rAllRisksFactors: no visible global function definition for ‘new’
rAssetDistribution: no visible global function definition for ‘new’
rDefaultSpread: no visible global function definition for ‘new’
rLiquiditySpread: no visible global function definition for ‘new’
rRealEstate: no visible global function definition for ‘new’
rShortRate: no visible global function definition for ‘new’
rStock: no visible global function definition for ‘new’
EuroCall_Stock_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
EuroCall_ZC_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
EuroPut_Stock_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
EuroPut_ZC_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
MartingaleTest,Scenarios: no visible global function definition for
  ‘plot’
MartingaleTest,Scenarios: no visible global function definition for
  ‘lines’
MartingaleTest,Scenarios: no visible global function definition for
  ‘title’
customPathsGeneration,Scenarios: no visible global function definition
  for ‘rnorm’
Undefined global functions or variables:
  lines new plot pnorm rnorm title
Consider adding
  importFrom("graphics", "lines", "plot", "title")
  importFrom("methods", "new")
  importFrom("stats", "pnorm", "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.Transition: no visible global function definition for ‘rnorm’
.Transition.DC: no visible global function definition for ‘runif’
CondPdf.CC.interval: no visible global function definition for ‘plot’
CondPdf.DC.interval: no visible global function definition for ‘plot’
Simu.Cond.HR: no visible global function definition for ‘rpois’
Simu.Cond.HR: no visible global function definition for ‘runif’
Simu.Cond.HR: no visible global function definition for ‘hist’
Simu.Cond.HR: no visible global function definition for ‘var’
Simu.HR: no visible global function definition for ‘rpois’
Simu.HR: no visible global function definition for ‘runif’
Simu.HR: no visible global function definition for ‘hist’
Simu.HR: no visible global function definition for ‘var’
Simu.PDMP: no visible global function definition for ‘plot’
Simu.PDMP.DC: no visible global function definition for ‘plot’
plotCHR: no visible global function definition for ‘plot’
plotHR: no visible global function definition for ‘plot’
Undefined global functions or variables:
  hist plot rnorm rpois runif var
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "rnorm", "rpois", "runif", "var")
to your NAMESPACE file.
EW : PhiP : Phi: no visible global function definition for ‘pnorm’
EWplot: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot pnorm
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
extfunnel: no visible global function definition for ‘qnorm’
extfunnel: no visible global function definition for ‘meta.summaries’
extfunnel: no visible global function definition for ‘flush.console’
extfunnel: no visible global function definition for ‘qt’
extfunnel: no visible global function definition for ‘dev.new’
extfunnel: no visible global function definition for ‘par’
extfunnel: no visible global function definition for ‘plot’
extfunnel: no visible global function definition for ‘polygon’
extfunnel: no visible global function definition for ‘segments’
extfunnel: no visible global function definition for ‘abline’
extfunnel: no visible global function definition for ‘axis’
extfunnel: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box dev.new flush.console meta.summaries par plot polygon
  qnorm qt segments
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "box", "par", "plot",
             "polygon", "segments")
  importFrom("stats", "qnorm", "qt")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
createFormula: no visible global function definition for ‘tail’
createFormula: no visible global function definition for ‘head’
createFormula: no visible global function definition for ‘as.formula’
ezsim: no visible global function definition for ‘runif’
plot.ezsim: no visible global function definition for ‘quantile’
plot.ezsim: no visible global function definition for ‘head’
plot.ezsim: no visible global function definition for ‘tail’
plot.ezsim: no visible global function definition for ‘plot’
plot.ezsim: no visible binding for global variable ‘dnorm’
plot.ezsim: no visible binding for global variable ‘pdf’
plot.ezsim: no visible global function definition for ‘dev.off’
plot.ezsim : <anonymous>: no visible global function definition for
  ‘dev.new’
plot.summary.ezsim: no visible global function definition for ‘head’
plot.summary.ezsim: no visible global function definition for ‘tail’
plot.summary.ezsim: no visible binding for global variable ‘pdf’
plot.summary.ezsim: no visible global function definition for ‘dev.off’
plot.summary.ezsim : <anonymous>: no visible global function definition
  for ‘dev.new’
Undefined global functions or variables:
  as.formula dev.new dev.off dnorm head pdf plot quantile runif tail
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "plot")
  importFrom("stats", "as.formula", "dnorm", "quantile", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
PTSingleAssetBarrierOption2: no visible global function definition for
  ‘new’
newton: no visible global function definition for ‘plot’
newton: no visible global function definition for ‘abline’
probInRange: no visible global function definition for ‘pnorm’
shortfall_risk: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline new plot pnorm
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "new")
  importFrom("stats", "pnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Killed
FDRreg: no visible global function definition for ‘dnorm’
colnormalize: no visible global function definition for ‘sd’
efron: no visible global function definition for ‘median’
efron: no visible global function definition for ‘hist’
efron: no visible global function definition for ‘glm’
efron: no visible binding for global variable ‘poisson’
efron: no visible global function definition for ‘qchisq’
efron: no visible global function definition for ‘predict’
efron: no visible global function definition for ‘quantile’
efron: no visible global function definition for ‘lm’
efron: no visible global function definition for ‘coef’
make.bspline.matrix: no visible global function definition for
  ‘quantile’
plotFDR: no visible global function definition for ‘hist’
plotFDR: no visible global function definition for ‘par’
plotFDR: no visible global function definition for ‘plot’
plotFDR: no visible global function definition for ‘axis’
plotFDR: no visible global function definition for ‘lines’
plotFDR: no visible global function definition for ‘legend’
plotFDR: no visible global function definition for ‘rug’
plotFDR: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis coef dnorm glm hist legend lines lm median par plot poisson
  predict qchisq quantile rug sd title
Consider adding
  importFrom("graphics", "axis", "hist", "legend", "lines", "par",
             "plot", "rug", "title")
  importFrom("stats", "coef", "dnorm", "glm", "lm", "median", "poisson",
             "predict", "qchisq", "quantile", "sd")
to your NAMESPACE file.
fgeasy: no visible global function definition for ‘dist’
fgeasy : cor.est: no visible global function definition for ‘cor.test’
fgeasy: no visible binding for global variable ‘var’
fgperm : runrand: no visible global function definition for ‘runif’
fgperm : runrand: no visible global function definition for ‘ave’
fgploc : runrand: no visible global function definition for ‘runif’
fgploc : runrand: no visible global function definition for ‘ave’
fyshuffle: no visible global function definition for ‘runif’
plot.fg: no visible global function definition for ‘par’
plot.fg: no visible global function definition for ‘plot’
plot.fg: no visible global function definition for ‘segments’
plot.fg: no visible binding for global variable ‘quantile’
plot.fg: no visible global function definition for ‘abline’
plot.fg: no visible global function definition for ‘axis’
summary.fg: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  abline ave axis cor.test dist par plot quantile runif segments var
Consider adding
  importFrom("graphics", "abline", "axis", "par", "plot", "segments")
  importFrom("stats", "ave", "cor.test", "dist", "quantile", "runif",
             "var")
to your NAMESPACE file.
Rd file 'POICalc.Rd':
  \examples lines wider than 100 characters:
        irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
                                  'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')

Rd file 'POIcoords_-.Rd':
  \examples lines wider than 100 characters:
        irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
                                  'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')

Rd file 'plotPOI.Rd':
  \examples lines wider than 100 characters:
          graphPOI@docs <- matrix(c(seq(1:nrow(graphPOI@objeto)), seq(1:nrow(graphPOI@objeto))), ncol = 2)
        graphPOI@objeto <- graphPOI@objeto <- rbind(c(0,.05), c(.05,0), c(0,-.05), c(-.05,0) ,round(circulo(0,0,.3,PLOT = FALSE),2))
         1 - (max(USArrests[,4]) - USArrests[,4]) / (max(max(USArrests[,4]) - USArrests[,4])),                                               ... [TRUNCATED]
        usaPOI@wordsInQuery <- c(paste('High', names(USArrests[,c(1,2,4)])), paste('Low', names(USArrests[,c(1,2,4)])))

These lines will be truncated in the PDF manual.
lsmacof: no visible global function definition for ‘cmdscale’
plotInc: no visible global function definition for ‘rainbow’
plotInc: no visible global function definition for ‘plot’
prepareCalib: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cmdscale lm plot rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "plot")
  importFrom("stats", "cmdscale", "lm")
to your NAMESPACE file.
GCV: no visible global function definition for ‘lm’
GCV: no visible global function definition for ‘resid’
ffplot: no visible global function definition for ‘par’
ffplot: no visible global function definition for ‘plot’
ffplot: no visible global function definition for ‘points’
ffplot: no visible global function definition for ‘legend’
flowfield: no visible global function definition for ‘write.table’
gpr: no visible global function definition for ‘quantile’
gpr: no visible global function definition for ‘var’
smoothp: no visible global function definition for ‘lm’
smoothp: no visible global function definition for ‘predict’
smoothp: no visible global function definition for ‘resid’
smoothp: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  legend lm optimize par plot points predict quantile resid var
  write.table
Consider adding
  importFrom("graphics", "legend", "par", "plot", "points")
  importFrom("stats", "lm", "optimize", "predict", "quantile", "resid",
             "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
ComputeDCT2FFT: no visible global function definition for ‘fft’
ComputeSemipgramFFT: no visible global function definition for ‘fft’
WaveVarFD: no visible global function definition for ‘modwt’
do.fd.estimate: no visible global function definition for
  ‘performParallel’
do.fd.estimate2d.simple: no visible global function definition for
  ‘median’
fd.Genton: no visible global function definition for ‘qn’
fd.estimate.matrix: no visible global function definition for
  ‘performParallel’
fd.plot.legend: no visible global function definition for ‘legend’
fd.plot.loglog: no visible global function definition for ‘plot’
fd.plot.loglog: no visible global function definition for ‘points’
fd.plot.loglog: no visible global function definition for ‘abline’
summary.FractalDim: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  abline fft legend median modwt performParallel plot points qn sd
Consider adding
  importFrom("graphics", "abline", "legend", "plot", "points")
  importFrom("stats", "fft", "median", "sd")
to your NAMESPACE file.
custom.draw.circle: no visible global function definition for ‘lines’
frcc: no visible binding for global variable ‘sd’
frcc: no visible global function definition for ‘cor.shrink’
frcc: no visible global function definition for ‘cor’
frcc: no visible global function definition for ‘p.asym’
generate_multivariate_normal_sample: no visible global function
  definition for ‘mvrnorm’
plot_units: no visible binding for global variable ‘sd’
plot_units: no visible global function definition for ‘plot’
plot_units: no visible global function definition for ‘points’
plot_units: no visible global function definition for ‘textxy’
plot_variables: no visible global function definition for ‘plot’
plot_variables: no visible global function definition for ‘points’
plot_variables: no visible global function definition for ‘textxy’
plot_variables: no visible global function definition for ‘segments’
Undefined global functions or variables:
  cor cor.shrink lines mvrnorm p.asym plot points sd segments textxy
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
.FunFEM.main: no visible global function definition for ‘kmeans’
.FunFEM.main: no visible global function definition for ‘rmultinom’
.FunFEM.main: no visible global function definition for ‘cutree’
.FunFEM.main: no visible global function definition for ‘hclust’
.FunFEM.main: no visible global function definition for ‘dist’
.FunFEM.main: no visible global function definition for ‘par’
.FunFEM.main: no visible global function definition for ‘plot’
.mstep: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov cutree dist hclust kmeans par plot rmultinom
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "cov", "cutree", "dist", "hclust", "kmeans",
             "rmultinom")
to your NAMESPACE file.
FPTsimul: no visible global function definition for ‘runif’
histplot: no visible global function definition for ‘dev.new’
histplot: no visible global function definition for ‘hist’
histplot: no visible global function definition for ‘par’
histplot: no visible global function definition for ‘plot’
histplot: no visible global function definition for ‘legend’
mdt: no visible binding for global variable ‘deltat’
plot.FPTdensity: no visible global function definition for ‘dev.new’
plot.FPTdensity: no visible global function definition for ‘plot’
res_summary: no visible global function definition for ‘write.table’
res_summary: no visible global function definition for ‘sd’
res_summary: no visible global function definition for ‘median’
vdt: no visible binding for global variable ‘deltat’
Undefined global functions or variables:
  deltat dev.new hist legend median par plot runif sd write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "legend", "par", "plot")
  importFrom("stats", "deltat", "median", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
CI.RMSEA: no visible global function definition for ‘qchisq’
CI.RMSEA: no visible global function definition for ‘pchisq’
GAIPE.RMSEA: no visible global function definition for ‘par’
GAIPE.RMSEA: no visible global function definition for ‘plot’
GAIPE.RMSEA: no visible global function definition for ‘abline’
GAIPE.RMSEA: no visible global function definition for ‘colors’
GAIPE.RMSEA: no visible global function definition for ‘text’
GAIPE.RMSEA: no visible global function definition for ‘arrows’
GAIPE.RMSEA: no visible global function definition for ‘points’
GAIPE.RMSEA: no visible global function definition for ‘axis’
GAIPE.RMSEA: no visible global function definition for ‘lines’
GAIPE.RMSEA: no visible global function definition for ‘legend’
GAIPE.RMSEA: no visible global function definition for ‘pchisq’
GAIPE.RMSEA: no visible global function definition for ‘qchisq’
GAIPE.RMSEA: no visible global function definition for ‘mtext’
GAIPE.RMSEA: no visible global function definition for ‘title’
PA.RMSEA: no visible global function definition for ‘pchisq’
PA.RMSEA: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  abline arrows axis colors legend lines mtext par pchisq plot points
  qchisq text title
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "abline", "arrows", "axis", "legend", "lines",
             "mtext", "par", "plot", "points", "text", "title")
  importFrom("stats", "pchisq", "qchisq")
to your NAMESPACE file.
cvriskMSM: no visible global function definition for ‘predict’
plotcvriskMSM: no visible global function definition for ‘plot’
plotcvriskMSM: no visible binding for global variable ‘lines’
plotcvriskMSM: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot predict
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
GAMBoost: no visible global function definition for ‘binomial’
GAMBoost: no visible global function definition for ‘gaussian’
GAMBoost: no visible global function definition for ‘poisson’
GAMBoost: no visible binding for global variable ‘sd’
GAMBoost: no visible global function definition for ‘Matrix’
calc.confidence.bands: no visible global function definition for
  ‘predict’
cv.GAMBoost: no visible global function definition for ‘binomial’
cv.GAMBoost : eval.fold: no visible global function definition for
  ‘predict’
cv.GAMBoost: no visible global function definition for ‘mclapply’
cv.GAMBoost: no visible binding for global variable ‘var’
estimPVal: no visible global function definition for ‘mclapply’
plot.GAMBoost: no visible global function definition for ‘plot’
plot.GAMBoost: no visible global function definition for ‘lines’
Undefined global functions or variables:
  Matrix binomial gaussian lines mclapply plot poisson predict sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "binomial", "gaussian", "poisson", "predict", "sd",
             "var")
to your NAMESPACE file.
contindic.gb2: no visible global function definition for ‘contour’
contindic.gb2: no visible global function definition for ‘box’
contindic.gb2: no visible global function definition for ‘mtext’
contprof.gb2: no visible global function definition for ‘image’
contprof.gb2: no visible global function definition for ‘heat.colors’
contprof.gb2: no visible global function definition for ‘contour’
contprof.gb2: no visible global function definition for ‘text’
contprof.gb2: no visible global function definition for ‘box’
dplot.cavgb2: no visible global function definition for ‘par’
dplot.cavgb2: no visible global function definition for ‘curve’
dplot.cavgb2: no visible global function definition for ‘legend’
dplot.cavgb2: no visible global function definition for ‘plot’
dplot.cavgb2: no visible global function definition for ‘lines’
dplot.cgb2: no visible global function definition for ‘curve’
dplot.cgb2: no visible global function definition for ‘lines’
dplot.cgb2: no visible global function definition for ‘legend’
plotsML.gb2: no visible global function definition for ‘par’
plotsML.gb2: no visible global function definition for ‘plot’
plotsML.gb2: no visible global function definition for ‘abline’
plotsML.gb2: no visible global function definition for ‘curve’
plotsML.gb2: no visible global function definition for ‘legend’
saveplot : <local>: no visible global function definition for ‘dev.set’
saveplot : <local>: no visible global function definition for
  ‘dev.print’
saveplot : <local>: no visible binding for global variable ‘pdf’
Undefined global functions or variables:
  abline box contour curve dev.print dev.set heat.colors image legend
  lines mtext par pdf plot text
Consider adding
  importFrom("grDevices", "dev.print", "dev.set", "heat.colors", "pdf")
  importFrom("graphics", "abline", "box", "contour", "curve", "image",
             "legend", "lines", "mtext", "par", "plot", "text")
to your NAMESPACE file.
coeplot: no visible global function definition for ‘plot’
coeplot: no visible global function definition for ‘axis’
coeplot: no visible global function definition for ‘lines’
coeplot: no visible global function definition for ‘title’
coeplot: no visible global function definition for ‘legend’
corplot: no visible global function definition for ‘par’
corplot: no visible global function definition for ‘pairs’
corplot: no visible global function definition for ‘strwidth’
lm.estimate: no visible global function definition for ‘as.formula’
lm.estimate: no visible global function definition for ‘glm’
panel.cor: no visible global function definition for ‘par’
panel.cor: no visible global function definition for ‘cor’
panel.cor: no visible global function definition for ‘strwidth’
panel.cor: no visible global function definition for ‘text’
panel.smooth.r: no visible global function definition for ‘par’
panel.smooth.r: no visible global function definition for ‘points’
panel.smooth.r: no visible global function definition for ‘lines’
posplot: no visible global function definition for ‘par’
posplot: no visible global function definition for ‘barplot’
posplot: no visible global function definition for ‘plot’
posplot: no visible global function definition for ‘points’
Undefined global functions or variables:
  as.formula axis barplot cor glm legend lines pairs par plot points
  strwidth text title
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "pairs",
             "par", "plot", "points", "strwidth", "text", "title")
  importFrom("stats", "as.formula", "cor", "glm")
to your NAMESPACE file.
plot.rbga: no visible global function definition for ‘par’
plot.rbga: no visible global function definition for ‘hist’
plot.rbga: no visible global function definition for ‘plot’
plot.rbga: no visible global function definition for ‘lines’
rbga: no visible global function definition for ‘runif’
rbga: no visible global function definition for ‘dnorm’
rbga.bin: no visible global function definition for ‘dnorm’
rbga.bin: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm hist lines par plot runif
Consider adding
  importFrom("graphics", "hist", "lines", "par", "plot")
  importFrom("stats", "dnorm", "runif")
to your NAMESPACE file.
splineAnalyze: no visible global function definition for ‘var’
splineAnalyze: no visible global function definition for ‘par’
splineAnalyze: no visible global function definition for ‘plot’
splineAnalyze: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines par plot var
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "var")
to your NAMESPACE file.
PAEA : <anonymous>: no visible global function definition for
  ‘integrate’
PAEAAnalysis: no visible global function definition for
  ‘txtProgressBar’
PAEAAnalysis : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
PAEAAnalysis: no visible global function definition for ‘par’
PAEAAnalysis: no visible global function definition for ‘barplot’
chdirSig: no visible global function definition for ‘prcomp’
chdirSig: no visible global function definition for ‘rchisq’
chdirSig: no visible global function definition for ‘txtProgressBar’
chdirSig : <anonymous> : <anonymous>: no visible global function
  definition for ‘setTxtProgressBar’
chdirplots : <anonymous>: no visible global function definition for
  ‘par’
chdirplots : <anonymous>: no visible global function definition for
  ‘plot’
chdirplots : <anonymous>: no visible global function definition for
  ‘arrows’
chdirplots : <anonymous>: no visible global function definition for
  ‘barplot’
multigmtPAEAAnalysis: no visible global function definition for
  ‘txtProgressBar’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘setTxtProgressBar’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘data’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘write.table’
Undefined global functions or variables:
  arrows barplot data integrate par plot prcomp rchisq
  setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("graphics", "arrows", "barplot", "par", "plot")
  importFrom("stats", "integrate", "prcomp", "rchisq")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
geoscaleBox: no visible global function definition for ‘boxplot’
geoscaleBox: no visible global function definition for ‘par’
geoscaleBox: no visible global function definition for ‘plot’
geoscaleBox: no visible global function definition for ‘text’
geoscaleBox: no visible global function definition for ‘segments’
geoscaleBox: no visible global function definition for ‘rect’
geoscaleBox: no visible global function definition for ‘rgb’
geoscaleBox: no visible global function definition for ‘polygon’
geoscaleBox: no visible global function definition for ‘points’
geoscaleBox: no visible global function definition for ‘axis’
geoscalePlot: no visible global function definition for ‘par’
geoscalePlot: no visible global function definition for ‘plot’
geoscalePlot: no visible global function definition for ‘text’
geoscalePlot: no visible global function definition for ‘segments’
geoscalePlot: no visible global function definition for ‘rect’
geoscalePlot: no visible global function definition for ‘rgb’
geoscalePlot: no visible global function definition for ‘points’
geoscalePlot: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis boxplot par plot points polygon rect rgb segments text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "boxplot", "par", "plot", "points",
             "polygon", "rect", "segments", "text")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gglasso.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘gglogo-alphabet.Rmd’ using rmarkdown

Attaching package: 'gglogo'

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

    fortify

Killed
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ggtern.Rcheck/00install.out’ for details.
acovamcmc: no visible global function definition for ‘rnorm’
acovamcmc: no visible global function definition for ‘rgamma’
acovamcmc: no visible binding for global variable ‘quantile’
acovamcmc: no visible global function definition for ‘quantile’
acovamcmc: no visible global function definition for ‘var’
plot.acovamcmc: no visible global function definition for ‘dev.new’
plot.acovamcmc: no visible global function definition for ‘par’
plot.acovamcmc: no visible global function definition for ‘plot’
plot.acovamcmc: no visible global function definition for ‘density’
plot.acovamcmc: no visible global function definition for ‘acf’
plot.acovamcmc: no visible global function definition for ‘contour’
plot.acovamcmc: no visible global function definition for ‘image’
plot.acovamcmc: no visible global function definition for ‘persp’
Undefined global functions or variables:
  acf contour density dev.new image par persp plot quantile rgamma
  rnorm var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "contour", "image", "par", "persp", "plot")
  importFrom("stats", "acf", "density", "quantile", "rgamma", "rnorm",
             "var")
to your NAMESPACE file.
CumulativeVarPlot: no visible global function definition for ‘plot’
CumulativeVarPlot: no visible global function definition for ‘axis’
PCplot: no visible global function definition for ‘par’
PCplot: no visible global function definition for ‘plot’
PCplot: no visible global function definition for ‘rainbow’
PCplot: no visible global function definition for ‘density’
gDist: no visible global function definition for ‘plot’
gDist: no visible global function definition for ‘density’
gDist: no visible global function definition for ‘abline’
gPCA.batchdetect: no visible global function definition for ‘var’
Undefined global functions or variables:
  abline axis density par plot rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "par", "plot")
  importFrom("stats", "density", "var")
to your NAMESPACE file.
Resdata : prepdata: no visible global function definition for ‘sqldf’
gpca : Build3d: no visible global function definition for ‘dev.new’
gpca : Build3d: no visible global function definition for
  ‘scatterplot3d’
gpca : Build3d: no visible global function definition for ‘text’
gpca : Build3d: no visible global function definition for ‘plot’
gpca : Build3d: no visible global function definition for ‘abline’
gpca : Build3d: no visible global function definition for ‘rect’
gpca: no visible global function definition for ‘cor’
gpca: no visible global function definition for ‘dev.new’
gpca: no visible global function definition for ‘plot’
gpca: no visible global function definition for ‘text’
gpca: no visible global function definition for ‘abline’
gpca: no visible global function definition for ‘rect’
gpca: no visible global function definition for ‘scatterplot3d’
gpca: no visible global function definition for ‘segments’
gpca: no visible global function definition for ‘points’
gpca: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline cor dev.new plot points rect scatterplot3d segments sqldf text
  write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "plot", "points", "rect", "segments",
             "text")
  importFrom("stats", "cor")
  importFrom("utils", "write.table")
to your NAMESPACE file.
gpfr: no visible global function definition for ‘rnorm’
gpfr: no visible global function definition for ‘runif’
gpfrpred : <anonymous>: no visible global function definition for
  ‘predict’
gpfrtrain: no visible global function definition for ‘nlminb’
gppredict: no visible global function definition for ‘predict’
gpr: no visible global function definition for ‘rnorm’
gpr: no visible global function definition for ‘runif’
gpr: no visible global function definition for ‘lm’
gpr: no visible global function definition for ‘resid’
gpr: no visible global function definition for ‘nlminb’
main1: no visible global function definition for ‘lm’
main1: no visible global function definition for ‘resid’
main2 : <anonymous>: no visible global function definition for
  ‘predict’
main2: no visible global function definition for ‘predict’
main3: no visible global function definition for ‘lm’
main3: no visible global function definition for ‘resid’
plot.gpfr: no visible global function definition for ‘polygon’
plot.gpfr: no visible global function definition for ‘rgb’
plot.gpfr: no visible global function definition for ‘matpoints’
plot.gpfr: no visible global function definition for ‘matlines’
plot.gpfr: no visible global function definition for ‘lines’
plot.gpr: no visible global function definition for ‘plot’
plot.gpr: no visible global function definition for ‘polygon’
plot.gpr: no visible global function definition for ‘rgb’
plot.gpr: no visible global function definition for ‘points’
plot.gpr: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines lm matlines matpoints nlminb plot points polygon predict resid
  rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "matlines", "matpoints", "plot",
             "points", "polygon")
  importFrom("stats", "lm", "nlminb", "predict", "resid", "rnorm",
             "runif")
to your NAMESPACE file.
GriegSmith: no visible global function definition for ‘is.ppp’
envelopes: no visible binding for global variable ‘quantile’
plot.GriegSmith: no visible global function definition for ‘plot’
plot.GriegSmith: no visible global function definition for ‘lines’
plot.GriegSmith: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis is.ppp lines plot quantile
Consider adding
  importFrom("graphics", "axis", "lines", "plot")
  importFrom("stats", "quantile")
to your NAMESPACE file.
gte: no visible global function definition for ‘model.extract’
gte: no visible global function definition for ‘model.matrix’
gte: no visible binding for global variable ‘sd’
gte: no visible global function definition for ‘dnorm’
plot.gte: no visible global function definition for ‘plot’
plot.gte: no visible global function definition for ‘par’
plot.gte: no visible global function definition for ‘polygon’
plot.gte: no visible global function definition for ‘gray’
plot.gte: no visible global function definition for ‘lines’
plot.gte: no visible global function definition for ‘legend’
Undefined global functions or variables:
  dnorm gray legend lines model.extract model.matrix par plot polygon
  sd
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "legend", "lines", "par", "plot", "polygon")
  importFrom("stats", "dnorm", "model.extract", "model.matrix", "sd")
to your NAMESPACE file.
PoincarePlot: no visible global function definition for ‘plot’
PoincarePlot: no visible global function definition for ‘lines’
PoincarePlot: no visible global function definition for ‘lowess’
hctest: no visible global function definition for ‘cor.test’
rdplot: no visible global function definition for ‘plot’
rdplot: no visible global function definition for ‘lines’
rdplot: no visible global function definition for ‘lowess’
rdplot: no visible global function definition for ‘rgb’
simer: no visible global function definition for ‘runif’
simer: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  cor.test lines lowess plot rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "cor.test", "lowess", "rnorm", "runif")
to your NAMESPACE file.
heatmap.plus: no visible binding for global variable ‘dist’
heatmap.plus: no visible binding for global variable ‘hclust’
heatmap.plus : <anonymous>: no visible global function definition for
  ‘reorder’
heatmap.plus: no visible global function definition for ‘as.dendrogram’
heatmap.plus: no visible global function definition for
  ‘order.dendrogram’
heatmap.plus: no visible binding for global variable ‘sd’
heatmap.plus: no visible global function definition for ‘par’
heatmap.plus: no visible global function definition for ‘layout’
heatmap.plus: no visible global function definition for ‘image’
heatmap.plus: no visible global function definition for ‘axis’
heatmap.plus: no visible global function definition for ‘mtext’
heatmap.plus: no visible global function definition for ‘plot’
heatmap.plus: no visible global function definition for ‘frame’
heatmap.plus: no visible global function definition for ‘title’
Undefined global functions or variables:
  as.dendrogram axis dist frame hclust image layout mtext
  order.dendrogram par plot reorder sd title
Consider adding
  importFrom("graphics", "axis", "frame", "image", "layout", "mtext",
             "par", "plot", "title")
  importFrom("stats", "as.dendrogram", "dist", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
HubNetwork: no visible global function definition for ‘rbinom’
HubNetwork: no visible global function definition for ‘runif’
HubNetwork: no visible global function definition for ‘cov2cor’
binaryMCMC: no visible global function definition for ‘rbinom’
image.hbn: no visible global function definition for ‘col2rgb’
image.hbn: no visible global function definition for ‘rgb’
image.hbn: no visible global function definition for ‘dev.new’
image.hbn: no visible global function definition for ‘par’
image.hbn: no visible global function definition for ‘image’
image.hcov: no visible global function definition for ‘col2rgb’
image.hcov: no visible global function definition for ‘rgb’
image.hcov: no visible global function definition for ‘dev.new’
image.hcov: no visible global function definition for ‘par’
image.hcov: no visible global function definition for ‘image’
image.hglasso: no visible global function definition for ‘col2rgb’
image.hglasso: no visible global function definition for ‘rgb’
image.hglasso: no visible global function definition for ‘dev.new’
image.hglasso: no visible global function definition for ‘par’
image.hglasso: no visible global function definition for ‘image’
plot.hbn: no visible global function definition for ‘rgb’
plot.hbn: no visible global function definition for ‘plot’
plot.hcov: no visible global function definition for ‘rgb’
plot.hcov: no visible global function definition for ‘plot’
plot.hglasso: no visible global function definition for ‘rgb’
plot.hglasso: no visible global function definition for ‘plot’
Undefined global functions or variables:
  col2rgb cov2cor dev.new image par plot rbinom rgb runif
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rgb")
  importFrom("graphics", "image", "par", "plot")
  importFrom("stats", "cov2cor", "rbinom", "runif")
to your NAMESPACE file.
compute.contrasts: no visible binding for global variable ‘sd’
compute.contrasts: no visible global function definition for ‘cor’
compute.contrasts: no visible global function definition for ‘sd’
plot.estfdr: no visible global function definition for ‘plot’
plot.hiertest: no visible global function definition for ‘plot’
plot.hiertest: no visible global function definition for ‘legend’
Undefined global functions or variables:
  cor legend plot sd
Consider adding
  importFrom("graphics", "legend", "plot")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
overlay.sim: no visible global function definition for ‘points’
plotDistr: no visible global function definition for ‘dev.hold’
plotDistr: no visible global function definition for ‘dev.flush’
plotDistr: no visible global function definition for ‘plot’
plotDistr: no visible global function definition for ‘segments’
Undefined global functions or variables:
  dev.flush dev.hold plot points segments
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold")
  importFrom("graphics", "plot", "points", "segments")
to your NAMESPACE file.
baumwelchcont: no visible global function definition for ‘dnorm’
hmmcontSimul: no visible global function definition for ‘rnorm’
hmmcontSimul: no visible global function definition for ‘rbinom’
plot.ContObservHMM: no visible global function definition for ‘plot’
plot.ContObservHMM: no visible global function definition for ‘lines’
statesDistributionsPlot: no visible global function definition for
  ‘dnorm’
statesDistributionsPlot: no visible global function definition for ‘sd’
statesDistributionsPlot: no visible global function definition for
  ‘plot’
statesDistributionsPlot: no visible global function definition for
  ‘lines’
statesDistributionsPlot: no visible global function definition for
  ‘legend’
summary.ContObservHMM: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dnorm legend lines plot rbinom rnorm sd
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "dnorm", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
dishonestCasino: no visible global function definition for ‘plot’
dishonestCasino: no visible global function definition for ‘axis’
dishonestCasino: no visible global function definition for ‘text’
dishonestCasino: no visible global function definition for ‘rect’
dishonestCasino: no visible global function definition for ‘rgb’
dishonestCasino: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis plot points rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "plot", "points", "rect", "text")
to your NAMESPACE file.
hpbayes.plot: no visible global function definition for ‘par’
hpbayes.plot: no visible global function definition for ‘plot’
hpbayes.plot: no visible global function definition for ‘points’
postpri.plot: no visible global function definition for ‘par’
postpri.plot: no visible global function definition for ‘plot’
postpri.plot: no visible global function definition for ‘points’
postpri.plot: no visible global function definition for ‘segments’
postpri.plot: no visible global function definition for ‘boxplot’
Undefined global functions or variables:
  boxplot par plot points segments
Consider adding
  importFrom("graphics", "boxplot", "par", "plot", "points", "segments")
to your NAMESPACE file.
Calculate3D: no visible global function definition for ‘persp’
CalculateHUM_Ex: no visible global function definition for ‘combn’
CalculateHUM_Plot: no visible global function definition for ‘plot’
CalculateHUM_Plot: no visible global function definition for ‘polygon’
CalculateHUM_Plot: no visible global function definition for ‘text’
CalculateHUM_Plot: no visible global function definition for ‘points’
CalculateHUM_Plot: no visible global function definition for ‘lines’
Undefined global functions or variables:
  combn lines persp plot points polygon text
Consider adding
  importFrom("graphics", "lines", "persp", "plot", "points", "polygon",
             "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
ibdhap.barplot: no visible global function definition for ‘plot’
ibdhap.barplot: no visible global function definition for ‘rect’
ibdhap.compare.loci: no visible global function definition for ‘hist’
ibdhap.compare.segs: no visible global function definition for ‘tail’
ibdhap.make.calls: no visible global function definition for
  ‘count.fields’
ibdhap.make.calls: no visible global function definition for
  ‘read.table’
ibdhap.make.true: no visible global function definition for
  ‘read.table’
ibdhap.names: no visible global function definition for ‘count.fields’
ibdhap.names: no visible global function definition for ‘read.table’
ibdhap.reduce.states: no visible global function definition for
  ‘read.table’
ibdhap.reduce.states: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  count.fields hist plot read.table rect tail write.table
Consider adding
  importFrom("graphics", "hist", "plot", "rect")
  importFrom("utils", "count.fields", "read.table", "tail",
             "write.table")
to your NAMESPACE file.
create.ibd.dat: no visible global function definition for ‘read.table’
create.pairs.frame: no visible global function definition for ‘terms’
ibd.moments: no visible global function definition for ‘var’
ibdreg: no visible global function definition for ‘terms’
ibdreg: no visible global function definition for ‘as.formula’
linkage.tests: no visible global function definition for ‘pchisq’
pchibar: no visible global function definition for ‘pchisq’
plot.linkage.all: no visible global function definition for ‘plot’
plot.linkage.all: no visible global function definition for ‘title’
plotpval: no visible global function definition for ‘plot’
plotpval: no visible global function definition for ‘lines’
sim.ibd.var: no visible global function definition for ‘read.table’
sim.mark.prop: no visible global function definition for ‘runif’
Undefined global functions or variables:
  as.formula lines pchisq plot read.table runif terms title var
Consider adding
  importFrom("graphics", "lines", "plot", "title")
  importFrom("stats", "as.formula", "pchisq", "runif", "terms", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
ICA: no visible global function definition for ‘runif’
plot.ICA: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
ICCbare: no visible global function definition for ‘na.omit’
ICCbare: no visible global function definition for ‘formula’
ICCbare: no visible global function definition for ‘replications’
ICCbare: no visible global function definition for ‘aggregate’
ICCbare: no visible global function definition for ‘anova’
ICCbare: no visible global function definition for ‘aov’
ICCbareF: no visible global function definition for ‘aggregate’
ICCest: no visible global function definition for ‘na.omit’
ICCest: no visible global function definition for ‘anova’
ICCest: no visible global function definition for ‘aov’
ICCest: no visible global function definition for ‘aggregate’
ICCest: no visible global function definition for ‘qf’
ICCest: no visible global function definition for ‘qnorm’
Nest: no visible global function definition for ‘qnorm’
effort : CIW: no visible global function definition for ‘qf’
effort: no visible global function definition for ‘plot’
effort: no visible global function definition for ‘axis’
effort: no visible global function definition for ‘lines’
effort: no visible global function definition for ‘legend’
Undefined global functions or variables:
  aggregate anova aov axis formula legend lines na.omit plot qf qnorm
  replications
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "plot")
  importFrom("stats", "aggregate", "anova", "aov", "formula", "na.omit",
             "qf", "qnorm", "replications")
to your NAMESPACE file.
INCAncinner : dian: no visible global function definition for ‘cutree’
INCAncinner : bestela: no visible global function definition for
  ‘cutree’
center: no visible global function definition for ‘var’
dbhatta: no visible global function definition for ‘as.dist’
dcor: no visible global function definition for ‘cor’
dcor: no visible global function definition for ‘as.dist’
dgower: no visible global function definition for ‘as.dist’
dmahal: no visible global function definition for ‘as.dist’
dproc2: no visible global function definition for ‘as.dist’
plot.incaix: no visible global function definition for ‘barplot’
plot.incanc: no visible global function definition for ‘plot’
plot.incanc: no visible global function definition for ‘lines’
plot.incanc: no visible global function definition for ‘legend’
selectioncluster : dian: no visible global function definition for
  ‘cutree’
selectioncluster : bestela: no visible global function definition for
  ‘cutree’
Undefined global functions or variables:
  as.dist barplot cor cutree legend lines plot var
Consider adding
  importFrom("graphics", "barplot", "legend", "lines", "plot")
  importFrom("stats", "as.dist", "cor", "cutree", "var")
to your NAMESPACE file.
A.dep.tests: no visible global function definition for ‘combn’
A.dep.tests: no visible global function definition for ‘pchisq’
dependogram: no visible global function definition for ‘makeCluster’
dependogram: no visible global function definition for
  ‘clusterSetupSPRNG’
dependogram: no visible global function definition for ‘clusterCall’
dependogram: no visible global function definition for ‘stopCluster’
dependogram: no visible global function definition for ‘combn’
dependogram: no visible global function definition for ‘plot’
dependogram: no visible global function definition for ‘points’
dependogram: no visible global function definition for ‘segments’
Undefined global functions or variables:
  clusterCall clusterSetupSPRNG combn makeCluster pchisq plot points
  segments stopCluster
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "pchisq")
  importFrom("utils", "combn")
to your NAMESPACE file.
Running ‘testthat.R’ [130s/143s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(interactions)
  > 
  > test_check("interactions")
  ── 1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157)  
  `print(p)` produced messages.
  
  ── 2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162)  
  `print(p)` produced messages.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 165 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157) 
  2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162) 
  
  Error: testthat unit tests failed
  Execution halted
ClearBottomMenuPlot: no visible global function definition for ‘rect’
InteractiveIGraph : mousedown: no visible global function definition
  for ‘grconvertX’
InteractiveIGraph : mousedown: no visible global function definition
  for ‘grconvertY’
InteractiveIGraph : dragmousemove: no visible global function
  definition for ‘grconvertX’
InteractiveIGraph : dragmousemove: no visible global function
  definition for ‘grconvertY’
InteractiveIGraph : dragmousemove: no visible global function
  definition for ‘polygon’
InteractiveIGraph : mouseup: no visible global function definition for
  ‘grconvertX’
InteractiveIGraph : mouseup: no visible global function definition for
  ‘grconvertY’
InteractiveIGraph : keybd: no visible global function definition for
  ‘par’
PlotRegionGeneral: no visible global function definition for ‘polygon’
plot.InteractiveIGraph: no visible global function definition for
  ‘plot’
plot.InteractiveIGraph: no visible global function definition for ‘par’
plot.Menu: no visible global function definition for ‘par’
plot.Menu: no visible binding for global variable ‘rect’
plot.MenuItem: no visible binding for global variable ‘strwidth’
plot.MenuItem: no visible binding for global variable ‘strheight’
plot.MenuItem: no visible binding for global variable ‘rect’
plot.MenuItem: no visible binding for global variable ‘text’
plot.MenuLine: no visible binding for global variable ‘rect’
Undefined global functions or variables:
  grconvertX grconvertY par plot polygon rect strheight strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "plot",
             "polygon", "rect", "strheight", "strwidth", "text")
to your NAMESPACE file.
interact: no visible global function definition for ‘cor’
plot.interact: no visible global function definition for ‘plot’
standardize.matrix: no visible binding for global variable ‘var’
standardize.matrix: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cor plot sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "sd", "var")
to your NAMESPACE file.
Mo.Th.Ra.: no visible global function definition for ‘aggregate’
daily_mean: no visible global function definition for ‘aggregate’
date.time: no visible global function definition for ‘chron’
date.time: no visible global function definition for ‘years’
date.time: no visible global function definition for ‘days’
date.time: no visible global function definition for ‘hours’
par_calibration: no visible global function definition for ‘date.mdy’
par_calibration: no visible global function definition for ‘as.date’
par_calibration: no visible global function definition for ‘aggregate’
plot_meas_sim: no visible global function definition for ‘as.date’
plot_meas_sim: no visible global function definition for ‘date.mdy’
plot_meas_sim: no visible global function definition for ‘plot’
plot_meas_sim: no visible global function definition for ‘par’
plot_meas_sim: no visible global function definition for ‘legend’
shape_calibration: no visible global function definition for ‘date.mdy’
shape_calibration: no visible global function definition for ‘as.date’
shape_calibration: no visible global function definition for
  ‘aggregate’
Undefined global functions or variables:
  aggregate as.date chron date.mdy days hours legend par plot years
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "aggregate")
to your NAMESPACE file.
icScoreTest: no visible global function definition for ‘pnorm’
icScoreTest: no visible global function definition for ‘pchisq’
icfit.formula: no visible global function definition for ‘terms’
icfit.formula: no visible global function definition for
  ‘model.extract’
icfitBootCI: no visible global function definition for ‘binom.test’
ictest.formula: no visible global function definition for
  ‘model.extract’
plot.icfit: no visible global function definition for ‘gray’
plot.icfit: no visible global function definition for ‘plot’
plot.icfit: no visible global function definition for ‘axis’
plot.icfit : polygon.icfit: no visible global function definition for
  ‘polygon’
scoresFromFit: no visible global function definition for ‘dnorm’
scoresFromFit: no visible global function definition for ‘qnorm’
wsrHLYpclt: no visible global function definition for ‘model.matrix’
wsrHLYpclt: no visible global function definition for ‘pchisq’
wsrHLYpclt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  axis binom.test dnorm gray model.extract model.matrix pchisq plot
  pnorm polygon qnorm terms
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "axis", "plot", "polygon")
  importFrom("stats", "binom.test", "dnorm", "model.extract",
             "model.matrix", "pchisq", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
interventionEffects: no visible binding for global variable ‘sd’
interventionEffects: no visible global function definition for ‘pt’
interventionEffects: no visible global function definition for ‘sd’
interventionalInference: no visible global function definition for ‘sd’
interventionalInferenceAdvanced: no visible global function definition
  for ‘sd’
linesROC: no visible global function definition for ‘segments’
plotMaxML: no visible global function definition for ‘plot’
plotMaxML: no visible global function definition for ‘segments’
Undefined global functions or variables:
  plot pt sd segments
Consider adding
  importFrom("graphics", "plot", "segments")
  importFrom("stats", "pt", "sd")
to your NAMESPACE file.
ILik : rbern: no visible global function definition for ‘runif’
ILik : q: no visible global function definition for ‘dnorm’
ILik : SlambdaG: no visible global function definition for ‘rnorm’
ILik : Pi_hat: no visible global function definition for ‘rnorm’
ILik : q: no visible global function definition for ‘dgamma’
ILik : SlambdaG: no visible global function definition for ‘rgamma’
ILik : Pi_hat: no visible global function definition for ‘rgamma’
ILik: no visible global function definition for ‘maxLik’
ILik: no visible global function definition for ‘coef’
ILik: no visible global function definition for ‘hessian’
ILik: no visible global function definition for ‘plot’
Undefined global functions or variables:
  coef dgamma dnorm hessian maxLik plot rgamma rnorm runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "dgamma", "dnorm", "rgamma", "rnorm",
             "runif")
to your NAMESPACE file.
f.B: no visible global function definition for ‘pnorm’
f.B.neglog.deriv: no visible global function definition for ‘pnorm’
f.B.neglog.deriv: no visible global function definition for ‘dnorm’
f.grovest3 : f.est: no visible global function definition for ‘survfit’
f.grovest3 : f.est: no visible global function definition for ‘plot’
f.grovest3 : f.est: no visible global function definition for ‘lines’
f.grovest3: no visible global function definition for ‘model.frame’
f.grovest3: no visible global function definition for ‘model.extract’
invGauss: no visible global function definition for ‘model.frame’
invGauss: no visible global function definition for ‘model.extract’
invGauss: no visible global function definition for ‘model.matrix’
predict.invGauss: no visible global function definition for
  ‘model.frame’
predict.invGauss: no visible global function definition for
  ‘model.extract’
predict.invGauss: no visible global function definition for
  ‘model.matrix’
predict.invGauss: no visible binding for global variable ‘formula’
predict.invGauss: no visible binding for global variable ‘data’
summary.invGauss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  data dnorm formula lines model.extract model.frame model.matrix plot
  pnorm survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "dnorm", "formula", "model.extract", "model.frame",
             "model.matrix", "pnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Rd file 'N2.cohen.kappa.Rd':
  \examples lines wider than 100 characters:
       N2.cohen.kappa(c(0.2, 0.25, 0.55), k1=0.6, k0=0.4)                                                            

