting from lines 195-198 (bossa-analysis.Rmd) 
Error: processing vignette ‘bossa-analysis.Rmd’ failed with diagnostics:
there is no package called 'phyloseq'
Execution halted
Package required but not available: ‘qicharts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘OpenStreetMap’ ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘prefmod’
Error in re-building vignettes:
  ...
Warning in eval(family$initialize) :
  non-integer counts in a binomial glm!

Error: processing vignette ‘BradleyTerry.Rnw’ failed with diagnostics:
 chunk 27 (label = student-specific_data) 
Error in library("prefmod") : there is no package called 'prefmod'
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union


Attaching package: 'dplyr'

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

    as_data_frame, groups, union

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 234-275 (BradleyTerryScalable.Rmd) 
Error: processing vignette ‘BradleyTerryScalable.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘installr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘Hmisc’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggfittext’

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

Packages suggested but not available for checking:
  ‘ggplot2’ ‘shinystan’ ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 33-45 (the_bridgedist_basics.Rmd) 
Error: processing vignette ‘the_bridgedist_basics.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘plotly’

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

Packages suggested but not available for checking: ‘rstan’ ‘rstanarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘rstan’ ‘bayesplot’ ‘shinystan’ ‘bridgesampling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘xergm’ ‘btergm’ ‘Hmisc’ ‘rstan’ ‘rstanarm’ ‘brms’
  ‘emmeans’
Running ‘test-all.R’ [20s/23s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("broom")
  Loading required package: broom
  ── 1. Error: (unknown) (@test-rstanarm.R#4)  ───────────────────────────────────
  there is no package called 'rstanarm'
  1: suppressPackageStartupMessages(library(rstanarm)) at testthat/test-rstanarm.R:4
  2: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
  3: library(rstanarm)
  4: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 673 SKIPPED: 14 FAILED: 1
  1. Error: (unknown) (@test-rstanarm.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 22-25 (bootstrapping.Rmd) 
Error: processing vignette ‘bootstrapping.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 23-35 (benchmarks.Rmd) 
Error: processing vignette ‘benchmarks.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘DiffBind’ ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘diagis’ ‘ggplot2’

Package suggested but not available for checking: ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: gbm
Loading required package: survival
Loading required package: lattice
Loading required package: splines
Loading required package: parallel
Loaded gbm 2.1.3

Error: processing vignette ‘pros.Rnw’ failed with diagnostics:
 chunk 2 
Error in library("pROC") : there is no package called 'pROC'
Execution halted
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘smoof’ ‘ggplot2’ ‘ggridges’
Error in re-building vignettes:
  ...
Quitting from lines 47-69 (Adapting_Algorithm_for_CAISEr.Rmd) 
Error: processing vignette ‘Adapting_Algorithm_for_CAISEr.Rmd’ failed with diagnostics:
there is no package called 'smoof'
Execution halted
Running ‘testthat.R’ [7s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(callr)
  > 
  > Sys.unsetenv("R_TESTS")
  > 
  > test_check("callr")
  ── 1. Error: debugger is called (@test-error.R#45)  ────────────────────────────
  Can't mock functions in base packages (utils)
  1: with_mock(`utils::debugger` = function(...) called <<- TRUE, r(function() {
         1 + "A"
     }, error = "debugger")) at testthat/test-error.R:45
  2: extract_mocks(new_values = new_values[!code_pos], .env = .env, eval_env = parent.frame())
  3: lapply(stats::setNames(nm = mock_qual_names), function(qual_name) {
         pkg_name <- gsub(pkg_and_name_rx, "\\1", qual_name)
         if (is_base_pkg(pkg_name)) {
             stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
         }
         name <- gsub(pkg_and_name_rx, "\\2", qual_name)
         if (pkg_name == "") 
             pkg_name <- .env
         env <- asNamespace(pkg_name)
         if (!exists(name, envir = env, mode = "function")) 
             stop("Function ", name, " not found in environment ", environmentName(env), 
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 28 SKIPPED: 0 FAILED: 1
  1. Error: debugger is called (@test-error.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘pheatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘vcd’
Packages required but not available: ‘ggplot2’ ‘caret’

Package suggested but not available for checking: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘alr4’
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: ‘expsmooth’ ‘forecast’

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

Package suggested but not available for checking: ‘GSIF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rms’ ‘vcdExtra’
Error in re-building vignettes:
  ...
Quitting from lines 153-156 (cate-vignette.Rnw) 
Error: processing vignette ‘cate-vignette.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘spacodiR’ ‘entropart’
Package required but not available: ‘season’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/cda.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘GDINA’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘eemR’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘colorspace’ ‘copula’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘scales’ ‘ggplot2’

Package suggested but not available for checking: ‘robustHD’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggrepel’ ‘scales’
Error in re-building vignettes:
  ...
Quitting from lines 63-74 (Census2016.Rmd) 
Error: processing vignette ‘Census2016.Rmd’ failed with diagnostics:
object ‘.CensusDataTables’ not found
Execution halted
Package required but not available: ‘ggmap’

Package suggested but not available for checking: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘cplm’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 160-170 (checkmate.Rmd) 
Error: processing vignette ‘checkmate.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘pROC’ ‘caret’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hmapSpectra
> ### Title: Seriated Heat Map for a Spectra Object
> ### Aliases: hmapSpectra
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> 
> data(SrE.IR)
> # Let's look just at the carbonyl region
> IR <- removeFreq(SrE.IR, rem.freq = SrE.IR$freq > 1850 | SrE.IR$freq < 1650)
> res <- hmapSpectra(IR, col = heat.colors(5), labCol = FALSE)
Error in hmapSpectra(IR, col = heat.colors(5), labCol = FALSE) : 
  You need to install package seriation to use this function
Execution halted
Running examples in ‘childsds-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: make_percentile_tab
> ### Title: calculate raw values
> ### Aliases: make_percentile_tab
> 
> ### ** Examples
> 
> ptab <- make_percentile_tab(ref = kro.ref,
+                             item = "height",
+                            perc = c(2.5,10,50,90,97.5),
+                            stack = TRUE)
Loading required namespace: reshape2
> 
> ggplot2::ggplot(ptab, ggplot2::aes(x = age, y = value, colour = variable)) +
+    ggplot2::geom_line() +
+    ggplot2::facet_wrap(~ sex, nrow = 2)
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Package suggested but not available for checking: ‘drc’
Package required but not available: ‘scales’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘scales’ ‘Hmisc’ ‘ggplot2’ ‘ggmap’

Package suggested but not available for checking: ‘choroplethrAdmin1’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘scales’ ‘ggplot2’
Packages required but not available:
  ‘factoextra’ ‘GGally’ ‘pheatmap’ ‘dendextend’ ‘viridis’ ‘ggplot2’
  ‘circlize’

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

Packages suggested but not available for checking:
  ‘dendextend’ ‘ComplexHeatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyverse’
Error in re-building vignettes:
  ...
Quitting from lines 61-65 (ciTools-binomial-vignette.Rmd) 
Error: processing vignette ‘ciTools-binomial-vignette.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
Packages required but not available: ‘ggplot2’ ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘brms’ ‘lmerTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘scales’

Package suggested but not available for checking: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rstan’ ‘ggplot2’

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

Package suggested but not available for checking: ‘dendextend’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 37-42 (using-clusternomics.Rmd) 
Error: processing vignette ‘using-clusternomics.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘copula’ ‘WeightedCluster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘quanteda’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘GGally’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘smoof’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggstance’

Package suggested but not available for checking: ‘WeightIt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 19-30 (codingMatrices.Rnw) 
Error: processing vignette ‘codingMatrices.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 110-112 (Temporal_Diversity_Indices.Rmd) 
Error: processing vignette ‘Temporal_Diversity_Indices.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘useful’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: coin
Loading required package: survival
Warning in .local(object, ...) :
  p-values may be incorrect due to violation
  of the subset pivotality condition

Error: processing vignette ‘coin_implementation.Rnw’ failed with diagnostics:
 chunk 27 (label = js-plot) 
Error in library("vcd") : there is no package called ‘vcd’
Execution halted
Packages required but not available: ‘ggplot2’ ‘haplo.stats’

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

Package suggested but not available for checking: ‘colorspace’

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

Package suggested but not available for checking: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 13-17 (noise.Rmd) 
Error: processing vignette ‘noise.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘colorspace’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘scales’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/colorspace.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘pcalg’ ‘backShift’
Packages required but not available: ‘Hmisc’ ‘SNPassoc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 199-221 (comtradr-vignette.Rmd) 
Error: processing vignette ‘comtradr-vignette.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘rminer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DendSer’
Error in re-building vignettes:
  ...
Quitting from lines 21-23 (chamber.Rmd) 
Error: processing vignette ‘chamber.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 239-240 (my-vignette.Rmd) 
Error: processing vignette ‘my-vignette.Rmd’ failed with diagnostics:
The package alpha.hull is required for this procedure, please install it
Execution halted
Running examples in ‘contoureR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: contourLinesR
> ### Title: Get Contour Lines (list)
> ### Aliases: contourLinesR
> 
> ### ** Examples
> 
> library(contoureR)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘rms’ ‘Hmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rstan’ ‘ggplot2’

Package suggested but not available for checking: ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘copula’ ‘vines’

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

Packages suggested but not available for checking: ‘lcopula’ ‘VineCopula’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘quanteda’
Packages suggested but not available for checking: ‘quanteda’ ‘RNewsflow’
Running examples in ‘corpustools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tCorpus$compare_documents
> ### Title: Calculate the similarity of documents
> ### Aliases: tCorpus$compare_documents compare_documents
> 
> ### ** Examples
> 
> d = data.frame(text = c('a b c d e',
+                         'e f g h i j k',
+                         'a b c'),
+                date = c('2010-01-01','2010-01-01','2012-01-01'))
> tc = create_tcorpus(d)
No existing document column (doc_column) specified. Using indices as id.
> 
> g = tc$compare_documents()
Error in tc$compare_documents() : 
  RNewsflow package needs to be installed in order to use document comparison methods
Execution halted
Package required but not available: ‘xcms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘seriation’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘forecast’ ‘hts’
Packages required but not available: ‘cosinor’ ‘ggplot2’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘hurricaneexposure’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘choroplethr’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 111-123 (countytimezones.Rmd) 
Error: processing vignette ‘countytimezones.Rmd’ failed with diagnostics:
there is no package called 'choroplethr'
Execution halted
Packages required but not available: ‘ggmap’ ‘ggplot2’ ‘rnoaa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘VIM’ ‘ggplot2’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘scales’

Package suggested but not available for checking: ‘viridis’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CREAM
> ### Title: CREAM is the main function for CORE identification
> ### Aliases: CREAM
> 
> ### ** Examples
> 
> CREAM(system.file("extdata", "A549_Chr21.bed", package = "CREAM"),
+ system.file("extdata", "A549_Chr21_COREs.bed", package = "CREAM"),
+ MinLength = 1000, peakNumMin = 2)
[1] "Please make sure there is no overlap between the input genomic regions. Overlap between the input regions may cause error."
[1] "Identifying window size for each Order"
[1] "Identifying COREs"
[1] "Filtering clusters of low order"
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/CREAM/extdata/A549_Chr21_COREs.bed': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: CREAM -> write.table -> file
Execution halted
Packages required but not available: ‘ggplot2’ ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggmcmc’

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

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

Package suggested but not available for checking: ‘ggplot2’

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

Package suggested but not available for checking: ‘adabag’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘qte’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 38-45 (csp.Rmd) 
Error: processing vignette ‘csp.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘rstan’

Package suggested but not available for checking: ‘shinystan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 12-17 (cubist.Rmd) 
Error: processing vignette ‘cubist.Rmd’ failed with diagnostics:
there is no package called 'caret'
Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘tidyverse’ ‘ggbeeswarm’
Error in re-building vignettes:
  ...
Quitting from lines 87-95 (how_to_test_CVs.Rmd) 
Error: processing vignette ‘how_to_test_CVs.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘cvxclustr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cvxclust
> ### Title: Convex Clustering Path via Variable Splitting Methods
> ### Aliases: cvxclust
> 
> ### ** Examples
> 
> ## Clusterpaths for Mammal Dentition
> data(mammals)
> X <- as.matrix(mammals[,-1])
> X <- t(scale(X,center=TRUE,scale=FALSE))
> n <- ncol(X)
> 
> ## Pick some weights and a sequence of regularization parameters.
> k <- 5
> phi <- 0.5
> w <- kernel_weights(X,phi)
> w <- knn_weights(w,k,n)
> gamma <- seq(0.0,43, length.out=100)
> 
> ## Perform clustering
> sol <- cvxclust(X,w,gamma)
Warning in cvxclust_ama(X, Lambda, ix - 1, M1 - 1, M2 - 1, s1, s2, w[w >  :
  The stepsize nu may be too large. Setting it to maximum of 1/n and 1/AnM.
> 
> ## Plot the cluster path
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package suggested but not available for checking: ‘leaflet’
Error in re-building vignettes:
  ...
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette ‘cycling_data_analysis.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
Execution halted
Packages required but not available: ‘scales’ ‘dendextend’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘treemap’
Package required but not available: ‘FrF2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: dams
Loading required package: ggplot2
Loading required package: maps
Loading required package: mapproj
Quitting from lines 67-71 (dams.Rmd) 
Error: processing vignette ‘dams.Rmd’ failed with diagnostics:
could not find function "ggplot"
Execution halted
Packages required but not available: ‘ggplot2’ ‘caret’

Packages suggested but not available for checking:
  ‘NeuralNetTools’ ‘gputools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘adegenet’ ‘ggplot2’ ‘pegas’ ‘SNPassoc’ ‘StAMPP’ ‘qvalue’ ‘plotly’

Packages suggested but not available for checking: ‘mmod’ ‘PopGenReport’

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

Packages suggested but not available for checking:
  ‘AdaptGauss’ ‘ProjectionBasedClustering’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘kableExtra’
Error in re-building vignettes:
  ...
Loading required package: lubridate

Attaching package: 'lubridate'

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

    date

Loading required package: stringr
Loading required package: Matrix
Loading required package: progress

Attaching package: 'data.table'

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

    hour, isoweek, mday, minute, month, quarter, second, wday,
    week, yday, year

Quitting from lines 16-54 (dataPreparation.Rmd) 
Error: processing vignette ‘dataPreparation.Rmd’ failed with diagnostics:
there is no package called 'kableExtra'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘colormap’

VignetteBuilder packages required for checking but not installed:
  ‘ggplot2’ ‘colormap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘caret’
Package required but not available: ‘DiagrammeR’

Package suggested but not available for checking: ‘treemap’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dbplot_bar
> ### Title: Bar plot
> ### Aliases: dbplot_bar
> 
> ### ** Examples
> 
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dbplot)
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: rlang
  
  Attaching package: 'rlang'
  
  The following objects are masked from 'package:testthat':
  
      is_false, is_null, is_true
  
  > library(dplyr)
  > library(ggplot2)
  Error in library(ggplot2) : there is no package called 'ggplot2'
  Execution halted
Package suggested but not available for checking: ‘dendextend’
Packages required but not available: ‘ggplot2’ ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggExtra’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘cowplot’ ‘ggplot2’
Package required but not available: ‘Deducer’

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

Depends: includes the non-default packages:
  ‘Deducer’ ‘psych’ ‘GPArotation’ ‘mvnormtest’ ‘irr’ ‘klaR’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘scales’ ‘effects’

Package suggested but not available for checking: ‘Hmisc’

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

Depends: includes the non-default packages:
  ‘JavaGD’ ‘Deducer’ ‘sp’ ‘maptools’ ‘OpenStreetMap’ ‘scales’ ‘rgdal’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 115-125 (ODE_parameter_inference.Rmd) 
Error: processing vignette ‘ODE_parameter_inference.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘DiagrammeR’
Packages required but not available: ‘rstan’ ‘ggplot2’ ‘seriation’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘viridis’

Packages suggested but not available for checking:
  ‘seriation’ ‘colorspace’ ‘NMF’ ‘heatmaply’ ‘d3heatmap’ ‘DendSer’
  ‘circlize’

Packages which this enhances but not available for checking:
  ‘ggdendro’ ‘labeltodendro’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘scales’ ‘caret’ ‘metacoder’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘seriation’ ‘gapmap’
Error in re-building vignettes:
  ...
Quitting from lines 27-32 (example_figures.Rmd) 
Error: processing vignette ‘example_figures.Rmd’ failed with diagnostics:
there is no package called 'seriation'
Execution halted
Packages required but not available: ‘ggplot2’ ‘drc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggrepel’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: densregion.survfit
> ### Title: Density regions for survival curves
> ### Aliases: densregion.survfit
> ### Keywords: aplot survival
> 
> ### ** Examples
> 
> library(survival)
Error in library(survival) : there is no package called ‘survival’
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette ‘DEoptim.Rnw’ failed with diagnostics:
 chunk 3 (label = figure1-code) 
Error in library("colorspace") : there is no package called ‘colorspace’
Execution halted
Packages required but not available: ‘scales’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘colorspace’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘scales’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘scales’
Running ‘has-devel.R’ [1s/2s]
  Running ‘test-that.R’ [60s/99s]
Running the tests in ‘tests/test-that.R’ failed.
Complete output:
  > library(testthat)
  > test_check("devtools")
  Loading required package: devtools
  
  Attaching package: 'devtools'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  ── 1. Failure: Github repos with submodules are identified correctly (@test-gith
  github_has_remotes(github_remote("armstrtw/rzmq")) not equal to TRUE.
  1 element mismatch
  
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 395 SKIPPED: 9 FAILED: 1
  1. Failure: Github repos with submodules are identified correctly (@test-github.r#82) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘MLInterfaces’

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

Packages suggested but not available for checking:
  ‘ggplot2’ ‘MEGENA’ ‘cowplot’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘Hmisc’ ‘NMF’ ‘caret’ ‘quantable’ ‘largeVis’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AgPalik
> ### Title: AgPalik
> ### Aliases: AgPalik
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(AgPalik)
> str(AgPalik$raw())
'data.frame':	241 obs. of  4 variables:
 $ wavelength: num  0.155 0.207 0.248 0.275 0.31 ...
 $ epsilon   : cplx  1+0i 1+0i 1+0i ...
 $ real      : num  1 1 1 1 1.01 ...
 $ imag      : num  5.84e-06 1.68e-05 3.04e-05 4.42e-05 7.16e-05 ...
> AgPalik$comment
$source
[1] "Silver in the visible, Palik"

$units
[1] "nanometres"

> demo(AgPalik)


	demo(AgPalik)
	---- ~~~~~~~

> library(dielectric)

> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Calls: demo -> source -> withVisible -> eval -> eval -> library
Execution halted
Packages required but not available: ‘missMethyl’ ‘methylumi’

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

Packages suggested but not available for checking:
  ‘DiffusionRgqd’ ‘DiffusionRjgqd’

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

Package suggested but not available for checking: ‘DiffusionRgqd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_R_NX
> ### Title: plot_R_NX
> ### Aliases: plot_R_NX
> 
> ### ** Examples
> 
> 
> ## define which methods to apply
> embed_methods <- c("Isomap", "PCA")
> ## load test data set
> data_set <- loadDataSet("3D S Curve", n = 1000)
> ## apply dimensionality reduction
> data_emb <- lapply(embed_methods, function(x) embed(data_set, x))
2018-01-11 06:01:48: Isomap START
2018-01-11 06:01:48: constructing knn graph
2018-01-11 06:01:48: calculating geodesic distances
2018-01-11 06:01:50: cmdscale
2018-01-11 06:01:53: post processing
> names(data_emb) <- embed_methods
> ## plot the R_NX curves:
> plot_R_NX(data_emb) +
+     ggplot2::theme(legend.title = ggplot2::element_blank(),
+                    legend.position = c(0.5, 0.1),
+                    legend.justification = c(0.5, 0.1))
Error in chckpkg("ggplot2") : 
  require 'ggplot2' package, install it using install.packages('ggplot2')
Calls: plot_R_NX -> chckpkg
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘alphahull’
Running ‘ggplot.R’ [0s/1s]
  Running ‘lasso.R’ [0s/1s]
Running the tests in ‘tests/lasso.R’ failed.
Complete output:
  > library(directlabels)
  > data(prostate,package="ElemStatLearn")
  > pros <- subset(prostate,select=-train,train==TRUE)
  > ycol <- which(names(pros)=="lpsa")
  > x <- as.matrix(pros[-ycol])
  > y <- pros[[ycol]]
  > library(lars)
  Loaded lars 1.2
  
  > fit <- lars(x,y,type="lasso")
  > beta <- scale(coef(fit),FALSE,1/fit$normx)
  > 
  > ## Degenerate case: one 0 curves.
  > beta[, "gleason"] <- 0
  > arclength <- rowSums(abs(beta))
  > path <- data.frame(
  +   step=as.integer(row(beta)),
  +   variable=colnames(beta)[as.integer(col(beta))],
  +   arclength=arclength[as.integer(row(beta))],
  +   standardized.coef=as.numeric(beta))
  > library(ggplot2)
  Error in library(ggplot2) : there is no package called 'ggplot2'
  Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggdendro’ ‘scales’ ‘seriation’
Packages suggested but not available for checking: ‘caret’ ‘pec’
Running examples in ‘discSurv-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aucUno
> ### Title: Area under the Curve Estimation
> ### Aliases: aucUno
> ### Keywords: survival
> 
> ### ** Examples
> 
> #####################################################
> # Example with cross validation and unemployment data 
> 
> library(Ecdat)
Loading required package: Ecfun

Attaching package: ‘Ecfun’

The following object is masked from ‘package:base’:

    sign


Attaching package: ‘Ecdat’

The following object is masked from ‘package:datasets’:

    Orange

> library(caret)
Error in library(caret) : there is no package called ‘caret’
Execution halted
Running ‘UnitTestsDiscSurvDataTransform.R’ [2s/3s]
  Running ‘UnitTestsDiscSurvEstimation.R’ [2s/3s]
  Running ‘UnitTestsDiscSurvEvalShort.R’ [5s/7s]
  Running ‘UnitTestsDiscSurvEvaluation.R’ [2s/3s]
Running the tests in ‘tests/UnitTestsDiscSurvEvaluation.R’ failed.
Complete output:
  > library(discSurv)
  > library(pec)
  Error in library(pec) : there is no package called 'pec'
  Execution halted
Packages required but not available: ‘caret’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘pheatmap’ ‘entropart’
Packages required but not available: ‘ggplot2’ ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘LBSPR’ ‘ggplot2’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: doBy

Error: processing vignette ‘LSmeans.Rnw’ failed with diagnostics:
 chunk 8 (label = simdat-fig) 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘vcd’

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

Packages which this enhances but not available for checking:
  ‘gurobi’ ‘Rmosek’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rms’
Error in re-building vignettes:
  ...
Quitting from lines 330-331 (dosresmeta.Rnw) 
Error: processing vignette ‘dosresmeta.Rnw’ failed with diagnostics:
there is no package called 'rms'
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggstance’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dpcr_density_table
> ### Title: Calculate Density of Multiple dPCR runs
> ### Aliases: dpcr_density_table
> ### Keywords: dplot hplot
> 
> ### ** Examples
> 
> dens <- dpcr_density_table(six_panels)
> 
> # create plot using ggplot2
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 16-40 (overview.Rmd) 
Error: processing vignette ‘overview.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘forecast’
Package required but not available: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [39s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("dplyr")
  ── 1. Error: FactorVisitor handles NA. #183 (@test-group-by.r#73)  ─────────────
  there is no package called 'MASS'
  1: group_by(MASS::survey, M.I) at testthat/test-group-by.r:73
  2: MASS::survey
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2891 SKIPPED: 3 FAILED: 1
  1. Error: FactorVisitor handles NA. #183 (@test-group-by.r#73) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 11-16 (dplyr.Rmd) 
Error: processing vignette ‘dplyr.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘rstan’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘ggplot2’

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

Package suggested but not available for checking: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘scales’ ‘caret’

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘frailtyEM’ ‘ggplot2’
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: optimx

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 110-117 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘rms’ ‘plotly’ ‘ggplot2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘incidence’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(earlyR)
  > 
  > test_check("earlyR")
  Error in library(incidence) : there is no package called 'incidence'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Packages required but not available:
  ‘caret’ ‘darch’ ‘ggplot2’ ‘pROC’ ‘scales’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EasyStrata
> ### Title: Function to run EasyStrata (v8.6).
> ### Aliases: EasyStrata
> 
> ### ** Examples
> 
> extDataDir=system.file("extdata", package="EasyStrata")
> ## Example Pipeline:
> ecfPipe=paste(extDataDir,"example_pipeline.ecf",sep="/")
> EasyStrata(ecfPipe)
Warning message:
In file(fileLog, open = "a") :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/EasyStrata/extdata/example_pipeline.ecf.out': Read-only file system
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 25-28 (ebayesthresh.Rmd) 
Error: processing vignette ‘ebayesthresh.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 29-31 (ecb_sdw.Rmd) 
Error: processing vignette ‘ecb_sdw.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘caret’ ‘WGCNA’

Packages suggested but not available for checking:
  ‘factoextra’ ‘ComplexHeatmap’ ‘circlize’ ‘pheatmap’ ‘viridis’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘d3heatmap’ ‘ggplot2’ ‘pheatmap’ ‘plotly’

Package suggested but not available for checking: ‘adegenet’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 12-18 (edgarWebR.Rmd) 
Error: processing vignette ‘edgarWebR.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘plotly’ ‘ggthemes’

Packages suggested but not available for checking: ‘GGally’ ‘scales’

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

Packages suggested but not available for checking: ‘cdom’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘vcd’

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

Package suggested but not available for checking: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘EnvStats’ ‘colourpicker’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘lumi’ ‘vsn’
Packages required but not available: ‘ggplot2’ ‘lmerTest’ ‘sjstats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggmap’ ‘HLMdiag’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘caret’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘bayesplot’ ‘mediation’ ‘lmerTest’

Packages which this enhances but not available for checking:
  ‘glmmADMB’ ‘rstanarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘colorspace’ ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spocc’
Error in re-building vignettes:
  ...
Loading required package: spocc
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'spocc'
Installing package into '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages'
(as 'lib' is unspecified)
Warning in install.packages("spocc", repos = "http://cran.us.r-project.org") :
  'lib = "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages"' is not writable
Quitting from lines 38-52 (ENMeval-vignette.Rmd) 
Error: processing vignette ‘ENMeval-vignette.Rmd’ failed with diagnostics:
unable to install packages
Execution halted
Packages required but not available: ‘Hmisc’ ‘vcd’

Package suggested but not available for checking: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘SensoMineR’ ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 50-69 (GLMs.Rmd) 
Error: processing vignette ‘GLMs.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dendextend’ ‘ggplot2’ ‘ggdendro’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘xcms’ ‘qvalue’

Package suggested but not available for checking: ‘faahKO’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: box.plot.wtd
> ### Title: weighted Boxplot
> ### Aliases: box.plot.wtd
> ### Keywords: boxplot
> 
> ### ** Examples
> 
> x<-rnorm(1000)
> g<-round(runif(1000))
> w<-abs(rnorm(1000))
> d<- data.frame(x, g, w)
> box.plot.wtd('x', 'g', w='w', data=d)
Error in library(Hmisc) : there is no package called ‘Hmisc’
Calls: box.plot.wtd -> library
Execution halted
Package required but not available: ‘timeROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘threejs’ ‘colorspace’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 122-133 (epitrix.Rmd) 
Error: processing vignette ‘epitrix.Rmd’ failed with diagnostics:
there is no package called 'incidence'
Execution halted
Package required but not available: ‘PairedData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘brms’ ‘ggplot2’ ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 54-57 (extending_etl.Rmd) 
Error: processing vignette ‘extending_etl.Rmd’ failed with diagnostics:
Please make sure that the 'ggplot2' package is installed
Execution halted
Running examples in ‘ETLUtils-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: write.dbi.ffdf
> ### Title: Write ffdf data to a database table by using a DBI connection.
> ### Aliases: write.dbi.ffdf
> 
> ### ** Examples
> 
> require(ff)
> 
> ##
> ## Example query using data in sqlite
> ##
> require(RSQLite)
Loading required package: RSQLite
> dbfile <- system.file("smalldb.sqlite3", package="ETLUtils")
> drv <- dbDriver("SQLite")
> query <- "select * from testdata limit 10000"
> x <- read.dbi.ffdf(query = query, dbConnect.args = list(drv = drv, dbname = dbfile),
+ first.rows = 100, next.rows = 1000, VERBOSE=TRUE)
read.dbi.ffdf 1..100 (100)  dbi-read=0.001sec ffdf-write=0.01sec
read.dbi.ffdf 101..1100 (1000)  dbi-read=0.002sec ffdf-write=0.006sec
read.dbi.ffdf 1101..2100 (1000)  dbi-read=0.002sec ffdf-write=0.007sec
read.dbi.ffdf 2101..2860 (760)  dbi-read=0.002sec ffdf-write=0.006sec
 dbi-read=0.007sec  ffdf-write=0.029sec  TOTAL=0.036sec
> 
> write.dbi.ffdf(x = x, name = "helloworld", row.names = FALSE, overwrite = TRUE,
+   dbConnect.args = list(drv = drv, dbname = dbfile),
+   by = 1000, VERBOSE=TRUE)
2018-01-11 04:13:45 dbWriteTable chunk 1/3
Error in rsqlite_send_query(conn@ptr, statement) : 
  attempt to write a readonly database
Calls: write.dbi.ffdf ... initialize -> initialize -> rsqlite_send_query -> .Call
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 59-68 (evergreenreviewgraphs.Rmd) 
Error: processing vignette ‘evergreenreviewgraphs.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘tmap’
Error in re-building vignettes:
  ...
Loading required package: xml2
trying URL ‘http://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ft2020_rk310.tsv.gz’
Content type 'application/octet-stream;charset=UTF-8' length 4328 bytes
==================================================
downloaded 4328 bytes

Table t2020_rk310 cached at /tmp/RtmpiUGQbw/eurostat/t2020_rk310_num_code_TF.rds
Quitting from lines 219-223 (eurostat_tutorial.Rmd) 
Error: processing vignette ‘eurostat_tutorial.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘scales’ ‘viridis’

Package suggested but not available for checking: ‘ggalt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘scales’ ‘tidyquant’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘geomorph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rrepast’ ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/expoRkit.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘propr’
Error in re-building vignettes:
  ...

Use 'expss_output_viewer()' to display tables in the RStudio Viewer.
 To return to the console output, use 'expss_output_default()'.

Quitting from lines 342-349 (TablesWithLabelsInR.Rmd) 
Error: processing vignette ‘TablesWithLabelsInR.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘colorspace’ ‘scales’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: eyelinker
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 110-113 (basics.Rmd) 
Error: processing vignette ‘basics.Rmd’ failed with diagnostics:
could not find function "ggplot"
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘dendextend’ ‘ggpubr’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggpubr’ ‘scales’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘pheatmap’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘OpenML’
Found the following significant warnings:
  Warning: ‘i’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fAsianOptions.Rcheck/00install.out’ for details.
Packages required but not available: ‘ggformula’ ‘mosaic’ ‘ggplot2’

Packages suggested but not available for checking:
  ‘mosaicCalc’ ‘Hmisc’ ‘vcd’ ‘corrgram’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘mosaic’ ‘mosaicCalc’

Packages suggested but not available for checking: ‘Hmisc’ ‘vcd’ ‘corrgram’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Packages required but not available: ‘DESeq2’ ‘destiny’ ‘pheatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

ROI.plugin.symphony: R Optimization Infrastructure
Registered solver plugins: nlminb, ecos, alabama, clp, cplex, deoptim, glpk, ipop, lpsolve, msbinlp, nloptr, optimx, quadprog, scs, symphony.
Default solver: auto.
Quitting from lines 19-22 (Multi-Objective_Optimization_case_study.Rmd) 
Error: processing vignette ‘Multi-Objective_Optimization_case_study.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
Package required but not available: ‘fdapace’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘refund’
Package suggested but not available for checking: ‘fds’
Running examples in ‘fdcov-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: classifier-com
> ### Title: Functional data classifier via concentration inequalities
> ### Aliases: classifier-com classif.com predict.classif.com
> 
> ### ** Examples
> 
> ## Not run: 
> ##D  library(fds);
> ##D  # Setup training data
> ##D  dat1 = rbind( 
> ##D    t(aa$y[,1:100]), t(ao$y[,1:100]), t(dcl$y[,1:100]), 
> ##D    t(iy$y[,1:100]), t(sh$y[,1:100]) 
> ##D  );
> ##D  # Setup testing data
> ##D  dat2 = rbind( 
> ##D    t(aa$y[,101:400]), t(ao$y[,101:400]), t(dcl$y[,101:400]), 
> ##D    t(iy$y[,101:400]), t(sh$y[,101:400]) 
> ##D  );
> ##D  
> ##D  datgrp = gl(5,100);
> ##D  clCom = classif.com( datgrp, dat1 );
> ##D  grp = predict( clCom, dat2, LOADING=TRUE );
> ##D  acc = c(
> ##D    sum( grp[1:300]==1 ), sum( grp[301:600]==2 ), sum( grp[601:900]==3 ), 
> ##D    sum( grp[901:1200]==4 ), sum( grp[1201:1500]==5 )
> ##D  )/300;
> ##D  print(rbind(gl(5,1),signif(acc,3)));
> ## End(Not run)
> ## Don't show: 
>  library(fds);
Error in library(fds) : there is no package called ‘fds’
Execution halted
Packages required but not available: ‘Fgmutils’ ‘ggplot2’ ‘randomcoloR’

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

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

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

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

Package suggested but not available for checking: ‘ggplot2’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FField-package
> ### Title: Force field simulation for a set of points
> ### Aliases: FField FField-package
> ### Keywords: package
> 
> ### ** Examples
> 
> # Repel points
> coords <-
+   FFieldPtRep(coords = cbind(mtcars$wt * 100 / max(mtcars$wt), 
+                              mtcars$mpg * 100 / max(mtcars$mpg)),
+               rep.fact = 40)
> head(mtcars)
                   mpg cyl disp  hp drat    wt  qsec vs am gear carb
Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1    4    1
Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2
Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1
> head(coords)
         x        y
1 45.11259 58.47014
2 54.19136 61.20140
3 40.34714 69.42976
4 62.48920 65.94822
5 59.81417 56.33633
6 66.54832 53.33343
>   
> # Demo
> FFieldPtRepDemo()
Error in library(ggplot2) : there is no package called ‘ggplot2’
Calls: FFieldPtRepDemo -> library
Execution halted
Packages required but not available: ‘yarrr’ ‘circlize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘colorplaner’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fiftystater)
  > 
  > test_check("fiftystater")
  ── 1. Error: (unknown) (@test_fifty_states.R#1)  ───────────────────────────────
  there is no package called 'ggplot2'
  1: library(ggplot2) at testthat/test_fifty_states.R:1
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_fifty_states.R#1) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 54-76 (fiftystater.Rmd) 
Error: processing vignette ‘fiftystater.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running ‘test-all.R’ [19s/25s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library('testthat')
  > library('finch')
  > 
  > test_check('finch')
  ── 1. Error: dwca_get - works with a zip file - read=FALSE (@test-dwca_get.R#21)
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/finch/examples/0000154-150116162929234/multimedia.txt': Read-only file system
  1: dwca_read(zip, read = FALSE) at testthat/test-dwca_get.R:21
  2: process(x)
  3: utils::unzip(x, exdir = dirpath)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 29 SKIPPED: 2 FAILED: 1
  1. Error: dwca_get - works with a zip file - read=FALSE (@test-dwca_get.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘diveRsity’
Error in re-building vignettes:
  ...
Quitting from lines 37-39 (lifeExpectancy.Rmd) 
Error: processing vignette ‘lifeExpectancy.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘EnvStats’ ‘revdbayes’
Packages suggested but not available for checking:
  ‘tidyverse’ ‘scales’ ‘ggthemes’ ‘ggraph’
Running examples in ‘fivethirtyeight-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: airline_safety
> ### Title: Should Travelers Avoid Flying Airlines That Have Had Crashes in
> ###   the Past?
> ### Aliases: airline_safety
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # To convert data frame to tidy data (long) format, run:
> library(tidyverse)
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 19-30 (bechdel.Rmd) 
Error: processing vignette ‘bechdel.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
Package required but not available: ‘mlr’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘plotly’ ‘smoof’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ActuDistns’ ‘colorspace’
Packages required but not available: ‘ggsn’ ‘ggmap’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘multipanelfigure’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘flowWorkspace’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘hrbrthemes’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘forecast’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘colorspace’ ‘ggplot2’

Package suggested but not available for checking: ‘expsmooth’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘allExamples.R’ [0s/1s]
  Running ‘rfPermute_supported.R’ [0s/1s]
  Running ‘stdUsage.R’ [15s/20s]
  Running ‘testBinaryClass.R’ [5s/6s]
  Running ‘testCaret.R’ [0s/0s]
Running the tests in ‘tests/testCaret.R’ failed.
Complete output:
  > ##test caret suuport
  > 
  > rm(list=ls())
  > library(caret)
  Error in library(caret) : there is no package called 'caret'
  Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘likert’
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 23-31 (Overview.Rmd) 
Error: processing vignette ‘Overview.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 50-83 (fourierin_details.Rmd) 
Error: processing vignette ‘fourierin_details.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking:
  ‘Rsocp’ ‘Rnlminb2’ ‘Rdonlp2’ ‘mvoutlier’
Packages required but not available: ‘forecast’ ‘fma’ ‘expsmooth’ ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 18-26 (Theory.Rmd) 
Error: processing vignette ‘Theory.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘refund’
Packages required but not available: ‘ggplot2’ ‘GGally’

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

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

Package suggested but not available for checking: ‘FrF2.catlg128’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘Hmisc’

Package suggested but not available for checking: ‘INLA’

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

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

Packages suggested but not available for checking: ‘Hmisc’ ‘pROC’ ‘rrlda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘RTCGA.rnaseq’ ‘ggplot2’
Packages required but not available: ‘forecast’ ‘rainbow’ ‘colorspace’

Package suggested but not available for checking: ‘fds’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘ggplot2’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 279-340 (rarity_indices.Rmd) 
Error: processing vignette ‘rarity_indices.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘furniture-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: table1
> ### Title: Table 1 for Simple and Stratified Descriptive Statistics
> ### Aliases: table1
> 
> ### ** Examples
> 
> ## Ficticious Data ##
> library(furniture)
> library(tidyverse)
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 39-44 (Furniture.Rmd) 
Error: processing vignette ‘Furniture.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 64-76 (subgroup_fusion.Rmd) 
Error: processing vignette ‘subgroup_fusion.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggthemes’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fuzzyjoin)
  > 
  > test_check("fuzzyjoin")
  Error in library(ggplot2) : there is no package called 'ggplot2'
  Calls: test_check ... suppressPackageStartupMessages -> withCallingHandlers -> library
  Execution halted
Packages required but not available: ‘ggplot2’ ‘scales’ ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘BayesX’ ‘R2BayesX’
Error in re-building vignettes:
  ...
Loading required package: R2BayesX
Installing package into '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages'
(as 'lib' is unspecified)

Error: processing vignette ‘gamboostLSS_Tutorial.Rnw’ failed with diagnostics:
 chunk 1 (label = init) 
Error in install.packages("R2BayesX", repos = repos) : 
  unable to install packages
Execution halted
Packages required but not available: ‘VineCopula’ ‘copula’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ga_parsimony
> ### Title: GA-PARSIMONY
> ### Aliases: ga_parsimony show,ga_parsimony-method
> ###   print,ga_parsimony-method print,ga_parsimony-method numericOrNA
> ### Keywords: optimize
> 
> ### ** Examples
> 
> 
> #################################
> ### Example 1: Classification ###
> #################################
> 
> # This a toy example that shows how to search, for the *iris* database, 
> # a parsimony classification NNET model with 'GAparsimony' 
> # and 'caret' packages. Validation errors and iterations have been
> # reduced to speedup the process
> 
> 
> # Training and testing Datasets
> library(caret)
Error in library(caret) : there is no package called ‘caret’
Execution halted
Packages suggested but not available for checking: ‘haplo.stats’ ‘rms’
Packages required but not available: ‘ggplot2’ ‘rstan’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Decathlon
> ### Title: Top performances in the Decathlon from 1985 to 2006.
> ### Aliases: Decathlon
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Decathlon, package="GDAdata")
> summary(Decathlon[, grep("P.*", names(Decathlon))])
   Polevault         P100m             Plj              Psp       
 Min.   :2.850   Min.   : 597.0   Min.   : 569.0   Min.   :418.0  
 1st Qu.:4.200   1st Qu.: 765.0   1st Qu.: 757.0   1st Qu.:622.0  
 Median :4.400   Median : 806.0   Median : 804.0   Median :672.0  
 Mean   :4.405   Mean   : 806.6   Mean   : 807.4   Mean   :674.6  
 3rd Qu.:4.650   3rd Qu.: 847.0   3rd Qu.: 857.0   3rd Qu.:726.0  
 Max.   :5.760   Max.   :1042.0   Max.   :1089.0   Max.   :941.0  
      Phj           P400m         P110h             Ppv              Pdt       
 Min.   : 396   Min.   :532   Min.   : 526.0   Min.   : 321.0   Min.   :231.0  
 1st Qu.: 696   1st Qu.:746   1st Qu.: 777.0   1st Qu.: 673.0   1st Qu.:600.0  
 Median : 749   Median :789   Median : 824.0   Median : 731.0   Median :655.0  
 Mean   : 749   Mean   :788   Mean   : 821.6   Mean   : 734.4   Mean   :657.8  
 3rd Qu.: 803   3rd Qu.:832   3rd Qu.: 868.0   3rd Qu.: 804.0   3rd Qu.:713.0  
 Max.   :1061   Max.   :998   Max.   :1044.0   Max.   :1152.0   Max.   :970.0  
      Pjt             P1500      
 Min.   : 330.0   Min.   :121.0  
 1st Qu.: 588.0   1st Qu.:607.0  
 Median : 644.0   Median :669.0  
 Mean   : 648.1   Mean   :661.7  
 3rd Qu.: 707.0   3rd Qu.:725.0  
 Max.   :1040.0   Max.   :946.0  
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package suggested but not available for checking: ‘WeightedCluster’
Packages suggested but not available for checking:
  ‘qvalue’ ‘haplo.stats’ ‘PredictABEL’
Packages required but not available: ‘ggnetwork’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘genderdata’ ‘ggplot2’
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 15-27 (predicting-gender.Rmd) 
Error: processing vignette ‘predicting-gender.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘scales’

Package suggested but not available for checking: ‘RHugin’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ProjectionBasedClustering’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘runTests.R’ [11s/12s]
Running the tests in ‘tests/runTests.R’ failed.
Complete output:
  > BiocGenerics:::testPackage("geno2proteo")
  Timing stopped at: 2.312 0.032 2.385
  Error in file(file, ifelse(append, "a", "w")) : 
    cannot open the connection
  In addition: Warning message:
  In file(file, ifelse(append, "a", "w")) :
    cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/geno2proteo/extdata/Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz_CDS_transcript.txt': Read-only file system
  Timing stopped at: 0.61 0 0.63
  Error in getWritablePathname.Arguments(static, ...) : 
    No write permission for directory: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/geno2proteo/extdata
  
  
  RUNIT TEST PROTOCOL -- Thu Jan 11 06:26:48 2018 
  *********************************************** 
  Number of test functions: 6 
  Number of errors: 2 
  Number of failures: 0 
  
   
  1 Test Suite : 
  geno2proteo RUnit Tests - 6 test functions, 2 errors, 0 failures
  ERROR in test_generatingCDSaaFile: Error in file(file, ifelse(append, "a", "w")) : 
    cannot open the connection
  ERROR in test_genomicLocToWholeDNASequence: Error in getWritablePathname.Arguments(static, ...) : 
    No write permission for directory: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/geno2proteo/extdata
  
  Test files with failing tests
  
     test_functionsInGeno2proteo.R 
       test_generatingCDSaaFile 
       test_genomicLocToWholeDNASequence 
  
  
  Error in BiocGenerics:::testPackage("geno2proteo") : 
    unit tests failed for package geno2proteo
  Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette ‘geno2proteoIntroduction.Rnw’ failed with diagnostics:
 chunk 3 (label = example_generatingCDSaaFile) 
Error in getWritablePathname.Arguments(static, ...) : 
  No write permission for directory: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/geno2proteo/extdata
Execution halted
Package required but not available: ‘circlize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reldist’
Packages suggested but not available for checking: ‘ggmap’ ‘ggplot2’
Error in re-building vignettes:
  ...
rgdal: version: 1.2-16, (SVN revision 701)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: /usr/share/gdal/2.2
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-6 
Loading required package: raster

Attaching package: 'raster'

The following object is masked _by_ '.GlobalEnv':

    values<-

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

    geom, values, values<-

Loading required package: lattice
Loading required package: latticeExtra
Loading required package: RColorBrewer
Quitting from lines 66-83 (plot_geotiff.Rmd) 
Error: processing vignette ‘plot_geotiff.Rmd’ failed with diagnostics:
there is no package called 'ggmap'
Execution halted
Packages required but not available: ‘inlmisc’ ‘ggplot2’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘plotly’

Packages suggested but not available for checking: ‘ggrepel’ ‘ggmap’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘scales’ ‘slackr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘viridis’
Error in re-building vignettes:
  ...
Quitting from lines 156-161 (gdfpd-vignette-introduction.Rmd) 
Error: processing vignette ‘gdfpd-vignette-introduction.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 75-80 (ghfd-vignette-Trades.Rmd) 
Error: processing vignette ‘ghfd-vignette-Trades.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘BETS’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘plotly’ ‘ggthemes’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 44-49 (gtdd-vignette_GetTDData.Rmd) 
Error: processing vignette ‘gtdd-vignette_GetTDData.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘scatterpie’ ‘ggplot2’ ‘ggrepel’ ‘circlize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘scales’ ‘plotly’

Package suggested but not available for checking: ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘geomnet’ ‘ggnetwork’ ‘GGally’ ‘ggmap’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggmcmc’ ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggforce’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘colourpicker’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘effects’ ‘ggplot2’ ‘scales’ ‘sjstats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘colourpicker’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘colorspace’ ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘mosaic’ ‘mosaicModel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘scales’

Packages suggested but not available for checking: ‘forecast’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggiraph’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggridges’

Packages suggested but not available for checking: ‘tidyverse’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘GGally’

Packages suggested but not available for checking: ‘rstan’ ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘productplots’ ‘plotly’

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

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tidyverse’ ‘ggplot2’ ‘scales’ ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘ggrepel’ ‘ggsci’ ‘cowplot’ ‘ggsignif’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘ggforce’ ‘scales’ ‘ggrepel’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘ggthemes’ ‘colourpicker’ ‘colorspace’ ‘GGally’ ‘munsell’
  ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘scales’

Packages suggested but not available for checking: ‘tidyverse’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘scales’ ‘ggplot2’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘colorspace’ ‘ggplot2’ ‘scales’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘VineCopula’ ‘ggplot2’ ‘copula’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: coda
##
## Markov Chain Monte Carlo Package (MCMCpack)
## Copyright (C) 2003-2018 Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
##
## Support provided by the U.S. National Science Foundation
## (Grants SES-0350646 and SES-0350613)
##
Quitting from lines 18-24 (mcmc.rmd) 
Error: processing vignette ‘mcmc.rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 117-117 (GMCM-JStatSoft.Rnw) 
Error: processing vignette ‘GMCM-JStatSoft.Rnw’ failed with diagnostics:
there is no package called 'Hmisc'
Execution halted
Package suggested but not available for checking: ‘Deducer’
Package suggested but not available for checking: ‘mediation’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘caret’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘copula’ ‘VineCopula’

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

Package suggested but not available for checking: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggdendro’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘vcd’ ‘colorspace’

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

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

Packages suggested but not available for checking:
  ‘taxstats’ ‘ggplot2’ ‘scales’ ‘viridis’ ‘ggrepel’

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘rms’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘DiagrammeR’ ‘bayesplot’
Running ‘testthat.R’ [1s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tensorflow)
  > library(greta)
  
  
    greta requires TensorFlow version 1.0.0 or higher, but TensorFlow isn't installed.
    Use install_tensorflow() to install the latest version.
  
  
  
  Attaching package: 'greta'
  
  The following objects are masked from 'package:stats':
  
      binomial, poisson
  
  The following objects are masked from 'package:base':
  
      %*%, beta, diag, gamma, sweep
  
  > 
  > test_check("greta")
  Error: 'dnst' is not an exported object from 'namespace:extraDistr'
  Execution halted
Package required but not available: ‘inlmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘egg’
Error in re-building vignettes:
  ...
Quitting from lines 24-33 (arrangeGrob.rmd) 
Error: processing vignette ‘arrangeGrob.rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Loading required package: XML

Attaching package: 'XML'

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

    toHTML


Error: processing vignette ‘import.Rnw’ failed with diagnostics:
 chunk 53 
Error in library(colorspace) : there is no package called 'colorspace'
Execution halted
Error in re-building vignettes:
  ...
Warning in yaml::yaml.load(string, ...) :
  R expressions in yaml.load will not be auto-evaluated by default in the near future
Warning in yaml::yaml.load(string, ...) :
  R expressions in yaml.load will not be auto-evaluated by default in the near future

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning in yaml::yaml.load(string, ...) :
  R expressions in yaml.load will not be auto-evaluated by default in the near future
Warning in yaml::yaml.load(string, ...) :
  R expressions in yaml.load will not be auto-evaluated by default in the near future
Quitting from lines 71-104 (cross-validation_with_groupdata2.Rmd) 
Error: processing vignette ‘cross-validation_with_groupdata2.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 397-414 (Growthcurver-vignette.Rmd) 
Error: processing vignette ‘Growthcurver-vignette.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘cellWise’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘aqp’ ‘plotKML’ ‘scales’

Packages suggested but not available for checking: ‘Hmisc’ ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 64-75 (Introduction.Rmd) 
Error: processing vignette ‘Introduction.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggthemes’ ‘plotKML’
Error in re-building vignettes:
  ...
Quitting from lines 135-153 (GSODR.Rmd) 
Error: processing vignette ‘GSODR.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘hts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mvoutlier’
Packages suggested but not available for checking: ‘nbpMatching’ ‘lmerTest’
Package required but not available: ‘ggtree’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 34-37 (hazus_demo.Rmd) 
Error: processing vignette ‘hazus_demo.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘rms’ ‘ggplot2’

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘caret’ ‘ggplot2’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘plotly’ ‘viridis’ ‘ggplot2’ ‘dendextend’ ‘scales’ ‘seriation’
  ‘colorspace’

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

Package suggested but not available for checking: ‘ggplot2’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: schooldata
> ### Title: School Data
> ### Aliases: schooldata
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(schooldata)
> # initial screening
> plot(schooldata)
> 
> # better plot
> library(corrgram)
Error in library(corrgram) : there is no package called ‘corrgram’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: car

Attaching package: 'candisc'

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

    cancor


Error: processing vignette ‘HE-examples.Rnw’ failed with diagnostics:
 chunk 21 (label = jury-mod3-eff) 
Error in library(effects) : there is no package called 'effects'
Execution halted
Packages required but not available: ‘cplm’ ‘DESeq2’

Package suggested but not available for checking: ‘glmmADMB’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: icea
> ### Title: Individualized cost-effectiveness analysis
> ### Aliases: icea icea_pw
> 
> ### ** Examples
> 
> # simulation output
> nsims <- 100
> sim <- data.frame(sim = rep(seq(nsims), 4),
+                c = c(rlnorm(nsims, 5, .1), rlnorm(nsims, 5, .1),
+                       rlnorm(nsims, 11, .1), rlnorm(nsims, 11, .1)),
+                e = c(rnorm(nsims, 8, .2), rnorm(nsims, 8.5, .1),
+                      rnorm(nsims, 11, .6), rnorm(nsims, 11.5, .6)),
+                strategy = rep(paste0("Strategy ", seq(1, 2)),
+                              each = nsims * 2),
+                grp = rep(rep(c("Group 1", "Group 2"),
+                              each = nsims), 2)
+ )
> 
> # icea
> icea.dt <- icea(sim, k = seq(0, 200000, 500), sim = "sim", strategy = "strategy",
+  grp = "grp", e = "e", c = "c")
> names(icea.dt)
[1] "summary" "mce"     "evpi"    "nmb"    
> # the probability that each strategy is the most cost-effective 
> # in each group with a willingness to pay of 20,000
> library("data.table")
> icea.dt$mce[k == 20000]
       k   strategy     grp prob
1: 20000 Strategy 1 Group 1 0.57
2: 20000 Strategy 2 Group 1 0.43
3: 20000 Strategy 1 Group 2 0.47
4: 20000 Strategy 2 Group 2 0.53
> 
> # icea_pw
> icea.pw.dt <-  icea_pw(sim,  k = seq(0, 200000, 500), comparator = "Strategy 1",
+                       sim = "sim", strategy = "strategy", e = "e", c = "c")
> names(icea.pw.dt)
[1] "summary" "delta"   "ceac"    "inmb"   
> # cost-effectiveness acceptability curve
> library("ggplot2")
Error in library("ggplot2") : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 162-170 (cea-vignette.Rmd) 
Error: processing vignette ‘cea-vignette.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggimage’ ‘ggplot2’

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

Packages suggested but not available for checking:
  ‘Rcmdr’ ‘RcmdrPlugin.HH’ ‘microplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggdendro’ ‘ggplot2’ ‘scales’

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

Package suggested but not available for checking: ‘pegas’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Highcharts (www.highcharts.com) is a Highsoft software product which is
not free for commercial and Governmental use
Quitting from lines 40-42 (charting-data-frames.Rmd) 
Error: processing vignette ‘charting-data-frames.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘rms’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘scales’ ‘effects’
Running examples in ‘HistData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Bowley
> ### Title: Bowley's data on values of British and Irish trade, 1855-1899
> ### Aliases: Bowley
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Bowley)
> 
> # plot the data 
> with(Bowley,plot(Year, Value, type='b', 
+ 	ylab="Value of British and Irish Exports",
+ 	main="Bowley's example of the method of smoothing curves"))
> 
> # find moving averages-- use center alignment (requires width=ODD)
> require(gtools, warn.conflicts=FALSE)
Loading required package: gtools
> mav3<-running(Bowley$Value, width=3, align="center")
> mav5<-running(Bowley$Value, width=5, align="center")
> mav9<-running(Bowley$Value, width=9, align="center")
> lines(Bowley$Year[2:44], mav3, col='blue', lty=2)
> lines(Bowley$Year[3:43], mav5, col='green3', lty=3)
> lines(Bowley$Year[5:41], mav9, col='brown', lty=4)
> 
> # add lowess smooth
> lines(lowess(Bowley), col='red', lwd=2)
> 
> require(ggplot2, warn.conflicts=FALSE)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> qplot(Year,Value, data=Bowley)+geom_smooth()
Error in qplot(Year, Value, data = Bowley) : 
  could not find function "qplot"
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggridges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘viridis’

Packages suggested but not available for checking: ‘rms’ ‘tables’ ‘plotly’

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HS.normal.means
> ### Title: The horseshoe prior for the sparse normal means problem
> ### Aliases: HS.normal.means
> 
> ### ** Examples
> 
> #Empirical Bayes example with 20 signals, rest is noise
> #Posterior mean for the signals is plotted
> #And variable selection is performed using the credible intervals
> #And the credible intervals are plotted
> truth <- c(rep(0, 80), rep(8, 20))
> data <-  truth + rnorm(100, 1)
> tau.hat <- HS.MMLE(data, Sigma2 = 1)
> res.HS1 <- HS.normal.means(data, method.tau = "fixed", tau = tau.hat,
+ method.sigma = "fixed", Sigma2 = 1)
[1] 1000
[1] 2000
[1] 3000
[1] 4000
[1] 5000
[1] 6000
> #Plot the posterior mean against the data (signals in blue)
> plot(data, res.HS1$BetaHat, col = c(rep("black", 80), rep("blue", 20)))
> #Find the selected betas (ideally, the last 20 are equal to 1)
> HS.var.select(res.HS1, data, method = "intervals")
  [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [38] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0
 [75] 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> #Plot the credible intervals
> library(Hmisc)
Error in library(Hmisc) : there is no package called ‘Hmisc’
Execution halted
Running examples in ‘HSAUR2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BCG
> ### Title: BCG Vaccine Data
> ### Aliases: BCG
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
>   data("BCG", package = "HSAUR2")
> 
>   ### sort studies w.r.t. sample size
>   BCG <- BCG[order(rowSums(BCG[,2:5])),]
> 
>   ### to long format
>   BCGlong <- with(BCG, data.frame(Freq = c(BCGTB, BCGVacc - BCGTB, 
+                                            NoVaccTB, NoVacc - NoVaccTB),
+                   infected = rep(rep(factor(c("yes", "no")), 
+                                  rep(nrow(BCG), 2)), 2),
+                   vaccined = rep(factor(c("yes", "no")), 
+                                  rep(nrow(BCG) * 2, 2)),
+                   study = rep(factor(Study, levels = as.character(Study)), 
+                               4)))
> 
>   ### doubledecker plot
>   library("vcd")
Error in library("vcd") : there is no package called ‘vcd’
Execution halted
Running examples in ‘HSAUR3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BCG
> ### Title: BCG Vaccine Data
> ### Aliases: BCG
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
>   data("BCG", package = "HSAUR3")
> 
>   ### sort studies w.r.t. sample size
>   BCG <- BCG[order(rowSums(BCG[,2:5])),]
> 
>   ### to long format
>   BCGlong <- with(BCG, data.frame(Freq = c(BCGTB, BCGVacc - BCGTB, 
+                                            NoVaccTB, NoVacc - NoVaccTB),
+                   infected = rep(rep(factor(c("yes", "no")), 
+                                  rep(nrow(BCG), 2)), 2),
+                   vaccined = rep(factor(c("yes", "no")), 
+                                  rep(nrow(BCG) * 2, 2)),
+                   study = rep(factor(Study, levels = as.character(Study)), 
+                               4)))
> 
>   ### doubledecker plot
>   library("vcd")
Error in library("vcd") : there is no package called ‘vcd’
Execution halted
Package required but not available: ‘caret’

Package suggested but not available for checking: ‘hyperSpec’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 101-141 (tables.Rmd) 
Error: processing vignette ‘tables.Rmd’ failed with diagnostics:
there is no package called 'Hmisc'
Execution halted
Package suggested but not available for checking: ‘HTSFilter’
Packages required but not available: ‘ggplot2’ ‘DESeq2’ ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘GGally’ ‘scales’ ‘EnvStats’ ‘viridis’ ‘colorspace’
Error in re-building vignettes:
  ...
Quitting from lines 21-25 (supplemental_vignette_age_dist.Rmd) 
Error: processing vignette ‘supplemental_vignette_age_dist.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggmap’ ‘ggplot2’

Package suggested but not available for checking: ‘hurricaneexposuredata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 41-46 (huxreg.Rmd) 
Error: processing vignette ‘huxreg.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘adegenet’
Running examples in ‘HWxtest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hwx.test
> ### Title: Test for HW by either full enumeration or Monte Carlo.
> ### Aliases: hwx.test
> 
> ### ** Examples
> 
> # Data from Louis and Dempster 1987 Table 2 and Guo and Thompson 1992 Figure 2:
> c <- c(0,3,1,5,18,1,3,7,5,2)
> hwx.test(c)

*****    Sample of 45 diploids with 4 alleles
Full enumeration of 162365 tables to test for HW

P value (LLR)   = 0.012945
P value (Prob)  = 0.017442
P value (U)     = 0.003343 (test for heterozygote excess)
P value (Chisq) = 0.020170
> # To see a histogram of the LLR statistic:
> hwx.test(c, histobins=TRUE)

*****    Sample of 45 diploids with 4 alleles
Full enumeration of 162365 tables to test for HW

P value (LLR)   = 0.012945
P value (Prob)  = 0.017442
P value (U)     = 0.003343 (test for heterozygote excess)
P value (Chisq) = 0.020170
Loading required namespace: ggplot2
Failed with error:  ‘there is no package called ‘ggplot2’’
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 6-18 (HWxtest.Rmd) 
Error: processing vignette ‘HWxtest.Rmd’ failed with diagnostics:
there is no package called 'adegenet'
Execution halted
Package required but not available: ‘InformationValue’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘DiagrammeR’ ‘pixiedust’

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

Package suggested but not available for checking: ‘SWAT2R’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘mixAK’ ‘dynsurv’
Packages required but not available: ‘coefplot’ ‘forecast’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
Packages required but not available: ‘ggplot2’ ‘ggrepel’

Package suggested but not available for checking: ‘caret’

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

Package suggested but not available for checking: ‘ie2miscdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ie2misc’ ‘ie2miscdata’ ‘qdap’
Packages suggested but not available for checking:
  ‘ie2misc’ ‘ie2miscdata’ ‘RcppOctave’ ‘optiRum’
Packages suggested but not available for checking: ‘NMF’ ‘scales’
Packages required but not available: ‘ggdendro’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘NSM3’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dae’ ‘ggplot2’ ‘Hmisc’ ‘GGally’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.cimg
> ### Title: Display an image using base graphics
> ### Aliases: plot.cimg
> 
> ### ** Examples
> 
> plot(boats,main="Boats") 
> plot(boats,axes=FALSE,xlab="",ylab="")
> 
> #Pixel values are rescaled to 0-1 by default, so that the following two plots are identical
> plot(boats)
> plot(boats/2,main="Rescaled")
> #If you don't want that behaviour, you can set rescale to FALSE, but
> #then you need to make sure values are in [0,1]
> try(plot(boats,rescale=FALSE)) #Error!
> try(plot(boats/255,rescale=FALSE)) #Works
> #You can specify a colour scale if you don't want the default one.
> #A colour scale is a function that takes pixels values and return an RGB code,
> #like R's rgb function,e.g.
> rgb(0,1,0)
[1] "#00FF00"
> #Let's switch colour channels
> cscale <- function(r,g,b) rgb(b,g,r)
> plot(boats/255,rescale=FALSE,colourscale=cscale)
> #Display slice of HSV colour space
> im <- imfill(255,255,val=1)
> im <- list(Xc(im)/255,Yc(im)/255,im) %>% imappend("c")
> plot(im,colourscale=hsv,rescale=FALSE,
+      xlab="Hue",ylab="Saturation")
> #In grayscale images, the colourscale function should take in a single value
> #and return an RGB code
> boats.gs <- grayscale(boats)
> #We use an interpolation function from package scales
> cscale <- scales::gradient_n_pal(c("red","purple","lightblue"),c(0,.5,1))
Error in loadNamespace(name) : there is no package called ‘scales’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Loading required package: plyr
Loading required package: magrittr

Attaching package: 'imager'

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

    add

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

    liply

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

    convolve, spectrum

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

    frame

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

    save.image

Quitting from lines 108-112 (gettingstarted.Rmd) 
Error: processing vignette ‘gettingstarted.Rmd’ failed with diagnostics:
there is no package called 'scales'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 26-35 (FunctionHelpers.Rmd) 
Error: processing vignette ‘FunctionHelpers.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘mediation’ ‘plotly’

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

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

Package suggested but not available for checking: ‘compareGroups’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘forecast’ ‘ggplot2’ ‘imputeTS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘cowplot’ ‘drc’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘iNEXT’

Package suggested but not available for checking: ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggthemes’

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

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘ggmap’ ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggfortify’

Package suggested but not available for checking: ‘INLA’

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

Package suggested but not available for checking: ‘colorspace’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘scales’

Package suggested but not available for checking: ‘caret’

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

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.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘Fgmutils’ ‘randomcoloR’ ‘rbokeh’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 120-137 (JacobiEigen.Rmd) 
Error: processing vignette ‘JacobiEigen.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘iClick’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘vcd’ ‘vcdExtra’ ‘GGally’ ‘afex’ ‘ggridges’

Package suggested but not available for checking: ‘semPlot’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘cowplot’ ‘weights’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘cowplot’ ‘Hmisc’

Package suggested but not available for checking: ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘clustMD’ ‘ggplot2’ ‘Hmisc’
Packages required but not available: ‘MVN’ ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘VineCopula’
Running ‘testthat.R’ [1s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(kdecopula)
  > 
  > test_check("kdecopula")
  ── 1. Error: (unknown) (@test-bandwidths.R#3)  ─────────────────────────────────
  there is no package called 'VineCopula'
  1: library(VineCopula) at testthat/test-bandwidths.R:3
  2: stop(txt, domain = NA)
  
  ── 2. Error: (unknown) (@test-dep-measures.R#4)  ───────────────────────────────
  there is no package called 'VineCopula'
  1: VineCopula::BiCopSim at testthat/test-dep-measures.R:4
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ── 3. Error: (unknown) (@test-generics.R#4)  ───────────────────────────────────
  there is no package called 'VineCopula'
  1: VineCopula::BiCopSim at testthat/test-generics.R:4
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test-bandwidths.R#3) 
  2. Error: (unknown) (@test-dep-measures.R#4) 
  3. Error: (unknown) (@test-generics.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: knitr
Loading required package: kfigr
knitr hook "anchor" is now available
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Quitting from lines 26-28 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
could not find function "qplot"
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 17-32 (cars.Rmd) 
Error: processing vignette ‘cars.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘knitr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: spin
> ### Title: Spin goat's hair into wool
> ### Aliases: spin
> 
> ### ** Examples
> 
> #' write normal text like this and chunk options like below
> 
> #+ label, opt=value
> 
> # /*
> #' these lines are treated as comments in spin()
> 1 + 1
[1] 2
> # */
> 
> (s = system.file("examples", "knitr-spin.R", package = "knitr"))
[1] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/knitr/examples/knitr-spin.R"
> spin(s)  # default markdown
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/knitr/examples/knitr-spin.Rmd': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: spin -> cat -> file
Execution halted
Packages suggested but not available for checking: ‘copula’ ‘Hmisc’
Error in re-building vignettes:
  ...
Quitting from lines 124-133 (labelVector.Rmd) 
Error: processing vignette ‘labelVector.Rmd’ failed with diagnostics:
there is no package called 'Hmisc'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘vcd’
Packages required but not available: ‘GGally’ ‘ggplot2’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rms’ ‘Hmisc’ ‘lmerTest’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggforce’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 55-71 (using-latex2exp.Rmd) 
Error: processing vignette ‘using-latex2exp.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘semPlot’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lawn_unkinkpolygon
> ### Title: Unkink polygon
> ### Aliases: lawn_unkinkpolygon
> 
> ### ** Examples
> 
> x <- '{
+   "type": "Feature",
+   "properties": {},
+   "geometry": {
+     "type": "Polygon",
+       "coordinates": [[[0, 0], [2, 0], [0, 2], [2, 2], [0, 0]]]
+    }
+ }'
> lawn_unkinkpolygon(x)
<FeatureCollection>
  Bounding box: 0.0 0.0 2.0 2.0
  No. features: 2
  No. points: 16
  Properties: NULL
> view(x)
Error: Please install leaflet
Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘colorspace’ ‘scales’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: grid
Loading required package: survival
Warning in methods:::bind_activation(TRUE) :
  methods:::bind_activation(TRUE) is deprecated;
 you should rather provide methods for cbind2() / rbind2()
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’

Error: processing vignette ‘addTracks.Rnw’ failed with diagnostics:
 chunk 14 (label = addQplot) 
Error in ggplotGrob({ : could not find function "ggplotGrob"
Execution halted
Packages required but not available: ‘ecd’ ‘scales’ ‘ggplot2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Error: processing vignette ‘LEAP_Vignette.Rnw’ failed with diagnostics:
 chunk 10 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘ggplot2’ ‘scales’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘Rcmdr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘mapview’ ‘mapedit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘demography’ ‘forecast’
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lifecontingencies.Rcheck/vign_test/lifecontingencies") :
  Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/pensionfunding.Rmd’
(Is a VignetteBuilder field missing?)
Package:  lifecontingencies
Authors:  Giorgio Alfredo Spedicato [cre,aut], Reinhold Kainhofer [ctb], Kevin J.
    Owens [ctb], Christophe Dutang [ctb], Ernesto Schirmacher[ctb], Gian Paolo Clemente [ctb]
Version:  1.3.2
Date:     2017-12-09
BugReport: http://github.com/spedygiorgio/lifecontingencies/issues

Loading required package: markovchain
Package:  markovchain
Version:  0.6.9.8-1
Date:     2017-08-15
BugReport: http://github.com/spedygiorgio/markovchain/issues

Loading required package: parallel

Error: processing vignette ‘mortality_projection.Rnw’ failed with diagnostics:
 chunk 2 (label = load) 
Error in library(demography) : there is no package called 'demography'
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘mlr’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘mlr’
Packages required but not available: ‘mlr’ ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: Matrix
Quitting from lines 95-108 (lmer.Rnw) 
Error: processing vignette ‘lmer.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘SPEI’
Found the following significant warnings:
  Warning: ‘nsimp’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/localdepth.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘mosaic’
Packages required but not available: ‘rms’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 7-30 (logitnorm.Rmd) 
Error: processing vignette ‘logitnorm.Rmd’ failed with diagnostics:
could not find function "exit"
Execution halted
Packages required but not available: ‘caret’ ‘pROC’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘colorspace’ ‘ggplot2’
Packages suggested but not available for checking: ‘rstan’ ‘rstanarm’
Packages suggested but not available for checking:
  ‘mediation’ ‘glmmADMB’ ‘lmerTest’ ‘rstan’ ‘rstanarm’
Error in re-building vignettes:
  ...
Quitting from lines 55-64 (lspline.Rmd) 
Error: processing vignette ‘lspline.Rmd’ failed with diagnostics:
there is no package called 'scales'
Execution halted
Packages suggested but not available for checking:
  ‘mcmcplots’ ‘ggmcmc’ ‘ggplot2’
Error in re-building vignettes:
  ...
Loading required package: mcmc
Loading required package: MHadaptive
Loading required package: MASS
Loading required package: numDeriv
Quitting from lines 13-17 (example-plots.Rmd) 
Error: processing vignette ‘example-plots.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘caret’ ‘Hmisc’
Running examples in ‘lulcc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: allow
> ### Title: Implement decision rules for land use change
> ### Aliases: allow
> 
> ### ** Examples
> 
> 
> ## Plum Island Ecosystems
> 
> ## load observed land use data
> obs <- ObsLulcRasterStack(x=pie,
+                    pattern="lu",
+                    categories=c(1,2,3),
+                    labels=c("forest","built","other"),
+                    t=c(0,6,14))
> 
> ## get land use values
> x <- getValues(obs[[1]])
> x <- x[!is.na(x)]
> 
> ## create vector of arbitrary land use history values
> hist <- sample(1:10, length(x), replace=TRUE)
> 
> ## calculate demand and get change direction for first timestep
> dmd <- approxExtrapDemand(obs=obs, tout=0:14)
Warning in total(x = obs) :
  missing argument 'categories': getting categories from 'x'
Error in loadNamespace(name) : there is no package called ‘Hmisc’
Calls: approxExtrapDemand ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages required but not available: ‘qgraph’ ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘caret’

Packages suggested but not available for checking: ‘moveHMM’ ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggmap’ ‘leaflet’ ‘clifro’

VignetteBuilder packages required for checking but not installed:
  ‘ggplot2’ ‘leaflet’ ‘clifro’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘R2wd’
Error in re-building vignettes:
  ...
Quitting from lines 33-38 (maddison_project_database.Rmd) 
Error: processing vignette ‘maddison_project_database.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘R2wd’ ‘ggplot2’
Running examples in ‘MAd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotcon
> ### Title: Meta Regression Scatterplot
> ### Aliases: plotcon
> ### Keywords: aplot
> 
> ### ** Examples
> 
> # SAMPLE DATA
> MA2 <-read.table(textConnection("
+ id       es1       var1 n.1 n.2 mod1 mod2
+ 1   1 0.5695938 0.04906967  26  30    a   20
+ 2   2 0.4123667 0.04362541  28  34    b   30
+ 3   3 0.4084333 0.04458363  34  28    a   25
+ 4   4 0.5014756 0.04186354  37  29    b   35
+ 5   5 0.5540745 0.04339382  31  32    b   40
+ 6   1 0.5695938 0.04906967  26  30    a   20
+ 7   2 0.4123667 0.04362541  28  34    b   30
+ 8   3 0.4084333 0.04458363  34  28    a   25
+ 9   4 0.5014756 0.04186354  37  29    b   35
+ 10  5 0.5540745 0.04339382  31  32    b   40"))
> 
> 
> # EXAMPLE
> plotcon(es1, var1, mod2, data=MA2, method= "fixed", modname="NULL",title="NULL")
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
Loading required package: metafor
Loading required package: Matrix
Loading 'metafor' package (version 2.0-0). For an overview 
and introduction to the package please type: help(metafor).
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: plotcon ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages required but not available:
  ‘forecast’ ‘forecastHybrid’ ‘colorspace’ ‘scales’ ‘ggplot2’ ‘munsell’
  ‘ggseas’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘tesseract’
Running examples in ‘magick-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: device
> ### Title: Magick Graphics Device
> ### Aliases: device image_graph image_device image_draw image_capture
> 
> ### ** Examples
> 
> # Regular image
> frink <- image_read("https://jeroen.github.io/images/frink.png")
> 
> # Produce image using graphics device
> fig <- image_graph(res = 96)
> ggplot2::qplot(mpg, wt, data = mtcars, colour = cyl)
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in tryCatch(evalq(sys.calls(), <environment>), error = function (x)  : 
  Magick device has zero pages
Fatal error: error during cleanup
Error in re-building vignettes:
  ...
Quitting from lines 425-429 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in tryCatch(evalq(sys.calls(), <environment>), error = function (x)  : 
  Magick device has zero pages
Fatal error: error during cleanup
Running examples in ‘MAGNAMWAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FormatMCLFastas
> ### Title: Format all raw GenBank fastas to single OrthoMCL compatible
> ###   fasta file
> ### Aliases: FormatMCLFastas
> 
> ### ** Examples
> 
> 
> dir <- system.file('extdata', 'fasta_dir', package='MAGNAMWAR')
> dir <- paste(dir,'/',sep='')
> formatted_file <- FormatMCLFastas(dir)
Warning in file.remove(outfile) :
  cannot remove file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta', reason 'Read-only file system'
Writing out to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta 
Warning in file(description = file.out, open = open) :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta': Read-only file system
Error in file(description = file.out, open = open) : 
  cannot open the connection
Calls: FormatMCLFastas -> <Anonymous> -> file
Execution halted
Packages required but not available: ‘beadarray’ ‘lumi’ ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘leaflet’ ‘plotly’
Packages required but not available: ‘forecast’ ‘smooth’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘leaflet’ ‘spocc’

Package suggested but not available for checking: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 95-100 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
Execution halted
Packages required but not available: ‘Hmisc’ ‘colorspace’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 338-346 (Introduction.Rmd) 
Error: processing vignette ‘Introduction.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘biomod2’
Error in re-building vignettes:
  ...
Loading required package: lme4
Loading required package: Matrix
Loading required package: parallel
This is marked 1.1.13


Error: processing vignette ‘markedVignette.Rnw’ failed with diagnostics:
 chunk 4 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/markmyassignment.Rcheck/00install.out’ for details.
Packages required but not available: ‘weights’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘extracat’ ‘scales’ ‘seriation’ ‘ggplot2’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spsurvey’
Error in re-building vignettes:
  ...
Quitting from lines 187-200 (MBHdesign.Rnw) 
Error: processing vignette ‘MBHdesign.Rnw’ failed with diagnostics:
there is no package called 'spsurvey'
Execution halted
Package suggested but not available for checking: ‘BayesX’
Packages required but not available: ‘ecr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘mosaic’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 50-60 (advanced.Rmd) 
Error: processing vignette ‘advanced.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 61-67 (cost-report-analysis.Rmd) 
Error: processing vignette ‘cost-report-analysis.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘Hmisc’

Depends: includes the non-default packages:
  ‘seqinr’ ‘pcaMethods’ ‘Matrix’ ‘ROCR’ ‘Hmisc’ ‘KernSmooth’ ‘seqLogo’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘scales’ ‘ggmap’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggthemes’ ‘ggplot2’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘cowplot’ ‘ggimage’ ‘shadowtext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘cowplot’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: codomToPropShared
> ### Title: Find proportion of shared alleles genetic distances from a
> ###   codominant alleles matrix
> ### Aliases: codomToPropShared
> 
> ### ** Examples
> 
> 
> radialData <- read.csv(system.file("extdata/radial.csv", package="memgene"))
> radialGen <- radialData[, -c(1,2)]
> radialDM <- codomToPropShared(radialGen)
Loading required package: adegenet
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘adegenet’
Error: memgene:  Please install the adegenet package to find the proportion of shared alleles
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 21-30 (memgeneTutorial.Rnw) 
Error: processing vignette ‘memgeneTutorial.Rnw’ failed with diagnostics:
there is no package called 'adegenet'
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘rstanarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘scales’ ‘ggfittext’ ‘ggrepel’ ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘edarf’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘preprocomb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘HTSFilter’ ‘DESeq2’
Error in re-building vignettes:
  ...

Error: processing vignette ‘metaRNASeq.Rnw’ failed with diagnostics:
 chunk 2 (label = loadparameters) 
Error in library(DESeq2) : there is no package called ‘DESeq2’
Execution halted
Package suggested but not available for checking: ‘semPlot’
Running examples in ‘MetaSubtract-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: meta.subtract
> ### Title: Subtracts GWAS results from one or more cohorts from the
> ###   meta-GWAS results
> ### Aliases: meta.subtract
> ### Keywords: Correct meta-GWAS results Leave-one-out
> 
> ### ** Examples
> 
> metafile="meta_results.txt"
> cohortfiles=c("cohort1_results.txt","cohort2_results.txt")
> # Subtract summary statistics of the two cohorts from the meta summary statistics in metafile.
> # Genomic control correction of the imported meta summary statistics will be undone using 
> # lambda.meta. Genomic control will be applied to the corrected meta summary statistics 
> # (gc_meta=TRUE by default) based on a lambda derived from the new meta summary statistics 
> # (calculate_lambda.meta=TRUE by default). The cohorts summary statistics will always be first 
> # corrected for genomic control before subtracting them from the meta summary statistics. By 
> # default, the lambda will be calculated from the data (calculate_lambdas.cohort=TRUE by default).
> m1<-meta.subtract(metafile=metafile, cohortfiles=cohortfiles, lambda.meta=1.046, 
+       dir=system.file("extdata", package="MetaSubtract"))
[1] "Thu Jan 11 04:40:06 2018"
Reading meta_results.txt 
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'MetaSubtract.log': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: meta.subtract -> write.table -> file
Execution halted
Packages required but not available: ‘nullabor’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘geiger’ ‘spacodiR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘RTisean’ ‘tsDyn’ ‘forecast’
Package suggested but not available for checking: ‘structSSI’
Package suggested but not available for checking: ‘VIM’
Package suggested but not available for checking: ‘MVN’
Running examples in ‘micompr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
MANOVA assumptions require 'MVN' and 'biotools' packages.
Error in `*tmp*`[[i]] : subscript out of bounds
Calls: assumptions -> assumptions.cmpoutput
Execution halted
Running ‘testthat.R’ [16s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright (c) 2016 Nuno Fachada
  > # Distributed under the MIT License (http://opensource.org/licenses/MIT)
  > 
  > library(testthat)
  > 
  > test_check("micompr")
  Loading required package: micompr
  ── 1. Error: assumptions.cmpoutput creates the correct object (@test_cmpoutput.R
  subscript out of bounds
  1: assumptions(cmp) at testthat/test_cmpoutput.R:214
  2: assumptions.cmpoutput(cmp)
  
  ── 2. Error: micomp assumptions have the correct properties (@test_micomp.R#281)
  subscript out of bounds
  1: assumptions(mic1a) at testthat/test_micomp.R:281
  2: assumptions.micomp(mic1a)
  3: lapply(obj, function(x) assumptions(x))
  4: FUN(X[[i]], ...)
  5: assumptions(x)
  6: assumptions.cmpoutput(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 363 SKIPPED: 0 FAILED: 2
  1. Error: assumptions.cmpoutput creates the correct object (@test_cmpoutput.R#214) 
  2. Error: micomp assumptions have the correct properties (@test_micomp.R#281) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 341-342 (paper.Rnw) 
Error: processing vignette ‘paper.Rnw’ failed with diagnostics:
subscript out of bounds
Execution halted
Running examples in ‘micropan-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bDist
> ### Title: Computes distances between sequences based on BLAST results
> ### Aliases: bDist
> 
> ### ** Examples
> 
> # Using BLAST result files in this package...
> # We need to uncompress them first:
> extdata.path <- file.path(path.package("micropan"),"extdata")
> filenames <- c("GID1_vs_GID1.txt",
+ "GID1_vs_GID2.txt",
+ "GID1_vs_GID3.txt",
+ "GID2_vs_GID1.txt",
+ "GID2_vs_GID2.txt",
+ "GID2_vs_GID3.txt",
+ "GID3_vs_GID1.txt",
+ "GID3_vs_GID2.txt",
+ "GID3_vs_GID3.txt")
> pth <- lapply( file.path( extdata.path, paste( filenames, ".xz", sep="" ) ), xzuncompress )
Warning in file(destname, open = "wb") :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/micropan/extdata/GID1_vs_GID1.txt': Read-only file system
Error in file(destname, open = "wb") : cannot open the connection
Calls: lapply -> FUN -> file
Execution halted
Packages required but not available: ‘Hmisc’ ‘HH’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Use the user-defined lambda vector.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 3.6867.
The penalty term is selected automatically with 50 candidates.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 4.9895.
The penalty term is selected automatically with 50 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 2.4657.
trying URL ‘http://www.cs.columbia.edu/~andrews/mil/data/MIL-Data-2002-Musk-Corel-Trec9.tgz’
Content type 'application/x-gzip' length 6249673 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