These lines will be truncated in the PDF manual.
residualplot: no visible global function definition for ‘predict’
residualplot: no visible global function definition for ‘rstandard’
residualplot: no visible global function definition for
  ‘complete.cases’
residualplot: no visible global function definition for ‘plot’
residualplot: no visible global function definition for ‘points’
residualplot: no visible global function definition for ‘lines’
residualplot: no visible global function definition for ‘smooth.spline’
residualplot: no visible global function definition for ‘sd’
residualplot: no visible global function definition for ‘rgb’
residualplot: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  complete.cases lines plot points polygon predict rgb rstandard sd
  smooth.spline
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "complete.cases", "predict", "rstandard", "sd",
             "smooth.spline")
to your NAMESPACE file.
getSysinfo: no visible global function definition for ‘sessionInfo’
getVecInfo: no visible global function definition for ‘sd’
isSeriesConstant: no visible global function definition for ‘median’
labelMargins: no visible global function definition for ‘mtext’
plotBG: no visible global function definition for ‘plot’
plotBG: no visible global function definition for ‘polygon’
plotBG: no visible global function definition for ‘par’
plotColorScale: no visible global function definition for ‘par’
plotColorScale: no visible global function definition for ‘text’
plotImageRotated: no visible global function definition for
  ‘heat.colors’
plotImageRotated: no visible global function definition for ‘par’
plotImageRotated: no visible global function definition for ‘plot’
plotImageRotated: no visible global function definition for ‘image’
plotImageRotated: no visible global function definition for ‘axis’
plotNLines: no visible global function definition for ‘par’
plotNLines: no visible global function definition for ‘plot’
plotNLines: no visible global function definition for ‘mtext’
plotNLines: no visible global function definition for ‘axis’
plotNLines: no visible global function definition for ‘points’
plotNLines: no visible global function definition for ‘sd’
userCoords: no visible global function definition for ‘par’
Undefined global functions or variables:
  axis heat.colors image median mtext par plot points polygon sd
  sessionInfo text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "axis", "image", "mtext", "par", "plot",
             "points", "polygon", "text")
  importFrom("stats", "median", "sd")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
Dependence on R version ‘3.4.4’ not with patchlevel 0
binteg: no visible global function definition for ‘contourLines’
binteg: no visible global function definition for ‘approx’
binteg: no visible global function definition for ‘par’
plot1: no visible global function definition for ‘plot’
plot1: no visible global function definition for ‘par’
plot1: no visible global function definition for ‘rect’
plot1: no visible global function definition for ‘axis’
plot1: no visible global function definition for ‘contour’
plot1: no visible global function definition for ‘contourLines’
plot1: no visible binding for global variable ‘approx’
plot1: no visible global function definition for ‘lines’
plot1: no visible global function definition for ‘text’
plot2: no visible global function definition for ‘plot’
plot2: no visible global function definition for ‘abline’
plot2: no visible global function definition for ‘lines’
plot2: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline approx axis contour contourLines legend lines par plot rect
  text
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "abline", "axis", "contour", "legend", "lines",
             "par", "plot", "rect", "text")
  importFrom("stats", "approx")
to your NAMESPACE file.
expression_up : <anonymous>: no visible global function definition for
  ‘quantile’
expression_up : <anonymous>: no visible global function definition for
  ‘IQR’
expression_up : <anonymous>: no visible global function definition for
  ‘median’
expression_up : <anonymous>: no visible global function definition for
  ‘sd’
plot_up: no visible global function definition for ‘plot’
plot_up: no visible global function definition for ‘text’
Undefined global functions or variables:
  IQR median plot quantile sd text
Consider adding
  importFrom("graphics", "plot", "text")
  importFrom("stats", "IQR", "median", "quantile", "sd")
to your NAMESPACE file.
as.matrix.multiPhylo : tip2tip: no visible global function definition
  for ‘cophenetic’
bw.nn : <anonymous>: no visible global function definition for
  ‘quantile’
dist.diss: no visible binding for global variable ‘median’
dist.diss: no visible global function definition for ‘dist’
hist.kdetrees: no visible binding for global variable ‘density’
kdetrees : cutoff: no visible global function definition for ‘quantile’
kdetrees.complete: no visible global function definition for ‘plot’
kdetrees.complete: no visible global function definition for ‘hist’
kdetrees.complete: no visible global function definition for
  ‘write.csv’
plot.kdetrees: no visible binding for global variable ‘density’
Undefined global functions or variables:
  cophenetic density dist hist median plot quantile write.csv
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "cophenetic", "density", "dist", "median",
             "quantile")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for ‘rbeta’
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for ‘runif’
calculate.power : <anonymous>: no visible binding for global variable
  ‘quantile’
generate.benchmark.data: no visible global function definition for
  ‘runif’
generate.benchmark.data: no visible global function definition for
  ‘rnorm’
generate.benchmark.data: no visible global function definition for
  ‘rbinom’
generate.patchwork.copula: no visible global function definition for
  ‘rbeta’
generate.patchwork.copula: no visible global function definition for
  ‘runif’
novelTest.chisq: no visible global function definition for ‘pchisq’
novelTest.chisq4nn: no visible global function definition for ‘pchisq’
optimise.copula.mi : <anonymous>: no visible global function definition
  for ‘optimize’
power.plot: no visible global function definition for ‘plot’
power.plot: no visible global function definition for ‘axis’
power.plot : <anonymous>: no visible global function definition for
  ‘points’
power.plot: no visible global function definition for ‘legend’
roc.plot: no visible global function definition for ‘colorRampPalette’
roc.plot : <anonymous>: no visible global function definition for
  ‘plot’
roc.plot : <anonymous> : <anonymous>: no visible global function
  definition for ‘points’
run.tests : <anonymous> : <anonymous>: no visible global function
  definition for ‘runif’
Undefined global functions or variables:
  axis colorRampPalette legend optimize pchisq plot points quantile
  rbeta rbinom rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "legend", "plot", "points")
  importFrom("stats", "optimize", "pchisq", "quantile", "rbeta",
             "rbinom", "rnorm", "runif")
to your NAMESPACE file.
image.kriging: no visible global function definition for ‘heat.colors’
image.kriging: no visible global function definition for ‘image’
kriging: no visible global function definition for ‘lm’
plot.kriging: no visible global function definition for ‘plot’
plot.kriging: no visible global function definition for ‘curve’
Undefined global functions or variables:
  curve heat.colors image lm plot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "curve", "image", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
kselection: no visible global function definition for ‘txtProgressBar’
kselection: no visible global function definition for
  ‘setTxtProgressBar’
plot.Kselection: no visible global function definition for ‘plot’
plot.Kselection: no visible global function definition for ‘lines’
plot.Kselection: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines plot setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
auc: no visible global function definition for ‘approx’
kulife.colors: no visible global function definition for ‘palette’
rootonorm: no visible global function definition for ‘sd’
rootonorm: no visible global function definition for ‘hist’
rootonorm: no visible global function definition for ‘pnorm’
rootonorm: no visible global function definition for ‘dnorm’
rootonorm: no visible global function definition for ‘plot’
rootonorm: no visible global function definition for ‘rect’
rootonorm: no visible global function definition for ‘lines’
rootonorm: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline approx dnorm hist lines palette plot pnorm rect sd
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "hist", "lines", "plot", "rect")
  importFrom("stats", "approx", "dnorm", "pnorm", "sd")
to your NAMESPACE file.
betabreaker: no visible global function definition for ‘predict’
coef.lars: no visible global function definition for ‘predict’
cv.lars: no visible global function definition for ‘predict’
cv.lars: no visible binding for global variable ‘var’
error.bars: no visible global function definition for ‘segments’
plot.lars: no visible global function definition for ‘plot’
plot.lars: no visible global function definition for ‘matplot’
plot.lars: no visible global function definition for ‘title’
plot.lars: no visible global function definition for ‘abline’
plot.lars: no visible global function definition for ‘axis’
plotCVLars: no visible global function definition for ‘plot’
predict.lars: no visible global function definition for ‘approx’
Undefined global functions or variables:
  abline approx axis matplot plot predict segments title var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "plot", "segments",
             "title")
  importFrom("stats", "approx", "predict", "var")
to your NAMESPACE file.
glassoscore: no visible global function definition for ‘var’
glassoscore: no visible global function definition for ‘pchisq’
lassoscore: no visible global function definition for ‘txtProgressBar’
lassoscore: no visible global function definition for
  ‘setTxtProgressBar’
lassoscore: no visible global function definition for ‘pchisq’
plot.glassoscore: no visible global function definition for ‘legend’
plot.lassoscore: no visible global function definition for ‘legend’
plot.mbscore: no visible global function definition for ‘legend’
qqpval: no visible global function definition for ‘ppoints’
qqpval: no visible global function definition for ‘qbeta’
qqpval: no visible global function definition for ‘points’
qqpval: no visible global function definition for ‘plot’
qqpval: no visible global function definition for ‘abline’
qqpval: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  abline legend pchisq plot points polygon ppoints qbeta
  setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("graphics", "abline", "legend", "plot", "points", "polygon")
  importFrom("stats", "pchisq", "ppoints", "qbeta", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Running ‘test-all.R’ [108s/115s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > #library(lavaSearch2)
  > suppressPackageStartupMessages(library("testthat"))
  > test_check("lavaSearch2")
  Loading required package: lavaSearch2
  Loading required package: ggplot2
  Loading required package: lava
  
  Attaching package: 'lava'
  
  The following object is masked from 'package:ggplot2':
  
      vars
  
  The following object is masked from 'package:testthat':
  
      compare
  
  lavaSearch2 version 1.5.4
  ── 1. Error: (unknown) (@test1-sCorrect-validObjects.R#48)  ────────────────────
  cannot coerce type 'closure' to vector of type 'any'
  Backtrace:
   1. lava::estimate(lvm(G ~ X1), data = d)
   2. lava:::estimate.lvm(lvm(G ~ X1), data = d)
   4. lava:::ordinal.estimate.hook(...)
   5. base::setdiff(lava::endogenous(x), bin)
   6. base::as.vector(y)
  
  ── 2. Error: (unknown) (@test2-modelsearch2.R#37)  ─────────────────────────────
  cannot coerce type 'closure' to vector of type 'any'
  Backtrace:
   1. lava::estimate(m, data = df.sim)
   2. lava:::estimate.lvm(m, data = df.sim)
   4. lava:::ordinal.estimate.hook(...)
   5. base::setdiff(lava::endogenous(x), bin)
   6. base::as.vector(y)
  
  ── 3. Error: (unknown) (@test3-multcomp.R#149)  ────────────────────────────────
  cannot coerce type 'closure' to vector of type 'any'
  Backtrace:
   1. lava::estimate(m.lvm, df.data)
   2. lava:::estimate.lvm(m.lvm, df.data)
   4. lava:::ordinal.estimate.hook(...)
   5. base::setdiff(lava::endogenous(x), bin)
   6. base::as.vector(y)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 464 | SKIPPED: 4 | WARNINGS: 2 | FAILED: 3 ]
  1. Error: (unknown) (@test1-sCorrect-validObjects.R#48) 
  2. Error: (unknown) (@test2-modelsearch2.R#37) 
  3. Error: (unknown) (@test3-multcomp.R#149) 
  
  Error: testthat unit tests failed
  Execution halted
ARConfIntEst: no visible global function definition for ‘sd’
PTLinkFunc: no visible global function definition for ‘pnorm’
PTLinkFunc: no visible global function definition for ‘qnorm’
PTMultiPeriodPD: no visible global function definition for ‘uniroot’
PTOnePeriodPD : f: no visible global function definition for ‘pbinom’
PTOnePeriodPD: no visible global function definition for ‘uniroot’
QMMGetRLogitPD: no visible global function definition for ‘ecdf’
QMMPDlinkFunc: no visible global function definition for ‘qnorm’
QMMPlot: no visible global function definition for ‘plot’
QMMPlot: no visible global function definition for ‘lines’
QMMPlot: no visible global function definition for ‘legend’
VDBCalibratePD: no visible global function definition for ‘ecdf’
VDBGetK: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  ecdf legend lines pbinom plot pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "ecdf", "pbinom", "pnorm", "qnorm", "sd",
             "uniroot")
to your NAMESPACE file.
AlternateSVD: no visible binding for global variable ‘sd’
IPOD: no visible global function definition for ‘mad’
IPOD: no visible global function definition for ‘pnorm’
Pvalue: no visible global function definition for ‘pf’
ROCplot: no visible global function definition for ‘png’
ROCplot: no visible global function definition for ‘matplot’
ROCplot: no visible global function definition for ‘legend’
ROCplot: no visible global function definition for ‘dev.off’
leapp: no visible global function definition for ‘png’
leapp: no visible global function definition for ‘plot’
leapp: no visible global function definition for ‘dev.off’
ridge: no visible global function definition for ‘sd’
ridge: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dev.off legend mad matplot pf plot png pnorm sd
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "matplot", "plot")
  importFrom("stats", "mad", "pf", "pnorm", "sd")
to your NAMESPACE file.
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lemon)
  > 
  > 
  > if (TRUE) {
  +   test_check("lemon")
  + } #else {
  ── 1. Failure: ggplot2 does not break lemon_plot by altering class (@test_lemon_
  `l + 1` threw an error with unexpected message.
  Expected match: "Don't know how to add 1 to a plot"
  Actual message: "Can't add `1` to a ggplot object."
  Backtrace:
   1. testthat::expect_error(...)
   6. ggplot2:::`+.gg`(l, 1)
   7. ggplot2:::add_ggplot(e1, e2, e2name)
   9. ggplot2:::ggplot_add.default(object, p, objectname)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 137 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: ggplot2 does not break lemon_plot by altering class (@test_lemon_plot.r#12) 
  
  Error: testthat unit tests failed
  Execution halted
plotBox: no visible global function definition for ‘sd’
plotBox: no visible global function definition for ‘rect’
plotBox: no visible global function definition for ‘qnorm’
plotBox: no visible global function definition for ‘segments’
plotInit: no visible global function definition for ‘plot’
plotInit: no visible global function definition for ‘runif’
plotInit: no visible global function definition for ‘mtext’
plotInit: no visible global function definition for ‘segments’
plotStack: no visible global function definition for ‘points’
Undefined global functions or variables:
  mtext plot points qnorm rect runif sd segments
Consider adding
  importFrom("graphics", "mtext", "plot", "points", "rect", "segments")
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
gen.lms: no visible global function definition for ‘na.omit’
plot.idf: no visible global function definition for ‘plot’
plot.idf: no visible global function definition for ‘mtext’
plot.idf: no visible global function definition for ‘points’
plot.idf: no visible global function definition for ‘segments’
plot.idf: no visible global function definition for ‘ftable’
plot.idf: no visible global function definition for ‘image’
plot.idf: no visible global function definition for ‘gray’
plot.idf: no visible global function definition for ‘abline’
plot.s.linlir: no visible global function definition for ‘plot’
plot.s.linlir: no visible global function definition for ‘mtext’
plot.s.linlir: no visible global function definition for ‘polygon’
plot.s.linlir: no visible global function definition for ‘points’
plot.s.linlir: no visible global function definition for ‘curve’
s.linlir: no visible global function definition for ‘na.omit’
s.linlir: no visible global function definition for ‘dbinom’
s.linlir: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline curve dbinom ftable gray image mtext na.omit pchisq plot
  points polygon segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "curve", "image", "mtext", "plot",
             "points", "polygon", "segments")
  importFrom("stats", "dbinom", "ftable", "na.omit", "pchisq")
to your NAMESPACE file.
EstimateProbability: no visible global function definition for
  ‘predict’
LOGICOIL: no visible binding for global variable ‘pssm’
LOGICOIL: no visible binding for global variable ‘LOGICOILfit’
LOGICOIL: no visible binding for global variable ‘Model_Parameters’
plot_LOGICOIL: no visible global function definition for ‘png’
plot_LOGICOIL: no visible global function definition for ‘par’
plot_LOGICOIL: no visible global function definition for ‘plot’
plot_LOGICOIL: no visible global function definition for ‘lines’
plot_LOGICOIL: no visible global function definition for ‘axis’
plot_LOGICOIL: no visible global function definition for ‘mtext’
plot_LOGICOIL: no visible global function definition for ‘legend’
plot_LOGICOIL: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  LOGICOILfit Model_Parameters axis dev.off legend lines mtext par plot
  png predict pssm
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par",
             "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:182:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:896:16: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:196:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
fplot: no visible global function definition for ‘rnorm’
fplot: no visible global function definition for ‘plot’
fplot: no visible global function definition for ‘segments’
fplot: no visible global function definition for ‘points’
fplot: no visible global function definition for ‘text’
fplot.foodweb: no visible global function definition for ‘plot’
fplot.foodweb: no visible global function definition for ‘segments’
fplot.foodweb: no visible global function definition for ‘points’
fplot.foodweb: no visible global function definition for ‘text’
gplot: no visible global function definition for ‘runif’
groupplot: no visible global function definition for ‘rnorm’
groupplot: no visible global function definition for ‘plot’
groupplot: no visible global function definition for ‘segments’
groupplot: no visible global function definition for ‘points’
groupplot: no visible global function definition for ‘text’
groupplot.foodweb: no visible global function definition for ‘rnorm’
groupplot.foodweb: no visible global function definition for ‘plot’
groupplot.foodweb: no visible global function definition for ‘segments’
groupplot.foodweb: no visible global function definition for ‘points’
groupplot.foodweb: no visible global function definition for ‘text’
Undefined global functions or variables:
  plot points rnorm runif segments text
Consider adding
  importFrom("graphics", "plot", "points", "segments", "text")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
learnPattern.default: no visible global function definition for ‘runif’
plot.learnPattern: no visible global function definition for ‘matplot’
plotMDS: no visible global function definition for ‘par’
plotMDS: no visible global function definition for ‘rainbow’
plotMDS: no visible global function definition for ‘plot’
plotMDS: no visible global function definition for ‘pairs’
visualizePattern: no visible global function definition for ‘par’
visualizePattern: no visible global function definition for ‘plot’
visualizePattern: no visible global function definition for ‘points’
visualizePattern: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend matplot pairs par plot points rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "matplot", "pairs", "par", "plot",
             "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘MLTA_Gollini_2019.Rmd’ using rmarkdown
Loading required package: MASS
Loading required package: ergm
Loading required package: network
network: Classes for Relational Data
Version 1.16.0 created on 2019-11-30.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.


ergm: version 3.10.4, created on 2019-06-10
Copyright (c) 2019, Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Carter T. Butts, University of California -- Irvine
                    Steven M. Goodreau, University of Washington
                    Pavel N. Krivitsky, University of Wollongong
                    Martina Morris, University of Washington
                    with contributions from
                    Li Wang
                    Kirk Li, University of Washington
                    Skye Bender-deMoll, University of Washington
                    Chad Klumb
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ergm").

NOTE: Versions before 3.6.1 had a bug in the implementation of the bd()
constriant which distorted the sampled distribution somewhat. In
addition, Sampson's Monks datasets had mislabeled vertices. See the
NEWS and the documentation for more details.

NOTE: Some common term arguments pertaining to vertex attribute and
level selection have changed in 3.10.0. See terms help for more
details. Use 'options(ergm.term=list(version="3.9.4"))' to use old
behavior.

Killed
SelectedInput:
  function(...)
SelectedInput.formula:
  function(..., data, control, metrics, stat, cutoff)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
ageprofile: no visible global function definition for ‘model.frame’
ageprofile: no visible binding for global variable ‘poisson’
ageprofile: no visible global function definition for ‘predict.gam’
ageprofile: no visible global function definition for ‘as.formula’
ageprofile: no visible global function definition for ‘summary.gam’
ageprofile: no visible global function definition for ‘contrasts<-’
ageprofile: no visible global function definition for ‘anova.gam’
plotap: no visible global function definition for ‘dev.new’
plotap: no visible global function definition for ‘plot’
plotap: no visible global function definition for ‘lines’
plotap: no visible global function definition for ‘points’
plotap: no visible global function definition for ‘legend’
splitter: no visible global function definition for ‘reshape’
tabm: no visible global function definition for ‘coef’
tabm: no visible global function definition for ‘AIC’
Undefined global functions or variables:
  AIC anova.gam as.formula coef contrasts<- dev.new legend lines
  model.frame plot points poisson predict.gam reshape summary.gam
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "AIC", "as.formula", "coef", "contrasts<-",
             "model.frame", "poisson", "reshape")
to your NAMESPACE file.
MAT: no visible global function definition for ‘dev.new’
MAT: no visible global function definition for ‘plot’
MAT: no visible global function definition for ‘points’
MAT: no visible global function definition for ‘abline’
MAT: no visible global function definition for ‘text’
MAT: no visible global function definition for ‘legend’
MAT: no visible global function definition for ‘lines’
MAT: no visible global function definition for ‘par’
MAT: no visible global function definition for ‘barplot’
MAT: no visible global function definition for ‘cor’
print.MAT: no visible global function definition for ‘sd’
print.MAT: no visible global function definition for ‘cor’
simM3PL: no visible global function definition for ‘rnorm’
simM3PL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline barplot cor dev.new legend lines par plot points rnorm runif
  sd text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "lines", "par",
             "plot", "points", "text")
  importFrom("stats", "cor", "rnorm", "runif", "sd")
to your NAMESPACE file.
Running ‘testthat.R’ [10m/11m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(matrixTests)
  > 
  > test_check("matrixTests")
  Killed
GSTplot : <anonymous>: no visible global function definition for
  ‘t.test’
GSTplot: no visible global function definition for ‘rt’
GSTplot: no visible global function definition for ‘layout’
GSTplot: no visible global function definition for ‘par’
GSTplot: no visible global function definition for ‘plot’
GSTplot: no visible global function definition for ‘text’
GSTplot: no visible global function definition for ‘lines’
GSTplot: no visible global function definition for ‘polygon’
GSTplot: no visible global function definition for ‘abline’
GSTplot: no visible global function definition for ‘ecdf’
GSTplot: no visible global function definition for ‘knots’
GSTplot : <anonymous>: no visible global function definition for ‘aov’
GSTplot: no visible global function definition for ‘qf’
MAVTn : <anonymous>: no visible global function definition for ‘aov’
MAVTn: no visible global function definition for ‘p.adjust’
MAVTn: no visible global function definition for ‘plot’
MAVTn: no visible global function definition for ‘par’
MAVTn: no visible global function definition for ‘abline’
MAVTn: no visible global function definition for ‘legend’
MAVTn: no visible global function definition for ‘locator’
Tols : olsf: no visible global function definition for ‘t.test’
Tols: no visible global function definition for ‘cor’
Undefined global functions or variables:
  abline aov cor ecdf knots layout legend lines locator p.adjust par
  plot polygon qf rt t.test text
Consider adding
  importFrom("graphics", "abline", "layout", "legend", "lines",
             "locator", "par", "plot", "polygon", "text")
  importFrom("stats", "aov", "cor", "ecdf", "knots", "p.adjust", "qf",
             "rt", "t.test")
to your NAMESPACE file.
MI.2: no visible global function definition for ‘xtabs’
RNASeq.Data: no visible binding for global variable ‘quantile’
loc.node: no visible global function definition for ‘head’
loc.node: no visible global function definition for ‘tail’
plotHybrid.Tree: no visible global function definition for ‘par’
plotHybrid.Tree: no visible global function definition for ‘plot’
plotHybrid.Tree: no visible global function definition for ‘text’
plotHybrid.Tree: no visible global function definition for ‘image’
plotHybrid.Tree: no visible global function definition for ‘grey’
plotHybrid.Tree: no visible global function definition for
  ‘heat.colors’
plotHybrid.Tree: no visible global function definition for ‘head’
plotHybrid.Tree: no visible global function definition for ‘segments’
plotbr: no visible global function definition for ‘segments’
Undefined global functions or variables:
  grey head heat.colors image par plot quantile segments tail text
  xtabs
Consider adding
  importFrom("grDevices", "grey", "heat.colors")
  importFrom("graphics", "image", "par", "plot", "segments", "text")
  importFrom("stats", "quantile", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
mcheatmaps : coscolorFun: no visible global function definition for
  ‘rgb’
mcheatmaps : halfcmat: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps : fullcmat: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘hclust’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘as.dist’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘sd’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘cophenetic’
mcheatmaps : printDiag: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps: no visible global function definition for ‘strwidth’
mcheatmaps: no visible global function definition for ‘pdf’
mcheatmaps: no visible global function definition for ‘plot.new’
mcheatmaps: no visible global function definition for ‘as.dendrogram’
mcheatmaps: no visible global function definition for ‘reorder’
mcheatmaps: no visible global function definition for ‘par’
mcheatmaps: no visible global function definition for ‘plot’
mcheatmaps: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps: no visible global function definition for ‘heat.colors’
mcheatmaps: no visible global function definition for ‘terrain.colors’
mcheatmaps: no visible global function definition for ‘as.dist’
mcheatmaps: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  as.dendrogram as.dist cophenetic dev.off hclust heat.colors
  order.dendrogram par pdf plot plot.new reorder rgb sd strwidth
  terrain.colors
Consider adding
  importFrom("grDevices", "dev.off", "heat.colors", "pdf", "rgb",
             "terrain.colors")
  importFrom("graphics", "par", "plot", "plot.new", "strwidth")
  importFrom("stats", "as.dendrogram", "as.dist", "cophenetic", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
plot.nsga2: no visible global function definition for ‘plot’
plot.nsga2: no visible global function definition for ‘lines’
plot.nsga2: no visible global function definition for ‘pairs’
plot.nsga2.collection: no visible global function definition for
  ‘devAskNewPage’
plot.nsga2.collection: no visible binding for global variable ‘plot’
Undefined global functions or variables:
  devAskNewPage lines pairs plot
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "lines", "pairs", "plot")
to your NAMESPACE file.
dometa: no visible global function definition for ‘qchisq’
dometa: no visible global function definition for ‘median’
dometa: no visible global function definition for ‘pchisq’
forestplot: no visible global function definition for ‘pchisq’
forestplot: no visible global function definition for ‘qnorm’
forestplot: no visible global function definition for ‘plot’
forestplot: no visible global function definition for ‘points’
forestplot: no visible global function definition for ‘text’
metagwa.files: no visible global function definition for ‘read.csv’
metagwa.files: no visible global function definition for ‘write.csv’
metagwa.tables: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  median pchisq plot points qchisq qnorm read.csv text write.csv
Consider adding
  importFrom("graphics", "plot", "points", "text")
  importFrom("stats", "median", "pchisq", "qchisq", "qnorm")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Dependence on R version ‘3.4.3’ not with patchlevel 0
calc_z_var: no visible binding for global variable ‘median’
diffScore: no visible global function definition for ‘new’
diffScore: no visible global function definition for ‘model.matrix’
logNORMcdf: no visible global function definition for ‘pnorm’
mGSZ.adj.mean.std: no visible binding for global variable ‘sd’
pick.data.cols: no visible binding for global variable ‘var’
plotProfile: no visible binding for global variable ‘quantile’
plotProfile: no visible global function definition for ‘plot’
plotProfile: no visible global function definition for ‘lines’
plotProfile: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines median model.matrix new plot pnorm quantile sd var
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("methods", "new")
  importFrom("stats", "median", "model.matrix", "pnorm", "quantile",
             "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
BCI: no visible global function definition for ‘quantile’
Metro_Hastings: no visible global function definition for ‘optim’
Metro_Hastings: no visible global function definition for ‘runif’
Metro_Hastings: no visible global function definition for ‘var’
plotMH: no visible global function definition for ‘hist’
plotMH: no visible global function definition for ‘plot’
plotMH: no visible global function definition for ‘frame’
plotMH: no visible global function definition for ‘text’
Undefined global functions or variables:
  frame hist optim plot quantile runif text var
Consider adding
  importFrom("graphics", "frame", "hist", "plot", "text")
  importFrom("stats", "optim", "quantile", "runif", "var")
to your NAMESPACE file.
migration.cv.in : <anonymous>: no visible global function definition
  for ‘sd’
migration.cv.out : <anonymous>: no visible global function definition
  for ‘sd’
migration.field.diagram: no visible global function definition for
  ‘plot’
migration.field.diagram: no visible global function definition for
  ‘lines’
migration.field.diagram: no visible global function definition for
  ‘text’
migration.field.diagram: no visible global function definition for
  ‘polygon’
migration.field.diagram: no visible global function definition for ‘lm’
migration.field.diagram: no visible global function definition for
  ‘predict’
migration.field.diagram: no visible global function definition for
  ‘points’
migration.field.diagram: no visible global function definition for
  ‘resid’
migration.field.diagram: no visible global function definition for
  ‘coef’
migration.field.diagram: no visible global function definition for
  ‘mtext’
migration.field.diagram: no visible global function definition for
  ‘density’
migration.field.diagram: no visible global function definition for
  ‘rug’
migration.gini.col : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.in : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.out : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.row : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.total: no visible global function definition for ‘dist’
Undefined global functions or variables:
  coef density dist lines lm mtext plot points polygon predict resid
  rug sd text
Consider adding
  importFrom("graphics", "lines", "mtext", "plot", "points", "polygon",
             "rug", "text")
  importFrom("stats", "coef", "density", "dist", "lm", "predict",
             "resid", "sd")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘milr-intro.Rmd’ using rmarkdown
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 2.8390.
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

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.
Warning: 'switch' is deprecated.
Use 'strip.position' instead.
See help("Deprecated")
The penalty term is selected automatically with 100 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 3.2909.
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.
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.
Killed
miney : plot.initial.matrix: no visible global function definition for
  ‘plot’
miney : plot.initial.matrix: no visible global function definition for
  ‘rect’
miney : plot.known.matrix: no visible global function definition for
  ‘plot’
miney : plot.known.matrix: no visible global function definition for
  ‘rect’
miney : plot.known.matrix: no visible global function definition for
  ‘text’
miney: no visible global function definition for ‘locator’
miney: no visible global function definition for ‘rect’
miney: no visible global function definition for ‘title’
Undefined global functions or variables:
  locator plot rect text title
Consider adding
  importFrom("graphics", "locator", "plot", "rect", "text", "title")
to your NAMESPACE file.
.FCLoess: no visible global function definition for ‘loess’
.FCLoessM: no visible global function definition for ‘loess’
.FCLoessM: no visible global function definition for ‘median’
.Import.Luminex: no visible global function definition for ‘read.csv’
.Intra.Me: no visible global function definition for ‘sd’
.Intra.Me: no visible global function definition for ‘quantile’
.Intra.Me: no visible global function definition for ‘qchisq’
.Intra.Median: no visible global function definition for ‘median’
.boxplot.rtprofile: no visible global function definition for ‘boxplot’
.denplot: no visible global function definition for ‘plot’
.denplot: no visible global function definition for ‘density’
.denplot: no visible global function definition for ‘abline’
.normalize.Luminex: no visible global function definition for ‘sd’
.normalize.qrtpcr: no visible global function definition for ‘density’
.validate.default: no visible global function definition for ‘t.test’
Undefined global functions or variables:
  abline boxplot density loess median plot qchisq quantile read.csv sd
  t.test
Consider adding
  importFrom("graphics", "abline", "boxplot", "plot")
  importFrom("stats", "density", "loess", "median", "qchisq", "quantile",
             "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
confusionBarplot: no visible global function definition for ‘par’
confusionBarplot: no visible global function definition for ‘barplot’
confusionBarplot: no visible global function definition for ‘lines’
confusionBarplot: no visible global function definition for ‘text’
confusionBarplot: no visible global function definition for ‘legend’
confusionBarplot: no visible global function definition for ‘axis’
confusionDendrogram: no visible global function definition for ‘plot’
confusionImage: no visible global function definition for ‘par’
confusionImage: no visible global function definition for ‘image’
confusionImage: no visible global function definition for ‘text’
confusionImage: no visible global function definition for ‘abline’
confusionImage: no visible global function definition for ‘axis’
confusionImage: no visible global function definition for ‘plot’
confusionImage: no visible global function definition for ‘mtext’
confusionStars: no visible global function definition for ‘par’
confusionStars: no visible global function definition for ‘stars’
confusionStars: no visible global function definition for ‘rect’
plot.mlearning: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline axis barplot image legend lines mtext par plot rect stars text
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "image", "legend",
             "lines", "mtext", "par", "plot", "rect", "stars", "text")
to your NAMESPACE file.
Mort1Dsmooth: no visible global function definition for ‘time’
Mort1Dsmooth: no visible global function definition for ‘glm’
Mort1Dsmooth: no visible binding for global variable ‘poisson’
Mort1Dsmooth_optimize: no visible global function definition for
  ‘median’
Mort2Dsmooth: no visible global function definition for ‘glm’
Mort2Dsmooth: no visible binding for global variable ‘poisson’
Mort2Dsmooth: no visible global function definition for ‘median’
Mort2Dsmooth_optimize: no visible global function definition for
  ‘median’
plot.HMDdata: no visible global function definition for ‘plot’
plot.Mort1Dsmooth: no visible global function definition for ‘matplot’
plot.Mort2Dsmooth: no visible global function definition for ‘quantile’
predict.Mort1Dsmooth: no visible global function definition for ‘glm’
predict.Mort1Dsmooth: no visible binding for global variable ‘poisson’
predict.Mort2Dsmooth: no visible global function definition for ‘glm’
predict.Mort2Dsmooth: no visible binding for global variable ‘poisson’
print.summary.Mort1Dsmooth: no visible global function definition for
  ‘quantile’
print.summary.Mort2Dsmooth: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  glm matplot median plot poisson quantile time
Consider adding
  importFrom("graphics", "matplot", "plot")
  importFrom("stats", "glm", "median", "poisson", "quantile", "time")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘mpa/R/zzz.R’:
  .First.lib calls:
    cat("\n mpa: CoWords Method")
    cat("\n ")
    cat("\n Universidad Nacional de Colombia")
    cat("\n ")
    cat("\n Elaborado por: Daniel Rodriguez <dhrodriguezt@unal.edu.co>")
    cat("\n                Campo Elias Pardo <cepardot@unal.edu.co>")
    cat("\n For help: ?mpa   \n\n")

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

diagram.mpa: no visible global function definition for ‘plot’
diagram.mpa: no visible global function definition for ‘abline’
diagram.mpa: no visible global function definition for ‘text’
plotmpa: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline plot text
Consider adding
  importFrom("graphics", "abline", "plot", "text")
to your NAMESPACE file.
mpcv: no visible binding for global variable ‘median’
mpcv: no visible global function definition for ‘cov’
mpcv: no visible global function definition for ‘dist’
plot.mpcv: no visible binding for global variable ‘median’
plot.mpcv: no visible global function definition for ‘par’
plot.mpcv: no visible global function definition for ‘plot’
plot.mpcv: no visible global function definition for ‘rect’
plot.mpcv: no visible global function definition for ‘lines’
plot.mpcv: no visible global function definition for ‘points’
plot.mpcv: no visible global function definition for ‘legend’
Undefined global functions or variables:
  cov dist legend lines median par plot points rect
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot", "points",
             "rect")
  importFrom("stats", "cov", "dist", "median")
to your NAMESPACE file.
MRwarp: no visible global function definition for ‘dev.new’
MRwarp: no visible global function definition for ‘plot’
MRwarp: no visible global function definition for ‘lines’
MRwarp: no visible global function definition for ‘points’
MRwarp: no visible global function definition for ‘hist’
Undefined global functions or variables:
  dev.new hist lines plot points
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "lines", "plot", "points")
to your NAMESPACE file.
msap: no visible global function definition for ‘packageVersion’
msap: no visible global function definition for ‘read.csv’
msap: no visible global function definition for ‘write.csv’
msap: no visible global function definition for ‘sd’
msap: no visible global function definition for ‘wilcox.test’
msap: no visible global function definition for ‘dist’
msap: no visible global function definition for ‘rainbow’
msap: no visible global function definition for ‘png’
msap: no visible global function definition for ‘legend’
msap: no visible global function definition for ‘dev.off’
pcoa: no visible global function definition for ‘cmdscale’
pcoa: no visible global function definition for ‘png’
pcoa: no visible global function definition for ‘par’
pcoa: no visible global function definition for ‘plot’
pcoa: no visible global function definition for ‘rainbow’
pcoa: no visible global function definition for ‘points’
pcoa: no visible global function definition for ‘dev.off’
pcoa: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  cmdscale dev.off dist legend packageVersion par plot png points
  rainbow read.csv sd wilcox.test write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow")
  importFrom("graphics", "legend", "par", "plot", "points")
  importFrom("stats", "cmdscale", "dist", "sd", "wilcox.test")
  importFrom("utils", "packageVersion", "read.csv", "write.csv")
to your NAMESPACE file.
CrossValidationMuFicokm: no visible global function definition for
  ‘covMatrix’
CrossValidationMuFicokmAll: no visible global function definition for
  ‘covMatrix’
MuFicokm: no visible global function definition for ‘km’
compute.beta.hat: no visible global function definition for ‘lm’
computeAuxVariables: no visible global function definition for
  ‘covMatrix’
kmCok: no visible global function definition for ‘new’
kmCok: no visible global function definition for ‘drop.response’
kmCok: no visible global function definition for ‘model.matrix’
kmCok: no visible global function definition for ‘covStruct.create’
kmCok: no visible global function definition for ‘validObject’
kmCok: no visible global function definition for ‘covParametersBounds’
kmCok: no visible binding for global variable ‘kmEstimate’
kmCok : cv: no visible global function definition for ‘leaveOneOut.km’
kmCok: no visible global function definition for ‘plot’
predict.kmCok: no visible global function definition for ‘model.matrix’
predict.kmCok: no visible global function definition for ‘covMat1Mat2’
predict.kmCok: no visible global function definition for ‘qnorm’
predict.kmCok: no visible global function definition for ‘qt’
predict.kmCok: no visible global function definition for ‘covMatrix’
summary.MuFicokm: no visible global function definition for
  ‘covparam2vect’
Undefined global functions or variables:
  covMat1Mat2 covMatrix covParametersBounds covStruct.create
  covparam2vect drop.response km kmEstimate leaveOneOut.km lm
  model.matrix new plot qnorm qt validObject
Consider adding
  importFrom("graphics", "plot")
  importFrom("methods", "new", "validObject")
  importFrom("stats", "lm", "model.matrix", "qnorm", "qt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
plotOptionValues: no visible global function definition for ‘plot’
plotOptionValues: no visible global function definition for ‘persp’
Undefined global functions or variables:
  persp plot
Consider adding
  importFrom("graphics", "persp", "plot")
to your NAMESPACE file.
betas_plot: no visible global function definition for ‘cov2cor’
betas_plot: no visible global function definition for
  ‘colorRampPalette’
betas_plot: no visible global function definition for ‘pdf’
betas_plot: no visible global function definition for ‘dev.off’
mhplot: no visible global function definition for ‘read.table’
mhplot: no visible global function definition for ‘pdf’
mhplot: no visible global function definition for ‘plot’
mhplot: no visible global function definition for ‘points’
mhplot: no visible global function definition for ‘abline’
mhplot: no visible global function definition for ‘axis’
mhplot: no visible global function definition for ‘dev.off’
multi_meta: no visible global function definition for ‘write.table’
multi_meta: no visible global function definition for ‘read.table’
multi_meta: no visible global function definition for ‘pchisq’
qqplotter: no visible global function definition for ‘read.table’
qqplotter: no visible global function definition for ‘qchisq’
qqplotter: no visible global function definition for ‘ppoints’
qqplotter: no visible global function definition for ‘median’
qqplotter: no visible global function definition for ‘pchisq’
qqplotter: no visible global function definition for ‘pdf’
qqplotter: no visible global function definition for ‘plot’
qqplotter: no visible global function definition for ‘abline’
qqplotter: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  abline axis colorRampPalette cov2cor dev.off median pchisq pdf plot
  points ppoints qchisq read.table write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "cov2cor", "median", "pchisq", "ppoints", "qchisq")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
.onAttach: no visible global function definition for
  ‘packageDescription’
genoudRob: no visible global function definition for ‘genoud’
get.XYdata: no visible global function definition for ‘terms’
get.xdata: no visible global function definition for ‘terms’
get.xdata: no visible global function definition for ‘model.matrix’
get.xy: no visible global function definition for ‘terms’
get.xynames: no visible global function definition for ‘terms’
get.ydata: no visible global function definition for ‘terms’
get.ydata: no visible global function definition for ‘model.response’
get.ydata: no visible global function definition for ‘model.frame’
mt.dev: no visible global function definition for ‘pt’
mt.dev.grad: no visible global function definition for ‘pt’
mt.dev.grad: no visible global function definition for ‘dt’
mt.mle: no visible global function definition for ‘optim’
multinomRob: no visible global function definition for ‘var’
plot.multinomRob: no visible global function definition for ‘par’
plot.multinomRob: no visible global function definition for ‘plot’
plot.multinomRob: no visible global function definition for ‘title’
rdirich: no visible global function definition for ‘rgamma’
residual.generator: no visible global function definition for ‘median’
rmultinomial: no visible global function definition for ‘runif’
rmultinomial: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  dt genoud median model.frame model.matrix model.response optim
  packageDescription par plot pt rbinom rgamma runif terms title var
Consider adding
  importFrom("graphics", "par", "plot", "title")
  importFrom("stats", "dt", "median", "model.frame", "model.matrix",
             "model.response", "optim", "pt", "rbinom", "rgamma",
             "runif", "terms", "var")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
plotFID: no visible global function definition for ‘plot’
plotFID: no visible global function definition for ‘points’
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
NAPPA: no visible binding for global variable ‘sd’
NAPPA: no visible global function definition for ‘sd’
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for ‘coef’
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for ‘lm’
calibrate.sigmoid.curve: no visible global function definition for
  ‘nls’
calibrate.sigmoid.curve: no visible binding for global variable
  ‘weights’
calibrate.sigmoid.curve: no visible global function definition for
  ‘coef’
calibrate.sigmoid.curve: no visible global function definition for
  ‘plot’
calibrate.sigmoid.curve: no visible global function definition for
  ‘rgb’
calibrate.sigmoid.curve: no visible global function definition for
  ‘box’
calibrate.sigmoid.curve: no visible global function definition for
  ‘axis’
calibrate.sigmoid.curve: no visible global function definition for
  ‘abline’
calibrate.sigmoid.curve: no visible global function definition for
  ‘lines’
calibrate.sigmoid.curve: no visible global function definition for
  ‘predict’
calibrate.sigmoid.curve: no visible global function definition for
  ‘smooth.spline’
calibrate.sigmoid.curve : <anonymous>: no visible global function
  definition for ‘nls’
calibrate.sigmoid.curve : <anonymous>: no visible binding for global
  variable ‘weights’
calibrate.sigmoid.curve: no visible binding for global variable ‘coef’
calibrate.sigmoid.curve: no visible global function definition for ‘pf’
calibrate.sigmoid.curve: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  abline axis box coef legend lines lm nls pf plot predict rgb sd
  smooth.spline weights
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "plot")
  importFrom("stats", "coef", "lm", "nls", "pf", "predict", "sd",
             "smooth.spline", "weights")
to your NAMESPACE file.
NB.estimator: no visible global function definition for ‘optimize’
NB.estimator: no visible global function definition for ‘uniroot’
NB.example.dataset: no visible global function definition for
  ‘write.table’
NB.plot.likelihood: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optimize plot uniroot write.table
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "optimize", "uniroot")
  importFrom("utils", "write.table")
to your NAMESPACE file.
population: no visible global function definition for ‘weighted.mean’
population: no visible global function definition for ‘rpois’
population: no visible global function definition for ‘lm’
population: no visible global function definition for ‘coefficients’
population: no visible global function definition for ‘sd’
population: no visible global function definition for ‘par’
population: no visible global function definition for ‘plot’
population: no visible global function definition for ‘lines’
Undefined global functions or variables:
  coefficients lines lm par plot rpois sd weighted.mean
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "coefficients", "lm", "rpois", "sd",
             "weighted.mean")
to your NAMESPACE file.
clustConfigurations: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
NPHMC: no visible global function definition for ‘integrate’
NPHMC: no visible global function definition for ‘qnorm’
NPHMC: no visible global function definition for ‘pnorm’
NPHMC: no visible global function definition for ‘plot’
NPHMC: no visible global function definition for ‘lines’
NPHMC: no visible global function definition for ‘smcure’
NPHMC: no visible global function definition for ‘coxph’
Undefined global functions or variables:
  coxph integrate lines plot pnorm qnorm smcure
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "integrate", "pnorm", "qnorm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘DBI’ ‘RJDBC’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘ODB-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ODB-package
> ### Title: Open Document Databases (.odb) management
> ### Aliases: ODB-package ODB
> 
> ### ** Examples
> 
> 
>   ## CONNECTION ##
>   
>   # Creation of a new .odb database
>   odb.create("test.odb", overwrite="do")
> 
>   # Connection to the file
>   odb <- odb.open("test.odb")
Error in validObject(.Object) : 
  invalid class “ODB” object: DBI connection is closed
Calls: odb.open ... new -> new -> initialize -> initialize -> validObject
Execution halted
Found an obsolete/platform-specific call in the following function:
  ‘comp.freq’
Found the platform-specific device:
  ‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
comp.freq: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
Rd file 'dmes.Rd':
  \examples lines wider than 100 characters:
     > #cf. Efron, B. & Tibshirani (1993). An Introduction to the Bootstrap. New York/London: Chapman&Hall.
     > #Ruscio, J. & Mullen, T. (2012). Confidence Intervals for the Probability of Superiority Effect Size Measure and the Area Under a Rec ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
genRidge: no visible global function definition for ‘plogis’
ordGene: no visible global function definition for ‘anova’
ordGene: no visible global function definition for ‘lm’
ordSelect: no visible binding for global variable ‘sd’
ordSmooth: no visible binding for global variable ‘sd’
plot.ordPen: no visible global function definition for ‘grey’
plot.ordPen: no visible global function definition for ‘devAskNewPage’
plot.ordPen: no visible global function definition for ‘plot’
plot.ordPen: no visible global function definition for ‘lines’
predict.ordPen: no visible global function definition for ‘plogis’
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis plot sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "anova", "lm", "plogis", "sd")
to your NAMESPACE file.
ORICC1: no visible binding for global variable ‘sd’
ORICC1: no visible global function definition for ‘write.table’
ORICC1: no visible global function definition for ‘postscript’
ORICC1: no visible global function definition for ‘jpeg’
ORICC1: no visible global function definition for ‘plot’
ORICC1: no visible global function definition for ‘points’
ORICC1: no visible global function definition for ‘dev.off’
ORICC1: no visible global function definition for ‘par’
ORICC2: no visible binding for global variable ‘sd’
ORICC2: no visible global function definition for ‘write.table’
ORICC2: no visible global function definition for ‘postscript’
ORICC2: no visible global function definition for ‘jpeg’
ORICC2: no visible global function definition for ‘plot’
ORICC2: no visible global function definition for ‘points’
ORICC2: no visible global function definition for ‘dev.off’
ORICC2: no visible global function definition for ‘par’
Undefined global functions or variables:
  dev.off jpeg par plot points postscript sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "postscript")
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
as_igraph : <anonymous>: no visible global function definition for
  ‘distHaversine’
as_igraph: no visible global function definition for ‘graph.edgelist’
as_igraph: no visible global function definition for ‘E’
as_igraph: no visible global function definition for ‘E<-’
as_sp_lines: no visible global function definition for ‘Lines’
as_sp_points: no visible global function definition for
  ‘SpatialPointsDataFrame’
as_sp_polygons: no visible global function definition for ‘Polygons’
as_sp_polygons: no visible global function definition for
  ‘SpatialPolygons’
as_sp_polygons: no visible global function definition for
  ‘SpatialPolygonsDataFrame’
make_SLDF: no visible global function definition for ‘SpatialLines’
make_SLDF: no visible global function definition for
  ‘SpatialLinesDataFrame’
osm_crs: no visible global function definition for ‘CRS’
plot.osmar: no visible global function definition for ‘gray’
plot_nodes: no visible global function definition for ‘points’
plot_nodes: no visible global function definition for ‘plot’
plot_ways: no visible global function definition for ‘plot’
plot_ways: no visible global function definition for ‘lines’
ways_nodes2Line: no visible global function definition for ‘Line’
ways_nodes2Polygon: no visible global function definition for ‘Polygon’
Undefined global functions or variables:
  CRS E E<- Line Lines Polygon Polygons SpatialLines
  SpatialLinesDataFrame SpatialPointsDataFrame SpatialPolygons
  SpatialPolygonsDataFrame distHaversine graph.edgelist gray lines plot
  points
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
Electre3_AlphaBetaThresholds: no visible global function definition for
  ‘plot’
Electre3_SimpleThresholds: no visible global function definition for
  ‘plot’
Electre_1: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
paf: no visible global function definition for ‘as.formula’
paf: no visible global function definition for ‘model.response’
paf: no visible global function definition for ‘model.frame’
paf: no visible global function definition for ‘model.matrix’
plot.paf: no visible global function definition for ‘plot’
plot.paf: no visible global function definition for ‘lines’
Undefined global functions or variables:
  as.formula lines model.frame model.matrix model.response plot
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
Rd file 'CalGIF.Rd':
  \examples lines wider than 100 characters:
     ###calculate the global influence factor (GIF) by using the random walk with restart (RWR) algorithm###
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 