Warning in fread("MilData/Musk/musk1norm.svm", header = FALSE) :
  Starting data input on line 2 and discarding line 1 because it has too few or too many items to be column names or data: # Generated by musk_2_svm(/pro/webagents/stu/mil//experiments/musk//data/clean1.data, /pro/webagents/stu/mil//experiments/musk//generate_data/clean1.svm)
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Quitting from lines 634-643 (milr-intro.Rmd) 
Error: processing vignette ‘milr-intro.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘dendextend’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mixAK’
Packages required but not available: ‘ggplot2’ ‘GGally’

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘DoE.base’ ‘FrF2’ ‘ggplot2’
Package required but not available: ‘daewr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘mixOmics’ ‘ggplot2’ ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Package 'mclust' version 5.4
Type 'citation("mclust")' for citing this R package in publications.
mixpack: a package for mixture components analysis
Quitting from lines 17-21 (mixture_components.Rmd) 
Error: processing vignette ‘mixture_components.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggmcmc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘pitchRx’ ‘viridis’ ‘ggplot2’ ‘plotly’
Error in re-building vignettes:
  ...
Quitting from lines 39-46 (pitch_plotting.Rmd) 
Error: processing vignette ‘pitch_plotting.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘mldr’
Package required but not available: ‘circlize’

Package suggested but not available for checking: ‘pROC’

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

Packages suggested but not available for checking:
  ‘cmaesr’ ‘ggplot2’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘adabag’ ‘caret’ ‘Hmisc’ ‘mldr’ ‘mlrMBO’ ‘pROC’ ‘rrlda’ ‘smoof’
  ‘sparsediscrim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘colorspace’ ‘dynsurv’
Error in re-building vignettes:
  ...
Loading required package: basefun
Loading required package: variables
Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/

Attaching package: 'flexsurv'

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

    Hgompertz, Hllogis, Hlnorm, Hweibull, dgompertz, dllogis,
    hgompertz, hllogis, hlnorm, hweibull, pgompertz, pllogis,
    qgompertz, qllogis, rgompertz, rllogis


Attaching package: 'grid'

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

    unit

Loading required package: RColorBrewer
Quitting from lines 22-63 (mlt.Rnw) 
Error: processing vignette ‘mlt.Rnw’ failed with diagnostics:
there is no package called 'colorspace'
Execution halted
Packages required but not available: ‘adegenet’ ‘pegas’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 304-389 (modcmfitrOverview.Rmd) 
Error: processing vignette ‘modcmfitrOverview.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘ModelGood-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AutoSelectLRM
> ### Title: Automated backward elemination for logistic regression
> ### Aliases: AutoSelectLRM
> 
> ### ** Examples
> 
> library(rms)
Error in library(rms) : there is no package called ‘rms’
Execution halted
Package required but not available: ‘mapedit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘smoof’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 106-114 (Basic_Usage.Rmd) 
Error: processing vignette ‘Basic_Usage.Rmd’ failed with diagnostics:
there is no package called 'smoof'
Execution halted
Package required but not available: ‘alphahull’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggmap’ ‘ggplot2’ ‘moveHMM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘geomorph’ ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spacodiR’
Running ‘testthat.R’ [4s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("MonoPhy")
  Loading required package: MonoPhy
  Loading required package: ape
  Loading required package: phytools
  Loading required package: maps
  Loading required package: phangorn
  Loading required package: RColorBrewer
  Loading required package: taxize
  ── 1. Error: Multifurcating solution1 is accurate (@test_solutions.R#38)  ──────
  there is no package called 'spacodiR'
  1: library(spacodiR) at testthat/test_solutions.R:38
  2: stop(txt, domain = NA)
  
  ── 2. Error: Multifurcating solution2 is accurate (@test_solutions.R#75)  ──────
  there is no package called 'spacodiR'
  1: library(spacodiR) at testthat/test_solutions.R:75
  2: stop(txt, domain = NA)
  
  ── 3. Error: Multifurcating solution3 is accurate (@test_solutions.R#112)  ─────
  there is no package called 'spacodiR'
  1: library(spacodiR) at testthat/test_solutions.R:112
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 24 SKIPPED: 0 FAILED: 3
  1. Error: Multifurcating solution1 is accurate (@test_solutions.R#38) 
  2. Error: Multifurcating solution2 is accurate (@test_solutions.R#75) 
  3. Error: Multifurcating solution3 is accurate (@test_solutions.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘moonBook-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ORplot
> ### Title: Plot for odds ratios for a S3 object of glm
> ### Aliases: ORplot
> 
> ### ** Examples
> 
> require(survival)
Loading required package: survival
> data(colon)
> out1=glm(status~sex+age+rx+obstruct+node4,data=colon)
> out2=glm(status~rx+node4,data=colon)
> ORplot(out1,type=2,show.CI=TRUE,xlab="This is xlab",main="Main Title")
Error in confint.glm(x) : package 'MASS' must be installed
Calls: ORplot ... suppressMessages -> withCallingHandlers -> confint -> confint.glm
Execution halted
Error in re-building vignettes:
  ...
Loading required package: bitops
Quitting from lines 17-19 (mortAAR_vignette-1.Rmd) 
Error: processing vignette ‘mortAAR_vignette-1.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
Packages suggested but not available for checking: ‘mosaic’ ‘ggformula’
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mosaicCore)
  > 
  > test_check("mosaicCore")
  ── 1. Error: favstats works (@test-df-stats.R#6)  ──────────────────────────────
  there is no package called 'mosaic'
  1: expect_equivalent(df_stats(~cesd, data = mosaicData::HELPmiss), mosaic::favstats(~cesd, 
         data = mosaicData::HELPmiss)) at testthat/test-df-stats.R:6
  2: quasi_label(enquo(expected), expected.label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: mosaic::favstats
  5: getExportedValue(pkg, name)
  6: asNamespace(ns)
  7: getNamespace(ns)
  8: tryCatch(loadNamespace(name), error = function(e) stop(e))
  9: tryCatchList(expr, classes, parentenv, handlers)
  10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  11: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 21 SKIPPED: 0 FAILED: 1
  1. Error: favstats works (@test-df-stats.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking: ‘mosaic’ ‘ggplot2’
Running examples in ‘mosaicData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SnowGR
> ### Title: Snowfall data for Grand Rapids, MI
> ### Aliases: SnowGR
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(SnowGR)
> if (require(mosaic)) {
+   favstats(SnowGR$Total)
+   histogram(~Total, data=SnowGR)
+   xyplot(Total ~ SeasonStart, SnowGR, type=c('p','smooth'))
+ }
Loading required package: mosaic
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mosaic’
> if (require(reshape2)) {
+   Snow2 <- melt(SnowGR, id=1:2)
+   names(Snow2)[3:4] <- c('Time','Snow')
+   bwplot(Snow ~ Time, Snow2)
+ }
Loading required package: reshape2
Error in bwplot(Snow ~ Time, Snow2) : could not find function "bwplot"
Execution halted
Packages required but not available:
  ‘caret’ ‘ggplot2’ ‘ggformula’ ‘tidyverse’

Package suggested but not available for checking: ‘mosaic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggformula’ ‘ggplot2’ ‘ggdendro’

Packages suggested but not available for checking: ‘fastR’ ‘vcd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggmap’
Error in re-building vignettes:
  ...
Loading required package: geosphere
Loading required package: sp
Loading required package: raster
Loading required package: rgdal
rgdal: version: 1.2-16, (SVN revision 701)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: /usr/share/gdal/2.2
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-6 
Warning in .local(x, y, time, data, proj, ...) :
  There were NA locations detected and omitted. Currently they are not stored in unusedrecords
Loading required package: ggmap
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggmap’
Loading required package: mapproj
Loading required package: maps

Error: processing vignette ‘move.Rnw’ failed with diagnostics:
 chunk 15 (label = googleplot) 
Error in ggmap(m) : could not find function "ggmap"
Execution halted
Packages required but not available: ‘ggplot2’ ‘RStoolbox’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘vcd’ ‘colorspace’ ‘corpus.useR.2008.abstracts’
Error in re-building vignettes:
  ...

Error: processing vignette ‘movMF.Rnw’ failed with diagnostics:
 chunk 1 
Error in loadNamespace(name) : there is no package called 'colorspace'
Execution halted
Packages required but not available: ‘ggplot2’ ‘scales’

Package suggested but not available for checking: ‘mvoutlier’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘leaflet’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘hydroPSO’

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

Depends: includes the non-default packages:
  ‘amap’ ‘clValid’ ‘cluster’ ‘fpc’ ‘mzR’ ‘xcms’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

Package suggested but not available for checking: ‘xcms’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: canabalt
> ### Title: The scores of the game Canabalt from Twitter
> ### Aliases: canabalt
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘forecast’ ‘Rssa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 121-130 (SIR-MCMC.Rmd) 
Error: processing vignette ‘SIR-MCMC.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ComplexHeatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘cplm’
Running examples in ‘musica-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compare
> ### Title: Compare decomposed variables
> ### Aliases: compare
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 17-20 (using_musica.Rmd) 
Error: processing vignette ‘using_musica.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘mutoss-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Qvalue
> ### Title: Storey's (2001) q-value Procedure...
> ### Aliases: Qvalue
> 
> ### ** Examples
> pval <- c(runif(50), runif(50, 0, 0.01))
> result <- Qvalue(pval)
Loading required package: qvalue
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘qvalue’
Package qvalue is required - should we install it?
Error in requireLibrary("qvalue") : 
  Required package qvalue should not be installed
Calls: Qvalue -> requireLibrary
Execution halted
Package required but not available: ‘rattle’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 31-43 (mvtboost_vignette.Rmd) 
Error: processing vignette ‘mvtboost_vignette.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘mwaved-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multiWaveD
> ### Title: Full mWaveD analysis
> ### Aliases: multiWaveD
> 
> ### ** Examples
> 
> library(mwaved)
> # Simulate the multichannel doppler signal.
> m <- 3
> n <- 2^10
> signal <- makeDoppler(n)
> # Noise levels per channel
> e <- rnorm(m * n)
> # Create Gamma blur
> shape <- seq(from = 0.5, to = 1, length = m)
> scale <- rep(0.25, m)
> G <- gammaBlur(n, shape = shape, scale = scale)
> # Convolve the signal
> X <- blurSignal(signal, G)
> # Create error with custom signal to noise ratio
> SNR <- c(10, 15, 20)
> sigma <- sigmaSNR(X, SNR)
> if (requireNamespace("fracdiff", quietly = TRUE)) {
+   alpha <- c(0.75, 0.8, 1)
+ } else {
+   alpha <- rep(1, m)
+ }
> E <- multiNoise(n, sigma, alpha)
> # Create noisy & blurred multichannel signal
> Y <- X + E
> # Compute mWaveD object
> mWaveDObj <- multiWaveD(Y, G = G, alpha = alpha)
> plot(mWaveDObj)
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: plot ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 14-53 (mWaveD.Rmd) 
Error: processing vignette ‘mWaveD.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘visdat’ ‘viridis’

Packages suggested but not available for checking: ‘wakefield’ ‘imputeTS’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘rstanarm’ ‘lmerTest’ ‘rstan’ ‘bayesplot’ ‘shinystan’

Package suggested but not available for checking: ‘afex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘openVA’
Package required but not available: ‘JBTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘heatmaply’ ‘ggplot2’ ‘dendextend’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_rank_intervals
> ### Title: Plot rank intervals
> ### Aliases: plot_rank_intervals
> 
> ### ** Examples
> 
> library(igraph)

Attaching package: ‘igraph’

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

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Quitting from lines 70-71 (partial_centrality.Rmd) 
Error: processing vignette ‘partial_centrality.Rmd’ failed with diagnostics:
ggplot2 needed for this function to work. Please install it.
Execution halted
Package required but not available: ‘WGCNA’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘qgraph’ ‘IsingFit’ ‘ggplot2’ ‘NetworkComparisonTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 11-19 (nifti_basics.Rmd) 
Error: processing vignette ‘nifti_basics.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘tidyverse’ ‘ggplot2’ ‘ggcorrplot’ ‘Hmisc’ ‘caret’

Package suggested but not available for checking: ‘lmerTest’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: download_nv_atlas
> ### Title: Download Neurovault Atlas and Label file
> ### Aliases: download_nv_atlas
> 
> ### ** Examples
> 
> res = download_nv_atlas(id = 1408)
GET command is:
Response [https://neurovault.org/api/atlases/1408/]
  Date: 2018-01-11 06:09
  Status: 200
  Content-Type: application/json; charset=utf-8
  Size: 751 B


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Unrecognized content encoding type. libcurl understands deflate, gzip content encodings.
Calls: download_nv_atlas ... request_fetch -> request_fetch.write_disk -> <Anonymous> -> .Call
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘NFPdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggthemes’ ‘ggplot2’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rstan’ ‘ggplot2’
Packages which this enhances but not available for checking:
  ‘jpndistrict’ ‘jpmesh’
Error in re-building vignettes:
  ...
This is lavaan 0.5-23.1097
lavaan is BETA software! Please report any bugs.
Quitting from lines 310-312 (NlsyAce.Rnw) 
Error: processing vignette ‘NlsyAce.Rnw’ failed with diagnostics:
there is no package called 'scales'
Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘Hmisc’ ‘TreeSim’
Running examples in ‘nLTT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_nltt_values
> ### Title: Collects the nLTT values of all phylogenies in the
> ###   melted/uncast/long form
> ### Aliases: get_nltt_values
> 
> ### ** Examples
> 
>   library(ape)
>   library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 62-67 (vignette_get_nltt_values.Rmd) 
Error: processing vignette ‘vignette_get_nltt_values.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘d3heatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘colorspace’ ‘ggplot2’

Package suggested but not available for checking: ‘RcppOctave’

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

Package suggested but not available for checking: ‘thief’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘choroplethr’ ‘ggplot2’ ‘hurricaneexposure’ ‘viridis’

Package suggested but not available for checking: ‘hurricaneexposuredata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘xpose4’

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

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.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘plotly’ ‘ggplot2’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘pheatmap’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘scales’ ‘ggthemes’ ‘GGally’
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 28-36 (observer-vignette.Rmd) 
Error: processing vignette ‘observer-vignette.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘marmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘marmap’
Packages required but not available: ‘ggplot2’ ‘cowplot’

Package suggested but not available for checking: ‘scales’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CDA2ODM
> ### Title: CDA2ODM
> ### Aliases: CDA2ODM
> ### Keywords: ODM
> 
> ### ** Examples
> 
> CDA2ODM(CDAfile=file.path(path.package("ODMconverter"),"extdata","CDA_letter_basic.xml"))
[1] "Generating /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/ODMconverter/extdata/CDA_letter_basic.xml.odm.xml"
Warning in file(file, if (append) "a" else "w") :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/ODMconverter/extdata/CDA_letter_basic.xml.odm.xml': Read-only file system
Error in file(file, if (append) "a" else "w") : 
  cannot open the connection
Calls: CDA2ODM -> sink -> file
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 119-127 (oecd_vignette_main.Rmd) 
Error: processing vignette ‘oecd_vignette_main.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘caret’ ‘scales’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘colorspace’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘InSilicoVA’ ‘ggplot2’

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [22s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  ── 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ────
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: nlme
This is mgcv 1.8-22. For overview type 'help("mgcv-package")'.
Quitting from lines 92-96 (opera-vignette.Rmd) 
Error: processing vignette ‘opera-vignette.Rmd’ failed with diagnostics:
there is no package called 'caret'
Execution halted
Package required but not available: ‘DepthProc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optimus)
  This is optimus 0.1.0, roll out!
  > 
  > test_check("optimus")
  ── 1. Error: find_optimal() stops with wrong data or arguments (@test-find_optim
  argument "quo" is missing, with no default
  1: expect_error(expr = optimus::find_optimal(data = mixed, clustering = counts_cutree, 
         family = "poisson"), message = "some.*") at testthat/test-find_optimal.R:38
  2: quasi_capture(enquo(object), capture_error, label = label)
  3: label %||% quo_label(quo)
  4: quo_label(quo)
  5: expr_label(quo_expr(quo))
  6: quo_expr(quo)
  7: quo_splice(duplicate(quo), warn = warn)
  8: switch_expr(x, language = {
         if (is_quosure(x)) {
             if (!is_false(warn)) {
                 if (is_string(warn)) {
                     msg <- warn
                 }
                 else {
                     msg <- "Collapsing inner quosure"
                 }
                 warn(msg)
                 warn <- FALSE
             }
             while (is_quosure(x)) {
                 x <- f_rhs(x)
             }
             if (!is_null(parent)) {
                 mut_node_car(parent, x)
             }
             quo_splice(x, parent, warn = warn)
         }
         else {
             quo_splice(node_cdr(x), warn = warn)
         }
     }, pairlist = {
         while (!is_null(x)) {
             quo_splice(node_car(x), x, warn = warn)
             x <- node_cdr(x)
         }
     })
  9: expr_type_of(.x)
  10: typeof(x)
  11: duplicate(quo)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 5 SKIPPED: 0 FAILED: 1
  1. Error: find_optimal() stops with wrong data or arguments (@test-find_optimal.R#38) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in kinship2::pedigree(id = Pedig$Indiv, dadid = Pedig$Sire, momid = Pedig$Dam,  :
  More than 25% of the gender values are 'unknown'
Quitting from lines 119-122 (ped-vignette.Rmd) 
Error: processing vignette ‘ped-vignette.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘VineCopula’ ‘tea’ ‘vcd’

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

Package suggested but not available for checking: ‘prefmod’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘caret’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 84-103 (ordinalClust.Rmd) 
Error: processing vignette ‘ordinalClust.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggthemes’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [19s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(origami)
  > 
  > test_check("origami")
  ── 1. Error: (unknown) (@test_overall_ts.R#2)  ─────────────────────────────────
  there is no package called 'forecast'
  1: library(forecast) at testthat/test_overall_ts.R:2
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 22 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_overall_ts.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 256-288 (generalizedCV.Rmd) 
Error: processing vignette ‘generalizedCV.Rmd’ failed with diagnostics:
there is no package called 'forecast'
Execution halted
Package required but not available: ‘OpenStreetMap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: knitcitations
Loading required package: OSTSC
Loading required package: keras
Loading required package: dummies
dummies-1.5.6 provided by Decision Patterns

Loading required package: pROC
Quitting from lines 518-526 (Over_Sampling_for_Time_Series_Classification.Rmd) 
Error: processing vignette ‘Over_Sampling_for_Time_Series_Classification.Rmd’ failed with diagnostics:
there is no package called 'pROC'
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggmap’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘cellWise’ ‘GGally’

Package suggested but not available for checking: ‘mbgraphic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘genealogicalSorting’ ‘phybase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggiraph’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 98-112 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘VineCopula’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggrepel’

Package suggested but not available for checking: ‘NMF’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: center_interval
> ### Title: Shift to the middle of each interval
> ### Aliases: center_interval
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 27-36 (padr.Rmd) 
Error: processing vignette ‘padr.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘pagenum-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pagenum
> ### Title: Put Page Numbers on Graphics
> ### Aliases: pagenum setPagenum getPagenum setPagenum getPagenum
> 
> ### ** Examples
> 
> # base graphics
> setPagenum(1)
> plot(Sepal.Length~Sepal.Width, data=iris, col=Species, pch=19)
> pagenum()
> 
> # lattice, date
> setPagenum(getPagenum()+1) # Manual increment
> require(lattice)
Loading required package: lattice
> xyplot(Sepal.Length~Sepal.Width, data=iris, groups=Species)
> pagenum(date=TRUE)
> 
> # ggplot2, top-right
> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> ggplot(iris, aes(x=Sepal.Width, y=Sepal.Length,
+   color=Species)) + geom_point() + theme_classic()
Error in ggplot(iris, aes(x = Sepal.Width, y = Sepal.Length, color = Species)) : 
  could not find function "ggplot"
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pagenum)
  > 
  > test_check("pagenum")
  ── 1. Error: (unknown) (@test_pagenum.R#17)  ───────────────────────────────────
  could not find function "ggplot"
  1: .handleSimpleError(function (e) 
     {
         handled <<- TRUE
         test_error <<- e
         options(expressions = expressions_opt_new)
         on.exit(options(expressions = expressions_opt), add = TRUE)
         e$expectation_calls <- frame_calls(11, 2)
         test_error <<- e
         register_expectation(e)
         e$handled <- TRUE
         test_error <<- e
     }, "could not find function \"ggplot\"", quote(ggplot(iris, aes(x = Sepal.Width, 
         y = Sepal.Length, color = Species)))) at testthat/test_pagenum.R:17
  2: eval(code, test_env)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_pagenum.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 74-79 (pagenum_examples.Rmd) 
Error: processing vignette ‘pagenum_examples.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘mcprofile’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_colour_poke
> ### Title: Add a pokemon palette to a ggplot2 colour or fill scale.
> ### Aliases: scale_color_poke scale_colour_poke scale_fill_poke
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘lmerTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘tables’ ‘rms’ ‘forecast’
Error in re-building vignettes:
  ...
Quitting from lines 13-18 (pander.Rmd) 
Error: processing vignette ‘pander.Rmd’ failed with diagnostics:
there is no package called 'tables'
Execution halted
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’

Error: processing vignette ‘parallelDist.Rnw’ failed with diagnostics:
 chunk 2 (label = performanceDtw) 
Error in ggplot(data = comparison, aes(x = expr, y = min, group = method,  : 
  could not find function "ggplot"
Execution halted
Package suggested but not available for checking: ‘pcalg’
Running examples in ‘ParallelPC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IDA_parallel
> ### Title: Estimate Total Causal Effects using the IDA_parallel Algorithm
> ### Aliases: IDA_parallel
> 
> ### ** Examples
> 
> ##########################################
> ## Using IDA_parallel without mem.efficeient
> ##########################################
> library(bnlearn)

Attaching package: ‘bnlearn’

The following object is masked from ‘package:stats’:

    sigma

> library(pcalg)
Error in library(pcalg) : there is no package called ‘pcalg’
Execution halted
Packages required but not available: ‘TIMP’ ‘colorspace’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘GGally’ ‘ggplot2’
Running ‘run-all.R’ [11s/14s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > library(BBmisc)
  > library(ParamHelpers)
  > 
  > test_check("ParamHelpers")
  ── 1. Error: plotYTrace works (@test_plotYTrace.R#28)  ─────────────────────────
  there is no package called 'ggplot2'
  1: renderYTraces(opt.paths, over.time = "dob") at testthat/test_plotYTrace.R:28
  2: ggplot2::ggplot
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  ── 2. Error: renderOptPathPlot (@test_renderOptPathPlot.R#19)  ─────────────────
  For renderOptPathPlot please install the following packages: GGally,ggplot2
  1: renderOptPathPlot(op0, iter = 0, alpha = FALSE) at testthat/test_renderOptPathPlot.R:19
  2: requirePackages(c("GGally", "ggplot2"), why = "renderOptPathPlot", default.method = "load")
  3: stopf("For %s please install the following packages: %s", why, ps)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1022 SKIPPED: 1 FAILED: 2
  1. Error: plotYTrace works (@test_plotYTrace.R#28) 
  2. Error: renderOptPathPlot (@test_renderOptPathPlot.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 26-34 (Simulating-Power.Rmd) 
Error: processing vignette ‘Simulating-Power.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘leaflet’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 67-110 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 97-113 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘parSim-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: parSim
> ### Title: Parallel Simulator
> ### Aliases: parSim parSim-package
> 
> ### ** Examples
> 
> # Some function we might use:
> bias <- function(x,y){abs(x-y)}
> 
> # Run the simulation:
> Results <- parSim(
+   # Any number of conditions:
+   sampleSize = c(50, 100, 250),
+   beta = c(0, 0.5, 1),
+   sigma = c(0.25, 0.5, 1),
+   
+   # Number of repititions?
+   reps = 25, # more is better!
+   
+   # Parallel?
+   nCores = 1,
+   
+   # Write to file?
+   write = FALSE,
+   
+   # Export objects (only needed when nCores > 1):
+   export = c("bias"),
+   
+   # R expression:
+   expression = {
+     # Load all R packages in the expression if needed
+     # library(...)
+     
+     # Want to debug? Enter browser() and run the function. Only works with nCores = 1!
+     # browser()
+     
+     # Enter whatever codes you want. I can use the conditions as objects.
+     X <- rnorm(sampleSize)
+     Y <- beta * X + rnorm(sampleSize, sigma)
+     fit <- lm(Y ~ X)
+     betaEst <- coef(fit)[2]
+     Rsquared <- summary(fit)$r.squared
+     
+     # Make a data frame with one row to return results (multple rows is 
+     # also possible but not reccomended):
+     data.frame(
+       betaEst = betaEst,
+       bias = bias(beta,betaEst),
+       Rsquared = Rsquared
+     )
+   }
+ )
> 
> # Analyze the results:
> library("ggplot2")
Error in library("ggplot2") : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘egcm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘partialAR’ ‘ggplot2’

Package suggested but not available for checking: ‘egcm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Errors in running code in vignettes:
when running code in ‘mob.Rnw’
  ...

> library("partykit")
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Loading required package: rpart

> options(prompt = "R> ", continue = "+  ", digits = 4, 
+     useFancyQuotes = FALSE)

> data("PimaIndiansDiabetes", package = "mlbench")

> pid_formula <- diabetes ~ glucose | pregnant + pressure + 
+     triceps + insulin + mass + pedigree + age

> logit <- function(y, x, start = NULL, weights = NULL, 
+     offset = NULL, ...) {
+     glm(y ~ 0 + x, family = binomial, start = start, ...)
+ }

> pid_tree <- mob(pid_formula, data = PimaIndiansDiabetes, 
+     fit = logit)

> pid_tree
Model-based recursive partitioning (logit)

Model formula:
diabetes ~ glucose | pregnant + pressure + triceps + insulin + 
    mass + pedigree + age

Fitted party:
[1] root
|   [2] mass <= 26.3: n = 167
|       x(Intercept)     xglucose 
|           -9.95151      0.05871 
|   [3] mass > 26.3
|   |   [4] age <= 30: n = 304
|   |       x(Intercept)     xglucose 
|   |           -6.70559      0.04684 
|   |   [5] age > 30: n = 297
|   |       x(Intercept)     xglucose 
|   |           -2.77095      0.02354 

Number of inner nodes:    2
Number of terminal nodes: 3
Number of parameters per node: 2
Objective function: 355.5

> pid_tree2 <- glmtree(diabetes ~ glucose | pregnant + 
+     pressure + triceps + insulin + mass + pedigree + age, data = PimaIndiansDiabetes, 
+     .... [TRUNCATED] 

> plot(pid_tree)

> plot(pid_tree2, tp_args = list(ylines = 1, margins = c(1.5, 
+     1.5, 1.5, 2.5)))
Loading required namespace: vcd
Failed with error:  'there is no package called 'vcd''

  When sourcing 'mob.R':
Error: Package 'vcd' is required for spine/CD plots
Execution halted
Error in re-building vignettes:
  ...
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Loading required package: rpart
Loading required package: RWeka
Loading required namespace: XML
Loading required package: XML

Attaching package: ‘XML’

The following object is masked from ‘package:tools’:

    toHTML

Loading required package: coin
Loading required package: survival
Loading required package: strucchange
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: Formula
Loading required package: modeltools
Loading required package: stats4

Attaching package: ‘party’

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

    cforest, ctree, ctree_control, edge_simple, mob,
    mob_control, node_barplot, node_bivplot, node_boxplot,
    node_inner, node_surv, node_terminal, varimp

Loading required namespace: vcd
Failed with error:  'there is no package called 'vcd''

Error: processing vignette ‘mob.Rnw’ failed with diagnostics:
 chunk 9 (label = PimaIndiansDiabetes-plot2) 
Error in terminal_panel(structure(list(node = structure(list(id = 1L,  : 
  Package 'vcd' is required for spine/CD plots
Execution halted
Packages suggested but not available for checking: ‘colorspace’ ‘vcd’
Error in re-building vignettes:
  ...
Loading required package: party
Loading required package: grid
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
Loading required package: strucchange
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: sandwich

Error: processing vignette ‘MOB.Rnw’ failed with diagnostics:
 chunk 19 (label = PimaIndiansDiabetes-plot) 
Error in terminal_panel(<S4 object of class structure("mob", package = "party")>) : 
  the `vcd' package is required for CD plots
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘tidyverse’
Error in re-building vignettes:
  ...
Quitting from lines 32-39 (passport.Rmd) 
Error: processing vignette ‘passport.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
Running examples in ‘PBImisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flu
> ### Title: Numbers of flu occurences in the 10 years period in the Poland.
> ### Aliases: flu
> ### Keywords: flu
> 
> ### ** Examples
> 
> data(flu)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘qvalue’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘phylosim’

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

Package suggested but not available for checking: ‘drc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘strvalidator’ ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘viridis’

Packages suggested but not available for checking: ‘adabag’ ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 734-750 (PDQutils.Rnw) 
Error: processing vignette ‘PDQutils.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘coefplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘viridis’ ‘ggthemes’
Running examples in ‘PeakError-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PeakError
> ### Title: PeakError
> ### Aliases: PeakError
> 
> ### ** Examples
> 
> x <- seq(5, 85, by=5)
> peaks <- rbind(Peaks("chr2", x, x+3),
+                Peaks("chr3", c(25, 38, 57), c(33, 54, 75)),
+                Peaks("chr4", c(5, 32, 38, 65), c(15, 35, 55, 85)),
+                Peaks("chr5", c(12, 26, 56, 75), c(16, 54, 59, 85)))
> regions <- NULL
> for(chr in 1:5){
+   regions <- rbind(regions, {
+     data.frame(chrom=paste0("chr", chr),
+                chromStart=c(10, 30, 50, 70),
+                chromEnd=c(20, 40, 60, 80),
+                annotation=c("noPeaks", "peakStart", "peakEnd", "peaks"))
+   })
+ }
> err <- PeakError(peaks, regions)
> ann.colors <-
+   c(noPeaks="#f6f4bf",
+     peakStart="#ffafaf",
+     peakEnd="#ff4c4c",
+     peaks="#a445ee")
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘penaltyLearning’
Running examples in ‘PeakSegDP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chr11ChIPseq
> ### Title: ChIP-seq aligned read coverage for 4 samples on a subset of
> ###   chr11
> ### Aliases: chr11ChIPseq
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(chr11ChIPseq)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘penaltyLearning’

Package suggested but not available for checking: ‘ggplot2’

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

Packages suggested but not available for checking: ‘riskRegression’ ‘Hmisc’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: detect
> ### Title: Detection probability in a single library of size N
> ### Aliases: detect
> 
> ### ** Examples
> 
> summary(detect())
    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
0.003628 0.061622 0.242643 0.360004 0.602151 0.999647 
> 
> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> lib <- libscheme("NNK", 7)
> qplot(detect(lib, size=10^8), weight=di, geom="histogram", data=lib$data)
Error in qplot(detect(lib, size = 10^8), weight = di, geom = "histogram",  : 
  could not find function "qplot"
Execution halted
Packages required but not available: ‘tidyverse’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'library' or 'require' calls in package code:
  ‘MASS’ ‘gamlss’ ‘quantreg’ ‘robustbase’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in ‘PerformanceAnalytics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Omega
> ### Title: calculate Omega for a return series
> ### Aliases: Omega
> 
> ### ** Examples
> 
> data(edhec)
>     Omega(edhec)
               Convertible Arbitrage CTA Global Distressed Securities
Omega (L = 0%)              2.602138   1.936841              3.230443
               Emerging Markets Equity Market Neutral Event Driven
Omega (L = 0%)         1.765435              6.213714     2.999655
               Fixed Income Arbitrage Global Macro Long/Short Equity
Omega (L = 0%)               2.585943     3.516616          2.438064
               Merger Arbitrage Relative Value Short Selling Funds of Funds
Omega (L = 0%)         4.595886       3.815368      1.228785       2.460153
>     Omega(edhec[,13],method="interp",output="point")
Error in loadNamespace(name) : there is no package called ‘Hmisc’
Calls: Omega ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Loading required package: xts
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric


Attaching package: ‘PerformanceAnalytics’

The following object is masked from ‘package:graphics’:

    legend

Warning in z + c(-1, 1) * sigma * qnorm((1 + conf.level)/2) :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in z + c(-1, 1) * sigma * qnorm((1 + conf.level)/2) :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in z + c(-1, 1) * sigma * qnorm((1 + conf.level)/2) :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in z + c(-1, 1) * sigma * qnorm((1 + conf.level)/2) :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in z + c(-1, 1) * sigma * qnorm((1 + conf.level)/2) :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in z + c(-1, 1) * sigma * qnorm((1 + conf.level)/2) :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.


Attaching package: ‘gplots’

The following object is masked from ‘package:PerformanceAnalytics’:

    textplot

The following object is masked from ‘package:stats’:

    lowess


Error: processing vignette ‘textplotPresentation-CRUG-2011.Rnw’ failed with diagnostics:
 chunk 5 (label = Hmiscformat) 
Error in library(Hmisc) : there is no package called ‘Hmisc’
Execution halted
Package required but not available: ‘seriation’

Packages suggested but not available for checking:
  ‘dendextend’ ‘dendextendRcpp’

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

Packages suggested but not available for checking:
  ‘ggspectra’ ‘ggplot2’ ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggspectra’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 25-30 (data-catalogue.Rmd) 
Error: processing vignette ‘data-catalogue.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘photobiologyLEDs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: leds.mspct
> ### Title: Spectral irradiance for diverse LEDs
> ### Aliases: leds.mspct
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(photobiology)
> library(ggspectra)
Error in library(ggspectra) : there is no package called ‘ggspectra’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 19-24 (user-guide.Rmd) 
Error: processing vignette ‘user-guide.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘ggspectra’
Error in re-building vignettes:
  ...
Quitting from lines 31-35 (dataplotsPlants.Rnw) 
Error: processing vignette ‘dataplotsPlants.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘quanteda’
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(phrasemachine)
  phrasemachine: Simple Phrase Extraction
  Version 1.1.2 created on 2017-05-29.
  copyright (c) 2016, Matthew J. Denny, Abram Handler, Brendan O'Connor.
  Type help('phrasemachine') or
  vignette('getting_started_with_phrasemachine') to get started.
  Development website: https://github.com/slanglab/phrasemachine
  > 
  > test_check("phrasemachine")
  ── 1. Error: See if tagging five documents works, and if coarsening works (@test
  there is no package called 'quanteda'
  1: quanteda::data_corpus_inaugural at testthat/test_POS_tag_documents.R:5
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ── 2. Error: See if extractor works (@test_extract_phrases.R#5)  ───────────────
  there is no package called 'quanteda'
  1: quanteda::data_corpus_inaugural at testthat/test_extract_phrases.R:5
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  Currently tagging document 1 of 1 
  Extracting phrases from document 1 of 1 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 10 SKIPPED: 0 FAILED: 2
  1. Error: See if tagging five documents works, and if coarsening works (@test_POS_tag_documents.R#5) 
  2. Error: See if extractor works (@test_extract_phrases.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 82-91 (getting_started_with_phrasemachine.Rmd) 
Error: processing vignette ‘getting_started_with_phrasemachine.Rmd’ failed with diagnostics:
there is no package called 'quanteda'
Execution halted
Package suggested but not available for checking: ‘OutbreakTools’
Packages required but not available: ‘geiger’ ‘ggplot2’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: equivalent_shifts
> ### Title: Find all equivalent shifts allocations and values.
> ### Aliases: equivalent_shifts
> 
> ### ** Examples
> 
> ## Simualte a tree
> set.seed(17920902)
> ntaxa = 20
> phylo <- TreeSim::sim.bd.taxa.age(n = ntaxa, numbsim = 1, lambda = 0.1,
+                                   mu = 0, age = 1, mrca = TRUE)[[1]]
Error in loadNamespace(name) : there is no package called ‘TreeSim’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Running ‘testthat_EM.R’ [3s/5s]
  Running ‘testthat_core.R’ [7s/9s]
  Running ‘testthat_independent.R’ [3s/4s]
  Running ‘testthat_shifts.R’ [5s/7s]
Running the tests in ‘tests/testthat_shifts.R’ failed.
Complete output:
  > library(testthat)
  > library(PhylogeneticEM)
  Loading required package: ape
  Loading required package: Matrix
  > 
  > test_check("PhylogeneticEM", filter = "shifts")
  ── 1. Error: Equivalent Shift - BM (@test-shifts-parsimonyNumber.R#41)  ────────
  there is no package called 'TreeSim'
  1: TreeSim::sim.bd.taxa.age at testthat/test-shifts-parsimonyNumber.R:41
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ── 2. Error: Equivalent Shift - OU (@test-shifts-parsimonyNumber.R#75)  ────────
  there is no package called 'TreeSim'
  1: TreeSim::sim.bd.taxa.age at testthat/test-shifts-parsimonyNumber.R:75
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 16 SKIPPED: 1 FAILED: 2
  1. Error: Equivalent Shift - BM (@test-shifts-parsimonyNumber.R#41) 
  2. Error: Equivalent Shift - OU (@test-shifts-parsimonyNumber.R#75) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: ape
Loading required package: Matrix
Quitting from lines 28-32 (tutorial.Rmd) 
Error: processing vignette ‘tutorial.Rmd’ failed with diagnostics:
there is no package called 'TreeSim'
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 16-43 (IdealWeightComparison.Rmd) 
Error: processing vignette ‘IdealWeightComparison.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘FrF2’ ‘DoE.base’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘pinnacle.data-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: USA_Election_2016
> ### Title: USA_Election_2016
> ### Aliases: USA_Election_2016
> ### Keywords: datasets
> 
> ### ** Examples
> 
> if (require("odds.converter")) {
+ library(tidyverse)
+ # What is Hilary Clinton's the highest implied winning probability at Pinnacle?
+ 
+ USA_Election_2016[which.min(USA_Election_2016$MoneyUS1),"EnteredDateTime"]
+ odds.converter::odds.us2prob(min(USA_Election_2016$MoneyUS1))
+ }
Loading required package: odds.converter
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 119-141 (Introduction.Rmd) 
Error: processing vignette ‘Introduction.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggsubplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'lubridate'

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

    date

Quitting from lines 529-552 (v10-performance.Rmd) 
Error: processing vignette ‘v10-performance.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘Hmisc’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggnetwork’ ‘ggplot2’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

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.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [44s/57s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PKNCA)
  > 
  > test_check("PKNCA")
  Provenance hash a generated on b with c.
  ── 1. Failure: pk.tss.stepwise.linear (@test-time.to.steady.state.R#284)  ──────
  pk.tss.stepwise.linear(...) not equal to data.frame(tss.stepwise.linear = 5).
  Component "tss.stepwise.linear": Modes: logical, numeric
  Component "tss.stepwise.linear": target is logical, current is numeric
  pk.tss.stepwise.linear no subject
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1189 SKIPPED: 2 FAILED: 1
  1. Failure: pk.tss.stepwise.linear (@test-time.to.steady.state.R#284) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 22-43 (AUC-Calculation-with-PKNCA.Rmd) 
Error: processing vignette ‘AUC-Calculation-with-PKNCA.Rmd’ failed with diagnostics:
there is no package called 'cowplot'
Execution halted
Packages suggested but not available for checking: ‘StatRank’ ‘kableExtra’
Error in re-building vignettes:
  ...
Quitting from lines 41-45 (Overview.Rmd) 
Error: processing vignette ‘Overview.Rmd’ failed with diagnostics:
there is no package called 'kableExtra'
Execution halted
Packages required but not available: ‘ggdendro’ ‘ggplot2’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘latticist’ ‘ggplot2’
Packages required but not available: ‘colorspace’ ‘aqp’ ‘scales’

Packages suggested but not available for checking:
  ‘spcosa’ ‘rgbif’ ‘Hmisc’ ‘GSIF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘scales’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘scales’ ‘crosstalk’

Packages suggested but not available for checking:
  ‘ggthemes’ ‘GGally’ ‘dendextend’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘mixOmics’ ‘SensoMineR’
Running examples in ‘PLSbiplot1-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Mag.Bmat.plot
> ### Title: Magnitude of the Partial Least Squares Regression (PLSR)
> ###   coefficients matrix
> ### Aliases: Mag.Bmat.plot
> 
> ### ** Examples
> 
> if(require(pls))
+ data(oliveoil, package="pls")
Loading required package: pls

Attaching package: ‘pls’

The following object is masked from ‘package:stats’:

    loadings

> X = as.matrix(oliveoil$chemical, ncol=5)
> dimnames(X) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Acidity","Peroxide","K232","K270","DK")))
> Y = as.matrix(oliveoil$sensory, ncol=6)
> dimnames(Y) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Yellow","Green","Brown","Glossy","Transp","Syrup")))
> Mag.Bmat.plot(X, Y, algorithm=mod.SIMPLS, A=2)
> 
> #nutrimouse data
> if(require(mixOmics))
+ data(nutrimouse, package="mixOmics")
Loading required package: mixOmics
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mixOmics’
> X1 = as.matrix(nutrimouse$lipid, ncol=21)
Error in as.matrix(nutrimouse$lipid, ncol = 21) : 
  object 'nutrimouse' not found
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 310-329 (plspm_introduction.Rnw) 
Error: processing vignette ‘plspm_introduction.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘mixOmics’ ‘rms’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘TripleR’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 17-19 (examples.Rmd) 
Error: processing vignette ‘examples.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
Package required but not available: ‘MDSMap’

Packages suggested but not available for checking: ‘Hmisc’ ‘NMF’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘adegenet’ ‘ggplot2’ ‘pegas’ ‘mmod’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘adegenet’ ‘ggplot2’ ‘pegas’

Package suggested but not available for checking: ‘cowplot’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Error: processing vignette ‘burkina-faso-females.Rnw’ failed with diagnostics:
 chunk 1 (label = sweave-setup) 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘PortfolioEffectHFT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘GGally’

Package suggested but not available for checking: ‘TreeSim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘lmerTest’ ‘ggplot2’ ‘ggsci’ ‘scales’

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘factoextra’
Error in re-building vignettes:
  ...
Quitting from lines 45-48 (fcm.Rmd) 
Error: processing vignette ‘fcm.Rmd’ failed with diagnostics:
there is no package called 'factoextra'
Execution halted
Packages suggested but not available for checking:
  ‘GGally’ ‘ggplot2’ ‘PPtreeViz’
Running examples in ‘PPforest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ternary_str
> ### Title: Data structure with the projected and boundary by node and
> ###   class.
> ### Aliases: ternary_str
> 
> ### ** Examples
> 
> #crab data set with all the observations used as training
> pprf.crab <- PPforest(data = crab, std =TRUE, class = "Type",
+  size.tr = 1, m = 100, size.p = .5, PPmethod = 'LDA')
>  require(dplyr)
Loading required package: dplyr

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> pl_ter <- function(dat, dx, dy ){
+   p1  <- dat[[1]] %>% dplyr::filter(pair %in% paste(dx, dy, sep = "-") ) %>%
+     dplyr::select(Class, x, y) %>%
+     ggplot2::ggplot(ggplot2::aes(x, y, color = Class)) +
+     ggplot2::geom_segment(data = dat[[2]], ggplot2::aes(x = x1, xend = x2,
+                                                y = y1, yend = y2), color = "black" ) +
+     ggplot2::geom_point(size = I(3), alpha = .5) +
+     ggplot2::labs(y = " ",  x = " ") +
+     ggplot2::theme(legend.position = "none", aspect.ratio = 1) +
+     ggplot2::scale_colour_brewer(type = "qual", palette = "Dark2") +
+     ggplot2::labs(x = paste0("T", dx, " "), y = paste0("T", dy, " ")) +
+     ggplot2::theme(aspect.ratio = 1)
+   p1
+ }
> #ternary plot in tree different selected dierections
>  pl_ter(ternary_str(pprf.crab, id = c(1, 2, 3), sp = 3, dx = 1, dy = 2), 1, 2 )
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: pl_ter ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Loading required package: PPforest
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: RColorBrewer
Loading required package: GGally
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'GGally'
Loading required package: gridExtra

Attaching package: 'gridExtra'

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

    combine

Loading required package: PPtreeViz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'PPtreeViz'
Quitting from lines 16-25 (PPforest-vignette.Rmd) 
Error: processing vignette ‘PPforest-vignette.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘precrec’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘PSF’ ‘forecast’ ‘imputeTestbench’

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

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

Packages suggested but not available for checking: ‘ggplot2’ ‘preproviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘caret’

Packages suggested but not available for checking: ‘preprocomb’ ‘preproviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘caret’ ‘ggplot2’ ‘ggdendro’

Package suggested but not available for checking: ‘preprocomb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘quanteda’ ‘ggplot2’ ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘viridis’
Error in re-building vignettes:
  ...
Quitting from lines 154-155 (prioritylasso_vignette.Rmd) 
Error: processing vignette ‘prioritylasso_vignette.Rmd’ failed with diagnostics:
there is no package called 'pROC'
Execution halted
Packages required but not available:
  ‘edeaR’ ‘DiagrammeR’ ‘ggplot2’ ‘ggthemes’ ‘plotly’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘edeaR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rfigshare’
Packages required but not available: ‘ggplot2’ ‘GeneralizedUmatrix’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘incidence’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘rstan’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘ggdendro’ ‘plotly’

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

Error: processing vignette ‘PRROC.Rnw’ failed with diagnostics:
 chunk 47 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘PogromcyDanych’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘TriMatch’ ‘ggthemes’

Package suggested but not available for checking: ‘multilevelPSA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘Hmisc’ ‘ggplot2’
Running examples in ‘pscl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: UKHouseOfCommons
> ### Title: 1992 United Kingdom electoral returns
> ### Aliases: UKHouseOfCommons
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(UKHouseOfCommons)
> tmp <- UKHouseOfCommons[,c("v1","v2","v3")] 
> summary(apply(tmp,1,sum))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.9999  1.0000  1.0000  1.0000  1.0000  1.0001 
> 
> col <- rep("black",dim(tmp)[1])
> col[UKHouseOfCommons$coninc==1] <- "blue"
> col[UKHouseOfCommons$labinc==1] <- "red"
> col[UKHouseOfCommons$libinc==1] <- "orange"
> 
> library(vcd)
Error in library(vcd) : there is no package called ‘vcd’
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  replaced special characters in figure filename "figure/Load RSEIS package" -> "figure/Load_RSEIS_package"
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  replaced special characters in figure filename "figure/AR prewhiten" -> "figure/AR_prewhiten"
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  replaced special characters in figure filename "figure/Sampling rate versus interval" -> "figure/Sampling_rate_versus_interval"
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  replaced special characters in figure filename "figure/Compute PSD with mtapspec" -> "figure/Compute_PSD_with_mtapspec"
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  replaced special characters in figure filename "figure/Structure of mtapspec-psd" -> "figure/Structure_of_mtapspec-psd"
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  replaced special characters in figure filename "figure/Comparative spectra: mtapspec vs pspectrum" -> "figure/Comparative_spectra:_mtapspec_vs_pspectrum"
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  replaced special characters in figure filename "figure/Interpolate results" -> "figure/Interpolate_results"
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  replaced special characters in figure filename "figure/Summarize regression statistics" -> "figure/Summarize_regression_statistics"
Quitting from lines 438-441 (psd_overview.Rnw) 
Error: processing vignette ‘psd_overview.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 403-408 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘qgraph’ ‘ggcorrplot’ ‘rstanarm’ ‘lmerTest’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘likert’
Errors in running code in vignettes:
when running code in ‘raschtree.Rnw’
  ...

> library("psychotree")
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Loading required package: rpart
Loading required package: psychotools

> data("SPISA", package = "psychotree")

> if (file.exists("raschtree-spisa.rda")) load("raschtree-spisa.rda") else {
+     my_first_raschtree <- raschtree(spisa ~ age + gender + semester + 
 .... [TRUNCATED] 

> file.remove("raschtree-spisa.rda")
[1] TRUE

> plot(my_first_raschtree)

> library("colorspace")

  When sourcing ‘raschtree.R’:
Error: there is no package called ‘colorspace’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Loading required package: rpart
Loading required package: psychotools

Error: processing vignette ‘raschtree.Rnw’ failed with diagnostics:
 chunk 10 (label = plot_raschtree_col) 
Error in library("colorspace") : there is no package called ‘colorspace’
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggdendro’ ‘kableExtra’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: publish.CauseSpecificCox
> ### Title: Tabulizing cause-specific hazard ratio from all causes with
> ###   confidence limits and Wald test p-values.
> ### Aliases: publish.CauseSpecificCox
> 
> ### ** Examples
> 
> library(riskRegression)
Error in library(riskRegression) : 
  there is no package called ‘riskRegression’
Execution halted
Packages required but not available: ‘ggmap’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [7s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pxweb)
  pxweb: R tools for PX-WEB API.
  Copyright (C) 2014 Mans Magnusson, Leo Lahti, Love Hansson
  https://github.com/ropengov/pxweb
  
  New PXWEB API(s):
   - prognos.konj.se
   - data.ssb.no
   - pxweb.asub.ax
   - makstat.stat.gov.mk
   - data.csb.gov.lv
  
  Use update_pxweb_apis() to update the api catalogue.
  > test_check("pxweb")
  ── 1. Failure: pxweb_api_class (@test-pxweb_api_class.R#20)  ───────────────────
  NOT(success)
  
  ── 2. Failure: pxweb_api_class (@test-pxweb_api_class.R#22)  ───────────────────
  "foo.bar" %in% unlist(lapply(api_catalogue(), function(X) X$api)) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 98 SKIPPED: 16 FAILED: 2
  1. Failure: pxweb_api_class (@test-pxweb_api_class.R#20) 
  2. Failure: pxweb_api_class (@test-pxweb_api_class.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘arulesCBA’
Packages required but not available: ‘Hmisc’ ‘colorspace’ ‘ggplot2’

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

Package suggested but not available for checking: ‘biom’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ARMA_GARCH
> ### Title: Fitting ARMA-GARCH Processes
> ### Aliases: fit_ARMA_GARCH
> ### Keywords: ts
> 
> ### ** Examples
> 
> library(rugarch)
Loading required package: parallel

Attaching package: ‘rugarch’

The following object is masked from ‘package:stats’:

    sigma

> library(copula)
Error in library(copula) : there is no package called ‘copula’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: parallel

Attaching package: 'rugarch'

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

    sigma

Loading required package: gsl
Loading required package: Matrix
Loading required package: mvtnorm
Loading required package: numDeriv
Loading required package: timeSeries
Loading required package: timeDate

Attaching package: 'timeSeries'

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

    returns


Attaching package: 'QRM'

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

    dGEV, dGPD, pGEV, pGPD, qGEV, qGPD, rGEV, rGPD

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

    lbeta

Quitting from lines 14-20 (VaR_bounds.Rmd) 
Error: processing vignette ‘VaR_bounds.Rmd’ failed with diagnostics:
there is no package called 'copula'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘GGally’
Error in re-building vignettes:
  ...
Quitting from lines 111-120 (wilcox1973.Rmd) 
Error: processing vignette ‘wilcox1973.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘scales’ ‘pROC’ ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘panel.R’ [3s/5s]
  Running ‘rq.R’ [3s/4s]
  Running ‘rq.fit.panel.R’ [0s/1s]
  Running ‘run-demos.R’ [2s/3s]
Running the tests in ‘tests/run-demos.R’ failed.
Complete output:
  > library(quantreg)
  Loading required package: SparseM
  
  Attaching package: 'SparseM'
  
  The following object is masked from 'package:base':
  
      backsolve
  
  > 
  > (dDIR <- system.file("demo", package = "quantreg"))
  [1] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/quantreg/demo"
  > setwd(dDIR)
  > set.seed(1) # since some demos randomly generate
  > 
  > cat("Running demos from package 'quantreg' : \n\n")
  Running demos from package 'quantreg' : 
  
  > for(ff in list.files(dDIR, pattern="\\.R$", full.names = TRUE)) {
  +    f <- basename(ff)
  +    cat("\n", f," :\n", paste(rep.int("-", nchar(f)), collapse=''),
  +        "\n", sep='')
  + 
  +    source(ff, echo = TRUE)
  + }
  
  Frank.R :
  -------
  
  > vFrank <- function(x, df, delta, u) -log(1 - (1 - 
  +     exp(-delta))/(1 + exp(-delta * pt(x, df)) * ((1/u) - 1)))/delta
  
  > FrankModel <- function(x, delta, mu, sigma, df, tau) {
  +     z <- qt(vFrank(x, df, delta, u = tau), df)
  +     mu + sigma * z
  + }
  
  > n <- 200
  
  > df <- 8
  
  > delta <- 8
  
  > set.seed(1989)
  
  > x <- sort(rt(n, df))
  
  > v <- vFrank(x, df, delta, u = runif(n))
  
  > y <- qt(v, df)
  
  > plot(x, y, pch = "o", col = "blue", cex = 0.25)
  Error in (function (file = if (onefile) "Rplots.pdf" else "Rplot%03d.pdf",  : 
    cannot open file 'Rplots.pdf'
  Calls: source ... eval -> plot -> plot.default -> dev.hold -> <Anonymous>
  Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘fastshp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 106-111 (R2admb.Rnw) 
Error: processing vignette ‘R2admb.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘lmerTest’ ‘ggplot2’ ‘afex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 78-88 (Performance.Rmd) 
Error: processing vignette ‘Performance.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘geiger’ ‘hierfstat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘radiant.data’ ‘ggplot2’ ‘scales’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘radiant.data’ ‘radiant.basics’ ‘NeuralNetTools’ ‘ggplot2’
  ‘data.tree’ ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘radiant.data’ ‘radiant.model’ ‘ggplot2’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘radiant.data’ ‘radiant.design’ ‘radiant.basics’ ‘radiant.model’
  ‘radiant.multivariate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 240-247 (single_cell_projections.Rmd) 
Error: processing vignette ‘single_cell_projections.Rmd’ failed with diagnostics:
there is no package called 'colorspace'
Execution halted
Package required but not available: ‘rags2ridges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 20-33 (ragtop_convertibles_in_r.Rmd) 
Error: processing vignette ‘ragtop_convertibles_in_r.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘colorspace’

Package suggested but not available for checking: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: sp

Attaching package: 'raster'

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

    distance

Quitting from lines 36-40 (raincpc_demo.Rmd) 
Error: processing vignette ‘raincpc_demo.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘colorspace’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘GGally’ ‘ggplot2’ ‘ggrepel’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rankhazard-package
> ### Title: Rank-hazard plots
> ### Aliases: rankhazard-package rankhazard
> ### Keywords: package hplot survival
> 
> ### ** Examples
> 
> library(survival)
> model <- coxph(Surv(time,status) ~ age + sex + ph.karno, data = cancer, x=TRUE)
> rankhazardplot(model, data=cancer)
Y-axis range:  0.608 1.49 
 
Relative hazards for each covarite: 
          Min. 1st Qu. Median 3rd Qu. Max.
age      0.743   0.917      1    1.08 1.27
sex      0.608   0.608      1    1.00 1.00
ph.karno 0.766   0.875      1    1.07 1.49
> library(rms)
Error in library(rms) : there is no package called ‘rms’
Execution halted
Packages required but not available: ‘scales’ ‘ggplot2’