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

These lines will be truncated in the PDF manual.
GOpredict: no visible global function definition for ‘fisher.test’
KEGGpredict: no visible global function definition for ‘fisher.test’
ProteinCluster: no visible global function definition for ‘ecdf’
ProteinCluster: no visible global function definition for ‘as.hclust’
ProteinCluster: no visible global function definition for
  ‘as.dendrogram’
ProteinCluster : addE: no visible global function definition for
  ‘is.leaf’
ProteinCluster: no visible global function definition for ‘plot’
SignificantSubcluster: no visible global function definition for
  ‘order.dendrogram’
SignificantSubcluster: no visible global function definition for
  ‘fisher.test’
SignificantSubcluster: no visible global function definition for ‘plot’
Undefined global functions or variables:
  as.dendrogram as.hclust ecdf fisher.test is.leaf order.dendrogram
  plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "as.dendrogram", "as.hclust", "ecdf",
             "fisher.test", "is.leaf", "order.dendrogram")
to your NAMESPACE file.
adalasso: no visible global function definition for ‘predict’
lm.ridge.univariate: no visible global function definition for ‘sd’
mylars: no visible global function definition for ‘predict’
mylars: no visible binding for global variable ‘var’
performance.pcor: no visible global function definition for
  ‘ggm.test.edges’
performance.pcor: no visible global function definition for ‘var’
ridge.cv: no visible global function definition for ‘coef’
ridge.cv: no visible global function definition for ‘plot’
Undefined global functions or variables:
  coef ggm.test.edges plot predict sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "predict", "sd", "var")
to your NAMESPACE file.
draw.pcaBootPlot: no visible global function definition for ‘plot’
draw.pcaBootPlot: no visible global function definition for ‘grid’
draw.pcaBootPlot: no visible global function definition for ‘points’
draw.pcaBootPlot: no visible global function definition for ‘symbols’
draw.pcaBootPlot: no visible global function definition for ‘legend’
pcaBootPlot: no visible global function definition for ‘prcomp’
pcaBootPlot: no visible global function definition for ‘cor’
pcaBootPlot: no visible global function definition for ‘quantile’
pcaBootPlot: no visible global function definition for ‘pdf’
pcaBootPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  cor dev.off grid legend pdf plot points prcomp quantile symbols
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "grid", "legend", "plot", "points", "symbols")
  importFrom("stats", "cor", "prcomp", "quantile")
to your NAMESPACE file.
peacf: no visible global function definition for ‘is.ts’
peacf: no visible global function definition for ‘cycle’
peacf: no visible global function definition for ‘ts.intersect’
peacf: no visible global function definition for ‘lag’
peacf: no visible global function definition for ‘ts’
peacf: no visible global function definition for ‘pchisq’
peacf.plot: no visible global function definition for ‘plot’
peacf.plot: no visible global function definition for ‘segments’
peacf.plot: no visible global function definition for ‘title’
pear: no visible global function definition for ‘cycle’
pear: no visible global function definition for ‘pchisq’
peboxplot: no visible global function definition for ‘cycle’
peboxplot: no visible global function definition for ‘boxplot’
peboxplot: no visible global function definition for ‘title’
peplot: no visible global function definition for ‘par’
peplot: no visible global function definition for ‘cycle’
peplot: no visible global function definition for ‘plot’
peplot: no visible global function definition for ‘identify’
peplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  boxplot cycle identify is.ts lag mtext par pchisq plot segments title
  ts ts.intersect
Consider adding
  importFrom("graphics", "boxplot", "identify", "mtext", "par", "plot",
             "segments", "title")
  importFrom("stats", "cycle", "is.ts", "lag", "pchisq", "ts",
             "ts.intersect")
to your NAMESPACE file.
PearsonICA: no visible global function definition for ‘rnorm’
PearsonICAdemo: no visible global function definition for ‘rnorm’
PearsonICAdemo: no visible global function definition for ‘dev.new’
PearsonICAdemo: no visible global function definition for ‘par’
PearsonICAdemo: no visible global function definition for ‘plot’
PearsonICAdemo: no visible global function definition for ‘axis’
PearsonICAdemo: no visible global function definition for ‘title’
PearsonICAdemo: no visible global function definition for ‘lines’
Undefined global functions or variables:
  axis dev.new lines par plot rnorm title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "axis", "lines", "par", "plot", "title")
  importFrom("stats", "rnorm")
to your NAMESPACE file.
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.
Running ‘testthat.R’ [10s/8s]
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
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  ── 2. Error: See if extractor works (@test_extract_phrases.R#7)  ───────────────
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  Currently tagging document 1 of 1 
  Extracting phrases from document 1 of 1 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: See if tagging five documents works, and if coarsening works (@test_POS_tag_documents.R#7) 
  2. Error: See if extractor works (@test_extract_phrases.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Rd file 'envelopeArea_and_Perimeter.Rd':
  \examples lines wider than 100 characters:
     cat("envelope area = ", envelopeStats["area"], " perimeter = ", envelopeStats["perimeter"],"\n")        
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")

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

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

These lines will be truncated in the PDF manual.
.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.
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.
Rd file 'ppoistweedie.Rd':
  \examples lines wider than 100 characters:
     layout.show(1)                                                                                                                          ... [TRUNCATED]

These lines will be truncated in the PDF 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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ABE.Rmd’ using rmarkdown
--- finished re-building ‘ABE.Rmd’

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

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

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

--- re-building ‘RSABE.Rmd’ using rmarkdown
Killed
--- re-building ‘vignette.Rmd’ using rmarkdown
--- finished re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(preText)
  preText: Diagnostics to Assess the Effects of Text Preprocessing Decisions
  Version 0.6.3 created on 2018-01-12.
  copyright (c) 2017, Matthew J. Denny, Penn State University
                      Arthur Spirling, NYU
  Type vignette('getting_started_with_preText') to get started.
  Development website: https://github.com/matthewjdenny/preText
  > 
  > test_check("preText")
  ── 1. Error: Small example works (@test_factorial_preprocessing.R#6)  ──────────
  unused argument (alist())
  Backtrace:
   1. documents[1:10, ]
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Small example works (@test_factorial_preprocessing.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
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.
.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.
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.
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.
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.
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.
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.
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.
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.
Rd file 'predict.randomGLM.Rd':
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, nCandidateCovariates=ncol(xTrain), nBags=30, keepModels = TRUE, nThreads = 1)

Rd file 'randomGLM.Rd':
  \usage lines wider than 90 characters:
       # Multi-level classification options - only apply to classification with multi-level response
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, xTest, classify=FALSE, nCandidateCovariates=ncol(xTrain), nBags=10, 

Rd file 'thinRandomGLM.Rd':
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, nCandidateCovariates=ncol(xTrain), nBags=30, keepModels = TRUE, nThreads = 1)

These lines will be truncated in the PDF manual.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
Running examples in ‘rcdk-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: eval.desc
> ### Title: Evaluate a Molecular Descriptor
> ### Aliases: eval.desc
> ### Keywords: programming
> 
> ### ** Examples
> 
> smiles <- c('CCC', 'c1ccccc1', 'CC(=O)C')
> mols <- sapply(smiles, parse.smiles)
> 
> dnames <- get.desc.names('constitutional')
Error in .jcall("org/guha/rcdk/descriptors/DescriptorUtilities", "[Ljava/lang/String;",  : 
  java.lang.NullPointerException
Calls: get.desc.names -> .jcall -> .jcheck
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘molform.Rmd’ using rmarkdown
Quitting from lines 37-42 (molform.Rmd) 
Error: processing vignette 'molform.Rmd' failed with diagnostics:
RcallMethod: invalid object parameter
--- failed re-building ‘molform.Rmd’

--- re-building ‘using-rcdk.Rmd’ using rmarkdown
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by RJavaTools to method java.util.Collections$UnmodifiableCollection$1.next()
WARNING: Please consider reporting this to the maintainers of RJavaTools
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Quitting from lines 318-320 (using-rcdk.Rmd) 
Error: processing vignette 'using-rcdk.Rmd' failed with diagnostics:
java.lang.NullPointerException
--- failed re-building ‘using-rcdk.Rmd’

SUMMARY: processing the following files failed:
  ‘molform.Rmd’ ‘using-rcdk.Rmd’

Error: Vignette re-building failed.
Execution halted
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.
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').
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: carData
  Loading required package: survival
  Loading required package: Formula
  > library(rddtools)
  Error in library(rddtools) : there is no package called 'rddtools'
  Execution halted
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.
Found the following significant warnings:
  Rreadsdpa.c:608:15: warning: ‘strncpy’ output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  Rreadsdpa.c:1041:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  Rreadsdpa.c:1042:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:164:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:165:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rdsdp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  compile.cc:292:69: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class re2::Prog::Inst’; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/re2r.Rcheck/00install.out’ for details.
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.
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.
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.
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.
Found the following significant warnings:
  Note: possible error in 'coord_trans(xtrans = "exp", ': unused arguments (xtrans = "exp", ytrans = "exp") 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RGraphics.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
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.
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.
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’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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.
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.
Rd file 'C.FRNN.FRST.Rd':
  \examples lines wider than 100 characters:
                     type.relation = c("tolerance", "eq.1"), t.implicator = "lukasiewicz")                                                   ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rpubchem)
  > 
  > test_check("rpubchem")
  ── 1. Failure: Assay description retrieves related AIDs (@test-getassay.R#4)  ──
  length(d$aids) > 0 isn't true.
  TRUE
  
  ── 2. Failure: Assay description retrieves related PMIDs (@test-getassay.R#9)  ─
  length(d$pmids) > 0 isn't true.
  TRUE
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 2 ]
  1. Failure: Assay description retrieves related AIDs (@test-getassay.R#4) 
  2. Failure: Assay description retrieves related PMIDs (@test-getassay.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
.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.
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.
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’

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.

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.
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.
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.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RVowpalWabbit.Rcheck/00install.out’ for details.
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.
.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.
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.
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.
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.
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.
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.
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 ‘SetMethods-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LR.intersect
> ### Title: Function for identifying contradictory simplifying assumptions
> ###   or easy counterfactuals.
> ### Aliases: LR.intersect
> ### Keywords: QCA
> 
> ### ** Examples
> 
> # Import your data. For example:
> 
> data(SCHF)
> 
> # Get the parsimonious solution:
> 
> sol_yp <- minimize(SCHF, outcome = "EXPORT",
+                 conditions = c("EMP","BARGAIN","UNI","OCCUP","STOCK", "MA"),
+                 incl.cut = .9, 
+                 include = "?", 					   
+                 details = TRUE, show.cases = TRUE)
Warning in if (all(target == toupper(target)) & expression != toupper(expression) &  :
  the condition has length > 1 and only the first element will be used

Error: Conditions 'empbcdef' do not match the set names from "snames" argument.

Execution halted
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.
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.
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.
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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/skeleSim.Rcheck/00install.out’ for details.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Rd file 'SyNet-package.rd':
  \examples lines wider than 100 characters:
       # Run NAM method on the previously inferred sympatry network                                           

Rd file 'acshgral.rd':
  \examples lines wider than 100 characters:
       #Display relationships into a parenthetical notation. You can track the indices of the species in the

Rd file 'gridinfer.rd':
  \examples lines wider than 100 characters:
       #are nested inside it. In a network analysis this kind of element will behave as intermediary node.  

Rd file 'reweight.rd':
  \examples lines wider than 100 characters:
       plot(unlist(ej),unlist(reweight(ej)), xlab = "Input matrix", ylab = "Reweighted matrix", main = "First reweighting")

These lines will be truncated in the PDF manual.
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.
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: ‘aws.polly’
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Running ‘testthat.R’ [17s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(uFTIR)
  Loading required package: parallel
  > 
  > test_check("uFTIR")
  ── 1. Error: Preprocess for SpectralPack object is reshaping the wavenumbers (@t
  there is no package called 'prospectr'
  Backtrace:
   1. base::library(prospectr)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 29 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Preprocess for SpectralPack object is reshaping the wavenumbers (@test-tile_functions.R#104) 
  
  Error: testthat unit tests failed
  Execution halted
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.
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.
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.
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.
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.
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.
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.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/x13binary.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [43s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xpose)
  Loading required package: ggplot2
  
  Attaching package: 'xpose'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("xpose")
  ── 1. Failure: parial xp_themes are properly added (@test-update_themes.R#39)  ─
  update_themes(xpdb = xpdb_ex_pk, xp_theme = c(point_color = "green"))$xp_theme not equivalent to `theme_xp_custom`.
  Component "labeller": target, current do not match when deparsed
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 521 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: parial xp_themes are properly added (@test-update_themes.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘aaSEA_Documentation.Rmd’ using rmarkdown
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 RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Quitting from lines 90-91 (aaSEA_Documentation.Rmd) 
Error: processing vignette 'aaSEA_Documentation.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘aaSEA_Documentation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    data       2.8Mb
    pictures   2.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    data    1.3Mb
    files   1.9Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    data  20.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    4.8Mb
    help   1.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       2.9Mb
    extdata   1.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ahn.Rmd’ using rmarkdown
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:
there is no package called 'webshot'
--- failed re-building ‘ahn.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rsvg’
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    extdata  12.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
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 49-64 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.4Mb
Package suggested but not available for checking: ‘ssh’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   2.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    testdata   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘antares.Rmd’ using rmarkdown
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.
--- finished re-building ‘antares.Rmd’

--- re-building ‘antaresH5.Rmd’ using rmarkdown
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 38-72 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘antaresH5.Rmd’

SUMMARY: processing the following file failed:
  ‘antaresH5.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘kebabs’
Error(s) in re-building vignettes:
  ...
--- re-building ‘apcluster.Rnw’ using knitr

Attaching package: 'apcluster'

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

    heatmap

Quitting from lines 387-408 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
object 'apres2c' not found
--- failed re-building ‘apcluster.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [20s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(apex)
  Loading required package: ape
  Loading required package: phangorn
  > 
  > test_check("apex")
  ── 1. Error: (unknown) (@test_export.R#8)  ─────────────────────────────────────
  subscript out of bounds
  Backtrace:
   1. apex::multidna2genind(x, mlst = TRUE, gapIsNA = TRUE)
   2. adegenet::df2genind(xdfnum, ploidy = 1, ind.names = x@labels)
   3. base::vapply(...)
   4. adegenet:::FUN(X[[i]], ...)
   5. base::rowSums(out[, i, drop = FALSE], na.rm = TRUE)
   6. base::is.data.frame(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 1 ]
  1. Error: (unknown) (@test_export.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘apex.Rmd’ using rmarkdown
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 294-299 (apex.Rmd) 
Error: processing vignette 'apex.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘apex.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘qCBA’
Error(s) in re-building vignettes:
  ...
--- re-building ‘arkhe.Rmd’ using rmarkdown
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.
Warning in normalizePath(f2) :
  path[1]="webshot1b231a4a5b98.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot1b231a4a5b98.png': No such file or directory
Quitting from lines 46-70 (arkhe.Rmd) 
Error: processing vignette 'arkhe.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘arkhe.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'oligo', 'pdInfoBuilder'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    help   1.1Mb
Running ‘testthat.R’ [19s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ARTool)
  > 
  > test_check("ARTool")
  ── 1. Failure: anova.art of Higgins1990Table5 matches results of the original AR
  `a` not equal to `ref`.
  Component "Term": 'current' is not a factor
  Component "Error": 'current' is not a factor
  
  ── 2. Failure: anova.art of Higgins1990Table5 matches results of the original AR
  `a` not equal to ref[-2].
  Component "Term": 'current' is not a factor
  
  ── 3. Failure: anova.art of Higgins1990Table1 matches results of the original AR
  `a` not equal to `ref`.
  Component "Term": 'current' is not a factor
  
  ── 4. Failure: anova.art of HigginsABC matches results of the original ARTool (@
  `a` not equal to `ref`.
  Component "Term": 'current' is not a factor
  Component "Error": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 108 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: anova.art of Higgins1990Table5 matches results of the original ARTool (@test.anova.art.R#45) 
  2. Failure: anova.art of Higgins1990Table5 matches results of the original ARTool (@test.anova.art.R#50) 
  3. Failure: anova.art of Higgins1990Table1 matches results of the original ARTool (@test.anova.art.R#69) 
  4. Failure: anova.art of HigginsABC matches results of the original ARTool (@test.anova.art.R#89) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   3.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    testdata   4.2Mb
Package suggested but not available for checking: ‘REBayes’
Error(s) in re-building vignettes:
  ...
--- re-building ‘asmapvignette.Rnw’ using knitr
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().
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc        2.4Mb
    full_doc   2.6Mb
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/augmentedRCBD.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [21s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(autocogs)
  > 
  > test_check("autocogs")
  ── 1. Error: ggplot2::geom_smooth (@test-plot_cogs.R#246)  ─────────────────────
  EXPR must be a length 1 vector
  Backtrace:
    1. ggplot2::qplot(cty, hwy, data = mpg, geom = "smooth")
    9. autocogs:::expect_auto_cogs(...)
   11. autocogs:::plot_cogs(.)
   19. autocogs:::get_layer_info(p, keep = keep_layers, ...)
   21. autocogs:::layer_info.ggplot(p, keep = keep, ...)
   22. base::lapply(...)
   23. autocogs:::FUN(X[[i]], ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 242 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: ggplot2::geom_smooth (@test-plot_cogs.R#246) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 73.8Mb
  sub-directories of 1Mb or more:
    java  73.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   3.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘BacArena-Introduction.Rmd’ using rmarkdown
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.
Loading required package: sybil
Loading required package: Matrix
Loading required package: lattice
Loading required package: ReacTran
Loading required package: rootSolve
Loading required package: deSolve
Loading required package: shape
BacArena paper: https://doi.org/10.1371/journal.pcbi.1005544
 Tutorials: https://bacarena.github.io
 Model import from SBML: https://github.com/euba/BacArena/wiki/Model-import
 Development and help: https://github.com/euba/bacarena
Warning in simEnv(arena, time = 10) :
  If growth is limited by maximum weight for an organism (max_weight=TRUE) it is recommended to use minimize total flux (sec_obj='mtf').
Quitting from lines 231-232 (BacArena-Introduction.Rmd) 
Error: processing vignette 'BacArena-Introduction.Rmd' failed with diagnostics:
Faceting variables must have at least one value
--- failed re-building ‘BacArena-Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘BacArena-Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Package suggested but not available for checking: ‘ArrayExpress’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘article2-vignette.Rnw’ using knitr
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-8'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Running ‘testthat.R’ [72s/109s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # 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(batchtools)
  > 
  > test_check("batchtools")
  ### [bt]: Setting seed to 2767 ...
  ── 1. Failure: addExperiments / user provided designs (@test_addExperiments.R#64
  `addExperiments(reg = reg, prob.designs = pd)` did not produce any warnings.
  
  ── 2. Failure: addExperiments / user provided designs (@test_addExperiments.R#67
  `addExperiments(reg = reg, prob.designs = pd)` did not produce any warnings.
  
  ### [bt]: Setting seed to 3080 ...
  ### [bt]: Setting seed to 3082 ...
  ### [bt]: Setting seed to 3081 ...
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1444 | SKIPPED: 11 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: addExperiments / user provided designs (@test_addExperiments.R#64) 
  2. Failure: addExperiments / user provided designs (@test_addExperiments.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   5.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.0Mb
    libs   1.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   4.2Mb
Running ‘testthat.R’ [21s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BayesPostEst)
  > 
  > test_check("BayesPostEst")
  ── 1. Failure: pars subsetting works (@test_mcmcTab.R#61)  ─────────────────────
  object$Variable not equal to factor(c(sprintf("b[%s]", 1:3))).
  Types not compatible: character is not integer
  
  ── 2. Failure: pars subsetting works (@test_mcmcTab.R#83)  ─────────────────────
  object$Variable not equal to factor(c(sprintf("b[%s]", 1:2))).
  Types not compatible: character is not integer
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 52 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: pars subsetting works (@test_mcmcTab.R#61) 
  2. Failure: pars subsetting works (@test_mcmcTab.R#83) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
Running ‘testthat.R’ [24s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bcgam)
  Loading required package: nimble
  nimble version 0.9.0 is loaded.
  For more information on NIMBLE and a User Manual,
  please visit http://R-nimble.org.
  
  Attaching package: 'nimble'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  > 
  > test_check("bcgam")
  thin = 1: tau, betalpha, sigma, eta
  ── 1. Error: (unknown) (@testthat.R#3)  ────────────────────────────────────────
  Failed to create the shared library.
  Backtrace:
   1. bcgam::bcgam(...)
   2. bcgam:::bcgam.fit(...)
   3. nimble::compileNimble(gaus)
   4. project$compileModel(units[[i]], control = control, showCompilerOutput = showCompilerOutput)
   5. cppProj$compileFile(compileList, showCompilerOutput)
   6. nimble:::compileDynamicRegistrations(showCompilerOutput = showCompilerOutput)
   7. nimble:::compileStaticCode(dllName, cppName, showCompilerOutput)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@testthat.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Bclim.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.7Mb
Package suggested but not available for checking: ‘BRugs’
Package suggested but not available for checking: ‘lumi’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Package suggested but not available for checking: ‘gifski’
installed size is 124.9Mb
  sub-directories of 1Mb or more:
    include  124.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in normalizePath(f2) :
  path[1]="webshot36192de4494c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot36192de4494c.png': No such file or directory
Quitting from lines 245-248 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘analysis.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    extdata   2.5Mb
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Running examples in ‘bigsnpr-Ex.R’ failed
The error most likely occurred in:

> ### Name: bed_tcrossprodSelf
> ### Title: Tcrossprod
> ### Aliases: bed_tcrossprodSelf
> 
> ### ** Examples
> 
> bedfile <- system.file("extdata", "example.bed", package = "bigsnpr")
> obj.bed <- bed(bedfile)
> 
> K <- bed_tcrossprodSelf(obj.bed)

 *** caught segfault ***
address f7c83000, cause 'invalid permissions'

Traceback:
 1: incr_FBM_mat(X, add)
 2: big_increment(K, tcrossprod(tmp))
 3: bed_tcrossprodSelf(obj.bed)
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
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.
Loading required package: correlbinom
Loading required package: Rmpfr
Loading required package: gmp

Attaching package: 'gmp'

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

    %*%, apply, crossprod, matrix, tcrossprod

C code of R package 'Rmpfr': GMP using 32 bits per limb


Attaching package: 'Rmpfr'

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

    outer

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

    dbinom, dgamma, dnorm, dpois, pnorm

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

    cbind, pmax, pmin, rbind

Quitting from lines 107-113 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
The melt generic in data.table has been passed a data.frame, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(rc.main.effects) or as.data.table(rc.main.effects). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is deprecated and you should be migrating your code away from using it.
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘BioCircos.Rmd’ using rmarkdown
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 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘BioCircos.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    extdata   7.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    doc       1.4Mb
    extdata   1.7Mb
Running examples in ‘bioRad-Ex.R’ failed
The error most likely occurred in:

> ### Name: beam_profile_overlap
> ### Title: Calculate overlap between a vertical profile ('vp') of
> ###   biological scatterers and the vertical radiation profile emitted by
> ###   the radar
> ### Aliases: beam_profile_overlap
> 
> ### ** Examples
> 
> # locate example volume file:
> pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
> 
> # load the example polar volume file:
> pvol <- read_pvolfile(pvolfile)
Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) : 
  HDF5. File accessibilty. Unable to open file.
Calls: read_pvolfile ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bioRad.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building ‘bioRad.Rmd’

--- re-building ‘rad_aero_19.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Welcome to bioRad version 0.5.0
Warning: Docker daemon not found
Warning: bioRad functionality requiring Docker has been disabled

To enable Docker functionality, first install Docker
--- finished re-building ‘rad_aero_19.Rmd’

--- re-building ‘range_correction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 63-70 (range_correction.Rmd) 
Error: processing vignette 'range_correction.Rmd' failed with diagnostics:
HDF5. File accessibilty. Unable to open file.
--- failed re-building ‘range_correction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
Running ‘testthat.R’ [8s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BisqueRNA)
  > 
  > test_check("BisqueRNA")
  ── 1. Error: Catches data where zero variance in training data (@test_ref_based.
  incorrect number of dimensions
  Backtrace:
   1. testthat::expect_equal(...)
   4. BisqueRNA::ReferenceBasedDecomposition(bulk.eset, sc.eset, use.overlap = F)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 49 | SKIPPED: 0 | WARNINGS: 9 | FAILED: 1 ]
  1. Error: Catches data where zero variance in training data (@test_ref_based.R#125) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘IHW’
Invalid maximum heap size: -Xmx4G
The specified size exceeds the maximum representable size.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
Found the following files/directories:
  ‘core’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
Running examples in ‘blockmodeling-Ex.R’ failed
The error most likely occurred in:

> ### Name: REGE
> ### Title: REGE - Algorithms for compiting (dis)similarities in terms of
> ###   regular equivalnece
> ### Aliases: REGE REGE.for REGE.nm.for REGE.ow REGE.ow.for REGE.ownm.for
> ###   REGD.for REGD.ow.for REGE.FC REGE.FC.ow REGD.ne.for REGD.ow.ne.for
> ###   REGE.ne.for REGE.nm.diag.for REGE.nm.ne.for REGE.ow.ne.for
> ###   REGE.ownm.diag.for REGE.ownm.ne.for
> ### Keywords: cluster graphs
> 
> ### ** Examples
> 
> n <- 20
> net <- matrix(NA, ncol = n, nrow = n)
> clu <- rep(1:2, times = c(5, 15))
> tclu <- table(clu)
> net[clu == 1, clu == 1] <- 0
> net[clu == 1, clu == 2] <- rnorm(n = tclu[1] * tclu[2], mean = 4, sd = 1) * sample(c(0, 1),
+    size = tclu[1] * tclu[2], replace = TRUE, prob = c(3/5, 2/5))
> net[clu == 2, clu == 1] <- 0
> net[clu == 2, clu == 2] <- 0
> 
> D <- REGE.for(M = net)$E # Any other REGE function can be used
> plot.mat(net, clu = cutree(hclust(d = as.dist(1 - D), method = "ward.D"),
+    k = 2))
> # REGE returns similarities, which have to be converted to
> # disimilarities
> 
> res <- optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss", blocks = "reg")


Starting optimization of the partiton 1 of 10 partitions.
Starting partition: 1 2 1 1 1 1 1 1 1 2 2 1 2 2 2 2 2 1 1 1 

 *** caught segfault ***
address 6f5ec1ac, cause 'memory not mapped'

Traceback:
 1: optParC(M = M, clu = temppar, approaches = approaches, blocks = blocks,     useMulti = useMulti, save.initial.param = save.initial.param.opt,     ...)
 2: optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss",     blocks = "reg")
An irrecoverable exception occurred. R is aborting now ...
Running ‘testthat.R’ [63s/69s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BMTME)
  > 
  > test_check("BMTME")
  ── 1. Failure: RandomPartition (@test.R#52)  ───────────────────────────────────
  RP_Test$Environments inherits from `character` not `factor`.
  
  ── 2. Failure: RandomPartition (@test.R#72)  ───────────────────────────────────
  RP_Test2$Traits inherits from `character` not `factor`.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 164 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: RandomPartition (@test.R#52) 
  2. Failure: RandomPartition (@test.R#72) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘BoolNet_package_vignette.Snw.Rnw’ using Sweave

Error: processing vignette 'BoolNet_package_vignette.Snw.Rnw' failed with diagnostics:
 chunk 13 
Error in net$interactions[[idx]][[functionIndices[idx]]] : 
  subscript out of bounds

--- failed re-building ‘BoolNet_package_vignette.Snw.Rnw’

SUMMARY: processing the following file failed:
  ‘BoolNet_package_vignette.Snw.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘break_caret.Rmd’ using rmarkdown
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.
Loading required package: lattice
Loading required package: ggplot2
--- finished re-building ‘break_caret.Rmd’

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

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

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

Cpu Limit Exceeded - core dumped
--- re-building ‘break_ranger.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- re-building ‘break_svm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_svm.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R     3.8Mb
    doc   2.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    bin    3.1Mb
    doc    1.3Mb
    libs   3.1Mb
Found the following significant warnings:
  Warning: namespace ‘DiffBind’ is not available and has been replaced
See ‘/home/ripley/R/packages/tests-devel/Brundle.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘simple_plotting.Rmd’ using rmarkdown
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: Removed 4550 row(s) containing missing values (geom_path).
Quitting from lines 173-174 (simple_plotting.Rmd) 
Error: processing vignette 'simple_plotting.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘simple_plotting.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.Rmd’ using rmarkdown
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.

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: 'c3'

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

    %>%

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

    grid, legend

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.
Warning in normalizePath(f2) :
  path[1]="webshot4be120cb73fc.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot4be120cb73fc.png': No such file or directory
Quitting from lines 56-65 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: ‘FastRWeb’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R        1.3Mb
    data     1.8Mb
    models   2.5Mb
Running ‘testthat.R’ [9m/17m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(caret)
  Loading required package: lattice
  Loading required package: ggplot2
  > 
  > test_check("caret")
  ── 1. Failure: Good names for dummies with reocurring patterns (@test_Dummies.R#
  all(exp_names_lvls %in% res_names_lvls) isn't true.
  
  ── 2. Error: Multiclass logloss returns expected values (@test_mnLogLoss.R#12)  
  'data$obs' should have levels consistent with 'lev'
  Backtrace:
   1. caret::mnLogLoss(test_dat1, classes)
  
  ── 3. Error: Twoclass logloss returns expected values (@test_mnLogLoss.R#38)  ──
  'data$obs' should have levels consistent with 'lev'
  Backtrace:
   1. caret::mnLogLoss(test_dat1.b, classes.b)
  
  ── 4. Failure: handles situation when there's a single column per transformation
  `preprocessed` not equal to data.frame(x = c("a", "a"), y = c(-0.5, 0.5)).
  Component "x": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 135 | SKIPPED: 33 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: Good names for dummies with reocurring patterns (@test_Dummies.R#126) 
  2. Error: Multiclass logloss returns expected values (@test_mnLogLoss.R#12) 
  3. Error: Twoclass logloss returns expected values (@test_mnLogLoss.R#38) 
  4. Failure: handles situation when there's a single column per transformation (@test_preProcess_internals.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cartograflow.Rmd’ using rmarkdown
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.

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: Use of `x$flowcum` is discouraged. Use `flowcum` instead.
Warning: Use of `x$linkcum` is discouraged. Use `linkcum` instead.
Warning: Use of `x$flowcum` is discouraged. Use `flowcum` instead.
Warning: Use of `x$flowcum` is discouraged. Use `flowcum` instead.
Quitting from lines 451-480 (cartograflow.Rmd) 
Error: processing vignette 'cartograflow.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘cartograflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
Package suggested but not available for checking: ‘iptools’
Running ‘testthat.R’ [85s/101s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(CHNOSZ)
  CHNOSZ version 1.3.5 (2020-02-16)
  reset: creating "thermo" object
  obigt: loading default database with 1849 aqueous, 3374 total species
  > 
  > # as fix for https://github.com/hadley/testthat/issues/129, https://github.com/hadley/testthat/issues/144
  > # (since we use makeCluster() etc via palply)
  > Sys.setenv("R_TESTS" = "") 
  > 
  > test_check("CHNOSZ")
  ── 1. Failure: add.protein works as expected (@test-add.protein.R#13)  ─────────
  `ip <- add.protein(aa)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 568 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 1 ]
  1. Failure: add.protein works as expected (@test-add.protein.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    doc    1.7Mb
    help   2.3Mb
Package suggested but not available for checking: ‘rggobi’
Running examples in ‘cleanNLP-Ex.R’ failed
The error most likely occurred in:

> ### Name: cnlp_annotate
> ### Title: Run the annotation pipeline on a set of documents
> ### Aliases: cnlp_annotate
> 
> ### ** Examples
> 
> cnlp_init_stringi()
> cnlp_annotate(un)
Error in stri_detect_regex(str, regex, ...) : 
  Start of codes indicating failure. (U_ILLEGAL_ARGUMENT_ERROR)
Calls: cnlp_annotate ... annotate_with_stringi -> <Anonymous> -> stri_detect_regex
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cleanNLP)
  > 
  > test_check("cleanNLP")
  ── 1. Error: testing stringi (@test-annotation.R#9)  ───────────────────────────
  Start of codes indicating failure. (U_ILLEGAL_ARGUMENT_ERROR)
  Backtrace:
   1. cleanNLP::cnlp_annotate(un, verbose = FALSE)
   2. cleanNLP:::annotate_with_stringi(input, verbose)
   3. stringi::stri_detect(...)
   4. stringi::stri_detect_regex(str, regex, ...)
  
  ── 2. Error: testing utils_tfidf (@test-tools.R#9)  ────────────────────────────
  Start of codes indicating failure. (U_ILLEGAL_ARGUMENT_ERROR)
  Backtrace:
   1. cleanNLP::cnlp_annotate(un, verbose = FALSE)
   2. cleanNLP:::annotate_with_stringi(input, verbose)
   3. stringi::stri_detect(...)
   4. stringi::stri_detect_regex(str, regex, ...)
  
  ── 3. Error: testing tidy_pca (@test-tools.R#20)  ──────────────────────────────
  Start of codes indicating failure. (U_ILLEGAL_ARGUMENT_ERROR)
  Backtrace:
   1. cleanNLP::cnlp_annotate(un, verbose = FALSE)
   2. cleanNLP:::annotate_with_stringi(input, verbose)
   3. stringi::stri_detect(...)
   4. stringi::stri_detect_regex(str, regex, ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: testing stringi (@test-annotation.R#9) 
  2. Error: testing utils_tfidf (@test-tools.R#9) 
  3. Error: testing tidy_pca (@test-tools.R#20) 
  
  Error: testthat unit tests failed
  Execution halted
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Package which this enhances but not available for checking: ‘RWeka’
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 43-45 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
More than one expression parsed
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘the_clusterR_package.Rmd’ using rmarkdown
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 403-416 (the_clusterR_package.Rmd) 
Error: processing vignette 'the_clusterR_package.Rmd' failed with diagnostics:
std::bad_alloc
--- failed re-building ‘the_clusterR_package.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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Error(s) in re-building vignettes:
  ...
--- re-building ‘codemeta-intro.Rmd’ using rmarkdown
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 85-86 (codemeta-intro.Rmd) 
Error: processing vignette 'codemeta-intro.Rmd' failed with diagnostics:
Timeout was reached: [sysreqs.r-hub.io] Operation timed out after 10003 milliseconds with 0 out of 0 bytes received
--- failed re-building ‘codemeta-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘codemeta-intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘fda7wnr6u.c’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Running-CoDiNA.Rmd’ using rmarkdown
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 100-105 (Running-CoDiNA.Rmd) 
Error: processing vignette 'Running-CoDiNA.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
--- failed re-building ‘Running-CoDiNA.Rmd’

SUMMARY: processing the following file failed:
  ‘Running-CoDiNA.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [93s/111s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat) 
  > library(codyn)
  > test_check("codyn")
  ── 1. Failure: rank_shift loads and returns correct result (@test_rank_shift.R#1
  result[, 1] inherits from `character` not `factor`.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 359 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: rank_shift loads and returns correct result (@test_rank_shift.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Getting_Started.Rmd’ using rmarkdown
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 44-47 (Getting_Started.Rmd) 
Error: processing vignette 'Getting_Started.Rmd' failed with diagnostics:

--- failed re-building ‘Getting_Started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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    doc       3.0Mb
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installed size is  5.4Mb
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    java   5.2Mb
Package suggested but not available for checking: ‘rscala’
installed size is  5.3Mb
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    doc   2.3Mb
installed size is  9.6Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_the_contact_package_v1.0.1.Rmd’ using rmarkdown
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 222-230 (Using_the_contact_package_v1.0.1.Rmd) 
Error: processing vignette 'Using_the_contact_package_v1.0.1.Rmd' failed with diagnostics:
invalid color name 'feed'
--- failed re-building ‘Using_the_contact_package_v1.0.1.Rmd’

SUMMARY: processing the following file failed:
  ‘Using_the_contact_package_v1.0.1.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘contrast.Rnw’ using Sweave
Loading required package: rms
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: ‘Hmisc’

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

    format.pval, units

Loading required package: SparseM

Attaching package: ‘SparseM’

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

    backsolve


Error: processing vignette 'contrast.Rnw' failed with diagnostics:
 chunk 8 (label = eachTest) 
Error in eval(predvars, data, env) : object 'diet' not found

--- failed re-building 'contrast.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘cooccurNet-Ex.R’ failed
The error most likely occurred in:

> ### Name: coocnet
> ### Title: coocnet
> ### Aliases: coocnet
> 
> ### ** Examples
> 
> cooccurNetwork  = coocnet(dataFile=getexample(dataType="protein"), dataType="protein")
reading file......
completed. (10,329)
preprocess file......Error in if (pred >= memsize * alpha || ncol > 150 || (nrow > 30000 &  : 
  missing value where TRUE/FALSE needed
Calls: coocnet ... cooccur.dataprepreprocess.preprocess -> inmemoryflag
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Extending-cooccurNet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 176-178 (Extending-cooccurNet.Rmd) 
Error: processing vignette 'Extending-cooccurNet.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘Extending-cooccurNet.Rmd’

SUMMARY: processing the following file failed:
  ‘Extending-cooccurNet.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘memory.limits’
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   5.9Mb
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Running ‘testthat.R’ [14s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(corpus)
  > 
  > test_check("corpus")
  -- 1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161
  invalid 'type' (list) of argument
  Backtrace:
    1. base::strsplit(capture_output(print(loc), width = 76), "\n")
    9. corpus:::print.corpus_text_locate(loc)
   10. corpus:::format.corpus_text_locate(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 581 | SKIPPED: 12 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    help   1.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Running examples in ‘CoSMoS-Ex.R’ failed
The error most likely occurred in:

> ### Name: acs
> ### Title: AutoCorrelation Structure
> ### Aliases: acs
> 
> ### ** Examples
> 
> 
> library(CoSMoS); library(ggplot2)
> 
> ## specify lag
> t <- 0:10
> 
> ## get the ACS
> f <- acs('fgn', t = t, H = .75)
> b <- acs('burrXII', t = t, scale = 1, shape1 = .6, shape2 = .4)
> w <- acs('weibull', t = t, scale = 2, shape = 0.8)
> p <- acs('paretoII', t = t, scale = 3, shape = 0.3)
> 
> ## visualize the ACS
> dta <- data.frame(t, f, b, w, p)
> 
> m.dta <- melt(dta, id.vars = 't')
Error in value[[3L]](cond) : 
  The melt generic in data.table has been passed a data.frame, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(dta) or as.data.table(dta). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is deprecated and you should be migrating your code away from using it.
Calls: melt ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Package required but not available: ‘SNPRelate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
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 399-421 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
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 cuminc(ftime = time, fstatus = risk, group = group, cencode = cens) :
  NAs introduced by coercion
Quitting from lines 176-180 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
NAs in foreign function call (arg 3)
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.4Mb
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    doc   8.0Mb
Found the following files/directories:
  ‘core’ ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
installed size is  7.7Mb
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    doc    1.5Mb
    libs   5.1Mb
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/csp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/ctsem.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'Rmosek', 'gurobi', 'Rcplex', 'rcbc'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    doc    1.3Mb
    help   1.1Mb
Running examples in ‘CVXR-Ex.R’ failed
The error most likely occurred in:

> ### Name: diag,Expression-method
> ### Title: Matrix Diagonal
> ### Aliases: diag,Expression-method diag
> 
> ### ** Examples
> 
> C <- Variable(3,3)
> obj <- Maximize(C[1,3])
> constraints <- list(diag(C) == 1, C[1,2] == 0.6, C[2,3] == -0.3, C == Variable(3,3, PSD = TRUE))
> prob <- Problem(obj, constraints)
> result <- solve(prob)

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

Traceback:
 1: scs::scs(A = args$A, b = args$b, obj = args$c, cone = cones,     control = control)
 2: solve_via_data(object@solver, data, warm_start, verbose, feastol,     reltol, abstol, num_iter, solver_opts, problem@.solver_cache)
 3: solve_via_data(object@solver, data, warm_start, verbose, feastol,     reltol, abstol, num_iter, solver_opts, problem@.solver_cache)
 4: reduction_solve_via_data(object@.solving_chain, object, data,     warm_start, verbose, feastol, reltol, abstol, num_iter, list(...))
 5: reduction_solve_via_data(object@.solving_chain, object, data,     warm_start, verbose, feastol, reltol, abstol, num_iter, list(...))
 6: psolve(a, solver = NA, ...)
 7: psolve(a, solver = NA, ...)
 8: solve(prob)
 9: solve(prob)
An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘cycling_data_analysis.Rmd’ using rmarkdown
Warning in engine$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 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘cycling_data_analysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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    libs   6.2Mb
installed size is  5.2Mb
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    doc   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
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 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
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Running examples in ‘dabestr-Ex.R’ failed
The error most likely occurred in:

> ### Name: dabest
> ### Title: Differences between Groups with Bootstrap Confidence Intervals
> ### Aliases: dabest
> 
> ### ** Examples
> 
> 
> # Performing unpaired (two independent groups) analysis.
> unpaired_mean_diff <- dabest(iris, Species, Petal.Width,
+                              idx = c("setosa", "versicolor"),
+                              paired = FALSE)
> 
> # Display the results in a user-friendly format.
> unpaired_mean_diff
DABEST (Data Analysis with Bootstrap Estimation) v0.2.3
=======================================================

Variable: Petal.Width 

Unpaired mean difference of versicolor (n=50) minus setosa (n=50)
 1.08 [95CI  1.01; 1.14]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

> 
> # Produce an estimation plot.
> plot(unpaired_mean_diff)
Error in loadNamespace(name) : there is no package called ‘plyr’
Calls: plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-dabestr.Rmd’ using rmarkdown
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.