Packages suggested but not available for checking: ‘gurobi’ ‘rgurobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘colorspace’
Packages required but not available: ‘pROC’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rattle’
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘colorspace’ ‘arulesViz’ ‘biclust’ ‘ggdendro’ ‘ggraptR’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘ChainLadder’ ‘FinCal’ ‘scales’
Packages required but not available: ‘rstan’ ‘bayesplot’ ‘ggplot2’

Packages suggested but not available for checking: ‘tidyverse’ ‘rstanarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: sp

Attaching package: 'dplyr'

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

    intersect, select, union

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

    filter, lag

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

    intersect, setdiff, setequal, union

rgdal: version: 1.2-16, (SVN revision 701)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: /usr/share/gdal/2.2
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-6 
Quitting from lines 29-36 (BGM_Spatial.Rmd) 
Error: processing vignette ‘BGM_Spatial.Rmd’ failed with diagnostics:
there is no package called 'scales'
Execution halted
Package required but not available: ‘oceanmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘aspace’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mudata2’

Package suggested but not available for checking: ‘ggplot2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘BCA’ ‘RcmdrMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘biclust’ ‘iBBiG’ ‘superbiclust’ ‘rqubic’ ‘s4vd’ ‘BiBitR’ ‘Rcmdr’
  ‘viridis’

Depends: includes the non-default packages:
  ‘biclust’ ‘fabia’ ‘iBBiG’ ‘superbiclust’ ‘BcDiag’ ‘rqubic’ ‘BicARE’
  ‘s4vd’ ‘BiBitR’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

Package suggested but not available for checking: ‘FrF2.catlg128’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ez’ ‘Rcmdr’ ‘RcmdrMisc’

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

Depends: includes the non-default packages:
  ‘Rcmdr’ ‘TeachingDemos’ ‘tseries’ ‘abind’ ‘MASS’ ‘xts’ ‘forecast’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

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

Package suggested but not available for checking: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘HH’ ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘ggplot2’ ‘ggthemes’ ‘scales’

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

Packages suggested but not available for checking: ‘ggplot2’ ‘scales’

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

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

Package suggested but not available for checking: ‘vcd’

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

Packages suggested but not available for checking:
  ‘qgraph’ ‘effects’ ‘vcd’ ‘gpairs’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘demography’ ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘colorspace’ ‘vcd’

Depends: includes the non-default packages:
  ‘Rcmdr’ ‘tcltk’ ‘car’ ‘RColorBrewer’ ‘colorspace’ ‘vcd’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘sutteForecastR’

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

Packages suggested but not available for checking: ‘colorspace’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘RCMIP5-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: worldPlot
> ### Title: Plot global data
> ### Aliases: worldPlot
> 
> ### ** Examples
> 
> d <- cmip5data(1970:1975)   # sample data
> worldPlot(d)
Error: requireNamespace(package = "ggplot2", quietly = T) is not TRUE
Execution halted
Running ‘testthat.R’ [111s/134s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("RCMIP5")
  Loading required package: RCMIP5
  ── 1. Error: worldPlot generates ggplot object (@test_worldPlot.R#19)  ─────────
  requireNamespace(package = "ggplot2", quietly = T) is not TRUE
  1: worldPlot(d) at testthat/test_worldPlot.R:19
  2: assert_that(requireNamespace("ggplot2", quietly = T))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 802 SKIPPED: 29 FAILED: 1
  1. Error: worldPlot generates ggplot object (@test_worldPlot.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 13-18 (purrr-e-rcongresso.Rmd) 
Error: processing vignette ‘purrr-e-rcongresso.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘rddtools’
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > # library(AER)
  > # library(sandwich)
  > # library(lmtest)
  > # library(Formula)
  > library(rddapp)
  > library(rdd)
  Loading required package: sandwich
  Loading required package: lmtest
  Loading required package: zoo
  
  Attaching package: 'zoo'
  
  The following objects are masked from 'package:base':
  
      as.Date, as.Date.numeric
  
  Loading required package: AER
  Loading required package: car
  Loading required package: survival
  Loading required package: Formula
  > library(rddtools)
  Error in library(rddtools) : there is no package called 'rddtools'
  Execution halted
Packages required but not available: ‘ggplot2’ ‘lpdensity’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: robustbase
Quitting from lines 42-47 (CreateRDML.Rmd) 
Error: processing vignette ‘CreateRDML.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running ‘testthat.R’ [82s/98s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rdomains)
  > 
  > test_check("rdomains")
  ── 1. Error: dmoz cat (@test-dmoz-cat.R#5)  ────────────────────────────────────
  HTTP error 404.
  1: get_dmoz_data() at testthat/test-dmoz-cat.R:5
  2: curl_download("https://github.com/soodoku/domain_classifier/blob/master/rdomains/data-raw/dmoz/dmoz_domain_category.zip?raw=true", 
         tmp)
  
  Shallalist Data saved to the following destination: ./ 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Error: dmoz cat (@test-dmoz-cat.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘ggplot2’ ‘scales’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 22-26 (mapDWD.Rmd) 
Error: processing vignette ‘mapDWD.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(quanteda)
  Error in library(quanteda) : there is no package called 'quanteda'
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: quanteda
Quitting from lines 146-152 (readtext_vignette.Rmd) 
Error: processing vignette ‘readtext_vignette.Rmd’ failed with diagnostics:
could not find function "corpus"
Execution halted
Package required but not available: ‘statsDK’

Package suggested but not available for checking: ‘ggplot2’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: step_window
> ### Title: Moving Window Functions
> ### Aliases: step_window tidy.step_window
> ### Keywords: datagen
> 
> ### ** Examples
> 
> library(recipes)
> library(dplyr)
> library(rlang)
> library(ggplot2, quietly = TRUE)
Error in library(ggplot2, quietly = TRUE) : 
  there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: broom

Attaching package: 'recipes'

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

    step

Quitting from lines 48-53 (Custom_Steps.Rmd) 
Error: processing vignette ‘Custom_Steps.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘prevR’ ‘scales’
Error in re-building vignettes:
  ...
Loading required package: recurse
Loading required package: scales
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'scales'
Quitting from lines 34-38 (recurse.Rmd) 
Error: processing vignette ‘recurse.Rmd’ failed with diagnostics:
could not find function "viridis_pal"
Execution halted
Packages suggested but not available for checking: ‘UsingR’ ‘vcd’
Error in re-building vignettes:
  ...
Failed with error:  'there is no package called 'kableExtra''
Quitting from lines 70-73 (BasicREDCapROperations.Rmd) 
Error: processing vignette ‘BasicREDCapROperations.Rmd’ failed with diagnostics:
there is no package called 'kableExtra'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 76-80 (rEDM-coprediction.Rmd) 
Error: processing vignette ‘rEDM-coprediction.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘isva’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘plotly’ ‘refund’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘caret’ ‘semPlot’ ‘colorspace’
Package which this enhances but not available for checking: ‘seriation’
Package required but not available: ‘PhaseType’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rcmdr’
Packages required but not available: ‘plotly’ ‘data.tree’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘OutbreakTools’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘DiagrammeR’
Running ‘testthat.R’ [49s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ReporteRs)
  Loading required package: ReporteRsjars
  > 
  > test_check("ReporteRs")
  ── 1. Error: (unknown) (@test-docx-plot.R#3)  ──────────────────────────────────
  there is no package called 'ggplot2'
  1: library(ggplot2) at testthat/test-docx-plot.R:3
  2: stop(txt, domain = NA)
  
  ── 2. Error: (unknown) (@test-pptx-plot.R#3)  ──────────────────────────────────
  there is no package called 'ggplot2'
  1: library(ggplot2) at testthat/test-pptx-plot.R:3
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 39 SKIPPED: 0 FAILED: 2
  1. Error: (unknown) (@test-docx-plot.R#3) 
  2. Error: (unknown) (@test-pptx-plot.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘useful’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: rivr
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
Quitting from lines 73-74 (quickstart.Rmd) 
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
could not find function "ggplot"
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘Hmisc’
Error in re-building vignettes:
  ...
Quitting from lines 29-33 (log_parsing.Rmd) 
Error: processing vignette ‘log_parsing.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘nhanesA’
Error in re-building vignettes:
  ...
Quitting from lines 13-17 (RFinfer-examples.Rmd) 
Error: processing vignette ‘RFinfer-examples.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘UsingR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘swfscMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 87-88 (vignette_RGCCA.Rmd) 
Error: processing vignette ‘vignette_RGCCA.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package which this enhances but not available for checking: ‘colorspace’
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘colorspace’ ‘Hmisc’ ‘munsell’ ‘pmg’ ‘Rcmdr’ ‘RGraphics’ ‘vcd’
  ‘vcdExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘plotly’ ‘ggplot2’
Packages required but not available: ‘ggplot2’ ‘rms’

Packages suggested but not available for checking: ‘Daim’ ‘pec’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: rivr
M1 profile specified. Computing upstream profile
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Quitting from lines 96-100 (quickstart.Rmd) 
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
could not find function "ggplot"
Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  libjson/Source/JSONGlobals.h:43:50: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
  libjson/Source/JSONGlobals.h:44:49: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
  JSONValidator.cpp:394:105: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
  JSONValidator.cpp:397:104: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RJSONIO.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘lmerTest’
Error in re-building vignettes:
  ...
Loading required package: Luminescence
Loading required package: magrittr
Welcome to the R package Luminescence version 0.7.5 [Built: 2018-01-11 02:40:35 UTC]
Die Ex vom Tatortreiniger: 'Das Ziel ist im Weg.'

Attaching package: 'RLumModel'

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

    model_LuminescenceSignals

Quitting from lines 25-28 (RLumModel_-_Getting_started_with_RLumModel.Rmd) 
Error: processing vignette ‘RLumModel_-_Getting_started_with_RLumModel.Rmd’ failed with diagnostics:
there is no package called 'kableExtra'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘merTools’
Error in re-building vignettes:
  ...
Loading required package: pwr
Loading required package: psych
Loading required package: RColorBrewer
Loading required package: plotrix

Attaching package: 'plotrix'

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

    rescale

Loading required package: rmcorr
Loading required package: lme4
Loading required package: Matrix
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Loading required package: merTools
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'merTools'
Warning in rmcorr(sub, newX, newY, exampleMat) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat2) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat3) :
  'sub' coerced into a factor
Quitting from lines 470-519 (Combined_paper_figures.Rmd) 
Error: processing vignette ‘Combined_paper_figures.Rmd’ failed with diagnostics:
could not find function "predictInterval"
Execution halted
Packages required but not available: ‘pegas’ ‘adegenet’

Package suggested but not available for checking: ‘ggplot2’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: group.CI
> ### Title: Group Confidence Interval
> ### Aliases: group.CI
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> require(latticeExtra)
Loading required package: latticeExtra
Loading required package: RColorBrewer
> with(group.CI(weight~feed,chickwts),
+  segplot(feed~weight.lower+weight.upper,center=weight.mean)
+ )
> 
> require(Hmisc)
Loading required package: Hmisc
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Hmisc’
> with(group.CI(Temp~Month,airquality),
+  xYplot(Cbind(Temp.mean,Temp.lower,Temp.upper)~numericScale(Month),type="b",ylim=c(60,90))
+ )
Error in xYplot(Cbind(Temp.mean, Temp.lower, Temp.upper) ~ numericScale(Month),  : 
  could not find function "xYplot"
Calls: with -> with.default -> eval -> eval
Execution halted
Packages required but not available: ‘Hmisc’ ‘ggplot2’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 208-221 (rte-vignette_creating_exams.Rmd) 
Error: processing vignette ‘rte-vignette_creating_exams.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking:
  ‘rrdf’ ‘geiger’ ‘rfigshare’
Running examples in ‘RNeXML-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_characters
> ### Title: Add character data to a nexml object
> ### Aliases: add_characters
> 
> ### ** Examples
> 
> library("geiger")
Error in library("geiger") : there is no package called ‘geiger’
Execution halted
Running ‘test-all.R’ [75s/130s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("RNeXML")
  Loading required package: RNeXML
  Loading required package: ape
  ── 1. Error: we can add multiple character matrices to a nexml file (@test_chara
  there is no package called 'geiger'
  1: library("geiger") at testthat/test_characters.R:106
  2: stop(txt, domain = NA)
  
  ── 2. Error: (unknown) (@test_comp_analysis.R#4)  ──────────────────────────────
  there is no package called 'geiger'
  1: library(geiger) at testthat/test_comp_analysis.R:4
  2: stop(txt, domain = NA)
  
  ── 3. Error: We can generate valid EML with uuid ids on all elements (@test_glob
  object 'geospiza' not found
  1: add_trees(geospiza$phy) at testthat/test_global_ids.R:9
  2: standardize_phylo_list(phy)
  3: is(phy, "list")
  
  Namespace prefix xhtml on div is not defined
  A nexml object representing:
   	 0 phylogenetic tree blocks, where: 
   	 block 1 contains NULL phylogenetic trees
  	 block 0 contains  phylogenetic trees 
   	 19 meta elements 
   	 0 character matrices 
   	 0 taxonomic units 
   Taxa: 	  ... 
  
   NeXML generated by RNeXML using schema version: 0.9 
   size: 21.8 Kb 
  Done simulation(s).
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 177 SKIPPED: 3 FAILED: 3
  1. Error: we can add multiple character matrices to a nexml file (@test_characters.R#106) 
  2. Error: (unknown) (@test_comp_analysis.R#4) 
  3. Error: We can generate valid EML with uuid ids on all elements (@test_global_ids.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: ape

Retrieving data for taxon 'Struthioniformes'


Retrieving data for taxon 'Tinamiformes'


Retrieving data for taxon 'Craciformes'


Retrieving data for taxon 'Galliformes'


Retrieving data for taxon 'Anseriformes'


Retrieving data for taxon 'Turniciformes'


Retrieving data for taxon 'Piciformes'


Retrieving data for taxon 'Galbuliformes'


Retrieving data for taxon 'Bucerotiformes'


Retrieving data for taxon 'Upupiformes'


Retrieving data for taxon 'Trogoniformes'


Retrieving data for taxon 'Coraciiformes'


Retrieving data for taxon 'Coliiformes'


Retrieving data for taxon 'Cuculiformes'


Retrieving data for taxon 'Psittaciformes'


Retrieving data for taxon 'Apodiformes'


Retrieving data for taxon 'Trochiliformes'


Retrieving data for taxon 'Musophagiformes'


Retrieving data for taxon 'Strigiformes'


Retrieving data for taxon 'Columbiformes'


Retrieving data for taxon 'Gruiformes'


Retrieving data for taxon 'Ciconiiformes'


Retrieving data for taxon 'Passeriformes'


Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 198-202 (metadata.Rmd) 
Error: processing vignette ‘metadata.Rmd’ failed with diagnostics:
there is no package called 'geiger'
Execution halted
Packages suggested but not available for checking:
  ‘dendextend’ ‘ggdendro’ ‘ggplot2’ ‘leaflet’ ‘plotly’
Packages required but not available: ‘ggplot2’ ‘scales’

Packages suggested but not available for checking: ‘leaflet’ ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘cowplot’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggmap’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘GGally’ ‘VIM’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: robustbase
Loading required package: xtable
Loading required package: GGally
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GGally’

Error: processing vignette ‘lmrob_simulation.Rnw’ failed with diagnostics:
 chunk 6 (label = fig-example-design) 
Error in ggpairs(df.r_25_5, axisLabels = "show", title = "rand_25_5: n=25, p=5") : 
  could not find function "ggpairs"
Execution halted
Packages required but not available: ‘ggplot2’ ‘perry’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sim.partially.matched
> ### Title: Simulate Paired, Independent, or Partially Matched Two-Sample
> ###   Data
> ### Aliases: r2sample sim.paired.with.replicates sim.partially.matched
> 
> ### ** Examples
> 
> dat=sim.partially.matched(m=10,n.x=5,n.y=4,distr="normal",
+     params=c("loc.2"=0,"rho"=0,"scale.2"=1),seed=1)
> X=dat$X; Y=dat$Y; Yprime=dat$Yprime    
> 
> dat=sim.partially.matched(m=10,n.x=5,n.y=4,distr="logistic",
+     params=c("loc.2"=0,"rho"=0,"scale.2"=1),seed=1)
Error in loadNamespace(name) : there is no package called ‘copula’
Calls: sim.partially.matched ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages suggested but not available for checking: ‘tables’ ‘Hmisc’
Package suggested but not available for checking: ‘data.tree’
Error in re-building vignettes:
  ...

Attaching package: 'rODE'

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

    step

Quitting from lines 27-65 (ErrorEuler.Rmd) 
Error: processing vignette ‘ErrorEuler.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘rollply-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: build_grid_ahull_fill
> ### Title: Regular grid in alpha-hull
> ### Aliases: build_grid_ahull_fill
> 
> ### ** Examples
> 
> 
> data(meadow)
> 
> # Plot a grid with diagnostics
> grid <- build_grid_ahull_fill(meadow[ ,c('lon','lat')], 10000,
+                               grid_opts = list(verbose = TRUE))
Error in build_grid_ahull_fill(meadow[, c("lon", "lat")], 10000, grid_opts = list(verbose = TRUE)) : 
  Alpha-hull-based grids require package alphahull
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rollply)
  > 
  > test_check("rollply")
  ── 1. Error: inahull_cpp works (@test_inahull.R#9)  ────────────────────────────
  there is no package called 'alphahull'
  1: library(alphahull) at testthat/test_inahull.R:9
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 1
  1. Error: inahull_cpp works (@test_inahull.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 21-27 (rollply.Rmd) 
Error: processing vignette ‘rollply.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggmap’ ‘viridis’
Error in re-building vignettes:
  ...
Quitting from lines 25-30 (graphics_of_pm_25_concentrations_in_several_countries.Rmd) 
Error: processing vignette ‘graphics_of_pm_25_concentrations_in_several_countries.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘mrfDepth’ ‘rrcovHD’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fulltext’
Non-standard file/directory found at top level:
  ‘Changelog.TMT’
Running examples in ‘rpdo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pdo
> ### Title: Pacific Decadal Oscillation Index
> ### Aliases: pdo
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(rpdo)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: parallel
Quitting from lines 7-13 (diagnostics.Rmd) 
Error: processing vignette ‘diagnostics.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 13-16 (visualization.Rmd) 
Error: processing vignette ‘visualization.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘plotly’ ‘GGally’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tidy.rsplit
> ### Title: Tidy Resampling Object
> ### Aliases: tidy.rsplit tidy.rset tidy.vfold_cv tidy.nested_cv
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: broom
Loading required package: tidyr

Attaching package: 'rsample'

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

    fill

Quitting from lines 48-52 (Recipes_and_rsample.Rmd) 
Error: processing vignette ‘Recipes_and_rsample.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘RSMET-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: meteofrance
> ### Title: Snow Weather Data in France
> ### Aliases: meteofrance
> 
> ### ** Examples
> 
>  
> 
> library(ggmap)
Error in library(ggmap) : there is no package called ‘ggmap’
Execution halted
Packages suggested but not available for checking:
  ‘emmeans’ ‘DoE.base’ ‘FrF2’
Package suggested but not available for checking: ‘NeuralNetTools’
Packages required but not available:
  ‘bayesplot’ ‘ggplot2’ ‘rstan’ ‘shinystan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘shinystan’ ‘bayesplot’

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

Packages suggested but not available for checking: ‘ggplot2’ ‘ggjoy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘bayesplot’ ‘rstan’ ‘rstanarm’ ‘shinystan’
Package which this enhances but not available for checking: ‘ggplot2’
Packages required but not available: ‘colorspace’ ‘inlmisc’

Package suggested but not available for checking: ‘leaflet’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rpca
> ### Title: Randomized principal component analysis (rpca).
> ### Aliases: rpca
> 
> ### ** Examples
> 
> 
> library('rsvd')
> #
> # Load Edgar Anderson's Iris Data
> #
> data('iris')
> 
> #
> # log transform
> #
> log.iris <- log( iris[ , 1:4] )
> iris.species <- iris[ , 5]
> 
> #
> # Perform rPCA and compute only the first two PCs
> #
> iris.rpca <- rpca(log.iris, k=2)
> summary(iris.rpca) # Summary
                         PC1   PC2
Explained variance     2.933 0.907
Standard deviations    1.712 0.952
Proportion of variance 0.733 0.227
Cumulative proportion  0.733 0.960
> print(iris.rpca) # Prints the rotations
Standard deviations:
[1] 1.712 0.952

Eigenvalues:
[1] 2.933 0.907

Rotation:
                PC1    PC2
Sepal.Length -0.504 -0.455
Sepal.Width   0.302 -0.889
Petal.Length -0.577 -0.034
Petal.Width  -0.567 -0.035
> 
> #
> # Use rPCA to compute all PCs, similar to \code{prcomp}
> #
> iris.rpca <- rpca(log.iris)
> summary(iris.rpca) # Summary
                         PC1   PC2   PC3   PC4
Explained variance     2.933 0.907 0.133 0.027
Standard deviations    1.712 0.952 0.365 0.166
Proportion of variance 0.733 0.227 0.033 0.007
Cumulative proportion  0.733 0.960 0.993 1.000
> print(iris.rpca) # Prints the rotations
Standard deviations:
[1] 1.712 0.952 0.365 0.166

Eigenvalues:
[1] 2.933 0.907 0.133 0.027

Rotation:
                PC1    PC2    PC3    PC4
Sepal.Length  0.504 -0.455  0.709  0.191
Sepal.Width  -0.302 -0.889 -0.331 -0.091
Petal.Length  0.577 -0.034 -0.219 -0.786
Petal.Width   0.567 -0.035 -0.583  0.580
> plot(iris.rpca) # Produce screeplot, variable and individuls factor maps.
Error: The package 'ggplot2' is needed for this function to work. Please install it.
Execution halted
Running examples in ‘rsvg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rsvg
> ### Title: Render SVG into Bitmap
> ### Aliases: rsvg rsvg_raw rsvg_webp rsvg_png rsvg_pdf rsvg_svg rsvg_ps
> 
> ### ** Examples
> 
> # create some svg
> options(example.ask=FALSE)
> tmp <- tempfile()
> svglite::svglite(tmp, width = 10, height = 7)
> ggplot2::qplot(mpg, wt, data = mtcars, colour = factor(cyl))
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette ‘rtf.Rnw’ failed with diagnostics:
 chunk 29 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘ggplot2’ ‘rbokeh’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘ggthemes’ ‘plotly’ ‘colourpicker’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘bang’ ‘revdbayes’
Unavailable namespace imported from by a ':::' call: ‘revdbayes’
  See the note in ?`:::` about the use of this operator.
Package required but not available: ‘mixOmics’

Package suggested but not available for checking: ‘emmeans’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘ggraph’
Running examples in ‘rvinecopulib-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.vinecop_dist
> ### Title: Plotting 'vinecop_dist' and 'vinecop' objects.
> ### Aliases: plot.vinecop_dist contour.vinecop_dist plot.vinecop
> ###   contour.vinecop plot.vinecop contour.vinecop_dist contour.vinecop
> ### Keywords: plot
> 
> ### ** Examples
> 
> # set up vine copula model
> d <- 20
> n <- 2e2
> u <- matrix(runif(n*d), n, d)
> vc <- vinecop(u, "indep")
> 
> # plot
> plot(vc, tree = c(1,2))
Error in plot.vinecop(vc, tree = c(1, 2)) : 
  The 'ggraph' package must be installed to plot.
Calls: plot -> plot.vinecop
Execution halted
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rvinecopulib)
  > 
  > test_check("rvinecopulib")
  ── 1. Error: plot functions work (@test_vinecop_dist.R#70)  ────────────────────
  The 'ggraph' package must be installed to plot.
  1: expect_silent(p <- plot(vc, edge_labels = "family", var_names = "legend")) at testthat/test_vinecop_dist.R:70
  2: quasi_capture(enquo(object), evaluate_promise)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  5: force(code)
  6: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  7: withVisible(code)
  8: eval_bare(get_expr(quo), get_env(quo))
  9: plot(vc, edge_labels = "family", var_names = "legend")
  10: plot.vinecop_dist(vc, edge_labels = "family", var_names = "legend")
  11: stop("The 'ggraph' package must be installed to plot.")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 81 SKIPPED: 0 FAILED: 1
  1. Error: plot functions work (@test_vinecop_dist.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘RVowpalWabbit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vw
> ### Title: Run the Vowpal Wabbit fast out-of-core learner
> ### Aliases: vw
> ### Keywords: misc
> 
> ### ** Examples
> 
>   ## also see demo(vw) from which this is a subset
> 
>   library(RVowpalWabbit)
> 
>   # Test 3: without -d, training only
>   # {VW} train-sets/0002.dat    -f models/0002.model
>   test3 <- c("-t", system.file("test", "train-sets", "0002.dat", package="RVowpalWabbit"),
+              "-f", system.file("test", "models", "0002.model", package="RVowpalWabbit"))
> 
>   res <- vw(test3)
Error in Rvw(args) : 
  can't open: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RVowpalWabbit/test/models/0002.model.writing for writing, exiting
Calls: vw -> Rvw -> .Call
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘viridis’ ‘ggdendro’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘Hmisc’ ‘vcd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multiCOBRA
> ### Title: Perform multiple COBRA runs
> ### Aliases: multiCOBRA
> 
> ### ** Examples
> 
> ## solve G11 problem nrun times  and plot the results of all nrun runs
> nrun=4
> feval=30
> 
> ## Defining the constraint problem: G11
> fn <- function(x) {
+   y<-x[1]*x[1]+((x[2]-1)^2)
+   y<-as.numeric(y)
+ 
+   g1 <- as.numeric(+(x[2] - x[1]^2))
+ 
+   return(c(objective=y, g1=g1))
+ }
> funcName="G11"
> d=2
> nConstraints<-1
> lower<-c(-1,-1)
> upper<-c(+1,+1)
> 
> ## Initializing and running cobra
> cobra <- cobraInit(xStart=c(0,0), fn=fn, fName=funcName, lower=lower, upper=upper,
+                    nConstraints=nConstraints,  feval=feval,
+                    initDesPoints=3*d, DOSAC=1,cobraSeed=1)
Error in loadNamespace(name) : there is no package called ‘scales’
Calls: cobraInit ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Loading required package: grid
Loading required package: polynom
Quitting from lines 409-415 (sadists.Rnw) 
Error: processing vignette ‘sadists.Rnw’ failed with diagnostics:
could not find function "qplot"
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘saeSim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: mvtnorm

Error: processing vignette ‘sc-intro.Rnw’ failed with diagnostics:
 chunk 1 
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘mixer’
Running examples in ‘satscanMapper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: satscanMapper
> ### Title: Function to map Results data produced by a SaTScan (TM) cluster
> ###   analysis
> ### Aliases: satscanMapper
> 
> ### ** Examples
> 
> ######
> #
> #  These examples focus on mapping the SaTScan (TM) data after the analysis
> #  has been completed.
> #  See the section on the CreateGeo4SS function for an example of how 
> #  to build a coordinates file (.geo) that matches the satscanMapper 
> #  boundary data.
> #
> ######
> 
> ######
> #
> #  Example # 1 - Mapping existing SaTScan (TM) results - "USStateLung" result files
> #     Make sure SaTScan (TM) results files are still located in the directories
> #     documented in the session saved (.prm) file.
> #
> #     This example maps data for the US States containing circular clusters.
> #
> #   Get location of .prm file and location to write mapping output files
> #
> 
> SSMInstDir <- system.file(package="satscanMapper", "extdata")
> 
> TT =c("Contiguous US States All Lung Cancer Mortality, 2004")
> 
> satscanMapper(resDir=SSMInstDir,                # path to .prm file location for output files. 
+                      prmFile  = "stateLung.prm", 
+                      title    = TT          )
Error in pdf(file = OutputFNpdf, width = vW, height = vH) : 
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/satscanMapper/extdata/stateLung-R01.pdf'
Calls: satscanMapper -> pdf
Execution halted
Package required but not available: ‘munsell’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 86-101 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘cowplot’ ‘ggstance’ ‘ggridges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggforce’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: nlme
Quitting from lines 147-161 (Estimating-effect-sizes.Rmd) 
Error: processing vignette ‘Estimating-effect-sizes.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘pROC’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ez’
Error in re-building vignettes:
  ...
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: ‘survey’

The following object is masked from ‘package:graphics’:

    dotchart


Error: processing vignette ‘SDaA_using_survey.Rnw’ failed with diagnostics:
 chunk 24 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘ggplot2’ ‘VIM’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotRules
> ### Title: Plot a rule set generated by a SDEFSR algorithm
> ### Aliases: plotRules
> 
> ### ** Examples
> 
> plotRules(habermanRules)
Package 'ggplot2' is not installed and must be installed to show the rule set plot. Do you want to install it? (Y/n): 
Error in plotRules(habermanRules) : Package ggplot2 is not available
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 538-540 (SDEFSRpackage.Rmd) 
Error: processing vignette ‘SDEFSRpackage.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘sdmpredictors-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_correlation
> ### Title: Plot the correlation matrix for the provided layercodes
> ### Aliases: plot_correlation
> 
> ### ** Examples
> 
> correlation <- layers_correlation(c("BO_calcite", "BO_damin", "MS_bathy_5m"))
> p <- plot_correlation(correlation)
Error: ggplot2 needed for the 'plot_correlation' function to work. Please install it.
Execution halted
Error in re-building vignettes:
  ...
Loading required package: raster
Loading required package: sp
Loading required package: rgdal
rgdal: version: 1.2-16, (SVN revision 701)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: /usr/share/gdal/2.2
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-6 
trying URL ‘http://sdmpredictors.samuelbosch.com/BO_ph_lonlat.tif’
Content type 'image/tiff' length 2518560 bytes (2.4 MB)
==================================================
downloaded 2.4 MB

trying URL ‘http://sdmpredictors.samuelbosch.com/BO_salinity_lonlat.tif’
Content type 'image/tiff' length 5841760 bytes (5.6 MB)
==================================================
downloaded 5.6 MB

trying URL ‘http://sdmpredictors.samuelbosch.com/BO_ph.tif’
Content type 'image/tiff' length 3201193 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

Quitting from lines 136-163 (quickstart.Rmd) 
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
ggplot2 needed for the 'plot_correlation' function to work. Please install it.
Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
[1] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sdmvspecies/external/env/bio1.bil" 
[2] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sdmvspecies/external/env/bio11.bil"
[3] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sdmvspecies/external/env/bio12.bil"
[4] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sdmvspecies/external/env/bio14.bil"
[5] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sdmvspecies/external/env/bio16.bil"
[6] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sdmvspecies/external/env/bio5.bil" 
[7] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sdmvspecies/external/env/bio7.bil" 

Error: processing vignette ‘sdmvspecies.Rnw’ failed with diagnostics:
 chunk 3 (label = bell_shaped_response_function) 
Error in library("ggplot2") : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘spsurvey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘scales’

Package suggested but not available for checking: ‘demography’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘geiger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggfortify’ ‘factoextra’ ‘ggdendro’ ‘plotly’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘lmerTest’ ‘Hmisc’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘quanteda’ ‘sentimentr’ ‘caret’ ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘qvalue’ ‘ggplot2’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dendextend’ ‘colorspace’

Packages suggested but not available for checking: ‘biclust’ ‘DendSer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘cowplot’ ‘caret’ ‘NMF’ ‘plotly’ ‘Hmisc’ ‘ggridges’

Packages suggested but not available for checking: ‘MAST’ ‘DESeq2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘tmap’ ‘ggplot2’ ‘mapview’
Error in re-building vignettes:
  ...
Quitting from lines 169-172 (sf5.Rmd) 
Error: processing vignette ‘sf5.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘SGP’
Package suggested but not available for checking: ‘threejs’
Error in re-building vignettes:
  ...
Loading required package: sp
rgeos version: 0.3-26, (SVN revision 560)
 GEOS runtime version: 3.6.2-CAPI-1.10.2 4d2925d6 
 Linking to sp version: 1.2-6 
 Polygon checking: TRUE 

Quitting from lines 221-222 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'scales'
Execution halted
Packages required but not available: ‘aqp’ ‘soilDB’ ‘Hmisc’ ‘scales’

Package suggested but not available for checking: ‘circlize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘alakazam’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggExtra’

Package suggested but not available for checking: ‘GGally’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aDataScene
> ### Title: A-Frame Scene with R data
> ### Aliases: aDataScene
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(scales)
Error in library(scales) : there is no package called ‘scales’
Execution halted
Packages required but not available: ‘heatmaply’ ‘viridis’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘difNLR’ ‘ggplot2’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘test-all.R’ [8s/15s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(shiny)
  > 
  > test_check("shiny")
  ── 1. Error: (unknown) (@test-plot-coordmap.R#2)  ──────────────────────────────
  there is no package called 'ggplot2'
  1: library(ggplot2) at testthat/test-plot-coordmap.R:2
  2: stop(txt, domain = NA)
  
  Unknown testing environment for test-staticdocs.R.
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 522 SKIPPED: 4 FAILED: 1
  1. Error: (unknown) (@test-plot-coordmap.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available:
  ‘bayesplot’ ‘colourpicker’ ‘ggplot2’ ‘rstan’ ‘threejs’

Package suggested but not available for checking: ‘rstanarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘viridis’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 42-50 (sigmoid.Rmd) 
Error: processing vignette ‘sigmoid.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘biclust’ ‘ComplexHeatmap’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘copula’ ‘ggplot2’ ‘Hmisc’
Packages suggested but not available for checking: ‘ggplot2’ ‘copula’
Package suggested but not available for checking: ‘robCompositions’
Error in re-building vignettes:
  ...
Loading required package: Rcpp
Loading required package: lattice
Loading required package: parallel
Loading required package: boot

Attaching package: ‘boot’

The following object is masked from ‘package:lattice’:

    melanoma

Loading required package: MASS

Error: processing vignette ‘simFrame-intro.Rnw’ failed with diagnostics:
 chunk 23 
Error in library("robCompositions") : 
  there is no package called ‘robCompositions’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 167-170 (Intro.Rmd) 
Error: processing vignette ‘Intro.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘DiagrammeR’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘simmer.plot’
Packages required but not available: ‘vcd’ ‘colorspace’ ‘VIM’ ‘EnvStats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘moveHMM’
Package suggested but not available for checking: ‘lmerTest’
Running ‘test-all.R’ [47s/57s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > if(require(testthat)) {
  + 
  +     test_check("simr")
  + }
  Loading required package: testthat
  Loading required package: simr
  Loading required package: lme4
  Loading required package: Matrix
  
  Attaching package: 'simr'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  ── 1. Error: lmer tests work (@test_testLibrary.R#52)  ─────────────────────────
  there is no package called 'lmerTest'
  1: doTest(fm1, fixed("x", "sa")) at testthat/test_testLibrary.R:52
  2: doTest.default(fm1, fixed("x", "sa"))
  3: test(object)
  4: test(., xname)
  5: lmerTest::summary
  6: getExportedValue(pkg, name)
  7: asNamespace(ns)
  8: getNamespace(ns)
  9: tryCatch(loadNamespace(name), error = function(e) stop(e))
  10: tryCatchList(expr, classes, parentenv, handlers)
  11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  12: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 100 SKIPPED: 2 FAILED: 1
  1. Error: lmer tests work (@test_testLibrary.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘colorspace’

Packages suggested but not available for checking: ‘Hmisc’ ‘copula’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addCondition
> ### Title: Add a single column to existing data set based on a condition
> ### Aliases: addCondition
> 
> ### ** Examples
> 
> 
> # New data set
> 
> def <- defData(varname = "x", dist = "categorical", formula = ".33;.33")
> def <- defData(def, varname="y", dist="uniform", formula="-5;5")
> 
> dt <- genData(1000, def)
> 
> # Define conditions
> 
> defC <- defCondition(condition = "x == 1", formula = "5 + 2*y-.5*y^2",
+                      variance = 1,dist = "normal")
> defC <- defCondition(defC, condition = "x == 2",
+                      formula = "3 - 3*y + y^2", variance = 2, dist="normal")
> defC <- defCondition(defC, condition = "x == 3",
+                      formula = "abs(y)", dist="poisson")
> 
> # Add column
> 
> dt <- addCondition(defC, dt, "NewVar")
> 
> # Plot data
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: data.table
Quitting from lines 38-282 (simstudy.Rmd) 
Error: processing vignette ‘simstudy.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running ‘testthat.R’ [51s/104s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Got this Sys.setenv line from https://github.com/luckyrandom/cmaker/blob/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0/tests/testthat.R
  > # so that devtools:check() won't hang.
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(simulator)
  
  Attaching package: 'simulator'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > 
  > test_check("simulator")
  ── 1. Failure: create makes a template that can be run without error (@test-crea
  any(grepl("error", readLines(a), ignore.case = TRUE)) isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 119 SKIPPED: 3 FAILED: 1
  1. Failure: create makes a template that can be run without error (@test-create.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-13

Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Quitting from lines 74-75 (elastic-net.Rmd) 
Error: processing vignette ‘elastic-net.Rmd’ failed with diagnostics:
To use this function, ggplot2 must be installed.
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 130-154 (uniform_rng_with_sitmo.Rmd) 
Error: processing vignette ‘uniform_rng_with_sitmo.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘Hmisc’ ‘sjPlot’
Running examples in ‘sjlabelled-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_term_labels
> ### Title: Retrieve labels of model terms from regression models
> ### Aliases: get_term_labels get_dv_labels
> 
> ### ** Examples
> 
> # use data set with labelled data
> data(efc)
> 
> fit <- lm(barthtot ~ c160age + c12hour + c161sex + c172code, data = efc)
> get_term_labels(fit)
                                   c160age 
                              "carer' age" 
                                   c12hour 
"average number of hours of care per week" 
                                   c161sex 
                          "carer's gender" 
                                  c172code 
              "carer's level of education" 
> 
> # make "education" categorical
> library(sjmisc)
> efc$c172code <- to_factor(efc$c172code)
> fit <- lm(barthtot ~ c160age + c12hour + c161sex + c172code, data = efc)
> get_term_labels(fit)
                                   c160age 
                              "carer' age" 
                                   c12hour 
"average number of hours of care per week" 
                                   c161sex 
                          "carer's gender" 
                                  c172code 
              "carer's level of education" 
                                 c172code1 
                  "low level of education" 
                                 c172code2 
         "intermediate level of education" 
                                 c172code3 
                 "high level of education" 
> 
> # get label of dv
> get_dv_labels(fit)
[1] "Total score BARTHEL INDEX"
> 
> # create "labelled" plot
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 62-67 (intro_sjlabelled.Rmd) 
Error: processing vignette ‘intro_sjlabelled.Rmd’ failed with diagnostics:
there is no package called 'Hmisc'
Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘Hmisc’ ‘sjPlot’ ‘sjstats’
Packages required but not available:
  ‘effects’ ‘ggeffects’ ‘ggplot2’ ‘merTools’ ‘scales’ ‘sjstats’

Packages suggested but not available for checking:
  ‘ggrepel’ ‘ggridges’ ‘lmerTest’ ‘rstanarm’

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

Packages suggested but not available for checking:
  ‘brms’ ‘ggplot2’ ‘Hmisc’ ‘lmerTest’ ‘pROC’ ‘rstanarm’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘adegenet’ ‘hierfstat’ ‘pegas’ ‘rmetasim’ ‘strataG’ ‘swfscMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: mosaic
Loading required package: Sleuth2
Quitting from lines 130-145 (chapter01-HortonMosaic.Rnw) 
Error: processing vignette ‘chapter01-HortonMosaic.Rnw’ failed with diagnostics:
could not find function "trellis.par.set"
Execution halted
Packages suggested but not available for checking: ‘Hmisc’ ‘mosaic’
Error in re-building vignettes:
  ...
Loading required package: mosaic
Loading required package: Sleuth3
Quitting from lines 130-145 (chapter01-HortonMosaic.Rnw) 
Error: processing vignette ‘chapter01-HortonMosaic.Rnw’ failed with diagnostics:
could not find function "trellis.par.set"
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 65-69 (slim.Rmd) 
Error: processing vignette ‘slim.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘Hmisc’ ‘colorspace’ ‘weights’

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

Package suggested but not available for checking: ‘demography’

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

Package suggested but not available for checking: ‘Mcomp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 161-165 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘aqp’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘aqp’ ‘munsell’

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

Packages suggested but not available for checking: ‘plotKML’ ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tdr’
Error in re-building vignettes:
  ...
Quitting from lines 23-25 (sophisthse_intro.Rmd) 
Error: processing vignette ‘sophisthse_intro.Rmd’ failed with diagnostics:
there is no package called 'forecast'
Execution halted
Error in re-building vignettes:
  ...
Sotkanet R tools (C) 2013-2017 rOpenGov
https://github.com/ropengov/sotkanet
Retrieving indicator 10013
Quitting from lines 99-114 (tutorial.Rmd) 
Error: processing vignette ‘tutorial.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘SciencesPo’
Package required but not available: ‘SpaDES.core’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘earlywarnings’
Packages required but not available: ‘ggplot2’ ‘RGraphics’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 643-691 (sparseHessianFD.Rnw) 
Error: processing vignette ‘sparseHessianFD.Rnw’ failed with diagnostics:
there is no package called 'scales'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 73-87 (sparseMVN.Rnw) 
Error: processing vignette ‘sparseMVN.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘leaflet’

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggpolypath’ ‘viridis’
Error in re-building vignettes:
  ...
Quitting from lines 25-45 (sfbabel.Rmd) 
Error: processing vignette ‘sfbabel.Rmd’ failed with diagnostics:
there is no package called 'viridis'
Execution halted
Packages suggested but not available for checking: ‘geiger’ ‘rgbif’
Packages required but not available:
  ‘hyperSpec’ ‘GGally’ ‘ggplot2’ ‘ggdendro’ ‘caret’ ‘qdap’ ‘xcms’
  ‘MAIT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rssa’ ‘ncdf.tools’ ‘JBTools’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_pop_totals
> ### Title: Plot characteristic summary output from
> ###   summarize_top_spew_region as totals
> ### Aliases: plot_pop_totals
> 
> ### ** Examples
> 
> data(tartanville)
> 
> tartanville_syneco <- spew(tartanville$pop_table, tartanville$shapefile, 
+                            tartanville$pums_h, tartanville$pums_p)
Loading required package: sp
[1] "Place has 0 Households!"
> plot_syneco(tartanville, tartanville_syneco, region_name = "Tartanville")
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: plot_syneco ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Running ‘testthat.R’ [32s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spew)
  > 
  > test_check("spew")
  ── 1. Error: functions for summarizing spew synecos in console (@test-summarize-
  there is no package called 'ggplot2'
  1: ggplot2::fortify at testthat/test-summarize-spew.R:6
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 100 SKIPPED: 7 FAILED: 1
  1. Error: functions for summarizing spew synecos in console (@test-summarize-spew.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
Quitting from lines 45-64 (spew-quickstart.Rmd) 
Error: processing vignette ‘spew-quickstart.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘ezsim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 187-193 (DPsplithalf-vignette.Rmd) 
Error: processing vignette ‘DPsplithalf-vignette.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘rgbif’ ‘rbison’ ‘rvertnet’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘R2BayesX’ ‘BayesX’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 30-35 (spThin_vignette.Rmd) 
Error: processing vignette ‘spThin_vignette.Rmd’ failed with diagnostics:
unable to install packages
Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
Quitting from lines 224-233 (CN_v2.Rmd) 
Error: processing vignette ‘CN_v2.Rmd’ failed with diagnostics:
there is no package called 'GGally'
Execution halted
Error in re-building vignettes:
  ...
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: 'survey'

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

    dotchart

Quitting from lines 31-47 (srvyr-vs-survey.Rmd) 
Error: processing vignette ‘srvyr-vs-survey.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘ssc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coBC
> ### Title: Train the Co-bagging model
> ### Aliases: coBC
> 
> ### ** Examples
> 
> # This example is part of CoBC demo.
> # Use demo(CoBC) to see all the examples.
> 
> ## Load Wine data set
> data(wine)
> 
> x <- wine[, -14] # instances without classes
> y <- wine[, 14] # the classes
> x <- scale(x) # scale the attributes
> 
> ## Prepare data
> set.seed(20)
> # Use 50% of instances for training
> tra.idx <- sample(x = length(y), size = ceiling(length(y) * 0.5))
> xtrain <- x[tra.idx,] # training instances
> ytrain <- y[tra.idx]  # classes of training instances
> # Use 70% of train instances as unlabeled set
> tra.na.idx <- sample(x = length(tra.idx), size = ceiling(length(tra.idx) * 0.7))
> ytrain[tra.na.idx] <- NA # remove class information of unlabeled instances
> 
> # Use the other 50% of instances for inductive testing
> tst.idx <- setdiff(1:length(y), tra.idx)
> xitest <- x[tst.idx,] # testing instances
> yitest <- y[tst.idx] # classes of testing instances
> 
> ## Example: Using the Euclidean distance in proxy package.
> m <- coBC(xtrain, ytrain, dist = "Euclidean")
> pred <- predict(m, xitest)
> caret::confusionMatrix(table(pred, yitest))
Error in loadNamespace(name) : there is no package called ‘caret’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages required but not available: ‘ggplot2’ ‘Hmisc’

Package suggested but not available for checking: ‘viridis’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘afex’ ‘lmerTest’
Error in re-building vignettes:
  ...
Quitting from lines 362-367 (using-standardize.Rmd) 
Error: processing vignette ‘using-standardize.Rmd’ failed with diagnostics:
there is no package called 'afex'
Execution halted
Package which this enhances but not available for checking: ‘rms’
Packages required but not available: ‘ggplot2’ ‘ggdendro’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘tidyverse’ ‘leaflet’
Error in re-building vignettes:
  ...
Loading required package: proxy

Attaching package: ‘proxy’

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

    as.dist, dist

The following object is masked from ‘package:base’:

    as.matrix

Loading required package: clue
Loading required package: survey
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: ‘survey’

The following object is masked from ‘package:graphics’:

    dotchart

Loading required package: RANN
Loading required package: lpSolve
Loading required package: Hmisc

Error: processing vignette ‘Statistical_Matching_with_StatMatch.Rnw’ failed with diagnostics:
 chunk 4 
Error in spearman2(n.income ~ area5 + urb + hsize + age + sex + marital +  : 
  could not find function "spearman2"
Execution halted
Running examples in ‘Stickbreaker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sim.data.from.priors.for.mod.selection
> ### Title: Simulate data from priors for doing model selection
> ### Aliases: sim.data.from.priors.for.mod.selection
> 
> ### ** Examples
> 
>  n.muts <- 4
>  n.muts <- length(Khan.data[1,])-1
>  geno.matrix <- Khan.data[,seq(1, n.muts)]
>  fit.matrix <- as.matrix(Khan.data[,(n.muts+1)])
>  outdir <- system.file("extdata",package="Stickbreaker")
>  file.name <- paste("Training_simulated_priors_fit_data_", n.muts, "muts.txt", sep="")
>  outpath <- paste(outdir, file.name, sep="/")
>  sim.data.from.priors.for.mod.selection(n.muts,
+    c(0.05, 0.5),
+    c(0, 0.25),
+    c(4),
+    1,
+    c(0.1, 10),
+    1.1,
+    1,
+    c(2,1),
+    outpath,
+    50,
+    coe.sim.model="identical",
+    coe.dist.par=NA,
+    print.interval=NA)
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Stickbreaker/extdata/Training_simulated_priors_fit_data_5muts.txt': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: sim.data.from.priors.for.mod.selection -> write.table -> file
Execution halted
Package required but not available: ‘stm’

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

Package suggested but not available for checking: ‘demography’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘ggmap’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘UsingR’
Package which this enhances but not available for checking: ‘tmap’
Packages required but not available:
  ‘apex’ ‘adegenet’ ‘copula’ ‘ggplot2’ ‘Hmisc’ ‘pegas’ ‘swfscMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘lmerTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: StructFDR
Loading required package: nlme
Loading required package: ape
Loading required package: cluster
Loading required package: dirmult
Loading required package: matrixStats
Loading required package: ggplot2
Loading required package: reshape
Quitting from lines 172-187 (StructFDR.Rmd) 
Error: processing vignette ‘StructFDR.Rmd’ failed with diagnostics:
could not find function "ggplot"
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘scales’ ‘ggdendro’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘caret’ ‘ggplot2’ ‘Hmisc’
Error in re-building vignettes:
  ...
Quitting from lines 191-213 (Guide-to-SuperLearner.Rmd) 
Error: processing vignette ‘Guide-to-SuperLearner.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘DoE.base’
Running examples in ‘support.BWS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bws.dataset
> ### Title: Creating a data set suitable for BWS analysis on the basis of
> ###   counting and modeling approaches
> ### Aliases: bws.dataset
> ### Keywords: datagen survival
> 
> ### ** Examples
> 
> ## load packages
> require(DoE.base) # include oa.design() used to generate a two-level OMED
Loading required package: DoE.base
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘DoE.base’
> require(crossdes) # include find.BIB() used to generate a BIBD
Loading required package: crossdes
Loading required package: AlgDesign
Loading required package: gtools
> require(survival) # include clogit() used to analyze responses
Loading required package: survival
> 
> ## case 1: BWS using a two-level OMED
> ## suppose that ten respondents answered twelve BWS questions valuing nine items
> 
> # create a two-level OMED with nine factors
> set.seed(123) # set seed for random number generator
> des1 <- oa.design(nfactors = 9, nlevels = 2)
Error in oa.design(nfactors = 9, nlevels = 2) : 
  could not find function "oa.design"
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘rms’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: schemper
> ### Title: Distance-based estimator of survival predictive accuracy
> ###   proposed by Schemper and Henderson
> ### Aliases: schemper
> ### Keywords: classif
> 
> ### ** Examples
> 
> 
> library(rms)
Error in library(rms) : there is no package called ‘rms’
Execution halted
Packages suggested but not available for checking:
  ‘colorspace’ ‘scales’ ‘INLA’ ‘ggplot2’
Packages required but not available: ‘rms’ ‘rstan’

Packages suggested but not available for checking: ‘shinystan’ ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘cowplot’ ‘ggthemes’ ‘viridis’

Package suggested but not available for checking: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggpubr’ ‘scales’ ‘survMisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘copula’ ‘tsDyn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘GGally’ ‘scales’

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

Packages suggested but not available for checking:
  ‘robets’ ‘scales’ ‘tidyquant’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [3s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(swirlify)
  > library(swirl)
  
  | Hi! Type swirl() when you are ready to begin.
  
  
  Attaching package: 'swirl'
  
  The following object is masked from 'package:testthat':
  
      skip
  
  > 
  > test_check("swirlify")
  ── 1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R
  all(correct_output %in% readLines(file.path(path, "test.log"))) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 7 SKIPPED: 0 FAILED: 1
  1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘ggplot2’ ‘ggmap’

Package suggested but not available for checking: ‘colorspace’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert.mpoly
> ### Title: Convert between mpoly and list representations of multivariate
> ###   polynomials
> ### Aliases: ' convert.mpoly '
> 
> ### ** Examples
> 
> # create an mpoly object here
> 
> # convert from mpoly to list representation
> library(mpoly)
Error in library(mpoly) : there is no package called ‘mpoly’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Loading required package: cubature
Loading required package: combinat

Attaching package: ‘combinat’

The following object is masked from ‘package:utils’:

    combn

Loading required package: multipol
Loading required package: abind

Attaching package: ‘multipol’

The following object is masked from ‘package:base’:

    single


Error: processing vignette ‘symmoments.rnw’ failed with diagnostics:
 chunk 13 (label = noncentral3a) 
Error in library(mpoly) : there is no package called ‘mpoly’
Execution halted
Packages suggested but not available for checking: ‘corrgram’ ‘vcd’
Running examples in ‘tabplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: num2fac
> ### Title: Transform a numerical vector to a factor
> ### Aliases: num2fac
> 
> ### ** Examples
> 
> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> data(diamonds)
Warning in data(diamonds) : data set ‘diamonds’ not found
> 
> diamonds$price2 <- num2fac(diamonds$price)
Loading required namespace: classInt
Error in quantile(num, na.rm = TRUE) : object 'diamonds' not found
Calls: num2fac -> quantile
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 19-24 (tabplot-timings.Rmd) 
Error: processing vignette ‘tabplot-timings.Rmd’ failed with diagnostics:
object ‘diamonds’ not found
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 91-94 (new-methods.Rmd) 
Error: processing vignette ‘new-methods.Rmd’ failed with diagnostics:
there is no package called 'forecast'
Execution halted
Packages required but not available: ‘pixiedust’ ‘ggplot2’ ‘viridis’

Package suggested but not available for checking: ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘LSAmitR’
Packages suggested but not available for checking: ‘rms’ ‘Hmisc’
Error in re-building vignettes:
  ...
Quitting from lines 13-18 (fda-example.Rmd) 
Error: processing vignette ‘fda-example.Rmd’ failed with diagnostics:
there is no package called 'Hmisc'
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘tcgsaseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘DESeq2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘tcpl’
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.