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 82-83 (using-dabestr.Rmd) 
Error: processing vignette 'using-dabestr.Rmd' failed with diagnostics:
there is no package called 'plyr'
--- failed re-building ‘using-dabestr.Rmd’

SUMMARY: processing the following file failed:
  ‘using-dabestr.Rmd’

Error: Vignette re-building failed.
Execution halted
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    Pied_Flycatchers_2   1.3Mb
    doc                  1.2Mb
installed size is  7.8Mb
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    java   7.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘get_started.Rmd’ using rmarkdown
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 26-34 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘get_started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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    doc       2.5Mb
    extdata   5.7Mb
installed size is  5.2Mb
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    doc    1.3Mb
    libs   2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘applications.Rmd’ using rmarkdown
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.
--- finished re-building ‘applications.Rmd’

--- re-building ‘data.tree.Rmd’ using rmarkdown
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 513-516 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘data.tree.Rmd’

SUMMARY: processing the following file failed:
  ‘data.tree.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘RPostgres’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    sample_data   3.6Mb
installed size is  5.1Mb
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    extdata   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘RC_units.Rmd’ using rmarkdown
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.
--- finished re-building ‘RC_units.Rmd’

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

--- re-building ‘sjukhus.Rmd’ using rmarkdown
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.
Joining, by = "key"
Joining, by = "key"
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 102-122 (sjukhus.Rmd) 
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sjukhus.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘delayed.Rmd’ using rmarkdown
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 97-98 (delayed.Rmd) 
Error: processing vignette 'delayed.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘delayed.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  7.3Mb
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    doc   5.9Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       5.0Mb
    extdata   2.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.0Mb
    help   1.6Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rmosek', 'Rsymphony'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    1.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘DGVM3D.Rmd’ using rmarkdown
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.
Loading required package: rgl
Loading required namespace: rmarkdown
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 230-234 (DGVM3D.Rmd) 
Error: processing vignette 'DGVM3D.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘DGVM3D.Rmd’

SUMMARY: processing the following file failed:
  ‘DGVM3D.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc           9.8Mb
    htmlwidgets   6.2Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc   9.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
Package suggested but not available for checking: ‘RcppRedis’
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    include  15.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   2.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Running examples in ‘dmdScheme-Ex.R’ failed
The error most likely occurred in:

> ### Name: report
> ### Title: Generic function for creating a report from an object 'x'
> ### Aliases: report report.character report.dmdScheme_validation
> 
> ### ** Examples
> 
> ## Report of `dmdScheme_validation`
> report( scheme_path_xlsx() )
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Running ‘testthat.R’ [32s/78s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(magrittr)
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > ##
  > library(dmdScheme)
  
  #############################################
  The cache will be in a temporary location and be deleted when you quit R.
  It is located at
     /tmp/RtmpXdayTK/working_dir/RtmpJfa4.x/dmdScheme_2ff72c92732a
  To make it permanent, call
     cache(createPermanent = TRUE)
  and restart R
  and a permanent cache will be created which will survive restarts.
  #############################################
  
  
  trying URL 'https://github.com/Exp-Micro-Ecol-Hub/dmdSchemeRepository/raw/master/schemes/dmdScheme_0.9.5.tar.gz'
  Content type 'application/octet-stream' length 27511 bytes (26 KB)
  ==================================================
  downloaded 26 KB
  
  Scheme definition `/tmp/RtmpXdayTK/working_dir/RtmpJfa4.x/file2ff7633924e1/dmdScheme_0.9.5.tar.gz, installed with
  name:    dmdScheme
  version: 0.9.5
  Theme switched to dmdScheme_0.9.5
  > ##
  > test_check("dmdScheme")
  terminate called after throwing an instance of 'Rcpp::exception'
    what():  Start tag expected, '<' not found [4]
Running ‘runit.R’ [17s/29s]
  Running ‘testthat.R’ [19s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > running_on_my_machines <- function() {
  +     sys_info <- Sys.info()
  +     r <- sys_info[["nodename"]] %in% c("h6", "h7") &&
  +         sys_info[["effective_user"]] == "qwer" &&
  +         .Platform[["OS.type"]] == "unix"
  +     return(r)
  + }
  > 
  > set_NOT_CRAN  <- function() {
  +     is_unset <- is.na(Sys.getenv("NOT_CRAN", unset = NA))
  +     if (running_on_my_machines() && is_unset)
  +         Sys.setenv("NOT_CRAN" = TRUE)
  + }
  > 
  > set_NOT_CRAN()
  > library("testthat")
  > library("document")
  > test_check("document")
  ── R CMD build ─────────────────────────────────────────────────────────────────
  * checking for file ‘.../DESCRIPTION’ ... OK
  * preparing ‘mini.mal’:
  * checking DESCRIPTION meta-information ... OK
  * checking for LF line-endings in source and make files and shell scripts
  * checking for empty or unneeded directories
  * building ‘mini.mal_2.0.0.tar.gz’
  
  ── 1. Error: (unknown) (@test_basic.R#13)  ─────────────────────────────────────
  Still alive
  Backtrace:
   1. document::document(file_name, check_package = TRUE, runit = TRUE)
   2. document:::check_package(...)
   3. rcmdcheck::rcmdcheck(...)
   4. rcmdcheck:::build_package(...)
   7. proc$get_built_file()
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@test_basic.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Packages which this enhances but not available for checking:
  'gurobi', 'Rmosek'
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DoE.multi.response)
  Loading required package: DoE.wrapper
  Loading required package: FrF2
  Loading required package: DoE.base
  Loading required package: grid
  Loading required package: conf.design
  
  Attaching package: 'DoE.base'
  
  The following objects are masked from 'package:stats':
  
      aov, lm
  
  The following object is masked from 'package:graphics':
  
      plot.design
  
  The following object is masked from 'package:base':
  
      lengths
  
  Loading required package: rsm
  
  Attaching package: 'DoE.wrapper'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > 
  > test_check("DoE.multi.response")
  ── 1. Error: (unknown) (@testufccd.R#8)  ───────────────────────────────────────
  non-numeric argument to binary operator
  Backtrace:
   1. DoE.multi.response::ufccd(x)
   2. DoE.wrapper::ccd.design(...)
   3. DoE.wrapper::ccd.augment(...)
   4. FrF2::add.center(cube, ncenter[1])
   7. base::substr(rostdrplev, punkt1 + 1, 999)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 23 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@testufccd.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
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 359-375 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
graphical parameter "col.axis" has the wrong length
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    DRomics-shiny   1.8Mb
    extdata         3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘userGuide.Rmd’ using rmarkdown
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.
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
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.
Warning in normalizePath(f2) :
  path[1]="webshotbc6538300b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotbc6538300b.png': No such file or directory
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘userGuide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    appinformation   4.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘dsa-vignette.Rmd’ using rmarkdown
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 37-38 (dsa-vignette.Rmd) 
Error: processing vignette 'dsa-vignette.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
--- failed re-building ‘dsa-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Designing-33PC.Rmd’ using rmarkdown
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 163-164 (Designing-33PC.Rmd) 
Error: processing vignette 'Designing-33PC.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Designing-33PC.Rmd’

SUMMARY: processing the following file failed:
  ‘Designing-33PC.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    1.8Mb
    libs   2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.8Mb
Running ‘testthat.R’ [74s/75s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("dynutils")
  Loading required package: dynutils
  
  Attaching package: 'dynutils'
  
  The following object is masked from 'package:testthat':
  
      has_names
  
  ── 1. Error: write_h5 and read_h5 works (@test-h5.R#11)  ───────────────────────
  HDF5-API H5T.c in H5Tget_class(): line 1876: not a datatype
          class: HDF5
          major: Invalid arguments to routine
          minor: Inappropriate type
  Backtrace:
   1. dynutils::read_h5(file)
   2. dynutils::read_h5_(file_h5)
   3. hdf5r::h5attr(file_h5, "object_class")
   4. attr_obj$read()
   5. hdf5r:::H5ToR_Pre(mem_type, nelem)
  
  ❌ Unable to read hdf5 files
  ── 2. Error: test_h5_installation works (@test-h5.R#17)  ───────────────────────
  HDF5-API H5T.c in H5Tget_class(): line 1876: not a datatype
          class: HDF5
          major: Invalid arguments to routine
          minor: Inappropriate type
  Backtrace:
   1. testthat::expect_true(test_h5_installation())
   4. dynutils::test_h5_installation()
   5. dynutils:::test_h5_installation_read(detailed, file)
   6. base::tryCatch(...)
   7. base:::tryCatchList(expr, classes, parentenv, handlers)
   8. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 402 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 2 ]
  1. Error: write_h5 and read_h5 works (@test-h5.R#11) 
  2. Error: test_h5_installation works (@test-h5.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
File ‘eaf/libs/eaf.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
    Objects: ‘eaf/eaf.o’, ‘eaf/io.o’, ‘mo-tools/hv.o’, ‘Repsilon.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.
Running examples in ‘eDMA-Ex.R’ failed
The error most likely occurred in:

> ### Name: BacktestDMA
> ### Title: Backtest measures for Dynamic Model Averaging and comparison
> ###   with Dynamic Model Selection
> ### Aliases: BacktestDMA
> 
> ### ** Examples
> 
> 
> library(eDMA)
> 
> ## load data
> data("USData")
> 
> ## do DMA, keep the first three predictors fixed and the intercept
> Fit <- DMA(GDPDEF ~ Lag(GDPDEF, 1) + Lag(GDPDEF, 2) + Lag(GDPDEF, 3) +
+             Lag(ROUTP, 1) + Lag(UNEMP, 1), data = USData, vDelta = c(0.9, 0.95, 0.99),
+             vKeep = c(1, 2, 3))

error: sort(): detected NaN
Error in funcEstimate_Eff_par(vY, mF, vDelta, dAlpha, vKeep, dBeta, bZellnerPrior,  : 
  sort(): detected NaN
Calls: DMA -> funcEstimate_Eff_par
Execution halted
Running ‘test-all.R’ [23s/76s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(eeptools)
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  ── 1. Failure: moves_calc gets the correct results (@test-calculators.R#210)  ──
  `moves` not equal to `correct_result`.
  Component "sid": Modes: character, numeric
  Component "sid": Attributes: < target is NULL, current is list >
  Component "sid": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 509 | SKIPPED: 0 | WARNINGS: 29 | FAILED: 1 ]
  1. Failure: moves_calc gets the correct results (@test-calculators.R#210) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc       5.3Mb
    extdata   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘EHRtemporalVariability.Rmd’ using rmarkdown
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.
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

Joining, by = "diagcode1"
Warning: Column `diagcode1` joining factor and character vector, coercing into character vector
# Missing values: 0 cases ( 0%)
# External causes codes: 0 cases ( 0%)
# V codes not mapped: 74330 cases ( 22.82%)
# Total ICD9-CM codes mapped: 146262 cases ( 44.9%)
# Unique ICD9-CM codes mapped: 3020
# Total PheWAS codes: 757
# ICD9 codes not mapped: 105180 cases ( 32.29%)
Quitting from lines 317-322 (EHRtemporalVariability.Rmd) 
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘EHRtemporalVariability.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    examples   4.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    xsd   4.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.6Mb
Running examples in ‘eNetXplorer-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotContingency
> ### Title: generates plot of response vs out-of-bag predictions across
> ###   classes
> ### Aliases: plotContingency
> 
> ### ** Examples
> 
> ## Don't show: 
> set.seed(123)
> fit = eNetXplorer(x=matrix(rnorm(120),ncol=4),y=c(rep(0,15),rep(1,15)),
+ family="binomial",n_run=5, n_perm_null=4,alpha=c(0.5,1))
Error during execution of alpha =  0.5 
> plot(x=fit,plot.type="contingency")
Error in if (x$family %in% c("binomial", "multinomial")) { : 
  argument is of length zero
Calls: plot -> plot.eNetXplorer
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    doc    3.4Mb
    help   3.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘epicontacts.Rmd’ using rmarkdown
Warning in engine$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 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘epicontacts.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EpiCurve.Rmd’ using rmarkdown
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.
Loading required package: ggplot2
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: ISOweek
Loading required package: scales
Quitting from lines 149-156 (EpiCurve.Rmd) 
Error: processing vignette 'EpiCurve.Rmd' failed with diagnostics:
Column `DateFactor` is unknown
--- failed re-building ‘EpiCurve.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epiflows-class.Rmd’ using rmarkdown
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.
--- finished re-building ‘epiflows-class.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
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 117-120 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘EpiSignalDetection-Ex.R’ failed
The error most likely occurred in:

> ### Name: runEpiSDReport
> ### Title: Run the EpiSignalDetection report (HTML markdown)
> ### Aliases: runEpiSDReport
> 
> ### ** Examples
> 
> #---> OR
> 
> #-- First setting the parameters to run the report for
> input <- list(
+ disease = "Salmonellosis",
+ country = "Portugal",
+ indicator = "Reported cases",
+ stratification = "Confirmed cases",
+ unit = "Month",
+ daterange = c("2011-01-01", "2016-12-31"),
+ algo = "FarringtonFlexible",
+ testingperiod = 6
+ )
> 
> #-- Second running the report based on the EpiSignalDetection::SignalData dataset
> #-- and store it in a temporary folder
> runEpiSDReport(input = input)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Running ‘sleep.R’
  Comparing ‘sleep.Rout’ to ‘sleep.Rout.save’ ... OK
  Running ‘testthat.R’ [69s/81s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(estimatr)
  > 
  > test_check("estimatr")
  ── 1. Error: FE matches lm_robust with one block (@test-lm-robust-fes.R#528)  ──
  contrasts can be applied only to factors with 2 or more levels
  Backtrace:
   1. estimatr::lm_robust(...)
   2. estimatr::lm_robust_fit(...)
   3. estimatr:::prep_data(...)
   5. stats::model.matrix.default(~0 + ., data = fe_dat)
   6. stats::`contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]])
  
  ── 2. Failure: Handle perfect fits appropriately (@test-lm-robust-fes.R#682)  ──
  tidy(rfo)[rfo$term == "X", ] not equivalent to tidy(ro)[ro$term == "X", ].
  Component "std.error": 'is.NA' value mismatch: 1 in current 0 in target
  Component "statistic": 'is.NA' value mismatch: 1 in current 0 in target
  Component "p.value": 'is.NA' value mismatch: 1 in current 0 in target
  Component "conf.low": 'is.NA' value mismatch: 1 in current 0 in target
  Component "conf.high": 'is.NA' value mismatch: 1 in current 0 in target
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1308 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: FE matches lm_robust with one block (@test-lm-robust-fes.R#528) 
  2. Failure: Handle perfect fits appropriately (@test-lm-robust-fes.R#682) 
  
  Error: testthat unit tests failed
  Execution halted
Undocumented S4 methods:
  generic 'plot' and siglist 'trialDesign_binom_one'
  generic 'plot' and siglist 'trialDesign_binom_two'
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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    exiftool  14.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_genExPrior.Rmd’ using rmarkdown
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 58-59 (using_genExPrior.Rmd) 
Error: processing vignette 'using_genExPrior.Rmd' failed with diagnostics:
Failed to create the shared library.
--- failed re-building ‘using_genExPrior.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘RWeka’
Package unavailable to check Rd xrefs: ‘RWeka’
Running ‘run-all.R’ [6s/18s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("farff")
  Loading required package: farff
  ── 1. Error: quick test with small arffs (@test_quick.R#6)  ────────────────────
  there is no package called 'RWeka'
  Backtrace:
   1. farff:::compareRWeka(INST_ARFF_DIR, "iris.arff", data.reader = dreader)
   2. RWeka::read.arff /home/ripley/R/packages/tests-devel/farff.Rcheck/tests/helper.R:17:2
   3. base::getExportedValue(pkg, name)
   4. base::asNamespace(ns)
   5. base::getNamespace(ns)
   6. base::loadNamespace(name)
   7. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8. base:::withOneRestart(expr, restarts[[1L]])
   9. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: quick test with small arffs (@test_quick.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Package suggested but not available for checking: ‘Rserve’
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/FastRWeb.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Running ‘spelling.R’
  Running ‘testthat.R’ [55s/67s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fgeo.analyze)
  > 
  > test_check("fgeo.analyze")
  ── 1. Failure: as.data.frame.tt_lst takes arguments via `...` (@test-as_tibble.R
  as.data.frame(tt_lst)[["sp"]] inherits from `character` not `factor`.
  
  ── 2. Failure: as.data.frame.demography_ctfs takes arguments via `...` (@test-as
  as.data.frame(result)[["groups"]] inherits from `character` not `factor`.
  
  $N2
  [1] 29
  
  $R
  [1] 3
  
  $rate
  [1] 0.02413113
  
  $lower
  [1] 0.0084585
  
  $upper
  [1] 0.06812388
  
  $time
  [1] 4.525246
  
  $date1
  [1] 18937.96
  
  $date2
  [1] 20600.72
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 305 | SKIPPED: 14 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: as.data.frame.tt_lst takes arguments via `...` (@test-as_tibble.R#31) 
  2. Failure: as.data.frame.demography_ctfs takes arguments via `...` (@test-as_tibble.R#129) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘quick_charts.Rmd’ using rmarkdown
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.

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 125-134 (quick_charts.Rmd) 
Error: processing vignette 'quick_charts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘quick_charts.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lifeExpectancy.Rmd’ using rmarkdown
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 76-77 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘lifeExpectancy.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    help   3.2Mb
Package suggested but not available for checking: ‘multipanelfigure’
Running examples in ‘float-Ex.R’ failed
The error most likely occurred in:

> ### Name: eigen
> ### Title: eigen
> ### Aliases: eigen eigen,float32-method
> 
> ### ** Examples
> 
> library(float)
> 
> s = flrunif(10, 3)
> cp = crossprod(s)
> 
> eigen(cp)
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    fonts   6.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    fonts   7.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘formattable-data-frame.Rmd’ using rmarkdown
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 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘formattable-data-frame.Rmd’

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

SUMMARY: processing the following file failed:
  ‘formattable-data-frame.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-formulaic.Rmd’ using rmarkdown
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 127-132 (Introduction-to-formulaic.Rmd) 
Error: processing vignette 'Introduction-to-formulaic.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Introduction-to-formulaic.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction-to-formulaic.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2', 'Rsymphony'
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    help   1.6Mb
    libs   5.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    2.1Mb
Packages suggested but not available for checking: 'RWeka', 'FSelector'
Package unavailable to check Rd xrefs: ‘FSelector’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data  16.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘futureheatwaves.Rmd’ using rmarkdown
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 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘futureheatwaves.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘chart_themes.Rmd’ using rmarkdown
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.
g3viz: visualizing gene/genome/gentics data for fun.
Any questions, please send emails to <g3viz.group@gmail.com>
Please send questions to cbioportal@googlegroups.com
Quitting from lines 48-58 (chart_themes.Rmd) 
Error: processing vignette 'chart_themes.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘chart_themes.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
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.
g3viz: visualizing gene/genome/gentics data for fun.
Any questions, please send emails to <g3viz.group@gmail.com>
Quitting from lines 103-114 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘chart_themes.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      2.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘gcbd.Rnw’ using Sweave
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
--- failed re-building ‘gcbd.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    L8NY18   2.1Mb
    doc      1.0Mb
    libs     2.3Mb
Running ‘testthat.R’ [31s/44s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(genBaRcode)
  > 
  > test_check("genBaRcode")
  ── 1. Failure: helper functions - com_pair (@test_helper_functions.R#72)  ──────
  test_dat$shared not equal to res$shared.
  Component "barcode": Modes: character, numeric
  Component "barcode": Attributes: < target is NULL, current is list >
  Component "barcode": target is character, current is factor
  Component "barcode": Modes: character, numeric
  Component "barcode": Attributes: < target is NULL, current is list >
  Component "barcode": target is character, current is factor
  
  ── 2. Failure: helper functions - com_pair (@test_helper_functions.R#73)  ──────
  test_dat$unique_sample1 not equal to res$unique_sample1.
  Component "barcode": Modes: character, numeric
  Component "barcode": Attributes: < target is NULL, current is list >
  Component "barcode": target is character, current is factor
  
  ── 3. Failure: helper functions - com_pair (@test_helper_functions.R#74)  ──────
  test_dat$unique_sample2 not equal to res$unique_sample2.
  Component "barcode": Modes: character, numeric
  Component "barcode": Attributes: < target is NULL, current is list >
  Component "barcode": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 47 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 3 ]
  1. Failure: helper functions - com_pair (@test_helper_functions.R#72) 
  2. Failure: helper functions - com_pair (@test_helper_functions.R#73) 
  3. Failure: helper functions - com_pair (@test_helper_functions.R#74) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R  10.3Mb
Package suggested but not available for checking: ‘reactome.db’
Running ‘test-all.R’ [32s/43s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > library("geojsonio")
  
  Attaching package: 'geojsonio'
  
  The following object is masked from 'package:base':
  
      pretty
  
  > test_check("geojsonio")
  ── 1. Failure: topojson_read works with file inputs (@test-topojson_read.R#11)  
  df$id inherits from `character` not `factor`.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 408 | SKIPPED: 23 | WARNINGS: 80 | FAILED: 1 ]
  1. Failure: topojson_read works with file inputs (@test-topojson_read.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [5s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(geojsonsf)
  > 
  > test_check("geojsonsf")
  ── 1. Failure: Factors are handled (@test-df_geojson.R#52)  ────────────────────
  as.character(geo) not equal to "{\"type\":\"FeatureCollection\",\"features\":[{\"type\":\"Feature\",\"properties\":{\"id\":1},\"geometry\":{\"type\":\"Point\",\"coordinates\":[1.0,0.0]}},{\"type\":\"Feature\",\"properties\":{\"id\":2},\"geometry\":{\"type\":\"Point\",\"coordinates\":[0.0,1.0]}}]}".
  1/1 mismatches
  x[1]: "{\"type\":\"FeatureCollection\",\"features\":[{\"type\":\"Feature\",\"pro
  x[1]: perties\":{\"id\":\"a\"},\"geometry\":{\"type\":\"Point\",\"coordinates\":
  x[1]: [1.0,0.0]}},{\"type\":\"Feature\",\"properties\":{\"id\":\"b\"},\"geometry
  x[1]: \":{\"type\":\"Point\",\"coordinates\":[0.0,1.0]}}]}"
  y[1]: "{\"type\":\"FeatureCollection\",\"features\":[{\"type\":\"Feature\",\"pro
  y[1]: perties\":{\"id\":1},\"geometry\":{\"type\":\"Point\",\"coordinates\":[1.0
  y[1]: ,0.0]}},{\"type\":\"Feature\",\"properties\":{\"id\":2},\"geometry\":{\"ty
  y[1]: pe\":\"Point\",\"coordinates\":[0.0,1.0]}}]}"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 485 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Factors are handled (@test-df_geojson.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    data  27.2Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R         9.1Mb
    extdata   1.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘geosample-vignette.Rnw’ using knitr
Loading required package: sf
Linking to GEOS 3.6.3, GDAL 2.2.4, PROJ 5.2.0
Loading required package: sp
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/
Loading required package: raster

Attaching package: 'raster'

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

    maxValue

Loading required package: pdist
Loading required package: Matrix
Quitting from lines 476-516 (geosample-vignette.Rnw) 
Error: processing vignette 'geosample-vignette.Rnw' failed with diagnostics:
cannot allocate vector of size 3.0 Gb
--- failed re-building ‘geosample-vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘geosample-vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
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 53-60 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    help   1.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggalluvial.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: ggplot2
Quitting from lines 36-46 (ggalluvial.rmd) 
Error: processing vignette 'ggalluvial.rmd' failed with diagnostics:
there is no package called 'plyr'
--- failed re-building ‘ggalluvial.rmd’

--- re-building ‘labels.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 31-40 (labels.rmd) 
Error: processing vignette 'labels.rmd' failed with diagnostics:
there is no package called 'plyr'
--- failed re-building ‘labels.rmd’

--- re-building ‘order-rectangles.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 43-46 (order-rectangles.rmd) 
Error: processing vignette 'order-rectangles.rmd' failed with diagnostics:
there is no package called 'plyr'
--- failed re-building ‘order-rectangles.rmd’

SUMMARY: processing the following files failed:
  ‘ggalluvial.rmd’ ‘labels.rmd’ ‘order-rectangles.rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'av', 'gifski'
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggBubbles.Rmd’ using rmarkdown
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.
Loading required package: knitr
Loading required package: ggplot2
Loading required package: ggBubbles
Quitting from lines 30-40 (ggBubbles.Rmd) 
Error: processing vignette 'ggBubbles.Rmd' failed with diagnostics:
could not find function "CRANpkg"
--- failed re-building ‘ggBubbles.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc         3.0Mb
    tutorials   1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggPredict.Rmd’ using rmarkdown
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.
Loading required package: ggplot2
`geom_smooth()` using formula 'y ~ x'
Loading required package: ggiraph
Loading required package: ggiraphExtra

Attaching package: 'ggiraphExtra'

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

    addLabelDf, getMapping

Loading required package: plyr
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 45-49 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘ggPredict.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
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.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
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.
Warning in normalizePath(f2) :
  path[1]="webshot36983e032e0.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot36983e032e0.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘ggPredict.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   2.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
Running examples in ‘ggraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: facet_graph
> ### Title: Create a grid of small multiples by node and/or edge attributes
> ### Aliases: facet_graph
> 
> ### ** Examples
> 
> library(tidygraph)

Attaching package: ‘tidygraph’

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

    filter

> gr <- as_tbl_graph(highschool) %>%
+   mutate(popularity = as.character(cut(centrality_degree(mode = 'in'),
+     breaks = 3,
+     labels = c('low', 'medium', 'high')
+   )))
> ggraph(gr) +
+   geom_edge_link() +
+   geom_node_point() +
+   facet_graph(year ~ popularity)
Using `stress` as default layout
Error in loadNamespace(name) : there is no package called ‘reshape2’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
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.

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: Matrix
Quitting from lines 185-186 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggseas.Rmd’ using rmarkdown
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 125-126 (ggseas.Rmd) 
Error: processing vignette 'ggseas.Rmd' failed with diagnostics:
Process terminated
--- failed re-building ‘ggseas.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/ggtern.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [15s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(glmdisc)
  > 
  > test_check("glmdisc")
  # weights:  9 (4 variable)
  initial  value 109.861229 
  iter  10 value 12.701739
  iter  20 value 5.686166
  iter  30 value 5.061799
  iter  40 value 4.906182
  iter  50 value 4.731498
  final  value 4.731498 
  stopped after 50 iterations
  # weights:  9 (4 variable)
  initial  value 109.861229 
  iter  10 value 12.701739
  iter  20 value 5.686166
  iter  30 value 5.061799
  iter  40 value 4.906182
  iter  50 value 4.731498
  final  value 4.731498 
  stopped after 50 iterations
  ── 1. Error: cutpoints works with continuous data (@test-method_cutpoints.R#10) 
  subscript out of bounds
  Backtrace:
   1. glmdisc::glmdisc(...)
  
  ── 2. Error: predict works with continuous data (@test-method_predict.R#11)  ───
  subscript out of bounds
  Backtrace:
   1. glmdisc::glmdisc(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 29 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: cutpoints works with continuous data (@test-method_cutpoints.R#10) 
  2. Error: predict works with continuous data (@test-method_predict.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘glmdisc.Rmd’ using rmarkdown
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.
Iteration 1 ended with a performance of aic = -Inf
Iteration 2 ended with a performance of aic = -130.824958263556
Iteration 3 ended with a performance of aic = -136.02676098584
Iteration 4 ended with a performance of aic = -136.443185202192
Iteration 5 ended with a performance of aic = -137.161824493705
Iteration 6 ended with a performance of aic = -134.265334250501
Iteration 7 ended with a performance of aic = -140.181725405014
Iteration 8 ended with a performance of aic = -135.151239342775
Iteration 9 ended with a performance of aic = -113.479632786418
Iteration 10 ended with a performance of aic = -121.213647435403
Iteration 11 ended with a performance of aic = -118.751232700537
Iteration 12 ended with a performance of aic = -106.250709892443
Iteration 13 ended with a performance of aic = -117.028352653963
Iteration 14 ended with a performance of aic = -132.299525514423
Iteration 15 ended with a performance of aic = -107.193688660066
Iteration 16 ended with a performance of aic = -125.263507376019
Iteration 17 ended with a performance of aic = -130.873039726077
Iteration 18 ended with a performance of aic = -132.70151289987
Iteration 19 ended with a performance of aic = -114.402843885835
Iteration 20 ended with a performance of aic = -113.369389483266
Iteration 21 ended with a performance of aic = -111.337231960417
Quitting from lines 298-301 (glmdisc.Rmd) 
Error: processing vignette 'glmdisc.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘glmdisc.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc         1.3Mb
    libs        1.8Mb
    test_data   1.3Mb
Running examples in ‘glmnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.cv.glmnet
> ### Title: plot the cross-validation curve produced by cv.glmnet
> ### Aliases: plot.cv.glmnet plot.cv.relaxed
> ### Keywords: models regression
> 
> ### ** Examples
> 
> 
> set.seed(1010)
> n = 1000
> p = 100
> nzc = trunc(p/10)
> x = matrix(rnorm(n * p), n, p)
> beta = rnorm(nzc)
> fx = (x[, seq(nzc)] %*% beta)
> eps = rnorm(n) * 5
> y = drop(fx + eps)
> px = exp(fx)
> px = px/(1 + px)
> ly = rbinom(n = length(px), prob = px, size = 1)
> cvob1 = cv.glmnet(x, y)
Error in intI(j, n = x@Dim[2], dn[[2]], give.dn = FALSE) : 
  'NA' indices are not (yet?) supported for sparse Matrices
Calls: cv.glmnet ... NextMethod -> predict.glmnet -> [ -> [ -> subCsp_cols -> intI
Execution halted
Packages required but not available: 'SeqArray', 'SeqVarTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘gprofiler2.Rmd’ using rmarkdown
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 239-240 (gprofiler2.Rmd) 
Error: processing vignette 'gprofiler2.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘gprofiler2.Rmd’

SUMMARY: processing the following file failed:
  ‘gprofiler2.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_graph4lg.Rmd’ using rmarkdown
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 267-268 (vignette_graph4lg.Rmd) 
Error: processing vignette 'vignette_graph4lg.Rmd' failed with diagnostics:
old version of unit class is no longer allowed
--- failed re-building ‘vignette_graph4lg.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette_graph4lg.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [38s/57s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > all.pkgs <- c("testthat", "dplyr", "dtplyr", "data.table", "magrittr", "survey", "zoo")
  > 
  > 
  > if (all(vapply(all.pkgs, requireNamespace, logical(1L), quietly = TRUE))) {
  +   
  +   library(testthat)
  +   library(grattan)
  +   library(hutils)
  +   library(data.table)
  +   library(magrittr)
  +   
  +   if (identical(Sys.getenv("CIRCLECI"), "true")) {
  +     test_check("grattan",
  +                reporter = JunitReporter$new(file = "junit_result.xml"))
  +   } else {
  +     test_check("grattan")
  +   }
  + }
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  ── 1. Error: Multiple People (@test_pension_supplement.R#59)  ──────────────────
  arguments imply differing number of rows: 1, 2
  Backtrace:
   1. testthat::expect_equal(...)
   4. grattan::pension_supplement(...)
   8. base::data.frame(..., check.names = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 833 | SKIPPED: 106 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Multiple People (@test_pension_supplement.R#59) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘profiling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Running ‘testthat.R’ [24s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gwsem)
  Loading required package: OpenMx
  To take full advantage of multiple cores, use:
    mxOption(key='Number of Threads', value=parallel::detectCores()) #now
    Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
  > 
  > test_check("gwsem")
  Error: C stack usage  273781876 is too close to the limit
  ── 1. Error: (unknown) (@test-covariate.R#36)  ─────────────────────────────────
  This model has 5 matrices, but the backend has returned 0 values
  Backtrace:
   1. gwsem::GWAS(...)
   2. OpenMx::mxRun(model)
   3. OpenMx:::runHelper(...)
   4. OpenMx:::updateModelMatrices(model, flatModel, output$matrices)
  
  ── 2. Error: (unknown) (@test-model.R#75)  ─────────────────────────────────────
  incompatible dimensions
  Backtrace:
   1. testthat::expect_equal(cor(ml$P, pgen$P), 1, tolerance = 0.001)
   4. stats::cor(ml$P, pgen$P)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 47 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 2 ]
  1. Error: (unknown) (@test-covariate.R#36) 
  2. Error: (unknown) (@test-model.R#75) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘growth.Rmd’ using rmarkdown
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.
Loading required package: OpenMx
To take full advantage of multiple cores, use:
  mxOption(key='Number of Threads', value=parallel::detectCores()) #now
  Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
Error: C stack usage  316970100 is too close to the limit
Quitting from lines 173-175 (growth.Rmd) 
Error: processing vignette 'growth.Rmd' failed with diagnostics:
This model has 4 matrices, but the backend has returned 0 values
--- failed re-building ‘growth.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 130.9Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    java  128.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    HaDeX   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
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.

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 40-43 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
prepare_Rd: it is not known that wchar_t is Unicode on this platform
Warning in deparse(ce, width.cutoff = 0.75 * getOption("width")) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(ce, width.cutoff = 0.75 * getOption("width")) :
  it is not known that wchar_t is Unicode on this platform
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_use.Rmd’ using rmarkdown
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 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Basic_use.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  readstat/readstat_convert.c:18:42: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:89:17: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:197:17: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/ripley/R/packages/tests-devel/haven.Rcheck/00install.out’ for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc           2.8Mb
    htmlwidgets   2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hchinamap.Rmd’ using rmarkdown
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.
trying URL 'https://czxb.github.io/br/chinadf.rda'
Content type 'application/octet-stream' length 3992 bytes
==================================================
downloaded 3992 bytes

Quitting from lines 50-58 (hchinamap.Rmd) 
Error: processing vignette 'hchinamap.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hchinamap.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    CWrappers_1.10.2   2.4Mb
    CWrappers_1.10.3   2.4Mb
    R                  1.1Mb
Running examples in ‘hdf5r-Ex.R’ failed
The error most likely occurred in:

> ### Name: H5A-class
> ### Title: Class for representing HDF5 attributes
> ### Aliases: H5A-class H5A
> 
> ### ** Examples
> 
> fname <- tempfile(fileext = ".h5")
> file <- H5File$new(fname, mode = "a")
> h5attr(file, "attr_numeric") <- rnorm(10)
> a <- file$attr_open("attr_numeric")
> a$get_info()
  corder_valid corder cset data_size
1            0      0    0        80
> a$attr_name()
[1] "attr_numeric"
> a$get_space()
Class: H5S
Type: Simple
Dims: 10
Maxdims: 10
> a$get_type()
Class: H5T_FLOAT
Datatype: H5T_IEEE_F64LE
> a$get_storage_size()
[1] 80
> a$read()
Error in H5ToR_Pre(mem_type, nelem) : HDF5-API Errors:
    error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
        class: HDF5
        major: Invalid arguments to routine
        minor: Inappropriate type
Calls: <Anonymous> -> H5ToR_Pre
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdf5r.Rmd’ using rmarkdown
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 159-160 (hdf5r.Rmd) 
Error: processing vignette 'hdf5r.Rmd' failed with diagnostics:
HDF5-API Errors:
    error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
        class: HDF5
        major: Invalid arguments to routine
        minor: Inappropriate type

--- failed re-building ‘hdf5r.Rmd’

SUMMARY: processing the following file failed:
  ‘hdf5r.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdnom.Rmd’ using rmarkdown
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.

(process:7388): Pango-WARNING **: failed to create cairo scaled font, expect ugly output. the offending font is 'Helvetica Medium 10.5'

(process:7388): Pango-WARNING **: font_face status is: no error has occurred

(process:7388): Pango-WARNING **: scaled_font status is: invalid matrix (not invertible)

(process:7388): Pango-WARNING **: shaping failure, expect ugly output. shape-engine='BasicEngineFc', font='Helvetica Medium 10.5', text='M'
Quitting from lines 367-379 (hdnom.Rmd) 
Error: processing vignette 'hdnom.Rmd' failed with diagnostics:
NA/NaN/Inf in foreign function call (arg 16)
--- failed re-building ‘hdnom.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘heatmaply.Rmd’ using rmarkdown
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.
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 1.0.0

Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.

The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>
======================

Quitting from lines 108-110 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘heatmaply.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   1.8Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Found the following significant warnings:
  mapping.cpp:95:58: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
See ‘/home/ripley/R/packages/tests-devel/hilbertSimilarity.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘RProtoBuf’
Package unavailable to check Rd xrefs: ‘RProtoBuf’
Running examples in ‘Hmisc-Ex.R’ failed
The error most likely occurred in:

> ### Name: summaryP
> ### Title: Multi-way Summary of Proportions
> ### Aliases: summaryP plot.summaryP ggplot.summaryP latex.summaryP
> ### Keywords: hplot category manip
> 
> ### ** Examples
> 
> n <- 100
> f <- function(na=FALSE) {
+   x <- sample(c('N', 'Y'), n, TRUE)
+   if(na) x[runif(100) < .1] <- NA
+   x
+ }
> set.seed(1)
> d <- data.frame(x1=f(), x2=f(), x3=f(), x4=f(), x5=f(), x6=f(), x7=f(TRUE),
+                 age=rnorm(n, 50, 10),
+                 race=sample(c('Asian', 'Black/AA', 'White'), n, TRUE),
+                 sex=sample(c('Female', 'Male'), n, TRUE),
+                 treat=sample(c('A', 'B'), n, TRUE),
+                 region=sample(c('North America','Europe'), n, TRUE))
> d <- upData(d, labels=c(x1='MI', x2='Stroke', x3='AKI', x4='Migraines',
+                  x5='Pregnant', x6='Other event', x7='MD withdrawal',
+                  race='Race', sex='Sex'))
Input object size:	 7272 bytes;	 12 variables	 100 observations
New object size:	10220 bytes;	12 variables	100 observations
> dasna <- subset(d, region=='North America')
> with(dasna, table(race, treat))
          treat
race        A  B
  Asian     8 10
  Black/AA 13  6
  White     4 10
> s <- summaryP(race + sex + ynbind(x1, x2, x3, x4, x5, x6, x7, label='Exclusions') ~
+               region + treat, data=d)
> # add exclude1=FALSE below to include female category
> plot(s, groups='treat')
Warning in matrix(0, n.row, n.col) :
  NAs introduced by coercion to integer range
Error in matrix(0, n.row, n.col) : invalid 'nrow' value (too large or NA)
Calls: <Anonymous> ... evaluate.legend -> do.call -> fun -> draw.key -> matrix
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hpackedbubble.Rmd’ using rmarkdown
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 35-49 (hpackedbubble.Rmd) 
Error: processing vignette 'hpackedbubble.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hpackedbubble.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.6Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   8.4Mb
    doc    2.3Mb
Running ‘testthat.R’ [4s/59s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("httr")
  Loading required package: httr
  ── 1. Failure: if request_perform() throws an error, RETRY passes it on (@test-r
  `RETRY(...)` threw an error with unexpected message.
  Expected match: "resolve host"
  Actual message: "Could not resolve: 98d90a2a254647889e2e4c236fb576cd.com (Domain name not found)"
  Backtrace:
   1. testthat::expect_error(...)
   6. httr::RETRY(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 158 | SKIPPED: 2 | WARNINGS: 4 | FAILED: 1 ]
  1. Failure: if request_perform() throws an error, RETRY passes it on (@test-retry.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
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.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 161-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hwordcloud.Rmd’ using rmarkdown
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 48-53 (hwordcloud.Rmd) 
Error: processing vignette 'hwordcloud.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hwordcloud.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘flowCore’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Running examples in ‘IAPWS95-Ex.R’ failed
The error most likely occurred in:

> ### Name: TDh
> ### Title: Temperature, Function of Density and Enthalpy
> ### Aliases: TDh
> 
> ### ** Examples
> 
> D <- 838.025
> h <- 977.181624
> T_Dh <- TDh(D,h)
Error(s) in re-building vignettes:
  ...
--- re-building ‘ibmsunburst.Rmd’ using rmarkdown
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 25-37 (ibmsunburst.Rmd) 
Error: processing vignette 'ibmsunburst.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘ibmsunburst.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: ‘BSgenome.Mmusculus.UCSC.mm10’
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
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 62-70 (example.Rmd) 
Quitting from lines 62-70 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
invalid connection
--- failed re-building ‘example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/home/ripley/R/packages/tests-devel/icd.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.5Mb
    doc    1.0Mb
Running ‘testthat.R’ [63s/69s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # this is common code to all the tests, each of which runs test_check with a
  > # different filter:
  > library("icd")
  > library("testthat", warn.conflicts = FALSE, quietly = TRUE)
  > icd:::.show_options()
  $icd.data.who_url
  [1] "https://icd.who.int/browse10"
  
  > # Definitely don't download data on CRAN
  > if (!icd:::.env_var_is_true("NOT_CRAN")) {
  +   old_offline <- options("icd.data.offline" = TRUE)
  +   on.exit(options(old_offline), add = TRUE)
  + } else {
  +   old_offline <- options("icd.data.offline" = FALSE)
  +   on.exit(options(old_offline), add = TRUE)
  + }
  > if (icd:::.env_var_is_true("ICD_TEST_SLOW")) {
  +   old_test_slow <- options("icd.test_slow" = TRUE)
  +   on.exit(options(old_test_slow), add = TRUE)
  + }
  > old_interact <- options("icd.data.interact" = FALSE)
  > on.exit(options(old_interact), add = TRUE)
  > icd:::.show_options()
  $icd.data.interact
  [1] FALSE
  
  $icd.data.offline
  [1] TRUE
  
  $icd.data.who_url
  [1] "https://icd.who.int/browse10"
  
  > testthat::test_check("icd")
  loading helper-base.R
  loading helper-icd10.R
  ── 1. Failure: van_walraven comodbidity index and score (@test-score.R#333)  ───
  van_walraven(mydf, visit_name = "id", icd_name = "value", return_df = TRUE) not equivalent to data.frame(id = factor(c(1, 2, 3)), vanWalraven = c(10, 12, -2)).
  Component "id": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 6000 | SKIPPED: 35 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: van_walraven comodbidity index and score (@test-score.R#333) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘model_details.Rmd’ using rmarkdown
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 25-32 (model_details.Rmd) 
Error: processing vignette 'model_details.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘model_details.Rmd’

--- re-building ‘parameter_details.Rmd’ using rmarkdown
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 24-31 (parameter_details.Rmd) 
Error: processing vignette 'parameter_details.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘parameter_details.Rmd’

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

SUMMARY: processing the following files failed:
  ‘model_details.Rmd’ ‘parameter_details.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ifa-Ex.R’ failed
The error most likely occurred in:

> ### Name: ifa.bic
> ### Title: A function to compute the BIC
> ### Aliases: ifa.bic
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(memory)

 *** caught segfault ***
address 144959bc, cause 'memory not mapped'

Traceback:
 1: sub(".*\\.", "", x)
 2: fileExt(file)
 3: data(memory)
An irrecoverable exception occurred. R is aborting now ...
Running examples in ‘ifaTools-Ex.R’ failed
The error most likely occurred in:

> ### Name: univariatePrior
> ### Title: Univariate priors commonly used in IFA models
> ### Aliases: univariatePrior
> 
> ### ** Examples
> 
> model <- univariatePrior("logit-norm", "x1", -1)
> model$priorParam$values[1,1] <- -.6
> model <- mxRun(model)
Running univariatePrior with 1 parameter
Error: C stack usage  296653972 is too close to the limit
Error: The job for model 'univariatePrior' exited abnormally with the error message: User interrupt
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pritikin-schmidt.Rnw’ using knitr
Quitting from lines 1347-1404 (pritikin-schmidt.Rnw) 
Error: processing vignette 'pritikin-schmidt.Rnw' failed with diagnostics:
Fit not achieved
--- failed re-building ‘pritikin-schmidt.Rnw’

SUMMARY: processing the following file failed:
  ‘pritikin-schmidt.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   6.5Mb
Package suggested but not available for checking: ‘tesseract’
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    doc       1.2Mb
    extdata   1.2Mb
    include   3.0Mb
    libs      6.3Mb
*** caught segfault ***
address f1000015, cause 'memory not mapped'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(p)
 4: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
 5: suppressMessages(loadNamespace(p))
 6: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
 7: suppressWarnings(suppressMessages(loadNamespace(p)))
 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(suppressWarnings(suppressMessages(loadNamespace(p))),     error = function(e) e)
12: tools:::.check_packages_used(package = "imager")
An irrecoverable exception occurred. R is aborting now ...
Running ‘testthat.R’ [71s/81s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(checkmate)
  > library(iml)
  > 
  > test_check("iml")
  ── 1. Failure: probs.to.labels (@test-utils.R#20)  ─────────────────────────────
  probs.to.labels(probs) not equal to `labels`.
  Component "..class": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 510 | SKIPPED: 0 | WARNINGS: 51 | FAILED: 1 ]
  1. Failure: probs.to.labels (@test-utils.R#20) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    help   1.8Mb
Package unavailable to check Rd xrefs: ‘minfi’
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
Unsupported platform: SunOS 5.10
For this platform, the path to the binary executable of X-13
has to be manually specified. See ?seasonal for details.
No path to the binary executable of X-13 specified.

You can set 'X13_PATH' manually if you intend to use your own
binaries. See ?seasonal for details.

Error in checkX13(fail = TRUE, fullcheck = FALSE, htmlcheck = FALSE) : 
  Process terminated
Calls: INFL.core_tf -> <Anonymous> -> checkX13
Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(inplace)
  > 
  > test_check("inplace")
  ── 1. Failure: in-place operators work in common cases (@test-operators.R#57)  ─
  `X` not identical to `X2`.
  Objects equal but not identical
  
  ── 2. Failure: in-place operators work in common cases (@test-sweep.R#49)  ─────
  `X` not identical to `X2`.
  Objects equal but not identical
  
  ── 3. Failure: in-place operators work in common cases (@test-sweep.R#50)  ─────
  `X` not identical to `X2`.
  Objects equal but not identical
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 805 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: in-place operators work in common cases (@test-operators.R#57) 
  2. Failure: in-place operators work in common cases (@test-sweep.R#49) 
  3. Failure: in-place operators work in common cases (@test-sweep.R#50) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    java   4.4Mb
Running ‘testthat.R’ [192s/224s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(interactions)
  > 
  > test_check("interactions")
  Failed with error:  'there is no package called 'brms''
  ── 1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157)  
  `print(p)` produced messages.
  
  ── 2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162)  
  `print(p)` produced messages.
  
  Failed with error:  'there is no package called 'brms''
  Failed with error:  'there is no package called 'rstanarm''
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 161 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157) 
  2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/IOHexperimenter.Rcheck/00install.out’ for details.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stringr)
  > library(io)
  Loading required package: filenamer
  > 
  > test_check("io")
  ── 1. Error: (unknown) (@test_read-write-read.R#8)  ────────────────────────────
  HDF5. File accessibilty. Unable to open file.
  Backtrace:
    1. io:::test_read_write_read(f)
    2. io::qread(infile) /home/ripley/R/packages/tests-devel/io.Rcheck/tests/helper.R:47:8
    4. io:::qread.hdf5(...)
   10. rhdf5::h5ls(file)
   11. rhdf5:::h5checktypeOrOpenLoc(file, readonly = TRUE, native = native)
   12. rhdf5::H5Fopen(file, "H5F_ACC_RDONLY", native = native)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test_read-write-read.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   7.7Mb
Package suggested but not available for checking: ‘redux’
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started-with-irg.Rmd’ using rmarkdown
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.
ndvi                    package:irg                    R Documentation

_R_a_w _N_D_V_I _T_i_m_e _S_e_r_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     A data.table containing NDVI samples for ten points over ten years
     (2002-2012).

_F_o_r_m_a_t:

     A data.table with 2530 rows and 5 variables:

        • id - individual identifier

        • yr - year of sample

        • DayOfYear - julian day/day of year of sample

        • NDVI - sampled value

        • SummaryQA - Summary quality assessment value

     SummaryQA details:

        • 0 - Good data, use with confidence

        • 1 - Marginal data, useful but look at detailed QA for more
          information

        • 2 - Pixel covered with snow/ice

        • 3 - Pixel is cloudy

_E_x_a_m_p_l_e_s:

     # Load data.table
     library(data.table)
     
     # Read example data
     ndvi <- fread(system.file("extdata", "ndvi.csv", package = "irg"))
     

Quitting from lines 99-153 (getting-started-with-irg.Rmd) 
Error: processing vignette 'getting-started-with-irg.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘getting-started-with-irg.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started-with-irg.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘isoband1.Rmd’ using rmarkdown
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.
--- finished re-building ‘isoband1.Rmd’

--- re-building ‘isoband2.Rmd’ using rmarkdown
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 56-97 (isoband2.Rmd) 
Error: processing vignette 'isoband2.Rmd' failed with diagnostics:
R: width or height exceeds limit `/home/ripley/R/Lib32-dev/isoband/extdata/ocean-cat.jpg[0]' @ error/cache.c/SetPixelCacheNexusPixels/5199
--- failed re-building ‘isoband2.Rmd’

--- re-building ‘isoband3.Rmd’ using rmarkdown
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.
--- finished re-building ‘isoband3.Rmd’

SUMMARY: processing the following file failed:
  ‘isoband2.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘isocat.Rmd’ using rmarkdown
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 206-214 (isocat.Rmd) 
Error: processing vignette 'isocat.Rmd' failed with diagnostics:
indivIDs must be of class 'vector' or 'factor'.
--- failed re-building ‘isocat.Rmd’

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

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

--- re-building ‘inspect.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 101-106 (inspect.Rmd) 
Error: processing vignette 'inspect.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘inspect.Rmd’

--- re-building ‘test.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 187-200 (test.Rmd) 
Error: processing vignette 'test.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘test.Rmd’

SUMMARY: processing the following files failed:
  ‘inspect.Rmd’ ‘test.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [17s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(janitor)
  
  Attaching package: 'janitor'
  
  The following objects are masked from 'package:stats':
  
      chisq.test, fisher.test
  
  > 
  > test_check("janitor")
  ── 1. Failure: totals col is correct (@test-add-totals.R#33)  ──────────────────
  untabyl(adorn_totals(ct, "col")) not equal to data.frame(...).
  Component "a": Modes: character, numeric
  Component "a": Attributes: < target is NULL, current is list >
  Component "a": target is character, current is factor
  
  ── 2. Failure: values are converted to NAs at the data.frame level (@test-clean-
  cleaned_df[[2]] not equal to factor(c(NA, NA, "b"), levels = c("a", "b")).
  Types not compatible: character is not integer
  
  Reading layer `nc' from data source `/home/ripley/R/Lib32-dev/sf/shape/nc.shp' using driver `ESRI Shapefile'
  Simple feature collection with 100 features and 14 fields
  geometry type:  MULTIPOLYGON
  dimension:      XY
  bbox:           xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
  epsg (SRID):    4267
  proj4string:    +proj=longlat +datum=NAD27 +no_defs
  ── 3. Failure: show_missing_levels parameter works (@test-tabyl.R#216)  ────────
  z %>% tabyl(a, b, new, show_missing_levels = TRUE) not equal to list(...).
  Component "lvl1": Attributes: < Component "core": Component "a": 'current' is not a factor >
  Component "lvl1": Component "a": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 554 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: totals col is correct (@test-add-totals.R#33) 
  2. Failure: values are converted to NAs at the data.frame level (@test-clean-NAs.R#31) 
  3. Failure: show_missing_levels parameter works (@test-tabyl.R#216) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/home/ripley/R/packages/tests-devel/JavaGD.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    dict   5.0Mb
Package suggested but not available for checking: ‘RProtoBuf’
Running examples in ‘joinet-Ex.R’ failed
The error most likely occurred in:

> ### Name: coef.joinet
> ### Title: Extract Coefficients
> ### Aliases: coef.joinet
> 
> ### ** Examples
> 
> n <- 50; p <- 100; q <- 3
> X <- matrix(rnorm(n*p),nrow=n,ncol=p)
> Y <- replicate(n=q,expr=rnorm(n=n,mean=rowSums(X[,1:5])))
> object <- joinet(Y=Y,X=X)
Error in approx(lambda, seq(lambda), sfrac) : 
  need at least two non-NA values to interpolate
Calls: joinet ... NextMethod -> predict.glmnet -> lambda.interp -> approx
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(joinet)
  > 
  > testthat::test_check(package="joinet",stop_on_warning=FALSE)
  ── 1. Error: (unknown) (@test.R#24)  ───────────────────────────────────────────
  need at least two non-NA values to interpolate
  Backtrace:
    1. joinet::joinet(...)
    2. glmnet::cv.glmnet(...)
    3. glmnet:::cv.glmnet.raw(...)
    5. glmnet:::buildPredmat.default(...)
    9. glmnet::predict.glmnet(...)
   10. glmnet:::lambda.interp(lambda, s)
   11. stats::approx(lambda, seq(lambda), sfrac)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 3 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@test.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘article.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building ‘article.Rmd’

--- re-building ‘joinet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 105-106 (joinet.Rmd) 
Error: processing vignette 'joinet.Rmd' failed with diagnostics:
need at least two non-NA values to interpolate
--- failed re-building ‘joinet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘kgc-fine.Rmd’ using rmarkdown
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.
Loading required package: shiny
Loading required package: shinythemes
Loading required package: plyr
Quitting from lines 37-53 (kgc-fine.Rmd) 
Error: processing vignette 'kgc-fine.Rmd' failed with diagnostics:
cannot allocate vector of size 640.7 Mb
--- failed re-building ‘kgc-fine.Rmd’

--- re-building ‘kgc-vignette.Rmd’ using rmarkdown
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.
Loading required package: shiny
Loading required package: shinythemes
Loading required package: plyr
--- finished re-building ‘kgc-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘kgc-fine.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘advanced.Rmd’ using rmarkdown
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.
Loading required package: Matrix
Loaded glmnet 3.0-2

--- finished re-building ‘advanced.Rmd’

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

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

Cpu Limit Exceeded - core dumped
--- re-building ‘knockoff.Rmd’ using rmarkdown
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.
Loading required package: Matrix
Loaded glmnet 3.0-2

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(KRIG)
  > 
  > test_check("KRIG")
  ── 1. Failure: Same result sequencial and parallel code (@test1.R#15)  ─────────
  `kw` not equal to `nw`.
  1/1 mismatches
  [1] 12691 - 6346 == 6346
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Same result sequencial and parallel code (@test1.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘copper_mining_2d.Rmd’ using rmarkdown
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.
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 120-123 (copper_mining_2d.Rmd) 
Error: processing vignette 'copper_mining_2d.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘copper_mining_2d.Rmd’

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

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

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

SUMMARY: processing the following file failed:
  ‘copper_mining_2d.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   3.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.3Mb
    help   1.2Mb
Running ‘config.R’
  Running ‘testthat.R’
Running the tests in ‘tests/config.R’ failed.
Complete output:
  > mac_dir <- "~/Documents/Rtest/"
  > win_dir <- "C:/Rtest"
  > linux_dir <- "~/Documents/Rtest"
  > 
  > switch(Sys.info()['sysname'],
  +        "Darwin" = {working_dir <- mac_dir},
  +        "Windows" = {working_dir <- win_dir},
  +        "Linux" = {working_dir <- linux_dir})
  > 
  > rds_file_name <- "./ranListSmall.rds"
  > llo_file_name <- "./ranListSmall.llo"
  > repeat_time <- 20
  > original <- FALSE
  > compress <- TRUE
  > 
  > # rds_file_name <- "./ranListMid.rds"
  > # llo_file_name <- "./ranListMid.llo"
  > # repeat_time <- 20
  > # original <- FALSE
  > # compress <- TRUE
  > 
  > options(list(largeList.report.progress = FALSE))
  > 
  > if (dir.exists(working_dir)) {
  +   setwd(working_dir)
  +   if (file.exists(rds_file_name)) {
  +     library(futile.logger)
  +     ready_to_test <- TRUE
  +   } else {
  +     ready_to_test <- FALSE
  +   }
  + } else {
  +   ready_to_test <- FALSE
  + }
  Error in dir.exists(working_dir) : object 'working_dir' not found
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_to_lavaanPlot.Rmd’ using rmarkdown
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 41-42 (Intro_to_lavaanPlot.Rmd) 
Error: processing vignette 'Intro_to_lavaanPlot.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Intro_to_lavaanPlot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘test-all.R’ [160s/207s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > #library(lavaSearch2)
  > suppressPackageStartupMessages(library("testthat"))
  > test_check("lavaSearch2")
  Loading required package: lavaSearch2
  Loading required package: ggplot2
  Loading required package: lava
  
  Attaching package: 'lava'
  
  The following object is masked from 'package:ggplot2':
  
      vars
  
  The following object is masked from 'package:testthat':
  
      compare
  
  lavaSearch2 version 1.5.4
  ── 1. Error: (unknown) (@test1-sCorrect-validObjects.R#48)  ────────────────────
  cannot coerce type 'closure' to vector of type 'any'
  Backtrace:
   1. lava::estimate(lvm(G ~ X1), data = d)
   2. lava:::estimate.lvm(lvm(G ~ X1), data = d)
   4. lava:::ordinal.estimate.hook(...)
   5. base::setdiff(lava::endogenous(x), bin)
   6. base::as.vector(y)
  
  ── 2. Error: (unknown) (@test2-modelsearch2.R#37)  ─────────────────────────────
  cannot coerce type 'closure' to vector of type 'any'
  Backtrace:
   1. lava::estimate(m, data = df.sim)
   2. lava:::estimate.lvm(m, data = df.sim)
   4. lava:::ordinal.estimate.hook(...)
   5. base::setdiff(lava::endogenous(x), bin)
   6. base::as.vector(y)
  
  ── 3. Error: (unknown) (@test3-multcomp.R#149)  ────────────────────────────────
  cannot coerce type 'closure' to vector of type 'any'
  Backtrace:
   1. lava::estimate(m.lvm, df.data)
   2. lava:::estimate.lvm(m.lvm, df.data)
   4. lava:::ordinal.estimate.hook(...)
   5. base::setdiff(lava::endogenous(x), bin)
   6. base::as.vector(y)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 464 | SKIPPED: 4 | WARNINGS: 2 | FAILED: 3 ]
  1. Error: (unknown) (@test1-sCorrect-validObjects.R#48) 
  2. Error: (unknown) (@test2-modelsearch2.R#37) 
  3. Error: (unknown) (@test3-multcomp.R#149) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.7Mb
    libs   2.3Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    geojson  11.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
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.

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 67-77 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘capped-axes.Rmd’ using rmarkdown
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.
--- finished re-building ‘capped-axes.Rmd’

--- re-building ‘facet-rep-labels.Rmd’ using rmarkdown
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.
--- finished re-building ‘facet-rep-labels.Rmd’

--- re-building ‘geoms.Rmd’ using rmarkdown
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 30-41 (geoms.Rmd) 
Error: processing vignette 'geoms.Rmd' failed with diagnostics:
invalid line type
--- failed re-building ‘geoms.Rmd’

--- re-building ‘gtable_show_lemonade.Rmd’ using rmarkdown
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 42-61 (gtable_show_lemonade.Rmd) 
Error: processing vignette 'gtable_show_lemonade.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘gtable_show_lemonade.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘geoms.Rmd’ ‘gtable_show_lemonade.Rmd’

Error: Vignette re-building failed.
Execution halted
Compilation used the following non-portable flag(s):
  ‘-mt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘batch_import.Rmd’ using rmarkdown
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.
--- finished re-building ‘batch_import.Rmd’

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

--- re-building ‘true_example.Rmd’ using rmarkdown
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 59-62 (true_example.Rmd) 
Error: processing vignette 'true_example.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘true_example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘lime-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_superpixels
> ### Title: Test super pixel segmentation
> ### Aliases: plot_superpixels
> 
> ### ** Examples
> 
> image <- system.file('extdata', 'produce.png', package = 'lime')
> 
> # plot with default settings
> plot_superpixels(image)

 *** caught segfault ***
address 2c, cause 'memory not mapped'

Traceback:
 1: magick_image_convolve_kernel(image, kernel, iterations, scaling,     bias)
 2: magick::image_convolve(contour, "Laplacian")
 3: plot_superpixels(image)
An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘Understanding_lime.Rmd’ using rmarkdown
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 262-263 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Understanding_lime.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘linkspotterVignette.Rmd’ using rmarkdown
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 109-112 (linkspotterVignette.Rmd) 
Error: processing vignette 'linkspotterVignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘linkspotterVignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R          1.8Mb
    doc        2.8Mb
    testdata   1.8Mb
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/lmSubsets.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘logisticRR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 162-169 (logisticRR.Rmd) 
Error: processing vignette 'logisticRR.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘logisticRR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Rsymphony’
Error(s) in re-building vignettes:
  ...
--- re-building ‘lspline.Rmd’ using rmarkdown
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 18-23 (lspline.Rmd) 
Error: processing vignette 'lspline.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘lspline.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LUCIDus-vignette.Rmd’ using rmarkdown
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 63-64 (LUCIDus-vignette.Rmd) 
Error: processing vignette 'LUCIDus-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘LUCIDus-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help   1.3Mb
Running examples in ‘lvmcomp-Ex.R’ failed
The error most likely occurred in:

> ### Name: StEM_mirt
> ### Title: Stochastic EM algorithm for solving multivariate item response
> ###   theory model
> ### Aliases: StEM_mirt
> 
> ### ** Examples
> 
> # run a toy example based on the M2PL model
> 
> # load a simulated dataset
> attach(data_sim_mirt)
> 
> # generate starting values for the algorithm
> A0 <- Q
> d0 <- rep(0, J)
> theta0 <- matrix(rnorm(N*K, 0, 1),N)
> sigma0 <- diag(1, K) 
> 
> # do the confirmatory MIRT analysis
> # to enable multicore processing, set parallel = T
> mirt_res <- StEM_mirt(response, Q, A0, d0, theta0, sigma0)

Step  1	| 
Step  2	| 
Step  3	| 
Step  4	|
Running examples in ‘lvnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: lvnet
> ### Title: Confirmatory Latent Variable Network Models
> ### Aliases: lvnet
> 
> ### ** Examples
> 
> # Load dataset:
> library("lavaan")
This is lavaan 0.6-5
lavaan is BETA software! Please report any bugs.

Attaching package: ‘lavaan’

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

    vech

> data(HolzingerSwineford1939)
> Data <- HolzingerSwineford1939[,7:15]
> 
> # Measurement model:
> Lambda <- matrix(0, 9, 3)
> Lambda[1:3,1] <- NA
> Lambda[4:6,2] <- NA
> Lambda[7:9,3] <- NA
> 
> # Fit CFA model:
> CFA <- lvnet(Data, lambda = Lambda)
Error: C stack usage  333091988 is too close to the limit
Error: The job for model 'model' exited abnormally with the error message: User interrupt
Execution halted
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    TS_files     6.0Mb
    base_files   6.5Mb
Packages suggested but not available for checking:
  'av', 'rsvg', 'tesseract', 'gifski'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Packages unavailable to check Rd xrefs: ‘rsvg’, ‘tesseract’, ‘gifski’, ‘av’
Running examples in ‘magick-Ex.R’ failed
The error most likely occurred in:

> ### Name: analysis
> ### Title: Image Analysis
> ### Aliases: analysis image_compare image_compare_dist image_fft
> 
> ### ** Examples
> 
> out1 <- image_blur(logo, 3)

 *** caught segfault ***
address 2c, cause 'memory not mapped'

Traceback:
 1: magick_image_blur(image, radius, sigma)
 2: image_blur(logo, 3)
An irrecoverable exception occurred. R is aborting now ...
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘MyMetadata.Rdata’ ‘MyMetadata.csv’ ‘MyintMatrix.Rdata’
  ‘MyintMatrix.csv’ ‘example’ ‘int.Rdata’ ‘int.binary.nex’
Error(s) in re-building vignettes:
  ...
--- re-building ‘manhattanly.Rmd’ using rmarkdown
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.
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘manhattanly.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘manipulateWidgets.Rmd’ using rmarkdown
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 normalizePath(f2) :
  path[1]="webshot1ec46762911.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot1ec46762911.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘manipulateWidgets.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.2Mb
    help   1.6Mb
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    mapdata  33.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data          1.0Mb
    doc           1.3Mb
    htmlwidgets   1.6Mb
    libs          3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
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 95-100 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    mapdata   4.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    java   3.4Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘MBNMAtime.Rmd’ using rmarkdown
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.
Reference treatment is `plac`

ET50 parameters (beta.2) are on exponential scale to ensure they take positive values on the natural scale
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   3.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   6.0Mb
Running examples in ‘mechkar-Ex.R’ failed
The error most likely occurred in:

> ### Name: exploreData
> ### Title: A tool for visual exploration of a dataset.
> ### Aliases: exploreData
> 
> ### ** Examples
> 
> ## --- Getting data stats for a given dataset ---
> data(iris)
> exploreData(data=iris, dir=tempdir())
Error in get_computer_type() : object 'computer.type' not found
Calls: exploreData -> get_computer_type
Execution halted
Package required but not available: ‘gdsfmt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   3.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Package suggested but not available for checking: ‘topGO’
Package required but not available: ‘metagenomeSeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs   1.7Mb
    misc   1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mfe-vignette.Rmd’ using rmarkdown
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 55-66 (mfe-vignette.Rmd) 
Error: processing vignette 'mfe-vignette.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building ‘mfe-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mgwrsar-basic_examples.Rmd’ using rmarkdown
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 91-94 (mgwrsar-basic_examples.Rmd) 
Error: processing vignette 'mgwrsar-basic_examples.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘mgwrsar-basic_examples.Rmd’

SUMMARY: processing the following file failed:
  ‘mgwrsar-basic_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [33s/43s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > #library(microsamplingDesign)
  > 
  > #source("generateTestData.R")
  > 
  > #test_check("microsamplingDesign")
  > 
  > testthat::test_check("microsamplingDesign")
  Loading required package: microsamplingDesign
  Loading required package: Rcpp
  start Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 cores── 1. Failure: fastRank schemes , default fixed options identcal results  (@test
  all.equal(getRanking(origExample), getRanking(fastExample)) isn't true.
  
  ── 2. Failure: Equal ranking SetOfSchemes (consistent with original ranking) (@t
  rankedSetOfSchemesOrig@ranking not equal to rankedSetOfSchemesNew@ranking.
  Component "name": 'current' is not a factor
  
  start Ranking Schemes on cluster with  2 cores── 3. Failure: Equal ranking timePoints (@testRankTimePoints.R#47)  ────────────
  rankTimePointsOrig@ranking not equal to rankedTimePointsNew@ranking.
  Component "name": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 19 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: fastRank schemes , default fixed options identcal results  (@testRankSetOfSchemes.R#87) 
  2. Failure: Equal ranking SetOfSchemes (consistent with original ranking) (@testRankSetOfSchemes.R#95) 
  3. Failure: Equal ranking timePoints (@testRankTimePoints.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following files/directories:
  ‘Summary.csv’ ‘Summary.txt’ ‘groupSKM.csv’ ‘groupSKM.txt’
  ‘groupTM.csv’ ‘groupTM.txt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Analysis.Rmd’ using rmarkdown
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.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.
Loading required package: Matrix
Quitting from lines 109-112 (Analysis.Rmd) 
Error: processing vignette 'Analysis.Rmd' failed with diagnostics:
objective in x0 returns NA
--- failed re-building ‘Analysis.Rmd’

--- re-building ‘Introduction.Rmd’ using rmarkdown
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.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.

(process:7971): Pango-WARNING **: failed to create cairo scaled font, expect ugly output. the offending font is 'Helvetica Medium 9.9599609375'

(process:7971): Pango-WARNING **: font_face status is: <unknown error status>

(process:7971): Pango-WARNING **: scaled_font status is: invalid matrix (not invertible)

(process:7971): Pango-WARNING **: shaping failure, expect ugly output. shape-engine='BasicEngineFc', font='Helvetica Medium 9.9599609375', text='m'
Loading required package: Matrix
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘Level2.Rmd’ using rmarkdown
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.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.
--- finished re-building ‘Level2.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'REBayes', 'Rmosek'
Packages unavailable to check Rd xrefs: ‘REBayes’, ‘Rmosek’
Packages suggested but not available for checking:
  'minfi', 'IlluminaHumanMethylation450kmanifest'
Running ‘testthat.R’ [235s/303s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("checkmate")
  > library("testthat")
  > library("mlr3")
  > library("paradox")
  > library("mlr3pipelines")
  > 
  > test_check("mlr3pipelines")
  Training debug.multi with input list(input_1 = 1, input_2 = 1)
  ── 1. Error: LearnerClassifAvg (@test_learner_weightedaverage.R#12)  ───────────
  <TaskClassif:tsk> has the following unsupported feature types: character
  Backtrace:
   1. lrn$train(tsk)
   2. mlr3::assert_learnable(task, self)
   3. mlr3misc::stopf(...)
  
  ── 2. Error: PipeOpRemoveConstants removes expected cols (@test_pipeop_removecon
  Target column 'target' must have at least two levels
  Backtrace:
   1. mlr3pipelines:::test_dropping(iris, iris, list())
   2. TaskClassif$new(...)
   3. .subset2(public_bind_env, "initialize")(...)
   4. private$.update_class_property()
   5. mlr3misc::stopf(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 7497 | SKIPPED: 44 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: LearnerClassifAvg (@test_learner_weightedaverage.R#12) 
  2. Error: PipeOpRemoveConstants removes expected cols (@test_pipeop_removeconstants.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘comparison_mlr3pipelines_mlr_sklearn.Rmd’ using rmarkdown
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.
--- finished re-building ‘comparison_mlr3pipelines_mlr_sklearn.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
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 172-173 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘FSelector’
Packages suggested but not available for checking:
  'classiFunc', 'FSelector', 'RWeka'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    data   2.4Mb
    help   1.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mnlogit.Rnw’ using Sweave
Package: mnlogit
Version: 1.2.6
Multinomial Logit Choice Models.
Scientific Computing Group, Sentrana Inc.
Loading required package: Formula
Loading required package: zoo

Attaching package: 'zoo'

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

    index

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

    as.Date, as.Date.numeric

Loading required package: lmtest

Attaching package: 'mlogit'

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

    hmftest, scoretest
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    doc  23.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘molaR_vignette.Rmd’ using rmarkdown
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.
Loading required package: alphahull
Loading required package: rgl
Loading required package: Rvcg
Quitting from lines 58-60 (molaR_vignette.Rmd) 
Error: processing vignette 'molaR_vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘molaR_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
Running examples in ‘monoreg-Ex.R’ failed
The error most likely occurred in:

> ### Name: monoreg
> ### Title: Bayesian monotonic regression
> ### Aliases: monoreg
> 
> ### ** Examples
> 
> library(monoreg)
> set.seed(1)
> # nobs <- 1000
> nobs <- 50
> sigma <- 0.01
> x1 <- runif(nobs)
> x2 <- runif(nobs)
> 
> # 6 different monotonic regression surfaces:
> # mu <- sqrt(x1)
> mu <- 0.5 * x1 + 0.5 * x2
> # mu <- pmin(x1, x2)
> # mu <- 0.25 * x1 + 0.25 * x2 + 0.5 * (x1 + x2 > 1.0)
> # mu <- 0.25 * x1 + 0.25 * x2 + 0.5 * (pmax(x1, x2) > 0.5)
> # mu <- ifelse((x1 - 1.0)^2 + (x2 - 1.0)^2 < 1.0, sqrt(1.0 - (x1 - 1.0)^2 - (x2 - 1.0)^2), 0.0)
> 
> y <- rnorm(nobs, mu, sigma)
> 
> # results <- monoreg(niter=15000, burnin=5000, adapt=5000, refresh=10, 
> results <- monoreg(niter=5000, burnin=2500, adapt=2500, refresh=10, 
+                    thin=5, birthdeath=10, seed=1, rhoa=0.1, rhob=0.1, 
+                    deltai=0.1, drange=2.0, predict=rep(1.0, nobs), 
+                    include=rep(1.0, nobs), response=y, offset=NULL, 
+                    axes=cbind(x1,x2), covariates=rep(1.0, nobs), 
+                    settozero=getcmat(2), package=rep(1,3)) 
Point process configuration:
1 0 1 
1 1 0 
1 0 0 
     
Packages:
1 
0 
Starting Gibbs sampler:

 *** caught segfault ***
address 6, cause 'memory not mapped'

Traceback:
 1: monoreg(niter = 5000, burnin = 2500, adapt = 2500, refresh = 10,     thin = 5, birthdeath = 10, seed = 1, rhoa = 0.1, rhob = 0.1,     deltai = 0.1, drange = 2, predict = rep(1, nobs), include = rep(1,         nobs), response = y, offset = NULL, axes = cbind(x1,         x2), covariates = rep(1, nobs), settozero = getcmat(2),     package = rep(1, 3))
An irrecoverable exception occurred. R is aborting now ...
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    R     2.3Mb
    doc   9.4Mb
Running ‘testthat.R’ [160s/230s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library("checkmate")
  > library("testthat")
  > library("ParamHelpers")
  > library("mlr")
  'mlr' is in maintenance mode since July 2019. Future development
  efforts will go into its successor 'mlr3' (<https://mlr3.mlr-org.com>).
  > library("mlrCPO")
  > 
  > test_check("mosmafs")
  Loading required package: mosmafs
  Loading required package: ecr
  Loading required package: BBmisc
  
  Attaching package: 'BBmisc'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  Loading required package: smoof
  
  Attaching package: 'ecr'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  
  Attaching package: 'mosmafs'
  
  The following objects are masked from 'package:ecr':
  
      getPopulations, getStatistics
  
  ── 1. Failure: multiFidelity with 2 columns (@test_customnsga2.R#232)  ─────────
  `slickEcr(...)` threw an error with unexpected message.
  Expected match: "Must be of type 'numeric', not 'factor'"
  Actual message: "Assertion on 'fidelity[[2]]' failed: Must be of type 'numeric', not 'character'."
  Backtrace:
    1. testthat::expect_error(...)
    6. mosmafs::slickEcr(...)
    7. mosmafs::initEcr(...)
    8. mosmafs:::checkFidelity(fidelity)
    9. checkmate::assertNumeric(fidelity[[2]], any.missing = FALSE)
   10. checkmate::makeAssertion(x, res, .var.name, add)
   11. checkmate:::mstop(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 458 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: multiFidelity with 2 columns (@test_customnsga2.R#232) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R             1.3Mb
    libs          7.2Mb
    mathematica   1.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mpMap2.Rnw’ using Sweave
Warning in mpcross(founders = founders, finals = finals, pedigree = pedigreeSF,  :
  Removing data for 1 markers, because these markers have NA founder alleles
Error in validObject(.Object) : 
  invalid class “geneticData” object: 1: Coding error for marker D1M3: Founder allele 10 was not present in @hetData[[3]]
invalid class “geneticData” object: 2: Coding error for marker D1M4: Founder allele 2 was not present in @hetData[[4]]
invalid class “geneticData” object: 3: Coding error for marker D1M4: Founder allele 3 was not present in @hetData[[4]]
invalid class “geneticData” object: 4: Coding error for marker D1M4: Founder allele 4 was not present in @hetData[[4]]
invalid class “geneticData” object: 5: Coding error for marker D1M5: Founder allele 1 was not present in @hetData[[5]]
invalid class “geneticData” object: 6: Omitting details of further coding errors

Error: processing vignette 'mpMap2.Rnw' failed with diagnostics:
 chunk 23 (label = rfExample) 
Error : C stack usage  349017336 is too close to the limit

Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Error in X[[i]] : invalid subscript type 'promise'
Calls: <Anonymous> ... gettextf -> sprintf -> gettext -> lapply -> tryCatch
Execution halted
Warning: stack imbalance in '{', 7 then -6

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

Traceback:
 1: cleanup(kill = tools::SIGKILL, detach = TRUE, shutdown = TRUE)
 2: (function (e) cleanup(kill = tools::SIGKILL, detach = TRUE, shutdown = TRUE))(<environment>)
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘msaR.Rmd’ using rmarkdown
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 30-37 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘msaR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Undocumented S4 methods:
  generic 'plot' and siglist 'Fit.class'
  generic 'plot' and siglist 'Mixture.fit.class'
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘msir.Rmd’ using rmarkdown
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 normalizePath(f2) :
  path[1]="webshot22bb54f3724.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot22bb54f3724.png': No such file or directory
Quitting from lines 102-104 (msir.Rmd) 
Error: processing vignette 'msir.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘msir.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/MultiBD.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package unavailable to check Rd xrefs: ‘RMark’
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    java  14.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    2.6Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    extdata  16.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.9Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ncmeta)
  > skip_on_os("solaris")
  Error: Reason: On Solaris
  Execution halted
Running examples in ‘NCutYX-Ex.R’ failed
The error most likely occurred in:

> ### Name: ancut
> ### Title: Cluster the Columns of Y into K Groups with the Help of External
> ###   Features X.
> ### Aliases: ancut
> 
> ### ** Examples
> 
> #This sets up the initial parameters for the simulation.
> library(MASS)#for mvrnorm
> library(fields)
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.5-1 (2019-12-12) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: ‘spam’

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

    backsolve, forwardsolve

Loading required package: maps
See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 
> n=30 #Sample size
> B=50 #Number of iterations in the simulated annealing algorithm.
> L=10000 #Temperature coefficient.
> p=50 #Number of columns of Y.
> q=p #Number of columns of X.
> h1=0.15
> h2=0.25
> 
> S=matrix(0.2,q,q)
> S[1:(q/2),(q/2+1):q]=0
> S[(q/2+1):q,1:(q/2)]=0
> S=S-diag(diag(S))+diag(q)
> 
> mu=rep(0,q)
> 
> W0=matrix(1,p,p)
> W0[1:(p/2),1:(p/2)]=0
> W0[(p/2+1):p,(p/2+1):p]=0
> Denum=sum(W0)
> 
> B2=matrix(0,q,p)
> for (i in 1:(p/2)){
+    B2[1:(q/2),i]=runif(q/2,h1,h2)
+    in1=sample.int(q/2,6)
+    B2[-in1,i]=0
+ }
> 
> for (i in (p/2+1):p){
+    B2[(q/2+1):q,i]=runif(q/2,h1,h2)
+    in2=sample(seq(q/2+1,q),6)
+    B2[-in2,i]=0
+ }
> 
> X=mvrnorm(n, mu, S)
> Z=X%*%B2
> Y=Z+matrix(rnorm(n*p,0,1),n,p)
> #Our method
> Res=ancut(Y=Y,X=X,B=B,L=L,alpha=0,ncv=3)
Error in if (J2 > J) { : missing value where TRUE/FALSE needed
Calls: ancut
Execution halted
Found the following significant warnings:
  generateData.cpp:105:18: warning: passing NULL to non-pointer argument 1 of ‘Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ [-Wconversion-null]
See ‘/home/ripley/R/packages/tests-devel/NestedCategBayesImpute.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘NetRep.Rmd’ using rmarkdown
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.

 *** caught segfault ***
address 0, cause 'memory not mapped'
Quitting from lines 245-251 (NetRep.Rmd) 
Warning: stack imbalance in 'lazyLoadDBfetch', 83 then 65
Error: processing vignette 'NetRep.Rmd' failed with diagnostics:
cannot get ALTVEC DATAPTR during GC
--- failed re-building ‘NetRep.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introducing_nhanesA.Rmd’ using rmarkdown
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 92-98 (Introducing_nhanesA.Rmd) 
Error: processing vignette 'Introducing_nhanesA.Rmd' failed with diagnostics:
Timeout was reached: [wwwn.cdc.gov] Resolving timed out after 10000 milliseconds
--- failed re-building ‘Introducing_nhanesA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   5.9Mb
installed size is 27.8Mb
  sub-directories of 1Mb or more:
    CppCode  10.4Mb
    R         6.3Mb
    include   5.3Mb
    libs      2.8Mb
    tests     1.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘geocode.Rmd’ using rmarkdown
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 127-133 (geocode.Rmd) 
Error: processing vignette 'geocode.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘geocode.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data      4.4Mb
    doc       1.2Mb
    reports   3.8Mb
Found the following significant warnings:
  WrapperNMFGPU.cpp:96:12: warning: converting ‘false’ to pointer type for argument 1 of ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, const _Alloc&) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ [-Wconversion-null]
See ‘/home/ripley/R/packages/tests-devel/nmfgpu4R.Rcheck/00install.out’ for details.
Running examples in ‘NMF-Ex.R’ failed
The error most likely occurred in:

> ### Name: NMFfitX-class
> ### Title: Virtual Class to Handle Results from Multiple Runs of NMF
> ###   Algorithms
> ### Aliases: NMFfitX-class
> 
> ### ** Examples
> 
> ## Don't show: 
> # roxygen generated flag
> options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
> ## End(Don't show)
> 
> # generate a synthetic dataset with known classes
> n <- 20; counts <- c(5, 2, 3);
> V <- syntheticNMF(n, counts)
> 
> # perform multiple runs of one algorithm (default is to keep only best fit)
> res <- nmf(V, 3, nrun=3)
# NOTE - CRAN check detected: limiting maximum number of cores [2/16]
Error in big.matrix(nrow = nrow(x), ncol = ncol(x), type = type, init = NULL,  : 
  Error: memory could not be allocated for instance of type big.matrix
Calls: nmf ... gVariable -> <Anonymous> -> <Anonymous> -> big.matrix
Timing stopped at: 0.031 0.035 0.068
Execution halted
Running ‘testthat.R’ [21s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(nnGarrote)
  > 
  > test_check("nnGarrote")
  Performing cross-validation for 1 values of the shrinkage parameter "lambda.nng":
   1 |── 1. Error: Warning for the non-negative garrote esitmator with more variables 
  'NA' indices are not (yet?) supported for sparse Matrices
  Backtrace:
    1. testthat::expect_warning(...)
    6. nnGarrote::cv.nnGarrote(...)
    7. nnGarrote::nnGarrote(...)
    9. glmnet::cv.glmnet(x.s, y.s, alpha = alpha)
   10. glmnet:::cv.glmnet.raw(...)
   12. glmnet:::buildPredmat.default(...)
   16. glmnet::predict.glmnet(...)
   18. nbeta[, lamlist$left, drop = FALSE]
   19. Matrix:::subCsp_cols(x, j, drop = drop)
   20. Matrix:::intI(j, n = x@Dim[2], dn[[2]], give.dn = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Warning for the non-negative garrote esitmator with more variables than observations when used with LS. (@test_nnGarrote_LS.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Package unavailable to check Rd xrefs: ‘redux’
Error(s) in re-building vignettes:
  ...
--- re-building ‘nonlinearTseries_quickstart.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 91-94 (nonlinearTseries_quickstart.Rmd) 
Error: processing vignette 'nonlinearTseries_quickstart.Rmd' failed with diagnostics:
need finite 'ylim' values
--- failed re-building ‘nonlinearTseries_quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    7.5Mb
    libs   1.0Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.0Mb
    doc    2.5Mb
    help   2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ODEnetwork.Rmd’ using rmarkdown
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 168-175 (ODEnetwork.Rmd) 
Error: processing vignette 'ODEnetwork.Rmd' failed with diagnostics:
Assertion failed. One of the following must apply:
 * checkDataFrame(events): May only contain the following types:
 * {factor,numeric,numeric}, but element 1 has type 'character'
 * checkDataFrame(events): Must have exactly 4 cols, but has 3 cols
--- failed re-building ‘ODEnetwork.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'RMark', 'R2ucare'
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    R        2.7Mb
    data     1.0Mb
    libs     4.1Mb
    models   4.4Mb
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: mxModelAverage
> ### Title: Information-Theoretic Model-Averaging and Multimodel Inference
> ### Aliases: mxModelAverage omxAkaikeWeights omxAICWeights
> 
> ### ** Examples
> 
> require(OpenMx)
> data(demoOneFactor)
> factorModel1 <- mxModel(
+ 	"OneFactor1",
+ 	mxMatrix(
+ 		"Full", 5, 1, values=0.8, 
+ 		labels=paste("a",1:5,sep=""),
+ 		free=TRUE, name="A"),
+ 	mxMatrix(
+ 		"Full", 5, 1, values=1,
+ 		labels=paste("u",1:5,sep=""),
+ 		free=TRUE, name="Udiag"),
+ 	mxMatrix(
+ 		"Symm", 1, 1, values=1,
+ 		free=FALSE, name="L"),
+ 	mxAlgebra(vec2diag(Udiag),name="U"),
+ 	mxAlgebra(A %*% L %*% t(A) + U, name="R"),
+ 	mxExpectationNormal(
+ 		covariance = "R",
+ 		dimnames = names(demoOneFactor)),
+ 	mxFitFunctionML(),
+ 	mxData(cov(demoOneFactor), type="cov", numObs=500))
> factorFit1 <- mxRun(factorModel1)
Running OneFactor1 with 10 parameters
> #Constrain unique variances equal:
> factorModel2 <- omxSetParameters(
+ 	model=factorModel1,labels=paste("u",1:5,sep=""),
+ 	newlabels="u",name="OneFactor2")
> factorFit2 <- mxRun(factorModel2)
Running OneFactor2 with 6 parameters
Error: C stack usage  270832788 is too close to the limit
Error: The job for model 'OneFactor2' exited abnormally with the error message: User interrupt
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    java     1.3Mb
    models   6.1Mb
Packages suggested but not available for checking:
  'gurobi', 'Rsymphony', 'lpsymphony'
Running ‘testthat.R’ [16s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(ordinalNet)
  > testthatInst <- require(testthat)
  Loading required package: testthat
  > 
  > if (testthatInst) test_check("ordinalNet")
  ── 1. Failure: Elastic net sratio matches glmnetcr::glmnet.cr (@test-ordinalNet.
  coef(o) not equal to `coefg`.
  3/7 mismatches (average diff: 0.475)
  [1] -0.572 - 0 == -0.572
  [3] -0.440 - 0 == -0.440
  [4] -0.413 - 0 == -0.413
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ]
  1. Failure: Elastic net sratio matches glmnetcr::glmnet.cr (@test-ordinalNet.R#213) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘OriGen/libs/OriGen.so’:
  Found ‘__f90_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_esfr’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_rewind’, possibly from ‘rewind’ (Fortran)
    Object: ‘OriGen.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    nifti   4.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rcpp_API.Rmd’ using rmarkdown
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.
--- finished re-building ‘Rcpp_API.Rmd’

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

--- re-building ‘introduction.Rmd’ using rmarkdown
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 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [6s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(oxcAAR)
  > 
  > test_check("oxcAAR")
  sh: /home/ripley/R/packages/tests-devel/oxcAAR.Rcheck/tests/testthat/ox_output.js: cannot execute
  ── 1. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  `quickSetupOxcal()` threw an error.
  Message: argument is of length zero
  Class:   simpleError/error/condition
  Backtrace:
   1. testthat::expect_error(quickSetupOxcal(), NA)
   6. oxcAAR::quickSetupOxcal()
  
  ── 2. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  dir.exists("OxCal/bin/") isn't true.
  
  ── 3. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  `%in%`(...) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 94 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#30) 
  2. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#31) 
  3. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#32) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic-usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 24-30 (basic-usage.Rmd) 
Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘basic-usage.Rmd’

SUMMARY: processing the following file failed:
  ‘basic-usage.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘graph_packing.Rmd’ using rmarkdown
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.
--- finished re-building ‘graph_packing.Rmd’

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

--- re-building ‘progressive_packing.Rmd’ using rmarkdown
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 196-217 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘progressive_packing.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 77-79 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
'names' attribute [3] must be the same length as the vector [2]
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Running ‘testthat.R’ [25s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PANICr)
  > 
  > test_check("PANICr")
  ── 1. Failure: Panic 10 demeaned consistency (@test_panic_io.R#25)  ────────────
  panic10(test1, nfac = 10L, k1 = 7, criteria = "IC1", demean = TRUE) not equal to `test_10_dm`.
  Component "MP.tests": Component "pool_test": Modes: character, numeric
  Component "MP.tests": Component "pool_test": Attributes: < target is NULL, current is list >
  Component "MP.tests": Component "pool_test": target is character, current is factor
  Component "MP.tests": Component "mp_test": Modes: character, numeric
  Component "MP.tests": Component "mp_test": Attributes: < target is NULL, current is list >
  Component "MP.tests": Component "mp_test": target is character, current is factor
  
  ── 2. Failure: Panic 10 non-demeaned consistency (@test_panic_io.R#40)  ────────
  panic10(test1, nfac = 10L, k1 = 7, criteria = "IC1", demean = FALSE) not equal to `test_10_ndm`.
  Component "MP.tests": Component "mp_test": Modes: character, numeric
  Component "MP.tests": Component "mp_test": Attributes: < target is NULL, current is list >
  Component "MP.tests": Component "mp_test": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: Panic 10 demeaned consistency (@test_panic_io.R#25) 
  2. Failure: Panic 10 non-demeaned consistency (@test_panic_io.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘run-all.R’ [25s/36s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > library(BBmisc)
  
  Attaching package: 'BBmisc'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  > library(ParamHelpers)
  > 
  > test_check("ParamHelpers")
  ── 1. Failure: requires works (@test_OptPath.R#198)  ───────────────────────────
  d[, 1:4] not equal to data.frame(...).
  Component "x": 'current' is not a factor
  
  ── 2. Error: plotEAF works (@test_plotEAF.R#27)  ───────────────────────────────
  groups must be a factor
  Backtrace:
   1. ParamHelpers::plotEAF(opt.paths)
   4. eaf:::eafplot.formula(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1050 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: requires works (@test_OptPath.R#198) 
  2. Error: plotEAF works (@test_plotEAF.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘functionMaximization.Rmd’ using rmarkdown
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.
  0.863 seconds

Starting Epoch 1 
  1) Fitting Gaussian Process...
  2) Running local optimum search...        0.524 seconds
  3) Running FUN 1 times in 1 thread(s)...  0.279 seconds

Starting Epoch 2 
  1) Fitting Gaussian Process...
  2) Running local optimum search...        0.894 seconds
  3) Running FUN 1 times in 1 thread(s)...  0.387 seconds



Warning in sink() : no sink to remove
Warning in sink() : no sink to remove
--- finished re-building ‘functionMaximization.Rmd’

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

--- re-building ‘tuningHyperparameters.Rmd’ using rmarkdown
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.
Error: segfault from C stack overflow
Warning in sink() : no sink to remove
Execution halted
SUMMARY: processing the following file failed:
  ‘tuningHyperparameters.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-parcoords-.Rmd’ using rmarkdown
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 27-30 (introduction-to-parcoords-.Rmd) 
Error: processing vignette 'introduction-to-parcoords-.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction-to-parcoords-.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        2.3Mb
    testdata   1.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    lib   4.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.1Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   8.4Mb
Package unavailable to check Rd xrefs: ‘tesseract’
Running examples in ‘pense-Ex.R’ failed
The error most likely occurred in:

> ### Name: coef.pense
> ### Title: Extract Model Coefficients
> ### Aliases: coef.pense
> 
> ### ** Examples
> 
> # Generate data with highly correlated groups of variables and some outliers
> set.seed(12345)
> n <- 50
> n_out <- 3
> p <- 20
> x <- 1 + matrix(rnorm(n * p), ncol = p)
> x[, 2] <- x[, 1] + rnorm(n, sd = 0.01)
> x[, 3] <- x[, 1] + rnorm(n, sd = 0.01)
> x[, 5] <- x[, 4] + rnorm(n, sd = 0.01)
> x[, 6] <- x[, 4] + rnorm(n, sd = 0.01)
> 
> y <- x %*% c(rep(c(2, 5), each = 3), numeric(p - 6)) + rnorm(n)
> 
> y[seq_len(n_out)] <- rnorm(n_out, -100, sd = 3)
> 
> # Compute the PENSE estimator
> set.seed(1234)
> est_en <- pense(x, y, alpha = 0.5, warm_reset = 1, cv_k = 3)

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

Traceback:
 1: enpy_exact(x, y, alpha, lambda, options, en_options)
 2: enpy(std_data$xs, std_data$yc, alpha, lambda, delta = pense_options$bdp,     cc = pense_options$cc, options = initest_options, en_options = en_options)
 3: pense_init_cold(x = x_train, y = y_train, lambda = job$lambda,     ...)
 4: FUN(X[[i]], ...)
 5: cluster$lapply(jobs_cold_est, get_cold_est, alpha = alpha, standardize = standardize,     pense_options = options, initest_options = init_options,     en_options = en_options)
 6: doTryCatch(return(expr), name, parentenv, handler)
 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8: tryCatchList(expr, classes, parentenv, handlers)
 9: tryCatch({    cold_inits <- cluster$lapply(jobs_cold_est, get_cold_est,         alpha = alpha, standardize = standardize, pense_options = options,         initest_options = init_options, en_options = en_options)}, error = function(e) {    cluster$stopCluster()    stop(e)})
10: pense(x, y, alpha = 0.5, warm_reset = 1, cv_k = 3)
An irrecoverable exception occurred. R is aborting now ...
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      4.5Mb
    data   3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
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 51-62 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data       2.4Mb
    examples   2.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   3.5Mb
Running ‘testthat.R’ [12s/17s]
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
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  ── 2. Error: See if extractor works (@test_extract_phrases.R#7)  ───────────────
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  Currently tagging document 1 of 1 
  Extracting phrases from document 1 of 1 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: See if tagging five documents works, and if coarsening works (@test_POS_tag_documents.R#7) 
  2. Error: See if extractor works (@test_extract_phrases.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting_started_with_phrasemachine.Rmd’ using rmarkdown
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 82-91 (getting_started_with_phrasemachine.Rmd) 
Error: processing vignette 'getting_started_with_phrasemachine.Rmd' failed with diagnostics:
unused argument (alist())
--- failed re-building ‘getting_started_with_phrasemachine.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Advanced_Usage.Rmd’ using rmarkdown
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 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Advanced_Usage.Rmd’

--- re-building ‘Basic_Use.Rmd’ using rmarkdown
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 30-32 (Basic_Use.Rmd) 
Error: processing vignette 'Basic_Use.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Basic_Use.Rmd’

SUMMARY: processing the following files failed:
  ‘Advanced_Usage.Rmd’ ‘Basic_Use.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_pifpaf_package.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: pifpaf
Loading required package: ggplot2
Running ‘test-async.R’ [1m/180m]
  Running ‘testthat.R’
Running the tests in ‘tests/test-async.R’ failed.
Complete output:
  > 
  > if (file.exists("async")) {
  +   library(testthat)
  +   library(pkgcache)
  +   test <- function() {
  +     package <- "pkgcache"
  +     env_test <- asNamespace("testthat")$env_test
  +     env_test$in_test <- TRUE
  +     env_test$package <- package
  +     on.exit({
  +       env_test$in_test <- FALSE
  +       env_test$package <- NULL
  +     })
  +     test_path <- "async"
  +     asNamespace("testthat")$test_package_dir(
  +       package = package, test_path = test_path,
  +       filter = NULL, reporter = "check")
  +   }
  +   test()
  + }
  
  Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pkgcache)
  > 
  > test_check("pkgcache")
  ── 1. Error: load_primary_pkgs (@test-metadata-cache.R#191)  ───────────────────
  No metadata available
  Backtrace:
   1. pkgcache:::synchronise(get_private(cmc)$load_primary_pkgs(oneday()))
   2. get_private(cmc)$load_primary_pkgs(oneday())
   3. pkgcache:::cmc__load_primary_pkgs(self, private, max_age)
   4. private$update_replica_rds(alert = FALSE)
   5. pkgcache:::cmc__update_replica_rds(self, private, alert)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 305 | SKIPPED: 28 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: load_primary_pkgs (@test-metadata-cache.R#191) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.png’
Running ‘testthat.R’ [9s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(plethem)
  You are now using PLETHEM.
                          If you have installed PLETHEM for the first time or have just updated it, please run setUserDb() to select an existing database or createUserDb() to create a new one.
  > 
  > test_check("plethem")
  ── 1. Error: Tissue volumes are less than 85% of body weight (@test_physio.R#19)
  invalid 'type' (list) of argument
  Backtrace:
   1. plethem::getLifecourseTissueVolumes(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 8 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: Tissue volumes are less than 85% of body weight (@test_physio.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
R: Fatal IO error 146 (Connection refused) on X server :5.0.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R             1.1Mb
    htmlwidgets   3.6Mb
Running ‘testthat.R’ [167s/208s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("plotly")
  Loading required package: ggplot2
  
  Attaching package: 'plotly'
  
  The following object is masked from 'package:ggplot2':
  
      last_plot
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following object is masked from 'package:graphics':
  
      layout
  
  > 
  > test_check("plotly")
  Visual testing is not enabled.
  OGR: Unsupported geometry type
  ── 1. Error: (unknown) (@test-cookbook-lines.R#192)  ───────────────────────────
  arguments imply differing number of rows: 0, 2
  Backtrace:
   1. base::data.frame(cond = levels(df$cond), xval = c(10, 11.5))
  
  ── 2. Failure: paths with the same color but different groups stay together (@te
  info$data[[1]]$name not identical to "positive".
  1/1 mismatches
  x[1]: "negative"
  y[1]: "positive"
  
  ── 3. Failure: paths with the same color but different groups stay together (@te
  info$data[[2]]$name not identical to "negative".
  1/1 mismatches
  x[1]: "positive"
  y[1]: "negative"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1375 | SKIPPED: 50 | WARNINGS: 63 | FAILED: 3 ]
  1. Error: (unknown) (@test-cookbook-lines.R#192) 
  2. Failure: paths with the same color but different groups stay together (@test-ggplot-path.R#51) 
  3. Failure: paths with the same color but different groups stay together (@test-ggplot-path.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [57s/66s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmml, quietly = T)
  > 
  > test_check("pmml")
  Error: segfault from C stack overflow
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘packages_and_functions.Rmd’ using rmarkdown
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.
--- finished re-building ‘packages_and_functions.Rmd’

--- re-building ‘xform_function.Rmd’ using rmarkdown
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.
Loading required package: XML
Quitting from lines 155-158 (xform_function.Rmd) 
Error: processing vignette 'xform_function.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘xform_function.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [52s/67s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmultinom)
  > 
  > test_check("pmultinom")
  ── 1. Failure: Correct behavior when target probability is 0 or 1 (@test_invertp
  invert.pmultinom(...) not equal to 0.
  1/1 mismatches
  [1] 6 - 0 == 6
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1561 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Correct behavior when target probability is 0 or 1 (@test_invertpmultinom.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in .arg_names_from_call(e[-1L]) :
  it is not known that wchar_t is Unicode on this platform
Warning in .arg_names_from_call(e[-1L]) :
  it is not known that wchar_t is Unicode on this platform
Warning in .arg_names_from_call(e[-1L]) :
  it is not known that wchar_t is Unicode on this platform
Warning in .arg_names_from_call(e[-1L]) :
  it is not known that wchar_t is Unicode on this platform
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘OpenCPU.Rmd’ using rmarkdown
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.
--- finished re-building ‘OpenCPU.Rmd’

--- re-building ‘vignette.Rmd’ using rmarkdown
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.
... activating corpus: GERMAPARLMINI
... activating corpus: REUTERS
Quitting from lines 140-141 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   4.0Mb
Package suggested but not available for checking: ‘ROI.plugin.symphony’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    java   5.7Mb
Undocumented S4 methods:
  generic 'plot' and siglist 'distribution'
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.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  11.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PPQnote.Rmd’ using rmarkdown
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.
--- finished re-building ‘PPQnote.Rmd’

--- re-building ‘PPQplan-vignette.Rmd’ using rmarkdown
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 normalizePath(f2) :
  path[1]="webshot18bb3daa67d2.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot18bb3daa67d2.png': No such file or directory
Quitting from lines 135-136 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PPQplan-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  StandardizeString.cpp:13:25: warning: passing NULL to non-pointer argument 1 of ‘Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]’ [-Wconversion-null]
See ‘/home/ripley/R/packages/tests-devel/PPRL.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘Rmosek’
Error(s) in re-building vignettes:
  ...
--- re-building ‘predict3d.Rmd’ using rmarkdown
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.
Loading required package: predict3d
Loading required package: rgl
Quitting from lines 55-58 (predict3d.Rmd) 
Error: processing vignette 'predict3d.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘predict3d.Rmd’

SUMMARY: processing the following file failed:
  ‘predict3d.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [11s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(preprocomb)
  > 
  > test_check("preprocomb")
  [1] "Running diagnostics on single preprocessors:"
  ── 1. Error: (unknown) (@tests.R#23)  ──────────────────────────────────────────
  Argument 'data' must have one and only one factor column.
  Backtrace:
   1. preprocomb::setgrid(phases = c("outliers"), data = modifiediris)
   2. preprocomb::testpreprocessors(unique(unlist(gridclassobject@grid)))
   3. preprocomb::initializedataclassobject(data)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 5 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@tests.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [8s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(preText)
  preText: Diagnostics to Assess the Effects of Text Preprocessing Decisions
  Version 0.6.3 created on 2018-01-12.
  copyright (c) 2017, Matthew J. Denny, Penn State University
                      Arthur Spirling, NYU
  Type vignette('getting_started_with_preText') to get started.
  Development website: https://github.com/matthewjdenny/preText
  > 
  > test_check("preText")
  ── 1. Error: Small example works (@test_factorial_preprocessing.R#6)  ──────────
  unused argument (alist())
  Backtrace:
   1. documents[1:10, ]
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Small example works (@test_factorial_preprocessing.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting_started_with_preText.Rmd’ using rmarkdown
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 60-69 (getting_started_with_preText.Rmd) 
Error: processing vignette 'getting_started_with_preText.Rmd' failed with diagnostics:
unused argument (alist())
--- failed re-building ‘getting_started_with_preText.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting_started_with_prewas.Rmd’ using rmarkdown
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 98-100 (getting_started_with_prewas.Rmd) 
Error: processing vignette 'getting_started_with_prewas.Rmd' failed with diagnostics:
Input must be a factor
--- failed re-building ‘getting_started_with_prewas.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'gurobi', 'lpsymphony', 'Rsymphony'
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRISMA.Rmd’ using rmarkdown
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 39-52 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘PRISMA.Rmd’

--- re-building ‘exclusionflowcharts.Rmd’ using rmarkdown
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 25-31 (exclusionflowcharts.Rmd) 
Error: processing vignette 'exclusionflowcharts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘exclusionflowcharts.Rmd’

SUMMARY: processing the following files failed:
  ‘PRISMA.Rmd’ ‘exclusionflowcharts.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc           9.3Mb
    htmlwidgets   2.7Mb
Running examples in ‘profile-Ex.R’ failed
The error most likely occurred in:

> ### Name: read_rprof
> ### Title: File I/O for profiler data
> ### Aliases: read_rprof read_pprof write_rprof write_pprof
> 
> ### ** Examples
> 
> rprof_file <- system.file("samples/rprof/1.out", package = "profile")
> ds <- read_rprof(rprof_file)
> ds
Profile data: 22 samples
> pprof_file <- tempfile("profile", fileext = ".pb.gz")
> write_pprof(ds, pprof_file)
Error: Package RProtoBuf is required to read pprof files.
Backtrace:
    █
 1. └─profile::write_pprof(ds, pprof_file)
 2.   └─profile:::ds_to_msg(x)
 3.     └─profile:::provide_proto()
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    extdata   8.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘quick_start.Rmd’ using rmarkdown
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.
Loading required package: Rcpp
Loading required package: rlang

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 33-34 (quick_start.Rmd) 
Quitting from lines 33-34 (quick_start.Rmd) 
Error: processing vignette 'quick_start.Rmd' failed with diagnostics:
invalid connection
--- failed re-building ‘quick_start.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data      1.8Mb
    extdata   2.8Mb
Undocumented S4 methods:
  generic 'plot' and siglist 'PSTf'
  generic 'plot' and siglist 'PSTr'
  generic 'plot' and siglist 'cprobd.list'
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘barebones_correlation.Rmd’ using rmarkdown
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.
--- finished re-building ‘barebones_correlation.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
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 97-103 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
invalid 'row.names' length
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    dict   5.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc        4.3Mb
    examples   2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Data_Model.Rmd’ using rmarkdown
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.
--- finished re-building ‘Data_Model.Rmd’

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

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

--- re-building ‘PWFSLSmoke.Rmd’ using rmarkdown
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 163-164 (PWFSLSmoke.Rmd) 
Error: processing vignette 'PWFSLSmoke.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘PWFSLSmoke.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
Running examples in ‘pyinit-Ex.R’ failed
The error most likely occurred in:

> ### Name: pyinit
> ### Title: PY (Pena-Yohai) initial estimates for S-estimates of regression
> ### Aliases: pyinit
> 
> ### ** Examples
> 
> # generate a simple synthetic data set for a linear regression model
> # with true regression coefficients all equal to one "(1, 1, 1, 1, 1)"
> set.seed(123)
> x <- matrix(rnorm(100*4), 100, 4)
> y <- rnorm(100) + rowSums(x) + 1
> # add masked outliers
> a <- svd(var(x))$v[,4]
> x <- rbind(x, t(outer(a, rnorm(20, mean=4, sd=1))))
> y <- c(y, rnorm(20, mean=-2, sd=.2))
> 
> # these outliers are difficult to find
> plot(lm(y~x), ask=FALSE)
> 
> # use pyinit to obtain estimated regression coefficients
> tmp <- pyinit(x=x, y=y, resid_keep_method='proportion', psc_keep = .5, resid_keep_prop=.5)

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

Traceback:
 1: pyinit(x = x, y = y, resid_keep_method = "proportion", psc_keep = 0.5,     resid_keep_prop = 0.5)
An irrecoverable exception occurred. R is aborting now ...
Running examples in ‘qad-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_density
> ### Title: Plot density of empirical checkerboard copula
> ### Aliases: plot_density
> 
> ### ** Examples
> 
> n <- 1000
> x <- runif(n,0,1)
> y <- runif(n,0,1)
> sample <- data.frame(x,y)
> plot(sample)
> 
> mass <- emp_c_copula(sample, resolution=8)
> plot_density(mass, density=TRUE)
Error in value[[3L]](cond) : 
  The melt generic in data.table has been passed a matrix, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(mass_matrix) or as.data.table(mass_matrix). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is deprecated and you should be migrating your code away from using it.
Calls: plot_density ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    staticdocs   3.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/qgg.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘orthography_processing.Rmd’ using rmarkdown
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.
--- finished re-building ‘orthography_processing.Rmd’

--- re-building ‘recoding_nominal_data.Rmd’ using rmarkdown
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 49-60 (recoding_nominal_data.Rmd) 
Error: processing vignette 'recoding_nominal_data.Rmd' failed with diagnostics:
factor level [3] is duplicated
--- failed re-building ‘recoding_nominal_data.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    data  12.9Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R         1.9Mb
    contrib   3.7Mb
    doc       3.2Mb
    libs      1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Qtools.Rmd’ using rmarkdown
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 124-146 (Qtools.Rmd) 
Error: processing vignette 'Qtools.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Qtools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    help   1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘quadmesh.Rmd’ using rmarkdown
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 20-35 (quadmesh.Rmd) 
Error: processing vignette 'quadmesh.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘quadmesh.Rmd’

--- re-building ‘topography.Rmd’ using rmarkdown
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 19-33 (topography.Rmd) 
Error: processing vignette 'topography.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘topography.Rmd’

SUMMARY: processing the following files failed:
  ‘quadmesh.Rmd’ ‘topography.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
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 83-117 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘wilcox1973.Rmd’ using rmarkdown
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 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘wilcox1973.Rmd’

SUMMARY: processing the following file failed:
  ‘wilcox1973.Rmd’

Error: Vignette re-building failed.
Execution halted
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Running ‘RUnit.R’ [149s/369s]
Running the tests in ‘tests/RUnit.R’ failed.
Complete output:
  > if (requireNamespace("RUnit", quietly=TRUE) && requireNamespace("RcppXPtrUtils", quietly=TRUE) && requireNamespace("r2sundials", quietly=TRUE) && requireNamespace("RcppArmadillo", quietly=TRUE)) {
  +    library(RUnit)
  +    library(RcppXPtrUtils)
  +    library(r2sundials)
  +    library(RcppArmadillo)
  + 
  +    testSuite <- defineTestSuite(
  +       name = "r2sundials unit tests",
  +       dirs = system.file("unitTests", package = "r2sundials"),
  +       testFuncRegexp = "^[Tt]est.+"
  +    )
  +    Sys.setenv("R_TESTS"="")
  +    tests <- runTestSuite(testSuite)
  + 
  +    printTextProtocol(tests)
  + 
  +    if (getErrors(tests)$nFail > 0) stop("RUnit test failure")
  +    if (getErrors(tests)$nErr > 0) stop("Errors in RUnit tests")
  + }
  Loading required package: rmumps
  CC: Warning: Optimizer level changed from 0 to 3 to support parallelized code.
  CC: Warning: Optimizer level changed from 0 to 3 to support parallelized code.
  CC: Warning: Optimizer level changed from 0 to 3 to support parallelized code.
  CC: Warning: Optimizer level changed from 0 to 3 to support parallelized code.
  terminate called after throwing an instance of 'Rcpp::exception'
    what():  CVode: At t = 6.69434e+10, mxstep steps taken before reaching tout.
Package unavailable to check Rd xrefs: ‘BRugs’
Error(s) in re-building vignettes:
  ...
--- re-building ‘RAbHIT-vignette.Rmd’ using rmarkdown
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.
Loading required package: ggplot2
RAbHIT version: 0.1.4
Quitting from lines 299-301 (RAbHIT-vignette.Rmd) 
Error: processing vignette 'RAbHIT-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘RAbHIT-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    app   6.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
Running ‘testthat.R’ [11s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(radjust)
  > test_check("radjust")
  ── 1. Failure: The examples work and the outputs are equal to the saved copies (
  `mice_rv_adaptive` not equivalent to eo$mice_rv_adaptive.
  Component "results_table": Component "name": target is character, current is factor
  
  ── 2. Failure: The examples work and the outputs are equal to the saved copies (
  `mice_rv_non_adpt_sel` not equivalent to eo$mice_rv_non_adpt_sel.
  Component "results_table": Component "name": target is character, current is factor
  
  ── 3. Failure: The examples work and the outputs are equal to the saved copies (
  `mice_rv_non_adpt` not equivalent to eo$mice_rv_non_adpt.
  Component "results_table": Component "name": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: The examples work and the outputs are equal to the saved copies (@test-radjust_sym.R#9) 
  2. Failure: The examples work and the outputs are equal to the saved copies (@test-radjust_sym.R#10) 
  3. Failure: The examples work and the outputs are equal to the saved copies (@test-radjust_sym.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.5Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    api           3.0Mb
    htmlwidgets   7.2Mb
Found the following files/directories:
  ‘blcs.dot’ ‘blcs.pdf’ ‘ex1.dot’ ‘ex1.pdf’ ‘ex1bridge1.dot’
  ‘ex1bridge1.pdf’ ‘ex1bridge2.dot’ ‘ex1bridge2.pdf’ ‘ex1bridge3.dot’
  ‘ex1bridge3.pdf’ ‘ex1effect1.dot’ ‘ex1effect1.pdf’ ‘ex1effect2.dot’
  ‘ex1effect2.pdf’ ‘gcmlinear.dot’ ‘gcmlinear.pdf’ ‘latent.dot’
  ‘latent.pdf’ ‘lcs.dot’ ‘lcs.pdf’ ‘mimic.dot’ ‘mimic.pdf’
Error(s) in re-building vignettes:
  ...
--- re-building ‘randomNames.Rmd’ using rmarkdown
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 13-26 (randomNames.Rmd) 
Error: processing vignette 'randomNames.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘randomNames.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [180s/437s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(randomsearch)
  Loading required package: ParamHelpers
  Loading required package: smoof
  Loading required package: checkmate
  > 
  > test_check("randomsearch")
  Error : [ENOENT] Failed to stat '/tmp/RtmpVcaqB6/working_dir/RtmpAxaidx/file2e19539d31a8/2_137': no such file or directory
  ── 1. Error: parallel randomsearch works with parallelMap (@test_randomsearch.R#
  [ENOENT] Failed to stat '/tmp/RtmpVcaqB6/working_dir/RtmpAxaidx/file2e19539d31a8/2_137': no such file or directory
  
  Backtrace:
   1. randomsearch::randomsearch(...)
   2. randomsearch:::randomsearch.smoof_function(...)
   3. parallelMap::parallelMap(...)
   4. parallelMap:::checkResultsAndStopWithErrorsMessages(res)
   5. parallelMap:::stopWithJobErrorMessages(...)
   6. BBmisc::stopf(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 69 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: parallel randomsearch works with parallelMap (@test_randomsearch.R#83) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
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.
Loading required package: Rcpp

Attaching package: 'lubridate'

The following objects are masked from 'package:data.table':

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

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

    date

Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 130-141 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.5Mb
    etc    2.2Mb
    po     1.5Mb
Package suggested but not available for checking: ‘av’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.7Mb
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    cont  25.9Mb
Running examples in ‘rchallenge-Ex.R’ failed
The error most likely occurred in:

> ### Name: icon
> ### Title: HTML code for icons.
> ### Aliases: icon
> 
> ### ** Examples
> 
> rmd <- '
+ ```{r}
+ library(rchallenge)
+ ```
+ <link rel="stylesheet" 
+  href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css">
+ `r icon("fa-user")`
+ `r icon("fa-user fa-lg")`
+ `r icon("fa-user fa-2x")`
+ `r icon("fa-user fa-3x")`
+ `r icon("fa-user fa-3x fa-border")`
+ '
> file <- tempfile()
> cat(rmd, file=file)
> writeLines(readLines(file))

```{r}
library(rchallenge)
```
<link rel="stylesheet" 
 href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css">
`r icon("fa-user")`
`r icon("fa-user fa-lg")`
`r icon("fa-user fa-2x")`
`r icon("fa-user fa-3x")`
`r icon("fa-user fa-3x fa-border")`
> rmarkdown::render(file)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rchallenge)
  > 
  > test_check("rchallenge")
  ── 1. Failure: pandoc available (@test-pandoc.R#2)  ────────────────────────────
  rmarkdown::pandoc_available("1.12.3") isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: pandoc available (@test-pandoc.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fuzzyrcmdrplugin.Rmd’ using rmarkdown
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 47-48 (fuzzyrcmdrplugin.Rmd) 
Error: processing vignette 'fuzzyrcmdrplugin.Rmd' failed with diagnostics:
Cluster setup failed. 1 worker of 1 failed to connect.
--- failed re-building ‘fuzzyrcmdrplugin.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.5Mb
    po    2.4Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    corpora   8.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    include   5.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘RcppCNPy-intro.Rmd’ using rmarkdown
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 95-104 (RcppCNPy-intro.Rmd) 
Error: processing vignette 'RcppCNPy-intro.Rmd' failed with diagnostics:
ImportError: No module named 'numpy'

Detailed traceback: 
  File "<string>", line 1, in <module>

--- failed re-building ‘RcppCNPy-intro.Rmd’

--- re-building ‘UsingReticulate.Rmd’ using rmarkdown
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 84-94 (UsingReticulate.Rmd) 
Error: processing vignette 'UsingReticulate.Rmd' failed with diagnostics:
ImportError: No module named 'numpy'
--- failed re-building ‘UsingReticulate.Rmd’

SUMMARY: processing the following files failed:
  ‘RcppCNPy-intro.Rmd’ ‘UsingReticulate.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    include   7.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    include   1.5Mb
    lib       3.0Mb
    libs      1.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    include   5.8Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    include   6.6Mb
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/RcppSimdJson.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [18s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RCSF)
  > 
  > test_check("RCSF")
  ── 1. Failure: csf algorithm works (@test-CSF.R#7)  ────────────────────────────
  length(id_ground) %in% c(15459L, 15453L) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: csf algorithm works (@test-CSF.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rdf_intro.Rmd’ using rmarkdown
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.

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 41-42 (rdf_intro.Rmd) 
Error: processing vignette 'rdf_intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘rdf_intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’ using rmarkdown
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.
Loading required package: rJava
Loading required package: Rdroolsjars

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: 'purrr'

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

    set_names

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Warning in if (class(intermediateOutput) == "list") { :
  the condition has length > 1 and only the first element will be used
Warning: filter_() is deprecated. 
Please use filter() instead

The 'programming' vignette or the tidyeval book can help you
to program with filter() : https://tidyeval.tidyverse.org
This warning is displayed once per session.
Warning in if (class(intermediateOutput) == "list") { :
  the condition has length > 1 and only the first element will be used
Quitting from lines 374-381 (Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd) 
Error: processing vignette 'Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘recexcavAAR-vignette-1.Rmd’ using rmarkdown
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 13-17 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-1.Rmd’

--- re-building ‘recexcavAAR-vignette-2.Rmd’ using rmarkdown
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 13-17 (recexcavAAR-vignette-2.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-2.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-2.Rmd’

--- re-building ‘recexcavAAR-vignette-3.Rmd’ using rmarkdown
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 13-17 (recexcavAAR-vignette-3.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-3.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-3.Rmd’

SUMMARY: processing the following files failed:
  ‘recexcavAAR-vignette-1.Rmd’ ‘recexcavAAR-vignette-2.Rmd’
  ‘recexcavAAR-vignette-3.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [88s/119s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(recipes)
  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
  
  
  Attaching package: 'recipes'
  
  The following object is masked from 'package:stats':
  
      step
  
  > 
  > if (requireNamespace("xml2")) {
  +   test_check("recipes", reporter = MultiReporter$new(reporters = list(JunitReporter$new(file = "test-results.xml"), CheckReporter$new())))
  + } else {
  +   test_check("recipes")
  + }
  Loading required namespace: xml2
  ── 1. Failure: add appropriate column with default settings (@test_intercept.R#2
  `rec_trans` not equal to `exp_res`.
  Incompatible type for column `cat`: x factor, y character
  
  ── 2. Failure: adds arbitrary numeric column (@test_intercept.R#33)  ───────────
  `rec_trans` not equal to `exp_res`.
  Incompatible type for column `cat`: x factor, y character
  
  ── 3. Failure: check_new_values works on factors (@test_newvalues.R#135)  ──────
  `res` not equal to `x1`.
  Incompatible type for column `a`: x factor, y character
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1431 | SKIPPED: 8 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: add appropriate column with default settings (@test_intercept.R#21) 
  2. Failure: adds arbitrary numeric column (@test_intercept.R#33) 
  3. Failure: check_new_values works on factors (@test_newvalues.R#135) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
Running ‘testthat.R’ [7s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rEDM)
  > 
  > if ("sample.kind" %in% names(formals(RNGkind)))
  + {
  +     suppressWarnings(RNGkind(sample.kind = "Rounding"))
  + }
  > 
  > test_check("rEDM")
  ── 1. Failure: multiview model_output works (@test_08_multiview.R#40)  ─────────
  digest::digest(round(model_output[, 1], 4)) not equal to "e5a987eb611ec1b250e616cb63e705e5".
  1/1 mismatches
  x[1]: "4a44297295aeb35b6fe54ef78e510397"
  y[1]: "e5a987eb611ec1b250e616cb63e705e5"
  
  ── 2. Failure: multiview model_output works (@test_08_multiview.R#42)  ─────────
  digest::digest(round(model_output[, 2], 4)) not equal to "3c35c2777121f5288749a397093b315f".
  1/1 mismatches
  x[1]: "6ce40d9c8cda41c48ab30216666c1b68"
  y[1]: "3c35c2777121f5288749a397093b315f"
  
  ── 3. Failure: multiview model_output works (@test_08_multiview.R#44)  ─────────
  digest::digest(round(model_output[, 3], 4)) not equal to "c00dbb731be86df5991ec0b46a1a5aee".
  1/1 mismatches
  x[1]: "60d6dd8107c0b095e993ba115cae9ced"
  y[1]: "c00dbb731be86df5991ec0b46a1a5aee"
  
  ── 4. Failure: beginning of range checking works (@test_11_error_checking.R#28) 
  Value hashes to e18b9aba52, not e5b3bb5459
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 190 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: multiview model_output works (@test_08_multiview.R#40) 
  2. Failure: multiview model_output works (@test_08_multiview.R#42) 
  3. Failure: multiview model_output works (@test_08_multiview.R#44) 
  4. Failure: beginning of range checking works (@test_11_error_checking.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘Rsymphony’

Package which this enhances but not available for checking: ‘Rcplex’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
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.

Attaching package: 'rENA'

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

    show

Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 107-117 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘getting-started.Rmd’

--- re-building ‘means-rotation.Rmd’ using rmarkdown
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.
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout


Attaching package: 'rENA'

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

    show

Quitting from lines 56-82 (means-rotation.Rmd) 
Error: processing vignette 'means-rotation.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘means-rotation.Rmd’

SUMMARY: processing the following files failed:
  ‘getting-started.Rmd’ ‘means-rotation.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [4s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(reshape2)
  > 
  > test_check("reshape2")
  ── 1. Failure: labels are correct when missing combinations dropped/kept (@test-
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 4 - 16 == -12
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 126 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: labels are correct when missing combinations dropped/kept (@test-cast.r#126) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘respirometry-Ex.R’ failed
The error most likely occurred in:

> ### Name: calc_MO2
> ### Title: Calculate metabolic rate
> ### Aliases: calc_MO2
> 
> ### ** Examples
> 
> # get O2 data
> file <- system.file('extdata', 'witrox_file.txt', package = 'respirometry')
> o2_data <- na.omit(import_witrox(file, split_channels = TRUE)$CH_4)
Warning in strsplit(raw, split = "\r\n", fixed = T) :
  input string 1 is invalid UTF-8
Error in grep("Date &Time [", f[1:20], fixed = TRUE):length(f) : 
  argument of length 0
Calls: na.omit -> import_witrox
Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’ [35s/71s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("retistruct")
  Loading required package: retistruct
  ── 1. Error: IDT format is read correctly (@test-format-idt.R#9)  ──────────────
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(r)
  
  ── 2. Error: Reconstruct SMI32 (CSV format) (@test-reconstruct.R#8)  ───────────
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(o)
  
  ── 3. Error: Reconstruct GMB530/R-CONTRA (IDT format) (@test-reconstruct.R#45)  
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(o)
  
  ── 4. Error: Serialisation works with a particular example (@test-reconstruct.R#
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(a, error = message)
  
  ── 5. Error: No regression on Issue #21 (@test-regressions.R#5)  ───────────────
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(a)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 138 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 5 ]
  1. Error: IDT format is read correctly (@test-format-idt.R#9) 
  2. Error: Reconstruct SMI32 (CSV format) (@test-reconstruct.R#8) 
  3. Error: Reconstruct GMB530/R-CONTRA (IDT format) (@test-reconstruct.R#45) 
  4. Error: Serialisation works with a particular example (@test-reconstruct.R#98) 
  5. Error: No regression on Issue #21 (@test-regressions.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘revgeo-Ex.R’ failed
The error most likely occurred in:

> ### Name: revgeo
> ### Title: Reverse Geocoding with the Photon Geocoder for OpenStreetMap,
> ###   Google Maps, and Bing.
> ### Aliases: revgeo
> ### Keywords: geocode reverse
> 
> ### ** Examples
> 
> revgeo(longitude=-77.0229529, latitude=38.89283435)
[1] "Getting geocode data from Photon: http://photon.komoot.de/reverse?lon=-77.0229529&lat=38.89283435"

Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rfm-customer-level-data.Rmd’ using rmarkdown
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.

Attaching package: 'dplyr'

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

    group_rows

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 230-274 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rfm-customer-level-data.Rmd’

--- re-building ‘rfm-transaction-level-data.Rmd’ using rmarkdown
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.

Attaching package: 'dplyr'

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

    group_rows

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 227-271 (rfm-transaction-level-data.Rmd) 
Error: processing vignette 'rfm-transaction-level-data.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rfm-transaction-level-data.Rmd’

SUMMARY: processing the following files failed:
  ‘rfm-customer-level-data.Rmd’ ‘rfm-transaction-level-data.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    help   2.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    doc       1.4Mb
    extdata   2.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘precipitation_stochastic_generation_v6.Rmd’ using rmarkdown
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.
Loading required package: copula
Loading required package: RGENERATE
Loading required package: RMAWGEN
Loading required package: chron
NOTE: The default cutoff when expanding a 2-digit year
to a 4-digit year will change from 30 to 69 by Aug 2020
(as for Date and POSIXct in base R.)
Loading required package: date
Loading required package: vars
Loading required package: MASS
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: urca
Loading required package: lmtest

Attaching package: 'vars'

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

    A

Loading required package: blockmatrix
Loading required package: Matrix
Loading required package: stringr

Attaching package: 'stringr'

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

    boundary


Attaching package: 'lubridate'

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

    days, hours, minutes, seconds, years

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

    interval

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

    date

Quitting from lines 50-63 (precipitation_stochastic_generation_v6.Rmd) 
Error: processing vignette 'precipitation_stochastic_generation_v6.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘precipitation_stochastic_generation_v6.Rmd’

SUMMARY: processing the following file failed:
  ‘precipitation_stochastic_generation_v6.Rmd’

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: ‘Rsymphony’
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc     3.8Mb
    fonts   1.6Mb
    libs    1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘WebGL.Rmd’ using rmarkdown
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 17-19 (WebGL.Rmd) 
Error: processing vignette 'WebGL.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘WebGL.Rmd’

--- re-building ‘legacyWebGL.Rmd’ using rmarkdown
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 17-19 (legacyWebGL.Rmd) 
Error: processing vignette 'legacyWebGL.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘legacyWebGL.Rmd’

--- re-building ‘rgl.Rmd’ using rmarkdown
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 16-19 (rgl.Rmd) 
Error: processing vignette 'rgl.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘rgl.Rmd’

SUMMARY: processing the following files failed:
  ‘WebGL.Rmd’ ‘legacyWebGL.Rmd’ ‘rgl.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'playwith', 'pmg', 'rggobi', 'SVGAnnotation'
Found the following significant warnings:
  Note: possible error in 'coord_trans(xtrans = "exp", ': unused arguments (xtrans = "exp", ytrans = "exp") 
See ‘/home/ripley/R/packages/tests-devel/RGraphics.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    extra  10.2Mb
Package required but not available: ‘RPostgres’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    help  10.6Mb
    libs   3.1Mb
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc          10.2Mb
    htmlwidgets   1.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_rhandsontable.Rmd’ using rmarkdown
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 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘intro_rhandsontable.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/ribiosUtils.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
Note: information on .o files is not available
File ‘/home/ripley/R/Lib32-dev/rJava/libs/rJava.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
File ‘rJava/libs/rJava.so’:
  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 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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    java  11.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘RLumModel_-_Getting_started_with_RLumModel.Rmd’ using rmarkdown
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.
Loading required package: Luminescence
Loading required package: magrittr
Welcome to the R package Luminescence version 0.9.7 [Built: 2020-03-07 10:12:16 UTC]
A trapped charge: 'I want to break free.'
--- finished re-building ‘RLumModel_-_Getting_started_with_RLumModel.Rmd’

--- re-building ‘RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd’ using rmarkdown
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.
Loading required package: Luminescence
Loading required package: magrittr
Welcome to the R package Luminescence version 0.9.7 [Built: 2020-03-07 10:12:16 UTC]
Any arbitrary independent OSL device manufacturer: 'Sure it will work, it was me who built it!'
Quitting from lines 125-154 (RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd) 
Error: processing vignette 'RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd’

--- re-building ‘RLumModel_-_Using_own_parameter_sets.Rmd’ using rmarkdown
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.
Loading required package: Luminescence
Loading required package: magrittr
Welcome to the R package Luminescence version 0.9.7 [Built: 2020-03-07 10:12:16 UTC]
Fast component to slow component: 'Life is short!'
--- finished re-building ‘RLumModel_-_Using_own_parameter_sets.Rmd’

SUMMARY: processing the following file failed:
  ‘RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    rmd   8.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.4Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    java  12.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R  11.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘robin.Rmd’ using rmarkdown
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.
Loading required package: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: gprege
Loading required package: gptk
Loading required package: Matrix
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.5-1 (2019-12-12) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

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

    det

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

    backsolve, forwardsolve

Loading required package: maps
See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 
Quitting from lines 80-81 (robin.Rmd) 
Error: processing vignette 'robin.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘robin.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'illuminaHumanv3.db'
Running examples in ‘RobStatTM-Ex.R’ failed
The error most likely occurred in:

> ### Name: lmrobdet.control
> ### Title: Tuning parameters for lmrobdetMM and lmrobdetDCML
> ### Aliases: lmrobdet.control
> 
> ### ** Examples
> 
> data(coleman, package='robustbase')
> m2 <- lmrobdetMM(Y ~ ., data=coleman, control=lmrobdet.control(refine.PY=50))

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

Traceback:
 1: pyinit::pyinit(x = X, y = y, intercept = FALSE, delta = dee,     cc = 1.54764, psc_keep = control$psc_keep * (1 - (p/n)),     resid_keep_method = control$resid_keep_method, resid_keep_thresh = control$resid_keep_thresh,     resid_keep_prop = control$resid_keep_prop, maxit = control$py_maxit,     eps = control$py_eps, mscale_maxit = control$mscale_maxit,     mscale_tol = control$mscale_tol, mscale_rho_fun = "bisquare")
 2: MMPY(X = x, y = y, control = control, mf = mf)
 3: lmrobdetMM(Y ~ ., data = coleman, control = lmrobdet.control(refine.PY = 50))
An irrecoverable exception occurred. R is aborting now ...
Running examples in ‘robust-Ex.R’ failed
The error most likely occurred in:

> ### Name: overlaidDenPlot.fdfm
> ### Title: Overlaid Density Plot
> ### Aliases: overlaidDenPlot.fdfm
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   data(los, package="robustbase")
>   los.fm <- fit.models(c(Robust = "fitdstnRob", MLE = "fitdstn"),
+                          x = los, densfun = "gamma")

 *** caught segfault ***
address 4, cause 'memory not mapped'

Traceback:
 1: Tabgamma(b1, b2, alpha1, alpha2, k, A, maxta, maxtc, maxit, til,     tol)
 2: gammaRob(x, ...)
 3: fitdstnRob(x = los, densfun = "gamma")
 4: eval(model.call, sys.parent())
 5: eval(model.call, sys.parent())
 6: fit.models(c(Robust = "fitdstnRob", MLE = "fitdstn"), x = los,     densfun = "gamma")
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.8Mb
    extdata   2.8Mb
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/rpg.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘NEWS.Rmd’ using rmarkdown
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.
--- finished re-building ‘NEWS.Rmd’

--- re-building ‘rpivotTableIntroduction.Rmd’ using rmarkdown
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 51-53 (rpivotTableIntroduction.Rmd) 
Error: processing vignette 'rpivotTableIntroduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘rpivotTableIntroduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/RPostgres.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rpredictit-vignette.Rmd’ using rmarkdown
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 54-56 (rpredictit-vignette.Rmd) 
Error: processing vignette 'rpredictit-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘rpredictit-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘diagnostics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: survival
Loading required package: Hmisc
Loading required package: lattice
Loading required package: Formula

Attaching package: 'Hmisc'

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

    format.pval, units

Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


Attaching package: 'dplyr'

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

    src, summarize

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 202-204 (diagnostics.Rmd) 
Error: processing vignette 'diagnostics.Rmd' failed with diagnostics:
contrasts can be applied only to factors with 2 or more levels
--- failed re-building ‘diagnostics.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘RScelestial-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 45-48 (RScelestial-vignette.Rmd) 
Error: processing vignette 'RScelestial-vignette.Rmd' failed with diagnostics:
Not compatible with requested type: [type=character; target=integer].
--- failed re-building ‘RScelestial-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following executable file:
  data/GH.RData
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/Rserve.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rnw’ using Sweave
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: ‘rsolr’

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

    ftable

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

    grouping


Error: processing vignette 'intro.Rnw' failed with diagnostics:
 chunk 3 (label = SolrFrame) 
Error in value[[3L]](cond) : Failed to retrieve schema.
rsolr requires schema via REST or as XML from admin module.
Error from REST: Error: Not Found



--- failed re-building ‘intro.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [31m/33m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(rsparse)
  > library(data.table)
  > library(Matrix)
  > options(rsparse_omp_threads = 1L)
  > logger = lgr::get_logger('rsparse')
  > logger$set_threshold('warn')
  > data("movielens100k")
  > test_check("rsparse")
Package required but not available: ‘GMMAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    4.9Mb
    libs  10.9Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs        8.5Mb
    unitTests   1.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Running examples in ‘rsubgroup-Ex.R’ failed
The error most likely occurred in:

> ### Name: CreateSDTask
> ### Title: Creates a Subgroup Discovery Task
> ### Aliases: CreateSDTask
> ### Keywords: subgroup task
> 
> ### ** Examples
> 
> # creating a task
> data(credit.data)
> 
> # task with binary target
> task <- CreateSDTask(credit.data, as.target("class", "good"))
Error in .jnew("org/vikamine/kernel/xpdl/ARFFAsStringDatasetProvider",  : 
  java.lang.UnsupportedClassVersionError: org/vikamine/kernel/xpdl/ARFFAsStringDatasetProvider : Unsupported major.minor version 52.0
Calls: CreateSDTask ... .CreateARFFProvider -> .CreateARFFProvider -> .jnew
Execution halted
Running ‘test.R’
Running the tests in ‘tests/test.R’ failed.
Complete output:
  > ###############################################################################
  > #    rsubgroup package R classes
  > # 
  > #    This file is part of the rsubgroup package.
  > #    Copyright (C) 2011-2019 by Martin Atzmueller
  > #    
  > #    This program is free software: you can redistribute it and/or modify
  > #    it under the terms of the GNU General Public License as published by
  > #    the Free Software Foundation, either version 3 of the License, or
  > #    (at your option) any later version.
  > 
  > #    This program is distributed in the hope that it will be useful,
  > #    but WITHOUT ANY WARRANTY; without even the implied warranty of
  > #    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > #    GNU General Public License for more details.
  > #    
  > #    You should have received a copy of the GNU General Public License
  > #    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  > #
  > #    Contact: Martin Atzmueller (martin@atzmueller.net)
  > ###############################################################################
  > library(rJava)
  > 
  > .jinit()
  > jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
  > if(substr(jv, 1L, 1L) == "1") {
  + 	jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))
  + 	if(jvn < 1.8) stop("Java 8 is needed for this package but not available")
  + } 
  Error: Java 8 is needed for this package but not available
  Execution halted
Running examples in ‘RSuite-Ex.R’ failed
The error most likely occurred in:

> ### Name: prj_pack
> ### Title: Prepares project source pack tagged with version.
> ### Aliases: prj_pack
> 
> ### ** Examples
> 
> # create exemplary project base folder
> prj_base <- tempfile("example_")
> dir.create(prj_base, recursive = TRUE, showWarnings = FALSE)
> 
> # start project
> prj <- prj_start("my_project", skip_rc = TRUE, path = prj_base)
2020-03-11 23:06:58 INFO:rsuite:Project my_project has structure compliant with current version of RSuite(v0.37.253).
2020-03-11 23:06:58 INFO:rsuite:Project my_project started.
> 
> # create package in the project
> prj_start_package("mypackage", prj = prj, skip_rc = TRUE)
2020-03-11 23:06:58 INFO:rsuite:Package mypackage started in project my_project.
> 
> # build project source pack
> pack_fpath <- prj_pack(prj = prj, path = tempdir(), pack_ver = "1.0")
2020-03-11 23:06:58 WARNING:rsuite:Project environment is not locked!
2020-03-11 23:06:58 INFO:rsuite:Exporting project from /tmp/Rtmpl2a4wG/working_dir/Rtmp6Gayf0/example_682b89d5071/my_project ...
2020-03-11 23:06:58 INFO:rsuite:Exporting project from /tmp/Rtmpl2a4wG/working_dir/Rtmp6Gayf0/example_682b89d5071/my_project ... done
2020-03-11 23:07:00 WARNING:rsuite:Zip building aborted for /tmp/Rtmpl2a4wG/working_dir/Rtmp6Gayf0/prjpack_my_project_1.0x.zip
2020-03-11 23:07:00 ERROR:rsuite:Failed to create pack file (zip returned non 0 return status).
Error: Failed to create pack file (zip returned non 0 return status).
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Skylark_example.Rmd’ using rmarkdown
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 171-172 (Skylark_example.Rmd) 
Error: processing vignette 'Skylark_example.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Skylark_example.Rmd’

--- re-building ‘rtrim_2_extensions.Rmd’ using rmarkdown
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 261-264 (rtrim_2_extensions.Rmd) 
Error: processing vignette 'rtrim_2_extensions.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘rtrim_2_extensions.Rmd’

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

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

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

--- re-building ‘TRIM_methods_v2.pdf.asis’ using asis
--- finished re-building ‘TRIM_methods_v2.pdf.asis’

SUMMARY: processing the following files failed:
  ‘Skylark_example.Rmd’ ‘rtrim_2_extensions.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    7.9Mb
    libs   2.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     3.1Mb
    doc   1.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘apply_any_r_function.Rmd’ using rmarkdown
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.
--- finished re-building ‘apply_any_r_function.Rmd’

--- re-building ‘built-in_functions.Rmd’ using rmarkdown
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.
--- finished re-building ‘built-in_functions.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 80-103 (runner_examples.Rmd) 
Error: processing vignette 'runner_examples.Rmd' failed with diagnostics:
Not compatible with requested type: [type=character; target=integer].
--- failed re-building ‘runner_examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    include   5.5Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs      3.0Mb
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/s2.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc           3.3Mb
    htmlwidgets   1.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘R-versus-CPP.Rmd’ using rmarkdown
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 63-72 (R-versus-CPP.Rmd) 
Error: processing vignette 'R-versus-CPP.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘R-versus-CPP.Rmd’

SUMMARY: processing the following file failed:
  ‘R-versus-CPP.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   3.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sankeywheel.Rmd’ using rmarkdown
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 43-44 (sankeywheel.Rmd) 
Error: processing vignette 'sankeywheel.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sankeywheel.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 63.6Mb
  sub-directories of 1Mb or more:
    extdata  63.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sass.Rmd’ using rmarkdown
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 50-51 (sass.Rmd) 
Error: processing vignette 'sass.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘sass.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rmosek', 'pogs'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    example   2.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data            1.5Mb
    vignette_data   2.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R   7.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.1Mb
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
Error(s) in re-building vignettes:
  ...
Cpu Limit Exceeded - core dumped
--- re-building ‘constraints.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: OpenMx
To take full advantage of multiple cores, use:
  mxOption(key='Number of Threads', value=parallel::detectCores()) #now
  Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
Warning: code chunks must not depend on the uncached chunk "difsim"
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘getting-started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘airway’
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs   1.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data        1.7Mb
    sequences   2.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.3Mb
Running examples in ‘SetMethods-Ex.R’ failed
The error most likely occurred in:

> ### Name: LR.intersect
> ### Title: Function for identifying contradictory simplifying assumptions
> ###   or easy counterfactuals.
> ### Aliases: LR.intersect
> ### Keywords: QCA
> 
> ### ** Examples
> 
> # Import your data. For example:
> 
> data(SCHF)
> 
> # Get the parsimonious solution:
> 
> sol_yp <- minimize(SCHF, outcome = "EXPORT",
+                 conditions = c("EMP","BARGAIN","UNI","OCCUP","STOCK", "MA"),
+                 incl.cut = .9, 
+                 include = "?", 					   
+                 details = TRUE, show.cases = TRUE)

 *** caught segfault ***
address 293506d0, cause 'memory not mapped'

Traceback:
 1: minimize(SCHF, outcome = "EXPORT", conditions = c("EMP", "BARGAIN",     "UNI", "OCCUP", "STOCK", "MA"), incl.cut = 0.9, include = "?",     details = TRUE, show.cases = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Packages suggested but not available for checking:
  'loomR', 'SDMTools', 'monocle'
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    doc     12.4Mb
    sqlite   1.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sf1.Rmd’ using rmarkdown
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.
--- finished re-building ‘sf1.Rmd’

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

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

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

--- re-building ‘sf5.Rmd’ using rmarkdown
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 213-215 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sf5.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SGPdata.Rmd’ using rmarkdown
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 13-28 (SGPdata.Rmd) 
Error: processing vignette 'SGPdata.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGPdata.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    doc   3.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SGP.Rmd’ using rmarkdown
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 13-29 (SGP.Rmd) 
Error: processing vignette 'SGP.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP.Rmd’

--- re-building ‘SGP_Data_Analysis.Rmd’ using rmarkdown
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 13-29 (SGP_Data_Analysis.Rmd) 
Error: processing vignette 'SGP_Data_Analysis.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Analysis.Rmd’

--- re-building ‘SGP_Data_Preparation.Rmd’ using rmarkdown
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 13-29 (SGP_Data_Preparation.Rmd) 
Error: processing vignette 'SGP_Data_Preparation.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Preparation.Rmd’

SUMMARY: processing the following files failed:
  ‘SGP.Rmd’ ‘SGP_Data_Analysis.Rmd’ ‘SGP_Data_Preparation.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    examples           2.2Mb
    framework7-5.1.3   1.7Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    www   9.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
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 89-90 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘getting-started.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sigminer.Rmd’ using rmarkdown
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.
stdin: not in compressed format
Quitting from lines 59-61 (sigminer.Rmd) 
Error: processing vignette 'sigminer.Rmd' failed with diagnostics:
missing required fields from MAF: Hugo_Symbol
--- failed re-building ‘sigminer.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using-SIMMS.Rmd’ using rmarkdown
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.
Loading required package: survival
Loading required package: MASS
Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 3.0-2

Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Quitting from lines 125-232 (Using-SIMMS.Rmd) 
Error: processing vignette 'Using-SIMMS.Rmd' failed with diagnostics:
unimplemented type 'list' in 'orderVector1'

--- failed re-building ‘Using-SIMMS.Rmd’

SUMMARY: processing the following file failed:
  ‘Using-SIMMS.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘clipper’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘simPATHy.Rmd’ using rmarkdown
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 263-269 (simPATHy.Rmd) 
Error: processing vignette 'simPATHy.Rmd' failed with diagnostics:
there is no package called 'clipper'
--- failed re-building ‘simPATHy.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘simPH-Ex.R’ failed
The error most likely occurred in:

> ### Name: coxsimPoly
> ### Title: Simulate quantities of interest for a range of values for a
> ###   polynomial nonlinear effect from Cox Proportional Hazards models
> ### Aliases: coxsimPoly
> 
> ### ** Examples
> 
> # Load Carpenter (2002) data
> data("CarpenterFdaData")
> 
> # Load survival package
> library(survival)
> 
> # Run basic model
> M1 <- coxph(Surv(acttime, censor) ~ prevgenx + lethal + deathrt1 +
+             acutediz + hosp01  + hhosleng + mandiz01 + femdiz01 +
+             peddiz01 + orphdum + natreg + I(natreg^2) +
+             I(natreg^3) + vandavg3 + wpnoavg3 +
+             condavg3 + orderent + stafcder, data = CarpenterFdaData)
> 
> # Simulate simpoly First Difference
> Sim1 <- coxsimPoly(M1, b = "natreg", qi = "First Difference",
+                 pow = 3, Xj = seq(1, 150, by = 5), nsim = 100)
All Xl set at 0.
Error in value[[3L]](cond) : 
  The melt generic in data.table has been passed a matrix, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(Temp) or as.data.table(Temp). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is deprecated and you should be migrating your code away from using it.
Calls: coxsimPoly ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘simPH-overview.Rnw’ using knitr
All Xl set to 0.
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
All Xl set to 0.
`geom_smooth()` using formula 'y ~ x'

Reminder (1): Currently SurvExpand does not support repeated events data.


Reminder (2): Times should be in 1 unit intervals, otherwise this could take awhile.


Converting "begin" to numeric. Things might get wacky. Please check.
Converting "end" to numeric. Things might get wacky. Please check.
Converting "event" to numeric. Things might get wacky. Please check.

Expanding data.

Keeping only needed observations.

Doing a final clean up.
All Xl set to 0.
Quitting from lines 408-412 (simPH-overview.Rnw) 
Error: processing vignette 'simPH-overview.Rnw' failed with diagnostics:
The melt generic in data.table has been passed a matrix, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(TVSim) or as.data.table(TVSim). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is deprecated and you should be migrating your code away from using it.
--- failed re-building ‘simPH-overview.Rnw’

SUMMARY: processing the following file failed:
  ‘simPH-overview.Rnw’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/skeleSim.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/slider.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   2.9Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    1.9Mb
Running examples in ‘somspace-Ex.R’ failed
The error most likely occurred in:

> ### Name: cnet
> ### Title: Complex network analysis
> ### Aliases: cnet
> 
> ### ** Examples
> 
> dummy <- owda[Time <= 1600] #toy example
> inp_som <- sominp(dummy)
> my_som <- somspa(inp_som, rlen = 100, grid = somgrid(3, 3, "hexagonal"))
> my_regions <- somregs(my_som, nregions = 6) 
> cnet(my_regions, n = 5, thres = 0.2)
Error in value[[3L]](cond) : 
  The melt generic in data.table has been passed a matrix, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(cor_regs(x, n)) or as.data.table(cor_regs(x, n)). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is deprecated and you should be migrating your code away from using it.
Calls: cnet ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘novel_solutions.Rmd’ using rmarkdown
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.
--- finished re-building ‘novel_solutions.Rmd’

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

--- re-building ‘understanding_sortable_js.Rmd’ using rmarkdown
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.
Warning in normalizePath(f2) :
  path[1]="webshot845181e29d1.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot845181e29d1.png': No such file or directory
Quitting from lines 71-72 (understanding_sortable_js.Rmd) 
Error: processing vignette 'understanding_sortable_js.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘understanding_sortable_js.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SourceSet.Rmd’ using rmarkdown
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.
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Identifing all possible orderings..
Total run time: 3.14 secs
Identifing all possible orderings..
Total run time: 1.53 secs
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘SourceSet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Found the following files/directories:
  ‘spacodi.formatted.txt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_sparkline.Rmd’ using rmarkdown
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 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘intro_sparkline.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    java   3.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Running examples in ‘spatial.tools-Ex.R’ failed
The error most likely occurred in:

> ### Name: tahoe_highrez_training
> ### Title: Point and polygon files for use with spatial.tools
> ### Aliases: tahoe_highrez_training
> ### Keywords: data
> 
> ### ** Examples
> 
> library("raster")
Loading required package: sp
> library("rgdal")
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.4, released 2018/03/19
 Path to GDAL shared files: /usr/local/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.4-1 
> tahoe_highrez_training_polygons <- readOGR(
+ 	dsn=system.file("external", package="spatial.tools"),layer="tahoe_highrez_training")
OGR data source with driver: ESRI Shapefile 
Source: "/home/ripley/R/Lib32-dev/spatial.tools/external", layer: "tahoe_highrez_training"
with 8 features
It has 2 fields
> spplot(tahoe_highrez_training_polygons,zcol="Class")
Warning in extend.limits(range(as.numeric(z), finite = TRUE)) :
  NAs introduced by coercion
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in seq.default(zrng[1], zrng[2], length.out = cuts + 2) : 
  'from' must be a finite number
Calls: spplot ... <Anonymous> -> levelplot.formula -> seq -> seq.default
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
Running examples in ‘SpatMCA-Ex.R’ failed
The error most likely occurred in:

> ### Name: spatmca
> ### Title: Regularized spatial MCA
> ### Aliases: spatmca
> 
> ### ** Examples
> 
> ############### 1D: regular locations ################################
> p <- q <- 20
> n <- 100
> x1 <- matrix(seq(-7, 7, length = p), nrow = p, ncol = 1)
> x2 <- matrix(seq(-7, 7, length = q), nrow = q, ncol = 1)
> u <- exp(-x1^2)/norm(exp(-x1^2), "F")
> v <- exp(-(x2 - 2)^2)/norm(exp(-(x2 - 2)^2), "F")
> Sigma <- array(0, c(p + q, p + q))
> Sigma[1:p, 1:p] <- diag(p)
> Sigma[(p + 1):(p + q), (p + 1):(p + q)] <- diag(p)
> Sigma[1:p, (p + 1):(p + q)] <- u%*%t(v)
> Sigma[(p + 1):(p + q), 1:p] <- t(Sigma[1:p, (p + 1):(p + q)])
> noise <- MASS::mvrnorm(n, mu = rep(0, p + q), Sigma = 0.001*diag(p + q))
> Y <- MASS:::mvrnorm(n, mu = rep(0, p + q), Sigma = Sigma) + noise
> Y1 <- Y[,1:p]
> Y2 <- Y[,-(1:p)]
> cv1 <- spatmca(x1, x2, Y1, Y2)

 *** caught segfault ***
address 275eae40, cause 'memory not mapped'
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    R      5.4Mb
    doc    5.1Mb
    help   5.3Mb
    libs   1.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    lsndata   2.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    lib       1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘staple_example.Rmd’ using rmarkdown
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.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   5.5Mb
Running examples in ‘starmie-Ex.R’ failed
The error most likely occurred in:

> ### Name: bestK
> ### Title: Determine a suitable K value from multiple Structure runs
> ### Aliases: bestK
> 
> ### ** Examples
> 
> multi_K <- exampleStructure("multiple_runs")
> # Run the evanno method and display diagnostic plots.
> evanno_results <- bestK(multi_K, method = "evanno")
Creating diagnostic plots for structure runs.
> # Run the default structure method and display diagnostic plots
> structure_results <- bestK(multi_K, "structure")
Creating diagnostic plots for structure runs.
> # find 'best' K according to results
> deltaK <- evanno_results$variable == 'delta K'
> max_deltaK <- which(evanno_results$value == max(evanno_results$value[deltaK], na.rm = TRUE))
> evanno_results[max_deltaK, ]
   K variable   value sd
16 4  delta K 104.815 NA
> lK <- structure_results$variable == 'L(K)'
> max_Lk <- which(structure_results$value == max(structure_results$value[lK], na.rm = TRUE))
> structure_results[max_Lk,]
    K variable   value       sd
5.1 5     L(K) -1410.7 2.687006
> # admixture example
> multi_K_admix <- exampleAdmixture()
> bestK(multi_K_admix)
Creating diagnositc plots for admixture runs
Error in value[[3L]](cond) : 
  The melt generic in data.table has been passed a data.frame, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(combineLogs(x)) or as.data.table(combineLogs(x)). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is deprecated and you should be migrating your code away from using it.
Calls: bestK ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    doc  10.6Mb
    nc    4.7Mb
XIO:  fatal IO error 146 (Connection refused) on X server ":5.0"
      after 0 requests (0 known processed) with 0 events remaining.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R          2.3Mb
    datasets   2.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.1Mb
Package suggested but not available for checking: ‘BSgenome.Ptroglodytes.UCSC.panTro5’
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘stRvignette.Rmd’ using rmarkdown
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 61-64 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
Process terminated
--- failed re-building ‘stRvignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [30m/32m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(subgroup.discovery)
  > 
  > test_check("subgroup.discovery")
Error(s) in re-building vignettes:
  ...
--- re-building ‘suddengains-tutorial.Rmd’ using rmarkdown
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 472-479 (suddengains-tutorial.Rmd) 
Error: processing vignette 'suddengains-tutorial.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘suddengains-tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘suddengains-tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    3.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Guide-to-CountVectorizer.Rmd’ using rmarkdown
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.
--- finished re-building ‘Guide-to-CountVectorizer.Rmd’

--- re-building ‘Guide-to-TfidfVectorizer.Rmd’ using rmarkdown
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.
--- finished re-building ‘Guide-to-TfidfVectorizer.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
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.
Error: segfault from C stack overflow
Execution halted
SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.8Mb
    help   1.0Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    data   3.3Mb
    doc    3.9Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘survsup_intro.Rmd’ using rmarkdown
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 92-96 (survsup_intro.Rmd) 
Error: processing vignette 'survsup_intro.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building ‘survsup_intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘svmpath/libs/svmpath.so’:
  Found ‘__f90_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__f90_eifr’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi30spec.o’, ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘__f90_esfr’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (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’
  Found ‘__f90_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__f90_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.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  5.7Mb
  sub-directories of 1Mb or more:
    extdata   4.6Mb
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/symengine.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘HTML.Rmd’ using rmarkdown
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.
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

Quitting from lines 44-45 (HTML.Rmd) 
Error: processing vignette 'HTML.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘HTML.Rmd’

--- re-building ‘tables.Rnw’ using Sweave
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: ‘Hmisc’

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

    format.pval, units

--- finished re-building ‘tables.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bibliography.Rmd’ using rmarkdown
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.
--- finished re-building ‘bibliography.Rmd’

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

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

--- re-building ‘seriation.Rmd’ using rmarkdown
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 230-276 (seriation.Rmd) 
Error: processing vignette 'seriation.Rmd' failed with diagnostics:
<BootCA> instance initialization:
* 'rows[[1]]' must be integer; not character.
* 'columns[[1]]' must be integer; not character.
--- failed re-building ‘seriation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
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.
--- finished re-building ‘example.Rmd’

--- re-building ‘fda-example.Rmd’ using rmarkdown
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 242-244 (fda-example.Rmd) 
Error: processing vignette 'fda-example.Rmd' failed with diagnostics:
attempt to set an attribute on NULL
--- failed re-building ‘fda-example.Rmd’

--- re-building ‘single-style.Rmd’ using rmarkdown
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.
--- finished re-building ‘single-style.Rmd’

--- re-building ‘summary-example.Rmd’ using rmarkdown
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.
--- finished re-building ‘summary-example.Rmd’

SUMMARY: processing the following file failed:
  ‘fda-example.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
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    doc           1.9Mb
    simulations   3.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.9Mb
Packages suggested but not available for checking:
  'lpsymphony', 'Rsymphony', 'gurobi'
Running ‘testthat.R’ [30s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(texPreview)
  > test_check("texPreview")
  ── 1. Error: (unknown) (@test-tex.R#115)  ──────────────────────────────────────
  R: delegate failed `'potrace' --svg --output '%o' '%i'' @ error/delegate.c/InvokeDelegate/1958
  Backtrace:
    1. testthat::describe(...)
    2. [ base::eval(...) ] with 1 more call
    5. texPreview:::tex_preview.xtable(...)
    7. texPreview:::tex_preview.character(...)
    8. texPreview:::tex_preview.default(...)
    9. texPreview:::tex_image(obj, stem, write_flag, overwrite)
   10. magick::image_write(imgOut, tex_path(fileDir, stem, dev = imgFormat))
   11. magick:::magick_image_write(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-tex.R#115) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.0Mb
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    data   2.8Mb
    doc    3.1Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   8.6Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    rda    7.7Mb
Running ‘testthat.R’ [54s/145s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(themetagenomics)
  Loading required package: Rcpp
  > 
  > test_check("themetagenomics")
  ── 1. Failure: prepare_data works with multiclass factor (@test-prepare.R#92)  ─
  `prepare_data(...)` did not produce any warnings.
  
  ── 2. Error: prepare_data works with multiclass factor and continuous (@test-pre
  undefined columns selected
  Backtrace:
   1. testthat::expect_equal(...)
   5. base::`[.data.frame`(x$modelframe, , c("Multi1", "Multi3", "Day"))
  
  ── 3. Error: prepare_data works with multiclass factor and spline (@test-prepare
  undefined columns selected
  Backtrace:
   1. testthat::expect_equal(...)
   5. base::`[.data.frame`(x$modelframe, , c("Multi1", "Multi3", "Day"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 45 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: prepare_data works with multiclass factor (@test-prepare.R#92) 
  2. Error: prepare_data works with multiclass factor and continuous (@test-prepare.R#139) 
  3. Error: prepare_data works with multiclass factor and spline (@test-prepare.R#168) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [23s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(theseus)
  > 
  > test_check("theseus")
  ── 1. Error: rename_column_to_other returns taxa names of correct length (@test-
  attempting to coerce non-factor
  Backtrace:
   1. base::table(...)
   2. theseus:::rename_column_to_other(df, tax_level = "Phylum", top_taxa)
   3. base::as.character.factor(df[[tax_level]])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: rename_column_to_other returns taxa names of correct length (@test-helpers.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘plot-smooths.Rmd’ using rmarkdown
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 172-177 (plot-smooths.Rmd) 
Error: processing vignette 'plot-smooths.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘plot-smooths.Rmd’

--- re-building ‘predict-gam.Rmd’ using rmarkdown
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.
--- finished re-building ‘predict-gam.Rmd’

SUMMARY: processing the following file failed:
  ‘plot-smooths.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Rblpapi’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Package unavailable to check Rd xrefs: ‘Rblpapi’
installed size is  6.7Mb
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    doc       1.5Mb
    extdata   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_tidyusda.Rmd’ using rmarkdown
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 72-89 (using_tidyusda.Rmd) 
Error: processing vignette 'using_tidyusda.Rmd' failed with diagnostics:
Timeout was reached: [quickstats.nass.usda.gov] Resolving timed out after 10010 milliseconds
--- failed re-building ‘using_tidyusda.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Tigger-Vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: ggplot2

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

sh: nproc:  not found
Quitting from lines 107-109 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command: 'Illegal seek'
--- failed re-building ‘Tigger-Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Tigger-Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
XIO:  fatal IO error 146 (Connection refused) on X server ":5.0"
      after 0 requests (0 known processed) with 0 events remaining.
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘toOrdinal.Rmd’ using rmarkdown
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 13-26 (toOrdinal.Rmd) 
Error: processing vignette 'toOrdinal.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘toOrdinal.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
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    data   4.8Mb
installed size is  5.3Mb
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    data   4.8Mb
Package suggested but not available for checking: ‘moveVis’
installed size is  5.6Mb
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    extdata   5.3Mb
Package unavailable to check Rd xrefs: ‘moveVis’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘TourDetrackeR.Rmd’ using rmarkdown
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.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Source : http://tile.stamen.com/toner/13/4056/2748.png
Source : http://tile.stamen.com/toner/13/4057/2748.png
Source : http://tile.stamen.com/toner/13/4056/2749.png
Source : http://tile.stamen.com/toner/13/4057/2749.png
Quitting from lines 106-108 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘TourDetrackeR.Rmd’

--- re-building ‘trackeR.Rnw’ using Sweave
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Loading required package: splines
Loading required package: Matrix

Attaching package: 'fda'

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

    matplot

--- finished re-building 'trackeR.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [10s/117s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(traitdataform)
  > 
  > test_check("traitdataform")
  ── 1. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#10)  ─────────
  Value hashes to 2448e3596a, not bc9f97d273
  
  ── 2. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#11)  ─────────
  Value hashes to 4381d5bd4d, not 74f9a02a12
  
  ── 3. Error: mapping of traits based on thesaurus works (@test.standardize.R#64)
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. traitdataform::standardize_traits(dataset2, thesaurus = traits2)
   2. base::droplevels(subset(out, traitNameStd == i)$traitUnitStd)
  
  ── 4. Error: factor level harmonizationworks (@test.standardize.R#81)  ─────────
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. traitdataform::standardize_traits(dd1)
   2. base::droplevels(subset(out, traitNameStd == i)$traitUnit)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 64 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#10) 
  2. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#11) 
  3. Error: mapping of traits based on thesaurus works (@test.standardize.R#64) 
  4. Error: factor level harmonizationworks (@test.standardize.R#81) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘traitdataform.Rmd’ using rmarkdown
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 310-312 (traitdataform.Rmd) 
Error: processing vignette 'traitdataform.Rmd' failed with diagnostics:
no applicable method for 'droplevels' applied to an object of class "character"
--- failed re-building ‘traitdataform.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    fonts   5.3Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   7.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(trustOptim)
  > 
  > test_check("trustOptim")
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
    50       0.000000       0.000000                    Success
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
   128       0.000000       0.000000                    Success
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
   287       0.000000       0.000000Radius of trust region is less than stop.trust.radius
  
  ── 1. Failure: Rosenbrock (@test_rosenbrock.R#67)  ─────────────────────────────
  opt0\$status does not match "Success".
  Actual value: "Radius of trust region is less than stop\.trust\.radius"
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
    65       0.000000       0.000000                    Success
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 15 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Rosenbrock (@test_rosenbrock.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/tsmp.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc     1.5Mb
    fonts   2.9Mb
installed size is 10.2Mb
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    doc     6.9Mb
    ubinc   2.2Mb
installed size is 12.5Mb
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    doc         7.3Mb
    dummydata   1.5Mb
    libs        1.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    extdata   2.6Mb
XIO:  fatal IO error 146 (Connection refused) on X server ":5.0"
      after 0 requests (0 known processed) with 0 events remaining.
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘TSstudio’
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
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 66-94 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   4.4Mb
Running examples in ‘umx-Ex.R’ failed
The error most likely occurred in:

> ### Name: RMSEA.summary.mxmodel
> ### Title: RMSEA function for MxModels
> ### Aliases: RMSEA.summary.mxmodel
> 
> ### ** Examples
> 
> require(umx)
> data(demoOneFactor)
> manifests = names(demoOneFactor)
> 
> m1 = umxRAM("One Factor", data = demoOneFactor, type = "cov",
+ 	umxPath("G", to = manifests),
+ 	umxPath(var = manifests),
+ 	umxPath(var = "G", fixedAt = 1.0)
+ )
A latent variable 'G' was created. 
Running One Factor with 10 parameters

 *** caught segfault ***
address 9d6bf516, cause 'memory not mapped'
Error(s) in re-building vignettes:
  ...
--- re-building ‘convexhull.Rmd’ using rmarkdown
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 93-98 (convexhull.Rmd) 
Error: processing vignette 'convexhull.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘convexhull.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    doc   1.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘upm-primer.Rmd’ using rmarkdown
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 70-71 (upm-primer.Rmd) 
Error: processing vignette 'upm-primer.Rmd' failed with diagnostics:
A variable(s) is listed by user as factors but data type in design matrix is not actually a factor. Reformat.
--- failed re-building ‘upm-primer.Rmd’

SUMMARY: processing the following file failed:
  ‘upm-primer.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.8Mb
Running ‘testthat.R’ [3s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(upwaver)
  > 
  > test_check("upwaver")
  ── 1. Failure: list_boards() works (@test-upwaver.R#29)  ───────────────────────
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 3 - 2 == 1
  
  ── 2. Failure: list_boards() works (@test-upwaver.R#34)  ───────────────────────
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 3 - 2 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 21 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: list_boards() works (@test-upwaver.R#29) 
  2. Failure: list_boards() works (@test-upwaver.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    data  14.9Mb
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    data  29.1Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   6.6Mb
Packages suggested but not available for checking: 'FSelector', 'RWeka'
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘varrank.Rmd’ using knitr
Loading required package: randomForest
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'randomForest'

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

    importance

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

    margin

Loading required package: parallel
Quitting from lines 122-125 (varrank.Rmd) 
Error: processing vignette 'varrank.Rmd' failed with diagnostics:
there is no package called 'FSelector'
--- failed re-building ‘varrank.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic_usage.Rmd’ using rmarkdown
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.

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 54-55 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘basic_usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_to_vegalite.Rmd’ using rmarkdown
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 24-36 (intro_to_vegalite.Rmd) 
Error: processing vignette 'intro_to_vegalite.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘intro_to_vegalite.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    doc    1.3Mb
    help   3.0Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   4.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-visNetwork.Rmd’ using rmarkdown
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 22-27 (Introduction-to-visNetwork.Rmd) 
Error: processing vignette 'Introduction-to-visNetwork.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Introduction-to-visNetwork.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction-to-visNetwork.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vortexRguide.Rmd’ using rmarkdown
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 284-288 (vortexRguide.Rmd) 
Error: processing vignette 'vortexRguide.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building ‘vortexRguide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’ [22s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(vroom)
  > 
  > if (requireNamespace("xml2")) {
  +   test_check("vroom", reporter = MultiReporter$new(reporters = list(JunitReporter$new(file = "test-results.xml"), CheckReporter$new())))
  + } else {
  +   test_check("vroom")
  + }
  Loading required namespace: xml2
  ── 1. Error: vroom works with many connections (@test-multi-file.R#90)  ────────
  Evaluation error: cannot open the connection.
  Backtrace:
   1. vroom::vroom(files)
   2. vroom:::vroom_(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 691 | SKIPPED: 5 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: vroom works with many connections (@test-multi-file.R#90) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  In for (i in seq_along(sigs)) { :
    closing unused connection 4 (/tmp/RtmpHkayQe/working_dir/RtmpFvaimx/file2e6161c16c1f/132.csv.gz)
  Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   6.6Mb
Package suggested but not available for checking: ‘rcdk’
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    client  10.1Mb
    doc      1.1Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    bn   7.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘wordcloud.Rmd’ using rmarkdown
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 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘wordcloud.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    data  13.4Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.9Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
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.
Loading required package: ggplot2
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Warning: Removed 10 rows containing non-finite values (stat_smooth).
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 5 row(s) containing missing values (geom_path).
Warning: Removed 10 rows containing missing values (geom_point).

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: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 214-234 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘x12’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/x12.Rcheck/00install.out’ for details.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/ripley/R/packages/tests-devel/x13binary.Rcheck/00install.out’ for details.
Running ‘test-all.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testit)
  > test_pkg('xaringan')
  Error from (function (input, output_format = NULL, output_file = NULL, output_dir = NULL,  ... 
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Running examples in ‘xgboost-Ex.R’ failed
The error most likely occurred in:

> ### Name: cb.gblinear.history
> ### Title: Callback closure for collecting the model coefficients history
> ###   of a gblinear booster during its training.
> ### Aliases: cb.gblinear.history
> 
> ### ** Examples
> 
> #### Binary classification:
> #
> # In the iris dataset, it is hard to linearly separate Versicolor class from the rest
> # without considering the 2nd order interactions:
> require(magrittr)
Loading required package: magrittr
> x <- model.matrix(Species ~ .^2, iris)[,-1]
> colnames(x)
 [1] "Sepal.Length"              "Sepal.Width"              
 [3] "Petal.Length"              "Petal.Width"              
 [5] "Sepal.Length:Sepal.Width"  "Sepal.Length:Petal.Length"
 [7] "Sepal.Length:Petal.Width"  "Sepal.Width:Petal.Length" 
 [9] "Sepal.Width:Petal.Width"   "Petal.Length:Petal.Width" 
> dtrain <- xgb.DMatrix(scale(x), label = 1*(iris$Species == "versicolor"))
> param <- list(booster = "gblinear", objective = "reg:logistic", eval_metric = "auc",
+               lambda = 0.0003, alpha = 0.0003, nthread = 2)
> # For 'shotgun', which is a default linear updater, using high eta values may result in
> # unstable behaviour in some datasets. With this simple dataset, however, the high learning
> # rate does not break the convergence, but allows us to illustrate the typical pattern of
> # "stochastic explosion" behaviour of this lock-free algorithm at early boosting iterations.
> bst <- xgb.train(param, dtrain, list(tr=dtrain), nrounds = 200, eta = 1.,
+                  callbacks = list(cb.gblinear.history()))
Error: segfault from C stack overflow
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xgboost)
  > 
  > test_check("xgboost")
  [1]	train-error:0.047136 
  Error: segfault from C stack overflow
  Execution halted
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    java  19.3Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.9Mb
Packages suggested but not available for checking: 'ChemmineR', 'fmcsR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.1Mb
Running ‘testthat.R’ [63s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xpose)
  Loading required package: ggplot2
  
  Attaching package: 'xpose'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("xpose")
  ── 1. Failure: parial xp_themes are properly added (@test-update_themes.R#39)  ─
  update_themes(xpdb = xpdb_ex_pk, xp_theme = c(point_color = "green"))$xp_theme not equivalent to `theme_xp_custom`.
  Component "labeller": target, current do not match when deparsed
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 521 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: parial xp_themes are properly added (@test-update_themes.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  yakmo.h:184:1: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/ripley/R/packages/tests-devel/yakmoR.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [17s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(yardstick)
  For binary classification, the first factor level is assumed to be the event.
  Set the global option `yardstick.event_first` to `FALSE` to change this.
  
  > 
  > test_check("yardstick")
  ── 1. Error: Three class (@test-prob-mn_log_loss.R#14)  ────────────────────────
  `truth` should be a factor but a character was supplied.
  Backtrace:
    1. testthat::expect_equal(...)
   13. yardstick:::metric_fn(...)
   14. yardstick::metric_vec_template(...)
   15. yardstick:::validate_truth_estimate_checks(...)
   16. yardstick:::validate_class(truth, "truth", cls[1])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 511 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Three class (@test-prob-mn_log_loss.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Undocumented S4 methods:
  generic 'plot' and siglist 'Zelig'
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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/aibd.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(attachment)
  > 
  > test_check("attachment")
  ── 1. Error: (unknown) (@test-to-description.R#8)  ─────────────────────────────
  object 'na.omit' is not exported by 'namespace:utils'
  Backtrace:
    1. attachment::att_to_description(path = dummypackage)
    3. attachment::att_from_namespace(path.n, document = document)
    4. devtools::document(dirname(path))
    7. roxygen2::roxygenise(pkg$path, roclets, load_code = load_code)
    8. roxygen2:::load_code(base_path)
    9. pkgload::load_all(path, helpers = FALSE, attach_testthat = FALSE)
   10. pkgload:::load_imports(path)
   11. pkgload:::process_imports(path)
   12. base::tryCatch(...)
   13. base:::tryCatchList(expr, classes, parentenv, handlers)
   14. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-to-description.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
---- unloading

 *** caught segfault ***
address 0x7f4f793abba0, cause 'invalid permissions'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Error(s) in re-building vignettes:
  ...
--- re-building ‘Examples_daily_response.Rmd’ using rmarkdown
Warning: Removed 92 row(s) containing missing values (geom_path).
Warning: Removed 71 row(s) containing missing values (geom_path).
Warning: Removed 124 row(s) containing missing values (geom_path).
Quitting from lines 229-245 (Examples_daily_response.Rmd) 
Error: processing vignette 'Examples_daily_response.Rmd' failed with diagnostics:
arguments imply differing number of rows: 6, 5
--- failed re-building ‘Examples_daily_response.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gglasso.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ggtern.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [128s/139s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(interactions)
  > 
  > test_check("interactions")
  ── 1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157)  
  `print(p)` produced messages.
  
  ── 2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162)  
  `print(p)` produced messages.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 165 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157) 
  2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘test-all.R’ [109s/116s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > #library(lavaSearch2)
  > suppressPackageStartupMessages(library("testthat"))
  > test_check("lavaSearch2")
  Loading required package: lavaSearch2
  Loading required package: ggplot2
  Loading required package: lava
  
  Attaching package: 'lava'
  
  The following object is masked from 'package:ggplot2':
  
      vars
  
  The following object is masked from 'package:testthat':
  
      compare
  
  lavaSearch2 version 1.5.4
  ── 1. Error: (unknown) (@test1-sCorrect-validObjects.R#48)  ────────────────────
  cannot coerce type 'closure' to vector of type 'any'
  Backtrace:
   1. lava::estimate(lvm(G ~ X1), data = d)
   2. lava:::estimate.lvm(lvm(G ~ X1), data = d)
   4. lava:::ordinal.estimate.hook(...)
   5. base::setdiff(lava::endogenous(x), bin)
   6. base::as.vector(y)
  
  ── 2. Error: (unknown) (@test2-modelsearch2.R#37)  ─────────────────────────────
  cannot coerce type 'closure' to vector of type 'any'
  Backtrace:
   1. lava::estimate(m, data = df.sim)
   2. lava:::estimate.lvm(m, data = df.sim)
   4. lava:::ordinal.estimate.hook(...)
   5. base::setdiff(lava::endogenous(x), bin)
   6. base::as.vector(y)
  
  ── 3. Error: (unknown) (@test3-multcomp.R#149)  ────────────────────────────────
  cannot coerce type 'closure' to vector of type 'any'
  Backtrace:
   1. lava::estimate(m.lvm, df.data)
   2. lava:::estimate.lvm(m.lvm, df.data)
   4. lava:::ordinal.estimate.hook(...)
   5. base::setdiff(lava::endogenous(x), bin)
   6. base::as.vector(y)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 464 | SKIPPED: 4 | WARNINGS: 2 | FAILED: 3 ]
  1. Error: (unknown) (@test1-sCorrect-validObjects.R#48) 
  2. Error: (unknown) (@test2-modelsearch2.R#37) 
  3. Error: (unknown) (@test3-multcomp.R#149) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:182:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:896:16: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:196:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
Running examples in ‘opencastR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: oc_api
> ### Title: Query Opencast base api
> ### Aliases: oc_api
> 
> ### ** Examples
> 
> Sys.setenv(OPENCAST_HOST = "https://legacy.opencast.org")
> Sys.setenv(OPENCAST_USERNAME = "admin")
> Sys.setenv(OPENCAST_PASSWORD = "opencast")
> 
> oc_api()
Error: lexical error: invalid char in json text.
                                       <!DOCTYPE HTML PUBLIC "-//W3C//
                     (right here) ------^
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting_started.Rmd’ using rmarkdown
Quitting from lines 39-40 (getting_started.Rmd) 
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
lexical error: invalid char in json text.
                                       <!DOCTYPE HTML PUBLIC "-//W3C//
                     (right here) ------^

--- failed re-building ‘getting_started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [9s/8s]
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
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  ── 2. Error: See if extractor works (@test_extract_phrases.R#7)  ───────────────
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  Currently tagging document 1 of 1 
  Extracting phrases from document 1 of 1 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: See if tagging five documents works, and if coarsening works (@test_POS_tag_documents.R#7) 
  2. Error: See if extractor works (@test_extract_phrases.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(preText)
  preText: Diagnostics to Assess the Effects of Text Preprocessing Decisions
  Version 0.6.3 created on 2018-01-12.
  copyright (c) 2017, Matthew J. Denny, Penn State University
                      Arthur Spirling, NYU
  Type vignette('getting_started_with_preText') to get started.
  Development website: https://github.com/matthewjdenny/preText
  > 
  > test_check("preText")
  ── 1. Error: Small example works (@test_factorial_preprocessing.R#6)  ──────────
  unused argument (alist())
  Backtrace:
   1. documents[1:10, ]
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Small example works (@test_factorial_preprocessing.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘R2019nCoV-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getMap
> ### Title: Getting real-time monitoring map of the 2019-nCoV virus
> ### Aliases: getMap
> 
> ### ** Examples
> 
> 
> x <- get_2019nCoV()
Error in file(con, "r") : 
  cannot open the connection to 'https://view.inews.qq.com/g2/getOnsInfo?name=disease_h5&callback=1580373566110'
Calls: get_2019nCoV -> <Anonymous> -> inside
Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rreadsdpa.c:608:15: warning: ‘strncpy’ output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  Rreadsdpa.c:1041:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  Rreadsdpa.c:1042:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:164:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:165:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rdsdp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  compile.cc:292:69: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class re2::Prog::Inst’; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/re2r.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [44s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rENA)
  
  Attaching package: 'rENA'
  
  The following object is masked from 'package:methods':
  
      show
  
  > 
  > test_check("rENA")
  ── 1. Failure: Verify binary/weighted accumulations with window > 1 are not equa
  any(as.matrix(win.4.binary$connection.counts) == as.matrix(win.4.sum$connection.counts)) not equal to `F`.
  1 element mismatch
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 160 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Verify binary/weighted accumulations with window > 1 are not equal (@test.weighted.single.window.R#30) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘UsingrerddapXtracto.Rmd’ using rmarkdown
Warning in make_crs(value) :
  the following proj4string elements are going to be ignored: +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0 ; remove the +init=epsg:XXXX to undo this
Warning in make_crs(value) :
  the following proj4string elements are going to be ignored: +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0 ; remove the +init=epsg:XXXX to undo this
Warning in make_crs(value) :
  the following proj4string elements are going to be ignored: +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0 ; remove the +init=epsg:XXXX to undo this
Warning in make_crs(value) :
  the following proj4string elements are going to be ignored: +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0 ; remove the +init=epsg:XXXX to undo this
Quitting from lines 524-534 (UsingrerddapXtracto.Rmd) 
Error: processing vignette 'UsingrerddapXtracto.Rmd' failed with diagnostics:
'Error {
    code=404;
    message="Not Found: Currently unknown datasetID=CORIOLIS_GLOBAL_NRTOA_OBS_TIME_SERIE_PSAL";
}
' does not exist in current working directory ('/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rerddapXtracto.Rcheck/vign_test/rerddapXtracto/vignettes').
--- failed re-building ‘UsingrerddapXtracto.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Note: possible error in 'coord_trans(xtrans = "exp", ': unused arguments (xtrans = "exp", ytrans = "exp") 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RGraphics.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-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’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-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’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RVowpalWabbit.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/skeleSim.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [17s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(uFTIR)
  Loading required package: parallel
  > 
  > test_check("uFTIR")
  ── 1. Error: Preprocess for SpectralPack object is reshaping the wavenumbers (@t
  there is no package called 'prospectr'
  Backtrace:
   1. base::library(prospectr)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 29 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Preprocess for SpectralPack object is reshaping the wavenumbers (@test-tile_functions.R#104) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [2s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(upwaver)
  > 
  > test_check("upwaver")
  ── 1. Failure: list_boards() works (@test-upwaver.R#29)  ───────────────────────
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 3 - 2 == 1
  
  ── 2. Failure: list_boards() works (@test-upwaver.R#34)  ───────────────────────
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 3 - 2 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 21 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: list_boards() works (@test-upwaver.R#29) 
  2. Failure: list_boards() works (@test-upwaver.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/x13binary.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(AER)
  Loading required package: car
  Loading required package: carData
  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: sandwich
  Loading required package: survival
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:car':
  
      recode
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(geepack)
  > library(survey)
  Loading required package: grid
  Loading required package: Matrix
  
  Attaching package: 'survey'
  
  The following object is masked from 'package:graphics':
  
      dotchart
  
  > library(testthat)
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:dplyr':
  
      matches
  
  > library(zeligverse)
  Error in library(zeligverse) : there is no package called 'zeligverse'
  Execution halted
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    R  13.7Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    extdata  11.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.8Mb
Package suggested but not available for checking: 'REBayes'
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "AWR.Kinesis"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('AWR.Kinesis')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
Error: connections left open:
	stdin (file)
Execution halted
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: install_aws_sdk
> ### Title: Install the AWS Java SDK
> ### Aliases: install_aws_sdk
> 
> ### ** Examples
> 
> ## Not run: 
> ##D install_aws_sdk()
> ## End(Not run)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.28 0.13 1.42 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.3Mb
    libs   1.8Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/BayesARIMAX.Rcheck/00install.out' for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 134.1Mb
  sub-directories of 1Mb or more:
    include  133.1Mb
Running 'spelling.R' [1s]
  Running 'testthat.R' [280s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(bigsnpr)
  Loading required package: bigstatsr
  > 
  > test_check("bigsnpr", filter = "7-")
  == testthat results  ===========================================================
  [ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
  > test_check("bigsnpr", filter = "1-")
  == testthat results  ===========================================================
  [ OK: 166 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
  > test_check("bigsnpr", filter = "2-")
  == testthat results  ===========================================================
  [ OK: 32 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 0 ]
  > test_check("bigsnpr", filter = "3-")
  -- 1. Failure: (unknown) (@test-3-plink-QC.R#14)  ------------------------------
  grepl("plink2", plink2) isn't true.
  
  -- 2. Error: (unknown) (@test-3-plink-QC.R#15)  --------------------------------
  '--version' not found
  Backtrace:
   1. base::system(paste(plink2, "--version"), intern = TRUE)
  
  == testthat results  ===========================================================
  [ OK: 12 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 2 ]
  1. Failure: (unknown) (@test-3-plink-QC.R#14) 
  2. Error: (unknown) (@test-3-plink-QC.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 59.6Mb
  sub-directories of 1Mb or more:
    include   8.6Mb
    lib      50.6Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.0Mb
Running examples in 'DALEXtra-Ex.R' failed
The error most likely occurred in:

> ### Name: explain_scikitlearn
> ### Title: Wrapper for Python Scikit-Learn Models
> ### Aliases: explain_scikitlearn
> 
> ### ** Examples
> 
> library("DALEXtra")
> if(DALEXtra:::is_conda()) {
+    # Explainer build (Keep in mind that 18th column is target)
+    titanic_test <- read.csv(system.file("extdata", "titanic_test.csv", package = "DALEXtra"))
+    # Keep in mind that when pickle is being built and loaded,
+    # not only Python version but libraries versions has to match aswell
+    explainer <- explain_scikitlearn(system.file("extdata", "scikitlearn.pkl", package = "DALEXtra"),
+    yml = system.file("extdata", "testing_environment.yml", package = "DALEXtra"),
+    data = titanic_test[,1:17], y = titanic_test$survived)
+    plot(model_performance(explainer))
+ 
+    # Predictions with newdata
+    predict(explainer, titanic_test[1:10,1:17])
+ 
+ } else {
+   print('Conda is required.')
+ }
There already exists environment named the same as it is specified in .yml file - myenv. It will be used
Warning in system2(command = python, args = paste0("\"", config_script,  :
  running command '"C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe" "D:/temp/RtmpmMO2lB/RLIBS_12c8033a42175/reticulate/config/config.py"' had status 2
Warning: Error in python_config(python_version, required_module, python_version, : Error 2 occurred running C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe 

Error: Yours environment has to match environment where pickle file was created. It also includes encoding, python version, and libraries version. Specifying .yml file or path to virtual environment may help. For more information look warnings() and then ?explain_scikitlearn
Execution halted
Running examples in 'DCD-Ex.R' failed
The error most likely occurred in:

> ### Name: DCD
> ### Title: Differential Community Detection for Paired Biological Networks,
> ###   for e.g. case vs control
> ### Aliases: DCD
> 
> ### ** Examples
> 
> 
> DCD_output <- DCD()
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> ## Not run: 
> ##D library(igraph)
> ##D g_A <- sample_grg(200, 0.15, torus=FALSE, coords = FALSE)
> ##D g_B <- permute(g_A,c(sample(20),21:200))
> ##D ground_truth <- c(rep(1,20),rep(0,180))
> ##D DCD_output2 <- DCD(g_A = g_A, g_B = g_B, method = "Spectral", mink = 7,
> ##D                    ground_truth = ground_truth, plot_flag = 1, color = "red",
> ##D                    iter = 1, cores = 1 )
> ##D   
> ## End(Not run)
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11578 (sockconn)
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/DeducerSpatial.Rcheck/00install.out' for details.
VanWaerdenTest.default: no visible global function definition for
  'deparse1'
Undefined global functions or variables:
  deparse1
Running examples in 'DescTools-Ex.R' failed
The error most likely occurred in:

> ### Name: VanWaerdenTest
> ### Title: van der Waerden Test
> ### Aliases: VanWaerdenTest VanWaerdenTest.default VanWaerdenTest.formula
> ### Keywords: htest
> 
> ### ** Examples
> 
> ## Hollander & Wolfe (1973), 116.
> ## Mucociliary efficiency from the rate of removal of dust in normal
> ##  subjects, subjects with obstructive airway disease, and subjects
> ##  with asbestosis.
> x <- c(2.9, 3.0, 2.5, 2.6, 3.2) # normal subjects
> y <- c(3.8, 2.7, 4.0, 2.4)      # with obstructive airway disease
> z <- c(2.8, 3.4, 3.7, 2.2, 2.0) # with asbestosis
> 
> VanWaerdenTest(list(x, y, z))
Error in deparse1(substitute(x)) : could not find function "deparse1"
Calls: VanWaerdenTest -> VanWaerdenTest.default
Execution halted
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11400 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11400 (sockconn)
Execution halted
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11866 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11866 (sockconn)
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/dyndimred.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/econetwork.Rcheck/00install.out' for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.5Mb
    libs      1.5Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      4.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.8Mb
Found the following significant warnings:
  Warning: namespace 'lme4' is not available and has been replaced
See 'd:/Rcompile/CRANpkg/local/3.6/GMMAT.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 130.5Mb
  sub-directories of 1Mb or more:
    java  128.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Running examples in 'icrf-Ex.R' failed
The error most likely occurred in:

> ### Name: getTree.icrf
> ### Title: Extract a single tree from an icrf object
> ### Aliases: getTree.icrf getTree
> 
> ### ** Examples
> 
> library(survival) # for Surv()
> data(rat2)
> L = ifelse(rat2$tumor, 0, rat2$survtime)
> R = ifelse(rat2$tumor, rat2$survtime, Inf)
> # Note that this is a toy example. Use a larger ntree and nfold in practice.
> ## Don't show: 
> set.seed(2)
> rats.icrf <-
+   icrf(Surv(L, R, type = "interval2") ~ dose.lvl + weight + male + cage.no,
+        data = rat2, ntree = 2, nfold = 2)
Error in icrf.default(m, L, R, ...) : 
  NA/NaN/Inf in foreign function call (arg 50)
Calls: icrf -> icrf.formula -> icrf.default
Execution halted
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.7Mb
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     15.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/ipmisc.Rcheck/00install.out' for details.
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 293
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11385 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11385 (sockconn)
Execution halted
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 284
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11493 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11493 (sockconn)
Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/JavaGD.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      2.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.1Mb
    libs   1.6Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
    proj   5.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   1.7Mb
Package unavailable to check Rd xrefs: 'REBayes'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.6Mb
    libs   1.4Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    R             1.1Mb
    libs         13.9Mb
    mathematica   1.5Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Found the following significant warnings:
  generateData.cpp:105:18: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/3.6/NestedCategBayesImpute.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/network.Rcheck/00install.out' for details.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    CppCode   2.6Mb
    R         6.0Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/nlcv.Rcheck/00install.out' for details.
Running 'testthat.R' [105s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > Sys.setenv("nlmixr_silent"="TRUE")
  > library(testthat)
  > library(nlmixr)
  > 
  > test_check("nlmixr")
  -- 1. Error: parsing functions fix drake compatibility (@test-drake.R#51)  -----
  object 'progress_bar' not found
  Backtrace:
    1. testthat::expect_equal(make(plan, cache = .cache), NULL)
    4. drake::make(plan, cache = .cache)
    6. drake::drake_config(...)
    7. drake:::logger(verbose = verbose, file = log_make)
    8. refclass_logger$new(verbose = verbose, file = file, progress_bar = progress_bar)
    9. methods::new(def, ...)
   11. methods::initialize(value, ...)
   12. methods::initRefFields(.Object, classDef, selfEnv, list(...))
  
  == testthat results  ===========================================================
  [ OK: 253 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: parsing functions fix drake compatibility (@test-drake.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [111s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > Sys.setenv("nlmixr_silent"="TRUE")
  > library(testthat)
  > library(nlmixr)
  > 
  > test_check("nlmixr")
  -- 1. Error: parsing functions fix drake compatibility (@test-drake.R#51)  -----
  object 'progress_bar' not found
  Backtrace:
    1. testthat::expect_equal(make(plan, cache = .cache), NULL)
    4. drake::make(plan, cache = .cache)
    6. drake::drake_config(...)
    7. drake:::logger(verbose = verbose, file = log_make)
    8. refclass_logger$new(verbose = verbose, file = file, progress_bar = progress_bar)
    9. methods::new(def, ...)
   11. methods::initialize(value, ...)
   12. methods::initRefFields(.Object, classDef, selfEnv, list(...))
  
  == testthat results  ===========================================================
  [ OK: 253 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: parsing functions fix drake compatibility (@test-drake.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Warning in system2(command = python, args = paste0("\"", config_script,  :
  running command '"C:/Users/CRAN/AppData/Local/r-miniconda/envs/r-reticulate/python.exe" "d:/RCompile/CRANpkg/lib/3.6/reticulate/config/config.py"' had status 2

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.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs   2.7Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    doc    2.3Mb
    help   2.7Mb
    libs   2.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    lib    5.6Mb
    libs   4.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.3Mb
Running examples in 'penDvine-Ex.R' failed
The error most likely occurred in:

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11817 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11817 (sockconn)
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   1.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/phateR.Rcheck/00install.out' for details.
Running 'testthat.R' [43s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(phenocamapi)
  Loading required package: data.table
  Loading required package: rjson
  Loading required package: RCurl
  > library(data.table)
  > 
  > test_check("phenocamapi")
  trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
  Content type 'application/octet-stream' length 203191 bytes (198 KB)
  ==================================================
  downloaded 198 KB
  
  -- 1. Failure: test getting awb data (@testphenocamapi.R#42)  ------------------
  `wb` not equal to "LIKELY_NO".
  target is NULL, current is character
  
  == testthat results  ===========================================================
  [ OK: 5 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: test getting awb data (@testphenocamapi.R#42) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'getting_started_phenocam_api.Rmd' using rmarkdown
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 203191 bytes (198 KB)
==================================================
downloaded 198 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/2013/05/dukehw_2013_05_31_150331.jpg'
Content type 'image/jpeg' length 470270 bytes (459 KB)
==================================================
downloaded 459 KB

Quitting from lines 282-298 (getting_started_phenocam_api.Rmd) 
Error: processing vignette 'getting_started_phenocam_api.Rmd' failed with diagnostics:
a character vector argument expected
--- failed re-building 'getting_started_phenocam_api.Rmd'

--- re-building 'phenocam_data_fusion.Rmd' using rmarkdown
Loading required package: rjson
Loading required package: RCurl
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 203191 bytes (198 KB)
==================================================
downloaded 198 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/oregonMP/ROI/oregonMP_EN_1000_3day.csv'
Content type 'application/octet-stream' length 269299 bytes (262 KB)
==================================================
downloaded 262 KB

--- finished re-building 'phenocam_data_fusion.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
    libs      1.5Mb
Running 'testthat.R' [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
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  -- 2. Error: See if extractor works (@test_extract_phrases.R#7)  ---------------
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  Currently tagging document 1 of 1 
  Extracting phrases from document 1 of 1 
  == testthat results  ===========================================================
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: See if tagging five documents works, and if coarsening works (@test_POS_tag_documents.R#7) 
  2. Error: See if extractor works (@test_extract_phrases.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.8Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R      6.8Mb
    data   4.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
Found the following significant warnings:
  StandardizeString.cpp:13:25: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/3.6/PPRL.Rcheck/00install.out' for details.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(preText)
  preText: Diagnostics to Assess the Effects of Text Preprocessing Decisions
  Version 0.6.3 created on 2018-01-12.
  copyright (c) 2017, Matthew J. Denny, Penn State University
                      Arthur Spirling, NYU
  Type vignette('getting_started_with_preText') to get started.
  Development website: https://github.com/matthewjdenny/preText
  > 
  > test_check("preText")
  -- 1. Error: Small example works (@test_factorial_preprocessing.R#6)  ----------
  unused argument (alist())
  Backtrace:
   1. documents[1:10, ]
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Small example works (@test_factorial_preprocessing.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc        4.1Mb
    examples   2.6Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       3.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.5Mb
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/randstr.Rcheck/00install.out' for details.
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ratelimitr)
  > 
  > test_check("ratelimitr")
  -- 1. Failure: rate limits still work in face of errors (@test-function-errors.R
  min(times, na.rm = TRUE) is not strictly more than `period`. Difference: -0.008
  
  == testthat results  ===========================================================
  [ OK: 18 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: rate limits still work in face of errors (@test-function-errors.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   3.8Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/Rblpapi.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/RBtest.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.2Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.8Mb
Found the following significant warnings:
  skein_block64.c:226:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.6/RDieHarder.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.7Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is 80.4Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.3Mb
    proj       5.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rglpk.Rcheck/00install.out' for details.
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/rJava.Rcheck/00install.out' for details.
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/3.6/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.6/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 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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rmagic.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/RNAseqNet.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    libs    1.7Mb
    tests   1.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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/3.6/Rserve.Rcheck/00install.out' for details.
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/3.6/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/3.6/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 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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Name: SolrList-class
> ### Title: SolrList
> ### Aliases: class:SolrList SolrList-class length,SolrList-method
> ###   names,SolrList-method [<-,SolrList,ANY,ANY,ANY-method
> ###   [[,SolrList,ANY-method [,SolrList-method [[,SolrList-method
> ###   [[<-,SolrList-method unique,SolrList-method searchDocs
> ###   searchDocs,Solr SolrList coerce,Solr,SolrList-method
> ###   coerce,SolrList,DocCollection-method show,SolrList-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  3.77 0.17 3.95 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    4.4Mb
    libs  17.8Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/rstap.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    Lib  11.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   1.8Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.3Mb
    libs   1.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/scattermore.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/scMappR.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.5Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R   7.2Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    www   8.1Mb
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(simpleCache)
  > 
  > test_check("simpleCache")
  -- 1. Failure: Direct lifespan specification is preferred to background option (
  `t0` not equal to file.info(fp)$ctime.
  1/1 mismatches
  [1] 2020-03-03 16:07:38 - 2020-03-03 16:07:38 == 0.0156 secs
  
  == testthat results  ===========================================================
  [ OK: 66 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Direct lifespan specification is preferred to background option (@test_cache_lifespan.R#123) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/skeleSim.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'SongEvo.Rmd' using rmarkdown
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/3.6/SongEvo.Rcheck/
vign_test/SongEvo/vignettes/SongEvo_files/figure-latex/Examine\%20population\%2
0size\%20over\%20time-1.pdf' not found.

Error: processing vignette 'SongEvo.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/3.6/SongEvo.Rcheck/vign_test/SongEvo/vignettes/SongEvo.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SongEvo.log for more info.
--- failed re-building 'SongEvo.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/StatDA.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.8Mb
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.7Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs     5.7Mb
    mylibs   1.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/tibble.Rcheck/00install.out' for details.
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/treefit.Rcheck/00install.out' for details.
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs  11.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.8Mb
installed size is 82.4Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    extdata   2.3Mb
    gdal      3.9Mb
    libs     69.0Mb
    proj      5.0Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ukpolice)
  > 
  > test_check("ukpolice")
  -- 1. Error: stop_and_search functions work (@test-stop-and-search.R#4)  -------
  HTTP error 502.
  Backtrace:
   1. ukpolice::ukc_stop_search_no_location(...)
   2. ukpolice:::ukc_get_data(query)
   4. jsonlite::fromJSON(paste0(baseurl, query))
   5. jsonlite:::parse_and_simplify(...)
   6. jsonlite:::parseJSON(txt, bigint_as_char)
   7. jsonlite:::parse_con(txt, bigint_as_char)
   9. base::open.connection(con, "rb")
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: stop_and_search functions work (@test-stop-and-search.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 66-94 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
HTTP error 502.
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.6Mb
    libs   2.3Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Error(s) in re-building vignettes:
--- re-building 'wCorrArguments.Rmd' using rmarkdown
Loading required package: knitr
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/3.6/wCorr.Rcheck/vi
gn_test/wCorr/vignettes/wCorrArguments_files/figure-latex/ML\%20RMSE\%20plot-1.
pdf' not found.

Error: processing vignette 'wCorrArguments.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/3.6/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrArguments.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrArguments.log for more info.
--- failed re-building 'wCorrArguments.Rmd'

--- re-building 'wCorrFormulas.Rmd' using rmarkdown
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/3.6/wCorr.Rcheck/vi
gn_test/wCorr/vignettes/wCorrFormulas_files/figure-latex/bias\%20Versus\%20rho-
1.pdf' not found.

Error: processing vignette 'wCorrFormulas.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/3.6/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrFormulas.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrFormulas.log for more info.
--- failed re-building 'wCorrFormulas.Rmd'

SUMMARY: processing the following files failed:
  'wCorrArguments.Rmd' 'wCorrFormulas.Rmd'

Error: Vignette re-building failed.
Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/x13binary.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building ‘aaSEA_Documentation.Rmd’ using rmarkdown
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 RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Warning in normalizePath(f2) :
  path[1]="webshot3f472895632b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot3f472895632b.png': No such file or directory
Quitting from lines 90-91 (aaSEA_Documentation.Rmd) 
Error: processing vignette 'aaSEA_Documentation.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘aaSEA_Documentation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/abcdeFBA.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.3Mb
Namespaces in Imports field not imported from:
  ‘httr’ ‘progress’
  All declared Imports should be used.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R  13.7Mb
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/adamethods.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘adapt_demo.Rmd’ using rmarkdown
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.
Error: processing vignette 'adapt_demo.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘adapt_demo.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.8Mb
    pictures   2.1Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ade4TkGUI.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
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No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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No protocol specified
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.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘filehash’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘amigaDiskFiles.Rmd’ using rmarkdown
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.
Error: processing vignette 'amigaDiskFiles.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘amigaDiskFiles.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/adiv.Rcheck/00install.out’ for details.
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘HiTC’
Package unavailable to check Rd xrefs: ‘HiTC’
Running examples in ‘admisc-Ex.R’ failed
The error most likely occurred in:

> ### Name: Interpret DNF/SOP expressions: compute, simplify, expand, translate
> ### Title: Functions to interpret and manupulate a SOP/DNF expression
> ### Aliases: compute sop simplify expand translate
> ### Keywords: functions
> 
> ### ** Examples
> 
> # -----
> # for compute()
> ## Not run: 
> ##D # make sure the package QCA is loaded
> ##D library(QCA)
> ##D data(LF)
> ##D compute("DEV*~IND + URB*STB", data = LF)
> ##D 
> ##D # calculating individual paths
> ##D compute("DEV*~IND + URB*STB", data = LF, separate = TRUE)
> ## End(Not run)
> 
> 
> # -----
> # for simplify(), also make sure the package QCA is loaded
> simplify("(A + B)(A + ~B)") # result is "A"

Error: Consider creating a truth table first, or formally specify the argument "outcome".

Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘adpss_ex.Rmd’ using rmarkdown
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.
Error: processing vignette 'adpss_ex.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘adpss_ex.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/afCEC.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘afpt-aerodynamic-model.Rmd’ using rmarkdown
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.
Error: processing vignette 'afpt-aerodynamic-model.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘afpt-aerodynamic-model.Rmd’

--- re-building ‘afpt-basic-usage.Rmd’ using rmarkdown
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.
Error: processing vignette 'afpt-basic-usage.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘afpt-basic-usage.Rmd’

--- re-building ‘afpt-multiple-birds.Rmd’ using rmarkdown
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.
Error: processing vignette 'afpt-multiple-birds.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘afpt-multiple-birds.Rmd’

SUMMARY: processing the following files failed:
  ‘afpt-aerodynamic-model.Rmd’ ‘afpt-basic-usage.Rmd’
  ‘afpt-multiple-birds.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘agridat-Ex.R’ failed
The error most likely occurred in:

> ### Name: baker.wheat.uniformity
> ### Title: Uniformity trial of wheat
> ### Aliases: baker.wheat.uniformity
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(baker.wheat.uniformity)
> dat <- baker.wheat.uniformity
> 
> require(desplot)
Loading required package: desplot
Error: package or namespace load failed for ‘desplot’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘stringi’
> desplot(yield ~ col*row, dat,
+         flip=TRUE, aspect=1,
+         main="baker.wheat.uniformity")
Error in desplot(yield ~ col * row, dat, flip = TRUE, aspect = 1, main = "baker.wheat.uniformity") : 
  could not find function "desplot"
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘agridat_data.Rmd’ using rmarkdown
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.
Error: processing vignette 'agridat_data.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘agridat_data.Rmd’

--- re-building ‘agridat_examples.Rmd’ using rmarkdown
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.
Error: processing vignette 'agridat_examples.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘agridat_examples.Rmd’

--- re-building ‘agridat_papadakis.Rmd’ using rmarkdown
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.
Error: processing vignette 'agridat_papadakis.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘agridat_papadakis.Rmd’

SUMMARY: processing the following files failed:
  ‘agridat_data.Rmd’ ‘agridat_examples.Rmd’ ‘agridat_papadakis.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ahn.Rmd’ using rmarkdown
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
--- failed re-building ‘ahn.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Biostrings’
Packages unavailable to check Rd xrefs: ‘Biostrings’, ‘Starr’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/AIG.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ggseas’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/akmedoids.Rcheck/00install.out’ for details.
Package required but not available: ‘org.Hs.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘allelic/libs/allelic.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/alphashape3d.Rcheck/00install.out’ for details.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
No protocol specified
No protocol specified
Error(s) in re-building vignettes:
  ...
--- re-building ‘amen.Rnw’ using knitr
Loading required package: network
network: Classes for Relational Data
Version 1.15 created on 2019-04-01.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.


Execution halted
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/analogueExtra.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/AnalyzeFMRI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/animalTrack.Rcheck/00install.out’ for details.
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    25.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   2.1Mb
Package suggested but not available for checking: ‘rhdf5’
Error(s) in re-building vignettes:
  ...
--- re-building ‘antares.Rmd’ using rmarkdown
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.
--- finished re-building ‘antares.Rmd’

--- re-building ‘antaresH5.Rmd’ using rmarkdown
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 38-72 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘antaresH5.Rmd’

SUMMARY: processing the following file failed:
  ‘antaresH5.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Anthropometry.Rcheck/00install.out’ for details.
installed size is 163.3Mb
  sub-directories of 1Mb or more:
    libs  162.9Mb
Packages suggested but not available for checking: 'Biostrings', 'kebabs'
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
Packages suggested but not available for checking:
  'RGtk2', 'gWidgetsRGtk2', 'cairoDevice'
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/aqr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/archiDART.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘argparse.Rrst’ using knitr
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'argparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
--- failed re-building ‘argparse.Rrst’

SUMMARY: processing the following file failed:
  ‘argparse.Rrst’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘arkhe.Rmd’ using rmarkdown
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.
Warning in normalizePath(f2) :
  path[1]="webshot2f253e2f778e.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot2f253e2f778e.png': No such file or directory
Quitting from lines 46-70 (arkhe.Rmd) 
Error: processing vignette 'arkhe.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘arkhe.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘AffymetrixDataTestFiles’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.2Mb
    testScripts   1.1Mb
Package suggested but not available for checking: ‘affxparser’
Package unavailable to check Rd xrefs: ‘affxparser’
Package suggested but not available for checking: ‘GLAD’
Packages suggested but not available for checking:
  'GLAD', 'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Package unavailable to check Rd xrefs: ‘GLAD’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Arothron.Rcheck/00install.out’ for details.
installed size is 37.9Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    libs  34.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.3Mb
Packages suggested but not available for checking: 'graph', 'Rgraphviz'
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/asbio.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  au.c:375:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int)') with an expression of type 'au_instance_t *(SEXP, float, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int)') [-Wincompatible-pointer-types]
  au.c:376:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int, int)') with an expression of type 'au_instance_t *(SEXP, float, int, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int, int)') [-Wincompatible-pointer-types]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/audio.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Data_Analysis_with_augmentedRCBD.Rmd’ using rmarkdown_notangle
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 57-76 (Data_Analysis_with_augmentedRCBD.Rmd) 
Error: processing vignette 'Data_Analysis_with_augmentedRCBD.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Data_Analysis_with_augmentedRCBD.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
Packages required but not available:
  'org.Hs.eg.db', 'ConsensusClusterPlus', 'clusterProfiler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
Found the following significant warnings:
  Warning: package ‘edgeR’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/babel.Rcheck/00install.out’ for details.
Running examples in ‘babette-Ex.R’ failed
The error most likely occurred in:

> ### Name: prepare_file_creation
> ### Title: Prepare for 'BEAST2' creating files
> ### Aliases: prepare_file_creation
> 
> ### ** Examples
> 
> library(testthat)
> 
> # For a test inference model, the files can be prepared
> inference_model <- create_test_inference_model()
> beast2_options <- create_beast2_options()
> expect_silent(prepare_file_creation(inference_model, beast2_options))
Error in prepare_file_creation(inference_model, beast2_options) : 
  Cannot create file '/Users/urbanek/Library/Caches/beast2_d5a24c974b.xml.state'. 
Maybe no permissions to write there?
Calls: expect_silent ... withCallingHandlers -> withVisible -> eval_bare -> prepare_file_creation
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BACA.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.3Mb
    libs   2.8Mb
Package suggested but not available for checking: ‘pcalg’
Package unavailable to check Rd xrefs: ‘pcalg’
installed size is 67.8Mb
  sub-directories of 1Mb or more:
    libs  66.7Mb
Running ‘test-all.R’ [1s/2s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Need at least two classes to do classification.
  1: samme(activity ~ ., train, test, 3, ntree = 5, trace = F) at /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bagRboostR.Rcheck/bagRboostR/tests/test_samme.R:6
  2: randomForest(formula, data = t, do.trace = trace, ntree = ntree, mtry = mtry)
  3: randomForest.formula(formula, data = t, do.trace = trace, ntree = ntree, mtry = mtry)
  4: randomForest.default(m, y, ...)
  5: stop("Need at least two classes to do classification.")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 39 SKIPPED: 0 FAILED: 1
  1. Error: samme returns a character vector of predicted classes (@test_samme.R#6) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
  Execution halted
Package suggested but not available for checking: ‘philr’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BALCONY.Rcheck/00install.out’ for details.
No protocol specified
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: package ‘edgeR’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BALLI.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: package ‘BiocParallel’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bapred.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.1Mb
    libs   3.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.0Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘article2-vignette.Rnw’ using knitr

Execution halted
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BAT.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BAwiR.Rcheck/00install.out’ for details.
installed size is 53.4Mb
  sub-directories of 1Mb or more:
    libs  51.5Mb
Package required but not available: ‘mritc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 54.1Mb
  sub-directories of 1Mb or more:
    libs  53.3Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  12.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  17.8Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs  13.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   3.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BayesXsrc.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.1Mb
Found the following significant warnings:
  sparseFactor.cpp:33:10: warning: explicitly assigning value of variable of type 'Rcpp::IntegerVector' (aka 'Vector<13>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BClustLonG.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘DNAcopy’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bcROCsurface.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'beadarrayExampleData', 'lumi'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/beadarrayFilter.Rcheck/00install.out’ for details.
Package required but not available: ‘rggobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 69.3Mb
  sub-directories of 1Mb or more:
    libs  67.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘beanz_vignettes.Rmd’ using rmarkdown
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.

Execution halted
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  35.1Mb
installed size is 131.4Mb
  sub-directories of 1Mb or more:
    include  131.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   7.4Mb
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BIGL.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘analysis.Rmd’ using rmarkdown
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.
No protocol specified
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in normalizePath(f2) :
  path[1]="webshot142971fec70e2.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot142971fec70e2.png': No such file or directory
Quitting from lines 245-248 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘analysis.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Rmpi’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      2.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      8.2Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
Package required but not available: ‘csaw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bioacoustics.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘BioCircos.Rmd’ using rmarkdown
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 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘BioCircos.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'BiocStyle', 'BiocVersion'
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Biocomb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BiodiversityR.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.1Mb
Packages required but not available: 'ChemmineR', 'fmcsR', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bios2mds.Rcheck/00install.out’ for details.
Package required but not available: ‘rpanel’

Package suggested but not available for checking: ‘soilphysics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘colorspace’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘deldir’ ‘rgl’ ‘tcltk’ ‘tcltk2’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages suggested but not available for checking: 'GO.db', 'org.Hs.eg.db'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BiSEp.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 53.5Mb
  sub-directories of 1Mb or more:
    libs  51.7Mb
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
Found the following executable file:
  inst/extdata/awt.gri
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is 36.8Mb
  sub-directories of 1Mb or more:
    libs  36.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Packages suggested but not available for checking:
  'graph', 'Rgraphviz', 'gRain'
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
Package suggested but not available for checking: ‘sangerseqR’
installed size is 335.2Mb
  sub-directories of 1Mb or more:
    include    8.5Mb
    lib      326.4Mb
installed size is 75.9Mb
  sub-directories of 1Mb or more:
    libs  75.4Mb
Found the following significant warnings:
  Warning: package ‘mixOmics’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bootsPLS.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘qvalue’
Package unavailable to check Rd xrefs: ‘qvalue’
Running examples in ‘Boptbd-Ex.R’ failed
The error most likely occurred in:

> ### Name: graphoptBbd
> ### Title: Creates the graphical layout of resultant optimal design
> ### Aliases: graphoptBbd
> ### Keywords: Graphical layout
> 
> ### ** Examples
> 
>     ##To create the graphical layout of the D-optimal block design
>     ##obtained using the treatment exchange algorithm for 
>     trt.N <- 10  #Number of treatments
>     blk.N <- 10  #Number of blocks
>     alpha <- 0.1 #alpha value 
>     beta  <- 0.1 #beta value 
>     OptdesF <- rbind(1:10, c(2:10,1)) #Bayesian A-optimal block design (loop design)
> 
>     graphoptBbd(trt.N = 10, blk.N = 10, alpha = 0.1, beta = 0.1, OptdesF, Optcrit = "A")
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "font".
Calls: graphoptBbd ... .tkplot.convert.font -> <Anonymous> -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bpca.Rcheck/00install.out’ for details.
Running examples in ‘bqror-Ex.R’ failed
The error most likely occurred in:

> ### Name: deviance3
> ### Title: Deviance Information Criteria for Ordinal Models with 3 outcomes
> ### Aliases: deviance3
> 
> ### ** Examples
> 
> set.seed(101)
> data("data25j3")
> x <- data25j3$x
> y <- data25j3$y
> p <- 0.25
> ans <- quan_reg3(y, x, mc = 50, p)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: quan_reg3 ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
No protocol specified

(R:60058): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brainKCCA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brainR.Rcheck/00install.out’ for details.
File ‘brainwaver/libs/brainwaver.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘connexity_small_world.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 36.0Mb
  sub-directories of 1Mb or more:
    libs  35.9Mb
Running examples in ‘breathteststan-Ex.R’ failed
The error most likely occurred in:

> ### Name: stan_fit
> ### Title: Bayesian Stan fit to 13C Breath Data
> ### Aliases: stan_fit
> 
> ### ** Examples
> 
> library(breathtestcore)
> suppressPackageStartupMessages(library(dplyr))
> d = breathtestcore::simulate_breathtest_data(n_records = 3) # default 3 records
> data = breathtestcore::cleanup_data(d$data)
> # Use more than 80 iterations and 4 chains for serious fits
> fit = stan_fit(data, chains = 1, iter = 80)
error occurred during calling the sampler; sampling not done
Stan model 'breath_test_1' does not contain samples.
Stan model 'breath_test_1' does not contain samples.
Stan model 'breath_test_1' does not contain samples.
Error in data.frame(pat_group_i = rep(1:n_record, each = chains * iter/2),  : 
  arguments imply differing number of rows: 120, 0
Calls: stan_fit -> data.frame
Execution halted
Running ‘testthat.R’ [6s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  arguments imply differing number of rows: 500, 0
  1: stan_fit(data, dose = dose, student_t_df = student_t_df, chains = chains, iter = iter) at testthat/test_stan_fit_2.R:21
  2: data.frame(pat_group_i = rep(1:n_record, each = chains * iter/2), m = as.vector(rstan::extract(fit, 
         permuted = TRUE, pars = "m")$m), beta = as.vector(rstan::extract(fit, permuted = TRUE, 
         pars = "beta")$beta), k = as.vector(rstan::extract(fit, permuted = TRUE, pars = "k")$k))
  3: stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows), 
         collapse = ", ")), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 7 FAILED: 2
  1. Error: Result with default parameters is tbl_df with required columns (@test_coef_by_group.R#16) 
  2. Error: Data that cannot be fitted with nls_list/nlme work with stan_fit (@test_stan_fit_2.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘hexbin’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'vsn', 'DESeq2', 'pasilla'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Brundle.Rcheck/00install.out’ for details.
installed size is 30.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  28.1Mb
installed size is 94.6Mb
  sub-directories of 1Mb or more:
    libs  93.9Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘simple_plotting.Rmd’ using rmarkdown
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: Removed 4550 rows containing missing values (geom_path).
Quitting from lines 173-174 (simple_plotting.Rmd) 
Error: processing vignette 'simple_plotting.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘simple_plotting.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘examples.Rmd’ using rmarkdown
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.

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: 'c3'

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

    %>%

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

    grid, legend

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.
Warning in normalizePath(f2) :
  path[1]="webshot17f0e554a7ebc.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot17f0e554a7ebc.png': No such file or directory
Quitting from lines 56-65 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘cairoDevice/R/zzz.R’:
  .onLoad calls:
    message("R session is headless; GTK+ not initialized.")

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

No protocol specified
Running examples in ‘cairoDevice-Ex.R’ failed
The error most likely occurred in:

> ### Name: Cairo
> ### Title: The Cairo Graphics Device
> ### Aliases: Cairo Cairo_pdf Cairo_ps Cairo_svg Cairo_png
> ### Keywords: device
> 
> ### ** Examples
> 
> Cairo()

(R:19967): Gdk-CRITICAL **: gdk_screen_get_width: assertion `GDK_IS_SCREEN (screen)' failed

(R:19967): Gdk-CRITICAL **: gdk_screen_get_width_mm: assertion `GDK_IS_SCREEN (screen)' failed

(R:19967): Gdk-CRITICAL **: gdk_screen_get_height: assertion `GDK_IS_SCREEN (screen)' failed

(R:19967): Gdk-CRITICAL **: gdk_screen_get_height_mm: assertion `GDK_IS_SCREEN (screen)' failed

(R:19967): GLib-GObject-WARNING **: invalid (NULL) pointer instance

(R:19967): GLib-GObject-CRITICAL **: g_signal_connect_data: assertion `G_TYPE_CHECK_INSTANCE (instance)' failed

(R:19967): Gtk-CRITICAL **: gtk_window_set_default_size: assertion `width >= -1' failed

(R:19967): Gtk-WARNING **: Screen for GtkWindow not set; you must always set
a screen for a GtkWindow before using the window

(R:19967): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:19967): Gdk-CRITICAL **: gdk_colormap_get_visual: assertion `GDK_IS_COLORMAP (colormap)' failed

(R:19967): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:19967): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:19967): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:19967): Gdk-CRITICAL **: gdk_window_new: assertion `GDK_IS_WINDOW (parent)' failed

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: Cairo()
An irrecoverable exception occurred. R is aborting now ...
Packages suggested but not available for checking:
  'GenomicRanges', 'IRanges', 'S4Vectors'
Package unavailable to check Rd xrefs: ‘GenomicRanges’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.1Mb
Package required and available but unsuitable version: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘limma’
Running examples in ‘caRpools-Ex.R’ failed
The error most likely occurred in:

> ### Name: carpools.hit.overview
> ### Title: Analysis: Analysis of pooled CRISPR screening data using a
> ###   Wilcoxon Test
> ### Aliases: carpools.hit.overview
> ### Keywords: ~Analysis
> 
> ### ** Examples
> 
> data(caRpools)
> 
> data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+   normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
+   control.picks=NULL)
> 
> 
> data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1,
+   fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
+   sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
+   fitType="parametric")
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘GenomeInfoDbData’
Calls: stat.DESeq ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CaRpools.Rmd’ using rmarkdown
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 940-945 (CaRpools.Rmd) 
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
Internal Server Error (HTTP 500).
--- failed re-building ‘CaRpools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘cartograflow.Rmd’ using rmarkdown
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.

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 normalizePath(f2) :
  path[1]="webshot87bf53b79c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot87bf53b79c.png': No such file or directory
Quitting from lines 451-480 (cartograflow.Rmd) 
Error: processing vignette 'cartograflow.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘cartograflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/cati.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.1Mb
    libs      3.2Mb
installed size is 120.7Mb
  sub-directories of 1Mb or more:
    libs  120.4Mb
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
comput: no visible global function definition for ‘cor’
img.estim.regul: no visible global function definition for ‘par’
img.estim.regul: no visible global function definition for ‘image’
img.estim.regul: no visible global function definition for
  ‘heat.colors’
img.estim.regul: no visible global function definition for ‘axis’
img.estim.regul: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘par’
img.matcor: no visible global function definition for ‘image’
img.matcor: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘abline’
img.matcor: no visible global function definition for ‘layout’
loo: no visible global function definition for ‘cor’
matcor: no visible global function definition for ‘cor’
plt.cc: no visible global function definition for ‘par’
plt.cc: no visible global function definition for ‘layout’
plt.indiv: no visible global function definition for ‘plot’
plt.indiv: no visible global function definition for ‘text’
plt.indiv: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘plot’
plt.var: no visible global function definition for ‘points’
plt.var: no visible global function definition for ‘text’
plt.var: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘lines’
rcc: no visible global function definition for ‘var’
rcc: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par plot
  points text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "plot", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
Package suggested but not available for checking: ‘graph’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   5.9Mb
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/changepoint.np.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘pbdMPI’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ChaosGame.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘multtest’
Packages suggested but not available for checking:
  'GenomicInteractions', 'Gviz', 'countreg'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
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.
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘Visualising_Interactions.Rmd’ using rmarkdown
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 41-105 (Visualising_Interactions.Rmd) 
Error: processing vignette 'Visualising_Interactions.Rmd' failed with diagnostics:
there is no package called 'GenomicInteractions'
--- failed re-building ‘Visualising_Interactions.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ComplexHeatmap’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   4.1Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/CleanBSequences.Rcheck/00install.out’ for details.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘getstarted.Rmd’ using rmarkdown
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 77-79 (getstarted.Rmd) 
Error: processing vignette 'getstarted.Rmd' failed with diagnostics:
cannot open the connection to 'https://dane.imgw.pl/data/dane_pomiarowo_obserwacyjne/dane_hydrologiczne/miesieczne/mies_info.txt'
--- failed re-building ‘getstarted.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/clpAPI.Rcheck/00install.out’ for details.
Package required but not available: ‘IsoGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/clusterSim.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘SingleCellExperiment’
Packages suggested but not available for checking:
  'Biobase', 'annotate', 'GO.db', 'moe430a.db'
Package unavailable to check Rd xrefs: ‘Biobase’
Error(s) in re-building vignettes:
  ...
--- re-building ‘clValid.Rnw’ using Sweave
Loading required package: cluster
Read 7 items
Loading required package: Biobase
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Biobase’
Loading required package: RankAggreg
Error: processing vignette 'clValid.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./clValid-022.pdf): PDF inclusion: required page 
does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘clValid.Rnw’

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

Error: Vignette re-building failed.
Execution halted
CMF: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Packages required but not available:
  'InteractionSet', 'GenomicInteractions',
  'BSgenome.Hsapiens.UCSC.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.4Mb
Package suggested but not available for checking: ‘limma’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/colourvision.Rcheck/00install.out’ for details.
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  28.7Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
Packages suggested but not available for checking:
  'inSilicoDb', 'mogene10sttranscriptcluster.db'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/CONDOP.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   11. pins::board_pin_store(...)
   13. pins:::board_pin_create.local(...)
   14. pins:::pin_registry_update(name = name, component = board$name)
   15. pins:::pin_registry_save_entries(entries, component)
   16. yaml::write_yaml(entries, pin_registry_config(component))
   17. base::file(file, "w", encoding = fileEncoding)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 22 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: tbl pin is created w/o error (@test-pins.R#16) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ConsRank.Rcheck/00install.out’ for details.
installed size is 51.1Mb
  sub-directories of 1Mb or more:
    libs  50.0Mb
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ConvergenceConcepts.Rcheck/00install.out’ for details.
Running examples in ‘ConvergenceConcepts-Ex.R’ failed
The error most likely occurred in:

> ### Name: investigate
> ### Title: Investigate examples and exercises from the paper
> ### Aliases: investigate
> ### Keywords: dplot iplot distribution htest
> 
> ### ** Examples
> 
> investigate()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: investigate ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/CoopGame.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/cops.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.0Mb
Package suggested but not available for checking: ‘ProData’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/corregp.Rcheck/00install.out’ for details.
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.8Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/CovTools.Rcheck/00install.out’ for details.
No protocol specified
prepare_Rd: RGL: unable to open X11 display
prepare_Rd: 'rgl_init' failed, running with rgl.useNULL = TRUE
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/cplexAPI.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
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 399-421 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Packages suggested but not available for checking:
  'AnnotationDbi', 'org.Hs.eg.db', 'clusterProfiler'
Error(s) in re-building vignettes:
--- re-building ‘case_study.Rmd’ using rmarkdown
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.
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.22.0 (2018-04-21) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

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

    getClasses, getMethods

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

    attach, detach, gc, load, save

R.utils v2.8.0 successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

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

    timestamp

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

    cat, commandArgs, getOption, inherits, isOpen, nullfile,
    parse, warnings


Attaching package: 'igraph'

The following object is masked from 'package:R.oo':

    hierarchy

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

    decompose, spectrum

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

    union

Quitting from lines 32-41 (case_study.Rmd) 
Error: processing vignette 'case_study.Rmd' failed with diagnostics:
there is no package called 'AnnotationDbi'
--- failed re-building ‘case_study.Rmd’

--- re-building ‘using_cRegulome.Rmd’ using rmarkdown
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.
Picking joint bandwidth of 0.0445
--- finished re-building ‘using_cRegulome.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/crs.Rcheck/00install.out’ for details.
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  23.4Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
Running examples in ‘ctDNAtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_mutations_read_counts
> ### Title: Counts ref and alt reads for a set of mutations
> ### Aliases: get_mutations_read_counts
> 
> ### ** Examples
> 
> data("mutations", package = "ctDNAtools")
> bamT1 <- system.file("extdata", "T1.bam", package = "ctDNAtools")
> get_mutations_read_counts(mutations = mutations[1:3, ], bam = bamT1)
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘GenomeInfoDbData’
Calls: get_mutations_read_counts ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    5. base::getNamespace(ns)
    6. base::loadNamespace(name)
    9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   13. base:::withOneRestart(expr, restarts[[1L]])
   14. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: (unknown) (@test-ctDNAtest.R#3) 
  2. Error: (unknown) (@test-fragment_size.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ctDNAtools.Rmd’ using rmarkdown
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 42-69 (ctDNAtools.Rmd) 
Error: processing vignette 'ctDNAtools.Rmd' failed with diagnostics:
there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
--- failed re-building ‘ctDNAtools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 93.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  90.8Mb
Package which this enhances but not available for checking: ‘pbdMPI’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/cubing.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/curvHDR.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘RGtk2’
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.0Mb
    libs   4.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘cycling_data_analysis.Rmd’ using rmarkdown
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 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘cycling_data_analysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
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 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/dartR.Rcheck/00install.out’ for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   3.5Mb
Package required but not available: ‘gWidgets2RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘get_started.Rmd’ using rmarkdown
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 26-34 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘get_started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 60.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  57.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘applications.Rmd’ using rmarkdown
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.
--- finished re-building ‘applications.Rmd’

--- re-building ‘data.tree.Rmd’ using rmarkdown
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.
Warning in normalizePath(f2) :
  path[1]="webshot157e81cd7762b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot157e81cd7762b.png': No such file or directory
Quitting from lines 513-516 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘data.tree.Rmd’

SUMMARY: processing the following file failed:
  ‘data.tree.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘gWidgetsRGtk2’
Package required but not available: ‘SDD’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 42.4Mb
  sub-directories of 1Mb or more:
    libs  42.2Mb
Package suggested but not available for checking: ‘WGCNA’
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
Error(s) in re-building vignettes:
--- re-building ‘RC_units.Rmd’ using rmarkdown
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.
--- finished re-building ‘RC_units.Rmd’

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

--- re-building ‘sjukhus.Rmd’ using rmarkdown
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.
Joining, by = "key"
Joining, by = "key"
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 102-122 (sjukhus.Rmd) 
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sjukhus.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘delayed.Rmd’ using rmarkdown
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 97-98 (delayed.Rmd) 
Error: processing vignette 'delayed.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘delayed.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 66.2Mb
  sub-directories of 1Mb or more:
    libs  63.6Mb
Package unavailable to check Rd xrefs: ‘WGCNA’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/depth.Rcheck/00install.out’ for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.5Mb
    libs   3.1Mb
Running examples in ‘DescTools-Ex.R’ failed
The error most likely occurred in:

> ### Name: VanWaerdenTest
> ### Title: van der Waerden Test
> ### Aliases: VanWaerdenTest VanWaerdenTest.default VanWaerdenTest.formula
> ### Keywords: htest
> 
> ### ** Examples
> 
> ## Hollander & Wolfe (1973), 116.
> ## Mucociliary efficiency from the rate of removal of dust in normal
> ##  subjects, subjects with obstructive airway disease, and subjects
> ##  with asbestosis.
> x <- c(2.9, 3.0, 2.5, 2.6, 3.2) # normal subjects
> y <- c(3.8, 2.7, 4.0, 2.4)      # with obstructive airway disease
> z <- c(2.8, 3.4, 3.7, 2.2, 2.0) # with asbestosis
> 
> VanWaerdenTest(list(x, y, z))
Error in deparse1(substitute(x)) : could not find function "deparse1"
Calls: VanWaerdenTest -> VanWaerdenTest.default
Execution halted
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rsymphony'
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DEVis.Rcheck/00install.out’ for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.6Mb
installed size is 52.9Mb
  sub-directories of 1Mb or more:
    libs  52.5Mb
Package required but not available: ‘ALL’

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

Package suggested but not available for checking: ‘org.Hs.eg.db’

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

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DGVM3D.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DiceView.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DiffusionRgqd.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DiffusionRimp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DiffusionRjgqd.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
Error(s) in re-building vignettes:
--- re-building ‘Part_1_Introduction.Rmd’ using rmarkdown
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.
--- finished re-building ‘Part_1_Introduction.Rmd’

--- re-building ‘Part_2_Transition_Densities.Rmd’ using rmarkdown
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 176-185 (Part_2_Transition_Densities.Rmd) 
Error: processing vignette 'Part_2_Transition_Densities.Rmd' failed with diagnostics:
there is no package called 'DiffusionRgqd'
--- failed re-building ‘Part_2_Transition_Densities.Rmd’

--- re-building ‘Part_3_Bivariate_Diffusions.Rmd’ using rmarkdown
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.
--- finished re-building ‘Part_3_Bivariate_Diffusions.Rmd’

--- re-building ‘DiffusionRjgqd_Paper.pdf.asis’ using asis
--- finished re-building ‘DiffusionRjgqd_Paper.pdf.asis’

--- re-building ‘DiffusionRjgqd_RepMaterials.html.asis’ using asis
--- finished re-building ‘DiffusionRjgqd_RepMaterials.html.asis’

--- re-building ‘Part_4_Likelihood_Inference.html.asis’ using asis
--- finished re-building ‘Part_4_Likelihood_Inference.html.asis’

SUMMARY: processing the following file failed:
  ‘Part_2_Transition_Densities.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Package suggested but not available for checking: ‘pcaL1’
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Directional.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/directPA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DirichletReg.Rcheck/00install.out’ for details.
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Error(s) in re-building vignettes:
--- re-building ‘brt.Rnw’ using Sweave
Loading required package: raster
Loading required package: sp
Loading required namespace: gbm
fitting final gbm model with a fixed number of 600 trees for Angaus
fitting final gbm model with a fixed number of 1800 trees for Angaus
gbm.simplify - version 2.9 
simplifying gbm.step model for Angaus with 11 predictors and 1000 observations 
original deviance = 0.6743(0.0269)
a fixed number of 5 drops will be tested
creating initial models...
dropping predictor: 1 2 3 4 5
processing final dropping of variables with full data
1-DSDam
2-SegLowFlow
3-USAvgT
4-SegTSeas
5-DSMaxSlope
fitting final gbm model with a fixed number of 1300 trees for Angaus
gbm.interactions - version 2.9
Cross tabulating interactions for gbm model with 11 predictors
1 2 3 4 5 6 7 8 9 10 
maximum value = 0.58


Error: processing vignette 'brt.Rnw' failed with diagnostics:
 chunk 12 (label = dismo-10) 
Error in library(gbm) : there is no package called ‘gbm’

--- failed re-building ‘brt.Rnw’

--- re-building ‘sdm.Rnw’ using Sweave
Loading required package: raster
Loading required package: sp
Checking rgeos availability: TRUE
Loading required namespace: XML
REQUEST_DENIED:Ayacucho+P.+Huamanga+Minas+Ckucho,Peru
REQUEST_DENIED:Ayacucho+P.+Huamanga+Minas+Ckucho,Peru
REQUEST_DENIED:Ayacucho+P.+Huamanga+Minas+Ckucho,Peru
REQUEST_DENIED:Ayacucho+P.+Huamanga+Minas+Ckucho,Peru
Loading required namespace: rgeos
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Warning in randomForest.default(m, y, ...) :
  The response has five or fewer unique values.  Are you sure you want to do regression?

Attaching package: ‘kernlab’

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

    buffer, rotated

Loading required namespace: gstat
Loading required namespace: deldir
--- finished re-building ‘sdm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Biobase’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DiversityOccupancy.Rcheck/00install.out’ for details.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include  16.2Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   3.6Mb
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DNLC.Rcheck/00install.out’ for details.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   9.2Mb
Package unavailable to check Rd xrefs: ‘doMPI’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/dpcR.Rcheck/00install.out’ for details.
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DRomics.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/drugCombo.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘userGuide.Rmd’ using rmarkdown
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.
No protocol specified
Warning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
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.
Warning in normalizePath(f2) :
  path[1]="webshot219036569873.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot219036569873.png': No such file or directory
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘userGuide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Designing-33PC.Rmd’ using rmarkdown
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 163-164 (Designing-33PC.Rmd) 
Error: processing vignette 'Designing-33PC.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Designing-33PC.Rmd’

SUMMARY: processing the following file failed:
  ‘Designing-33PC.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/dti.Rcheck/00install.out’ for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.8Mb
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs  23.3Mb
Running ‘testthat.R’ [36s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ── 2. Error: Perform dimred dm_destiny  ────────────────────────────────────────
  Please install the following packages: 
    "destiny"
  Backtrace:
   1. dyndimred:::method_fun(small_expr)
   2. dynutils::install_packages("destiny")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 191 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 2 ]
  1. Error: Perform dimred dm_destiny 
  2. Error: Perform dimred dm_destiny 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
    libs   2.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Package suggested but not available for checking: ‘dyndimred’
Package unavailable to check Rd xrefs: ‘dyndimred’
Running ‘testthat.R’ [85s/84s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   3. base::getExportedValue(pkg, name)
   4. base::asNamespace(ns)
   5. base::getNamespace(ns)
   6. base::loadNamespace(name)
   7. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8. base:::withOneRestart(expr, restarts[[1L]])
   9. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1269 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: Testing add_dimred including calculation of dimred (@test-wrap_add_dimred.R#110) 
  2. Error: Test get_dimred (@test-wrap_add_dimred.R#278) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs        8.4Mb
    shiny_app   1.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.7Mb
Running examples in ‘ebirdst-Ex.R’ failed
The error most likely occurred in:

> ### Name: compute_ppms
> ### Title: Computes the Predictive Performance Metrics for a spatiotemporal
> ###   extent
> ### Aliases: compute_ppms
> 
> ### ** Examples
> 
> # download and load example data
> sp_path <- ebirdst_download("example_data", tifs_only = FALSE)
Warning in dir.create(path, recursive = TRUE) :
  cannot create dir '/Users/urbanek/Library/Application Support/ebirdst', reason 'Read-only file system'
Warning in utils::download.file(s3_files$s3_path[i], s3_files$local_path[i],  :
  URL https://ebirdst-data.s3.amazonaws.com/yebsap-ERD2018-EBIRD_SCIENCE-20191030-3abe59ca-example/data/yebsap-ERD2018-EBIRD_SCIENCE-20191030-3abe59ca-example_srd_raster_template.tif: cannot open destfile '/Users/urbanek/Library/Application Support/ebirdst/yebsap-ERD2018-EBIRD_SCIENCE-20191030-3abe59ca-example/data/yebsap-ERD2018-EBIRD_SCIENCE-20191030-3abe59ca-example_srd_raster_template.tif', reason 'No such file or directory'
Warning in utils::download.file(s3_files$s3_path[i], s3_files$local_path[i],  :
  download had nonzero exit status
Error in ebirdst_download("example_data", tifs_only = FALSE) : 
  Error downloading files from AWS S3
Execution halted
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   1. ebirdst::ebirdst_download("example_data", tifs_only = FALSE)
  
  ── 3. Error: (unknown) (@test_ppms.R#3)  ───────────────────────────────────────
  Error downloading files from AWS S3
  Backtrace:
   1. ebirdst::ebirdst_download("example_data", tifs_only = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 1 | WARNINGS: 9 | FAILED: 3 ]
  1. Error: (unknown) (@test_loading.R#3) 
  2. Error: (unknown) (@test_plotting.R#3) 
  3. Error: (unknown) (@test_ppms.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: package ‘edgeR’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/edgeRun.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/edrGraphicalTools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/eegkit.Rcheck/00install.out’ for details.
installed size is 75.5Mb
  sub-directories of 1Mb or more:
    libs  74.9Mb
Package suggested but not available for checking: ‘BiocStyle’
Error(s) in re-building vignettes:
--- re-building ‘EHRtemporalVariability.Rmd’ using rmarkdown
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.
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

Joining, by = "diagcode1"
Warning: Column `diagcode1` joining factor and character vector, coercing into character vector
# Missing values: 0 cases ( 0%)
# External causes codes: 0 cases ( 0%)
# V codes not mapped: 74330 cases ( 22.82%)
# Total ICD9-CM codes mapped: 146262 cases ( 44.9%)
# Unique ICD9-CM codes mapped: 3020
# Total PheWAS codes: 757
# ICD9 codes not mapped: 105180 cases ( 32.29%)
Quitting from lines 317-322 (EHRtemporalVariability.Rmd) 
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘EHRtemporalVariability.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘elementR-Ex.R’ failed
The error most likely occurred in:

> ### Name: elementR_project
> ### Title: Object elementR_project
> ### Aliases: elementR_project
> 
> ### ** Examples
> 
> ## create a new elementR_repStandard object based on the "filePath" 
> ## from a folder containing sample replicate
> 
> filePath <- system.file("Example_Session", package="elementR")
> 
> exampleProject <- elementR_project$new(filePath)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: <Anonymous> ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Packages suggested but not available for checking:
  'hgu133plus2.db', 'lumi', 'GO.db'
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  11.2Mb
Running examples in ‘EmiStatR-Ex.R’ failed
The error most likely occurred in:

> ### Name: CInp2TS
> ### Title: Function to convert Constant Input to Time Series
> ### Aliases: CInp2TS
> ### Keywords: CInp2TS
> 
> ### ** Examples
> 
> library(EmiStatR)
> library(zoo)

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

> 
> data("Esch_Sure2010")
> data("qs_factor")
> 
> cinp            <- 150 # water consumption [m3/h]
> prec            <- Esch_Sure2010[1:1000,] # selecting just the first 1,000 rows
> 
> cinp.daily.file <- qs_factor
> cinp.weekly     <- list(mon=1, tue=.83, wed=.83, thu=.83, fri=1, sat=1.25, sun=1.25)  
> # factors average to 1
> cinp.seasonal   <- list(jan=.79, feb=.79, mar=1.15, apr=1.15, may=1.15, jun=1.15,
+                         jul=1.15, aug=1.15, sep=1.15, oct=1.15, nov=.79, dec=.79) 
> # factors average to 1
> ts1 <- CInp2TS(cinp, prec, cinp.daily.file, cinp.weekly, cinp.seasonal)
Error in `[.xts`(cinp.ts.deltap, 1:nrow(P1), ) : subscript out of bounds
Calls: CInp2TS -> [ -> [.xts
Execution halted
Package suggested but not available for checking: ‘taxadb’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/EMMIXcskew.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/empiricalFDR.DESeq2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/emstreeR.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘epicontacts.Rmd’ using rmarkdown
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.
Warning in normalizePath(f2) :
  path[1]="webshotb53a10875b16.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotb53a10875b16.png': No such file or directory
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘epicontacts.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epiflows-class.Rmd’ using rmarkdown
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.
--- finished re-building ‘epiflows-class.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
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 117-120 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EpiReport_Vignette.Rmd’ using rmarkdown
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 367-368 (EpiReport_Vignette.Rmd) 
Error: processing vignette 'EpiReport_Vignette.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
--- failed re-building ‘EpiReport_Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   1.8Mb
Package required but not available: ‘rpanel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Errors in running code in vignettes:
when running code in ‘ESEA.Rnw’
  ...

> PathwayNetwork <- Results[[2]][[1]]

> SavePathway2File(PathwayNetwork, layout = layout.circle, 
+     file = "Graph")
[1] "...writing to file"

  When sourcing ‘ESEA.R’:
Error: there is no package called ‘graph’
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ESEA.Rnw’ using Sweave
Loading required package: igraph

Attaching package: ‘igraph’

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

    decompose, spectrum

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

    union

Loading required package: XML
Loading required package: parmigene

Error: processing vignette 'ESEA.Rnw' failed with diagnostics:
 chunk 11 
Error in loadNamespace(name) : there is no package called ‘graph’

--- failed re-building ‘ESEA.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/etasFLP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  gradHess.cpp:27:7: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
  gradHess.cpp:69:7: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
  gradHess.cpp:119:7: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/evgam.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Evomorph.Rcheck/00install.out’ for details.
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    exiftool  13.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ExomeDepth.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Malformed Description field: should contain one or more complete sentences.
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.4Mb
Running ‘runit.R’ [35s/58s]
Running the tests in ‘tests/runit.R’ failed.
Last 13 lines of output:
  test_touch: (1 checks) ... OK (2.01 seconds)
  --------------------------- 
  Test file: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fakemake.Rcheck/fakemake/runit_tests/runit-throw.R 
  test_exception: (1 checks) ... OK (0 seconds)
  --------------------------- 
  Test file: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fakemake.Rcheck/fakemake/runit_tests/runit-xmake.R 
  test_make_full_tree: (4 checks) ... OK (0.03 seconds)
  test_make_missing: (2 checks) ... OK (0.02 seconds)
  test_make_newer: (2 checks) ... OK (1.04 seconds)
  test_make_phony: (3 checks) ... OK (2.04 seconds)
  test_make_prerequisite: (3 checks) ... OK (1.04 seconds)
  test_make_sink: (2 checks) ... OK (0.01 seconds)
  test_make_source_files: (0 checks) ... OK (0 seconds)
  Error: RUnit failed.
  Execution halted
Found the following significant warnings:
  Warning: ‘i’ is used uninitialized in this function [-Wuninitialized]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fAsianOptions.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.1Mb
installed size is 42.3Mb
  sub-directories of 1Mb or more:
    libs  42.1Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  16.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.5Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      6.9Mb
Packages suggested but not available for checking: 'DESeq2', 'destiny'
Error(s) in re-building vignettes:
  ...
--- re-building ‘FateID.Rmd’ using rmarkdown
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 141-142 (FateID.Rmd) 
Error: processing vignette 'FateID.Rmd' failed with diagnostics:
there is no package called 'destiny'
--- failed re-building ‘FateID.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/FcircSEC.Rcheck/00install.out’ for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is 39.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  36.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fdaPDE.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fdasrvf.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
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.
Loading required package: rainbow
Loading required package: MASS
Loading required package: pcaPP
Loading required package: RCurl
Loading required package: bitops

Execution halted
Packages required and available but unsuitable versions: 'stats', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘test-as-dgCMatrix.R’ [2s/2s]
  Running ‘test-empty_array.R’ [2s/2s]
  Running ‘test-existence_collision.R’ [2s/2s]
  Running ‘test-hash.mapping.R’ [2s/2s]
  Running ‘test-hashing.R’ [2s/2s]
Running the tests in ‘tests/test-hashing.R’ failed.
Last 13 lines of output:
  +     if (class(e)[1] != "std::invalid_argument") stop(e)
  +     if (conditionMessage(e) != "