Error: processing vignette ‘tcpl_Overview.Rnw’ failed with diagnostics:
 chunk 4 
Error in rsqlite_send_query(conn@ptr, statement) : 
  attempt to write a readonly database
Execution halted
Packages required but not available:
  ‘leaflet’ ‘threejs’ ‘d3heatmap’ ‘plotly’ ‘DiagrammeR’ ‘scales’
  ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘arulesViz’ ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/tesseract.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 29-51 (GIAValidationExample.Rmd) 
Error: processing vignette ‘GIAValidationExample.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘GGally’

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

Packages which this enhances but not available for checking: ‘rms’ ‘xergm’
Packages required but not available:
  ‘ggplot2’ ‘plotly’ ‘rstan’ ‘scales’ ‘stm’

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘phyloseq’ ‘tidyverse’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘forecast’ ‘hts’ ‘forecTheta’ ‘ggplot2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: S3 methods ‘complete.data.frame’, ‘complete_.data.frame’, ‘drop_na.data.frame’, ‘drop_na.default’, ‘drop_na_.data.frame’, ‘expand.data.frame’, ‘expand.default’, ‘expand.grouped_df’, ‘expand_.data.frame’, ‘extract.data.frame’, ‘extract.default’, ‘extract_.data.frame’, ‘fill.data.frame’, ‘fill.default’, ‘fill.grouped_df’, ‘fill_.data.frame’, ‘full_seq.Date’, ‘full_seq.POSIXct’, ‘full_seq.numeric’, ‘gather.data.frame’, ‘gather.default’, ‘gather_.data.frame’, ‘nest.data.frame’, ‘nest.default’, ‘nest_.data.frame’, ‘replace_na.data.frame’, ‘separate.data.frame’, ‘separate.default’, ‘separate_.data.frame’, ‘separate_rows.data.frame’, ‘separate_rows.default’, ‘separate_rows_.data.frame’, ‘spread.data.frame’, ‘spread.default’, ‘spread_.data.frame’, ‘unite.data.frame’, ‘unite.default’, ‘unite_.data.frame’, ‘unnest.data.frame’, ‘unnest.default’, ‘unnest_.data.frame’ were declared in NAMESPACE but not found
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/tibbletime.Rcheck/00install.out’ for details.
Packages required but not available: ‘ggplot2’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘rstanarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tidyverse’ ‘ggplot2’ ‘scales’ ‘timetk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘quanteda’ ‘ggplot2’ ‘scales’ ‘stm’
Running examples in ‘tidytext-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lda_tidiers
> ### Title: Tidiers for LDA objects from the topicmodels package
> ### Aliases: lda_tidiers tidy.LDA augment.LDA glance.LDA
> 
> ### ** Examples
> 
> 
> if (requireNamespace("topicmodels", quietly = TRUE)) {
+   set.seed(2016)
+   library(dplyr)
+   library(topicmodels)
+ 
+   data("AssociatedPress", package = "topicmodels")
+   ap <- AssociatedPress[1:100, ]
+   lda <- LDA(ap, control = list(alpha = 0.1), k = 4)
+ 
+   # get term distribution within each topic
+   td_lda <- tidy(lda)
+   td_lda
+ 
+   library(ggplot2)
+ 
+   # visualize the top terms within each topic
+   td_lda_filtered <- td_lda %>%
+     filter(beta > .004) %>%
+     mutate(term = reorder(term, beta))
+ 
+   ggplot(td_lda_filtered, aes(term, beta)) +
+     geom_bar(stat = "identity") +
+     facet_wrap(~ topic, scales = "free") +
+     theme(axis.text.x = element_text(angle = 90, size = 15))
+ 
+   # get classification of each document
+   td_lda_docs <- tidy(lda, matrix = "gamma")
+   td_lda_docs
+ 
+   doc_classes <- td_lda_docs %>%
+     group_by(document) %>%
+     top_n(1) %>%
+     ungroup()
+ 
+   doc_classes
+ 
+   # which were we most uncertain about?
+   doc_classes %>%
+     arrange(gamma)
+ }

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 13-17 (tf_idf.Rmd) 
Error: processing vignette ‘tf_idf.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘ggtree’ ‘treeio’
Error in re-building vignettes:
  ...
Quitting from lines 60-71 (smells.Rmd) 
Error: processing vignette ‘smells.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘abd’ ‘mosaic’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘alakazam’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggthemes’ ‘leaflet’
Packages required but not available: ‘ggplot2’ ‘mtconnectR’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCalendarHeatmap
> ### Title: Calendar Heatmap
> ### Aliases: plotCalendarHeatmap
> 
> ### ** Examples
> 
> dates = timeSequence(from = '2012-01-01', to = '2012-12-31', by = 'day')
>    plotCalendarHeatmap(as.Date(dates), 1:366)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
Loading required package: plyr

Attaching package: ‘plyr’

The following object is masked from ‘package:lubridate’:

    here

Error in ggplot(tp, aes(monthweek, weekday, fill = values)) : 
  could not find function "ggplot"
Calls: plotCalendarHeatmap
Execution halted
Package required but not available: ‘forecast’

Packages suggested but not available for checking:
  ‘robets’ ‘scales’ ‘tidyverse’ ‘tidyquant’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 18-23 (tintHTML.Rmd) 
Error: processing vignette ‘tintHTML.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘scales’

Package which this enhances but not available for checking: ‘ggplot2’
Packages required but not available: ‘leaflet’ ‘mapview’

Package suggested but not available for checking: ‘ggplot2’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gg_na
> ### Title: Plot missing data
> ### Aliases: gg_na
> ### Keywords: NA
> 
> ### ** Examples
> 
> # What a mess. 
> # Feature 10 is missing a lot. Observations 25 and 35 are completely missing.
> # Most of features 40-45 are missing, except for the first few observations.
> set.seed(2016-07-12)
> x <- matrix(1, nrow=50, ncol=50)
> x[sample(prod(dim(x)), 100)] <- NA
> x <- data.frame(x)
> x$X10[sample(length(x$X10), 25)] <- NA
> x[c(25, 35), ] <- NA
> x[1:40, 40:45] <- NA
> gg_na(x)
Error: ggplot2 and reshape2 packages needed for this function to work. Please install them.
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘ggthemes’ ‘scales’ ‘ggmap’ ‘GGally’

Package suggested but not available for checking: ‘ggnetwork’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: display_xy
> ### Title: Display tour path with a scatterplot
> ### Aliases: display_xy animate_xy
> 
> ### ** Examples
> 
> animate_xy(flea[, 1:6])
Using half_range 0.98
> animate(flea[, 1:6], tour_path=grand_tour(), display=display_xy())
Using half_range 0.98
> animate(flea[, 1:6], tour_path=grand_tour(),
+   display=display_xy(axes = "bottomleft"))
Using half_range 0.98
> animate(flea[, 1:6], tour_path=grand_tour(),
+   display=display_xy(half_range = 0.5))
> animate_xy(flea[, 1:6], tour_path=little_tour())
Using half_range 0.98
> animate_xy(flea[, 1:3], tour_path=guided_tour(holes), sphere = TRUE)
Value 0.474 39.1% better (0.653 away) - NEW BASIS
Using half_range 0.69
> animate_xy(flea[, 1:6], center = FALSE)
Using half_range 1.9
> 
> # The default axes are centered, like a biplot, but there are other options
> animate_xy(flea[, 1:6], axes = "bottomleft")
Using half_range 0.98
> animate_xy(flea[, 1:6], axes = "off")
Using half_range 0.98
> animate_xy(flea[, 1:6], dependence_tour(c(1, 2, 1, 2, 1, 2)),
+   axes = "bottomleft")
Using half_range 0.98
> require(colorspace)
Loading required package: colorspace
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘colorspace’
> pal <- rainbow_hcl(length(levels(flea$species)))
Error in rainbow_hcl(length(levels(flea$species))) : 
  could not find function "rainbow_hcl"
Execution halted
Packages suggested but not available for checking: ‘rmongodb’ ‘ggplot2’
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'tcpl'
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.
toxboot 0.1.1
MongoDB settings (?toxbootConf):
  TOXBOOT_HOST: NA
  TOXBOOT_DBNS: NA
  TOXBOOT_USER: NA
  TOXBOOT_DB: NA
MySQL settings:
  Host: Not Configured
  Database: Not Configured
  User: Not Configured
Loading required package: DBI
Quitting from lines 27-35 (toxboot.Rmd) 
Error: processing vignette ‘toxboot.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggthemes’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggmap’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘OpenStreetMap’
Error in re-building vignettes:
  ...
Loading required package: trapezoid
Loading required package: plyr
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’

Error: processing vignette ‘trapezoid.Rnw’ failed with diagnostics:
 chunk 2 (label = trapezoid) 
Error in ggplot(data = data.frame(x, density), aes(x = x, y = density)) : 
  could not find function "ggplot"
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette ‘treecm.Rnw’ failed with diagnostics:
 chunk 14 (label = exStabilization5) 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘phyloseq’ ‘ggplot2’

Package suggested but not available for checking: ‘adaptiveGPCA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘colorspace’ ‘ggplot2’

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

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

Package suggested but not available for checking: ‘ggplot2’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stick_to
> ### Title: Work on a specific attribute within a pipeline
> ### Aliases: stick_to stick_to_ unstick
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(observer)
> 
> df <- ggplot2::diamonds %>% 
+   mutate(depth2 = 100*2*z/(x+y)) %>% 
+   observe_if(abs(depth-depth2) < 1)
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: %>% ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages required but not available: ‘ggplot2’ ‘scales’ ‘ez’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘SIBER’

Package suggested but not available for checking: ‘MCMCvis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 13-16 (quickstart.Rmd) 
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ICtest’ ‘forecast’

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

Package suggested but not available for checking: ‘FinTS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘hts’
Running ‘testthat.R’ [26s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(rlang)
  > library(tibble)
  > library(lubridate)
  
  Attaching package: 'lubridate'
  
  The following object is masked from 'package:base':
  
      date
  
  > library(testthat)
  
  Attaching package: 'testthat'
  
  The following objects are masked from 'package:rlang':
  
      is_false, is_null, is_true
  
  > library(tsibble)
  
  Attaching package: 'tsibble'
  
  The following object is masked from 'package:lubridate':
  
      interval
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("tsibble")
  ── 1. Error: Test a hts (@test-ts-tsibble.R#35)  ───────────────────────────────
  there is no package called 'hts'
  1: hts::htseg1 at testthat/test-ts-tsibble.R:35
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ── 2. Error: Test a tsibble with composite keys (@test-tsibble-ts.R#46)  ───────
  there is no package called 'hts'
  1: hts::htseg1 at testthat/test-tsibble-ts.R:46
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 215 SKIPPED: 0 FAILED: 2
  1. Error: Test a hts (@test-ts-tsibble.R#35) 
  2. Error: Test a tsibble with composite keys (@test-tsibble-ts.R#46) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘MAPA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘bfast’ ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 41-43 (example.Rmd) 
Error: processing vignette ‘example.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 105-107 (ExamplesTukeytrendtest.Rnw) 
Error: processing vignette ‘ExamplesTukeytrendtest.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘mapview’
Running examples in ‘uavRmp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read_gpx
> ### Title: Read GPX file
> ### Aliases: read_gpx
> 
> ### ** Examples
> 
> ## for visualisation we are using mapview
> require(mapview)
Loading required package: mapview
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mapview’
> ## assign  GPX file
> gpxFN <- system.file("extdata", "flighttrack.gpx", package = "uavRmp")
> 
> ## read it
> gpx <- read_gpx(gpxFN, layers=c("tracks"))
> 
> ## plot it
> mapview::mapview(gpx)
Error in loadNamespace(name) : there is no package called ‘mapview’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages required but not available: ‘ggmap’ ‘ggplot2’ ‘ggthemes’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ImbC
> ### Title: Synthetic Imbalanced Data Set for a Multi-class Task
> ### Aliases: ImbC
> ### Keywords: datasets
> 
> ### ** Examples
> 
> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> data(ImbC)
> summary(ImbC)
       X1              X2         Class    
 Min.   :-13.5843   cat :300   normal:859  
 1st Qu.: -2.6930   dog :400   rare1 : 10  
 Median : -0.1592   fish:300   rare2 :131  
 Mean   : -0.1064                          
 3rd Qu.:  2.4633                          
 Max.   : 12.7836                          
> ggplot(data=ImbC, aes(x=X2, y=X1, color=Class))+geom_jitter()
Error in ggplot(data = ImbC, aes(x = X2, y = X1, color = Class)) : 
  could not find function "ggplot"
Execution halted
Running examples in ‘ukgasapi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dataItemExplorer
> ### Title: Data Item Explorer API
> ### Aliases: dataItemExplorer
> 
> ### ** Examples
> 
> # Specify the data item(s) to enquire from API
> dataitems <- c('Storage Injection, Actual',
+                'Storage Withdrawal, Actual')
> 
> # Initialise API (requires internet connection for this step)
> response <- dataItemExplorer(dataitems,
+                              fromdate = '2013-10-01',
+                              todate='2015-09-30')
*   Trying 40.127.139.252...
* TCP_NODELAY set
* Connected to marketinformation.natgrid.co.uk (40.127.139.252) port 80 (#0)
> POST /MIPIws-public/public/publicwebservice.asmx HTTP/1.1
Host: marketinformation.natgrid.co.uk
Accept: text/xml
Content-Type: application/soap+xml; charset=utf-8
Content-Length: 655

* upload completely sent off: 655 out of 655 bytes
< HTTP/1.1 200 OK
< Cache-Control: private, max-age=0
< Content-Length: 518779
< Content-Type: application/soap+xml; charset=utf-8
< Server: Microsoft-IIS/10.0
< X-AspNet-Version: 4.0.30319
< X-Powered-By: ASP.NET
< Set-Cookie: ARRAffinity=656be05bcb90b8383e83555c0a718d835067bc586deb0215c9a10d4c84a7f80b;Path=/;HttpOnly;Domain=marketinformation.natgrid.co.uk
< Date: Thu, 11 Jan 2018 07:25:15 GMT
< 
* Connection #0 to host marketinformation.natgrid.co.uk left intact
> 
> # Visualise the results on a chart
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘ggplot2’ ‘AdaptGauss’

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

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggforce’
Error in re-building vignettes:
  ...
Error : cannot convert cm*km/h/s into cm/s
Quitting from lines 384-387 (measurement_units_in_R.Rmd) 
Error: processing vignette ‘measurement_units_in_R.Rmd’ failed with diagnostics:
there is no package called 'ggforce'
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

If you use data from the unvotes package, please cite the following:

Erik Voeten "Data and Analyses of Voting in the UN General Assembly" Routledge Handbook of International Organization, edited by Bob Reinalda (published May 27, 2013)
Warning: code chunks must not depend on the uncached chunk "joined"
Warning: Column `rcid` has different attributes on LHS and RHS of join
Warning: code chunks must not depend on the uncached chunk "by_country_year"

Attaching package: 'lubridate'

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

    date

Quitting from lines 76-87 (unvotes.Rmd) 
Error: processing vignette ‘unvotes.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘mcmcplots’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘data.tree’ ‘DiagrammeR’ ‘GGally’ ‘ggplot2’ ‘ggrepel’ ‘ggridges’
  ‘scales’ ‘viridis’

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

Packages suggested but not available for checking: ‘ggplot2’ ‘vcd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_usmap
> ### Title: Conveniently plot basic US map
> ### Aliases: plot_usmap
> 
> ### ** Examples
> 
> plot_usmap()
Error in plot_usmap() : 
  Please install `ggplot2`. Use: install.packages("ggplot2")
Execution halted
Running ‘testthat.R’ [6s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(usmap)
  > 
  > test_check("usmap")
  ── 1. Error: (unknown) (@test-plot.R#4)  ───────────────────────────────────────
  Please install `ggplot2`. Use: install.packages("ggplot2")
  1: plot_usmap() at testthat/test-plot.R:4
  2: stop("Please install `ggplot2`. Use: install.packages(\"ggplot2\")")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 52 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-plot.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 21-22 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
Please install `ggplot2`. Use: install.packages("ggplot2")
Execution halted
Package required but not available: ‘mldr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘cowplot’ ‘ggplot2’ ‘scales’

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

Packages suggested but not available for checking: ‘effects’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘adegenet’ ‘ggplot2’ ‘poppr’ ‘scales’
Running ‘testthat.R’ [55s/66s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library("testthat")
  > #library("vcfR")
  > #
  > #
  > test_check("vcfR")
  Loading required package: vcfR
  
     *****       ***   vcfR   ***       *****
     This is vcfR 1.6.0 
       browseVignettes('vcfR') # Documentation
       citation('vcfR') # Citation
     *****       *****      *****       *****
  
  Failed with error:  'there is no package called 'adegenet''
  ── 1. Failure: vcfR2genind works (@test_conversion.R#15)  ──────────────────────
  `my_genind` inherits from `matrix` not `genind`.
  
  ── 2. Error: vcfR2genlight works (@test_conversion.R#22)  ──────────────────────
  there is no package called 'adegenet'
  1: suppressMessages(library(adegenet)) at testthat/test_conversion.R:22
  2: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
  3: library(adegenet)
  4: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 442 SKIPPED: 5 FAILED: 2
  1. Failure: vcfR2genind works (@test_conversion.R#15) 
  2. Error: vcfR2genlight works (@test_conversion.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Failed with error:  'there is no package called 'adegenet''
Quitting from lines 83-86 (converting_data.Rmd) 
Error: processing vignette ‘converting_data.Rmd’ failed with diagnostics:
there is no package called 'poppr'
Execution halted
Packages required but not available: ‘drc’ ‘ggplot2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘colorspace’ ‘vcd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘ggbeeswarm’
Error in re-building vignettes:
  ...
Loading required package: sm
Package 'sm', version 2.2-5.4: type help(sm) for summary information

Error: processing vignette ‘methodComparison.Rnw’ failed with diagnostics:
 chunk 18 (label = showDiamond) 
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Execution halted
Running examples in ‘viridisLite-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: viridis
> ### Title: Matplotlib 'viridis' color map
> ### Aliases: viridis viridisMap magma inferno plasma
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘scales’ ‘colorspace’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘colourpicker’ ‘ggraph’
Packages required but not available: ‘ggmap’ ‘marmap’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘viridis’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect,
    is.unsorted, lapply, lengths, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans,
    rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Quitting from lines 74-84 (my-vignette.Rmd) 
Error: processing vignette ‘my-vignette.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 35-60 (vtreatRareLevels.Rmd) 
Error: processing vignette ‘vtreatRareLevels.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘bayesplot’ ‘rstan’ ‘ggplot2’

Package suggested but not available for checking: ‘diagis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘shinystan’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coor.graph
> ### Title: Coordinated singing graphs
> ### Aliases: coor.graph
> 
> ### ** Examples
> 
> {
+ 
+ # First set temporary folder
+ setwd(tempdir())
+ 
+ # load simulate singing events  (see data documentation)
+ data(sim.coor.sing)
+ 
+ # make coor.graphs in tiff format
+ coor.graph(X = sim.coor.sing, ovlp = TRUE, only.coor = FALSE, xl =2, res =80, 
+ it = "tiff", img = TRUE)
+ 
+ 
+ #' # make coor.graphs in graphic device format
+ cgs <- coor.graph(X = sim.coor.sing, ovlp = TRUE, only.coor = FALSE, img = FALSE)
+ 
+ cgs
+ }
Error in coor.graph(X = sim.coor.sing, ovlp = TRUE, only.coor = FALSE,  : 
  'install ggplot2 to use coor.graph()'
Execution halted
Packages required but not available: ‘colorspace’ ‘ggplot2’

Package suggested but not available for checking: ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 193-201 (Using_the_wbstats_package.Rmd) 
Error: processing vignette ‘Using_the_wbstats_package.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘pROC’ ‘ggplot2’
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("WeightedROC")
  Loading required package: WeightedROC
  ── 1. Error: aSAH (@test-auc.R#101)  ───────────────────────────────────────────
  there is no package called 'pROC'
  1: library(pROC) at testthat/test-auc.R:101
  2: stop(txt, domain = NA)
  
  label
  -1 
   4 
  label
  1 
  4 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 44 SKIPPED: 0 FAILED: 1
  1. Error: aSAH (@test-auc.R#101) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette ‘Definition.Rnw’ failed with diagnostics:
 chunk 1 (label = curve) 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘cobalt’

Package suggested but not available for checking: ‘sbw’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multilinestring
> ### Title: Make WKT multilinestring objects
> ### Aliases: multilinestring
> 
> ### ** Examples
> 
> ## empty multilinestring
> multilinestring("empty")
[1] "MULTILINESTRING EMPTY"
> # multilinestring("stuff")
> 
> # character string
> x <- "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> multilinestring(x)
[1] "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> 
> # data.frame
> df <- data.frame(long = c(30, 45, 10), lat = c(20, 40, 40))
> df2 <- data.frame(long = c(15, 40, 10), lat = c(5, 10, 20))
> multilinestring(df, df2, fmt=0)
[1] "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> multilinestring(df, df2, fmt=0) %>% lint
[1] TRUE
> multilinestring(df, df2) %>% wktview(zoom=3)
Error: Please install leaflet
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 64-80 (who_vignette.Rmd) 
Error: processing vignette ‘who_vignette.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘ggraph’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 13-20 (united_nations.Rmd) 
Error: processing vignette ‘united_nations.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘leaflet’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addFlexTables
> ### Title: Read Word document with bookmarks and create other Word document
> ###   with rendered tables in place.
> ### Aliases: addFlexTables
> 
> ### ** Examples
> 
> library(ReporteRs)
Loading required package: ReporteRsjars
> ft_mtcars <- vanilla.table(mtcars)
> ft_iris <- vanilla.table(iris)
> FT <- list(ft_mtcars=ft_mtcars,ft_iris=ft_iris)
> addFlexTables(
+   paste(examplePath(),'templates/templateFT.docx',sep = ''),
+   paste(examplePath(),'results/resultFT.docx',sep = ''),
+   FT)
Error in writeDoc.docx(doc, docxOut) : 
  writeDoc: Cannot write to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/WordR/examples/results/resultFT.docx
Calls: addFlexTables -> <Anonymous> -> writeDoc.docx
Execution halted
Packages suggested but not available for checking: ‘colorspace’ ‘ez’
Error in re-building vignettes:
  ...
Loading required package: WRS2
Loading required package: beanplot
Loading required package: car
Loading required package: MASS
Loading required package: colorspace
Loading required package: reshape
Loading required package: ez
Loading required package: MBESS
Quitting from lines 445-446 (WRS2.Rnw) 
Error: processing vignette ‘WRS2.Rnw’ failed with diagnostics:
could not find function "rainbow_hcl"
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 57-82 (wrswoR.Rmd) 
Error: processing vignette ‘wrswoR.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘caret’ ‘EnvStats’ ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘btergm’ ‘GERGM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘DiagrammeR’ ‘vcd’
Error in re-building vignettes:
  ...
Loading required package: xgboost
Loading required package: Matrix
Loading required package: data.table
Loading required package: vcd
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'vcd'
Installing package into '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages'
(as 'lib' is unspecified)
Warning in install.packages("vcd") :
  'lib = "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages"' is not writable
Quitting from lines 28-32 (discoverYourData.Rmd) 
Error: processing vignette ‘discoverYourData.Rmd’ failed with diagnostics:
unable to install packages
Execution halted
Error in re-building vignettes:
  ...
Loading required package: XLConnect
Loading required package: XLConnectJars
XLConnect 0.2-13 by Mirai Solutions GmbH [aut],
  Martin Studer [cre],
  The Apache Software Foundation [ctb, cph] (Apache POI),
  Graph Builder [ctb, cph] (Curvesapi Java library)
http://www.mirai-solutions.com ,
http://miraisolutions.wordpress.com
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’

Error: processing vignette ‘XLConnect.Rnw’ failed with diagnostics:
 chunk 20 (label = AdvancedExampleP5) 
Error in ggplot(gcurr, aes(Date, Value, colour = Currency)) : 
  could not find function "ggplot"
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggforce’ ‘vpc’

Package suggested but not available for checking: ‘plotly’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bam_to_reads
> ### Title: Convert BAM files into BED files containing the reads overlaping
> ###   the specified annotations.
> ### Aliases: bam_to_reads
> 
> ### ** Examples
> 
> bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
> data(annotations)
> bam_to_reads(bamfile, annotations)
Error in FUN(X[[i]], ...) : failed to build index
  file: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Calls: bam_to_reads -> .index_bam
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 48-60 (yCrypticRNAs.Rmd) 
Error: processing vignette ‘yCrypticRNAs.Rmd’ failed with diagnostics:
failed to build index
  file: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Execution halted
Packages suggested but not available for checking: ‘copula’ ‘ggplot2’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘zdat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(abjutils)
  > 
  > test_check("abjutils")
  ── 1. Failure: rm_accent is the converted version of a string with all non-ASCII
  rm_accent(acute) not equal to `nudeAcute`.
  1/1 mismatches
  x[1]: "'a'e'i'o'u'A'E'I'O'U'y'Y"
  y[1]: "aeiouAEIOUyY"
  
  ── 2. Failure: rm_accent is the converted version of a string with all non-ASCII
  rm_accent(circunflex) not equal to `nudeCircunflex`.
  1/1 mismatches
  x[1]: "^a^e^i^o^u^A^E^I^O^U"
  y[1]: "aeiouAEIOU"
  
  ── 3. Failure: rm_accent is the converted version of a string with all non-ASCII
  rm_accent(tilde) not equal to `nudeTilde`.
  1/1 mismatches
  x[1]: "~a~o~A~O~n~N"
  y[1]: "aoAOnN"
  
  ── 4. Failure: rm_accent is the converted version of a string with all non-ASCII
  rm_accent(umlaut) not equal to `nudeUmlaut`.
  1/1 mismatches
  x[1]: "\"a\"e\"i\"o\"u\"A\"E\"I\"O\"U\"y"
  y[1]: "aeiouAEIOUy"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 10 SKIPPED: 0 FAILED: 4
  1. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#30) 
  2. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#32) 
  3. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#33) 
  4. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data       2.8Mb
    pictures   2.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 15-19 (ALA4R.Rmd) 
Error: processing vignette 'ALA4R.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Package required but not available: ‘RWeka’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 39-73 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘MBESS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘kebabs’
Error in re-building vignettes:
  ...
Quitting from lines 31-44 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
there is no package called 'kebabs'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.




More than one TSN found for taxon 'Canis lupus'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Canis latrans'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Acer saccharum'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Castor canadensis'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Alces alces'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Acer rubrum'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Vulpes vulpes'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Salix babylonica'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Odocoileus virginianus'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Betula alleghaniensis'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Rangifer tarandus'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Juniperus occidentalis'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Pinus strobus'!

            Enter rownumber of taxon (other inputs will return 'NA'):
Running examples in ‘AR1seg-Ex.R’ failed
The error most likely occurred in:

> ### Name: AR1seg-package
> ### Title: Segmentation of an AR(1) Gaussian process
> ### Aliases: AR1seg-package AR1seg
> 
> ### ** Examples
> 
> library(AR1seg)
> data(y)
> res=AR1seg_func(y,Kmax=15,rho=TRUE)
Error in cumsum(datasize)[breaks[k, 1:k]] : 
  only 0's may be mixed with negative subscripts
Calls: AR1seg_func -> Segmentor -> Segmentor.default
Execution halted
Error in re-building vignettes:
  ...
Warning in summary.cross(cross) :
  Some markers at the same position on chr 1B1,1D,2B,2D1,3A,3B,3D,4A,5A,5B,5D,6D,7A,7B,7D; use jittermap().
Warning in summary.cross(cross) :
  Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
  (Perhaps it is in basepairs?)
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7,L.8,L.9; use jittermap().
Warning in heatMap(mapBC6, chr = c("L.3", "L.5", "L.8", "L.9"), lmax = 70) :
  Running est.rf.
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7; use jittermap().
Running examples in ‘autothresholdr-Ex.R’ failed
The error most likely occurred in:

> ### Name: auto_thresh
> ### Title: Automatically threshold an image.
> ### Aliases: auto_thresh auto_thresh_mask auto_thresh_apply_mask
> 
> ### ** Examples
> 
> img <- EBImage::readImage(system.file("extdata", "eg.tif",
+                           package = "autothresholdr"), as.is = TRUE)
> auto_thresh(img, "huang")
Error in rJava::.jnew("Auto_Threshold_R") : 
  java.lang.UnsupportedClassVersionError: Auto_Threshold_R : Unsupported major.minor version 52.0
Calls: auto_thresh -> <Anonymous> -> .External
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 40-43 (autothresholdr.Rmd) 
Error: processing vignette 'autothresholdr.Rmd' failed with diagnostics:
java.lang.UnsupportedClassVersionError: Auto_Threshold_R : Unsupported major.minor version 52.0
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.6Mb
installed size is 73.8Mb
  sub-directories of 1Mb or more:
    java  73.8Mb
File ‘aylmer/libs/aylmer.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘aylmer.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘aylmer.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.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
Package suggested but not available for checking: ‘sybilSBML’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
Package suggested but not available for checking: ‘mzR’
Package suggested but not available for checking: ‘BayesXsrc’
Package unavailable to check Rd xrefs: ‘BayesXsrc’
Installation failed.
See ‘/home/ripley/R/packages/tests32/BANOVA.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 46-49 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted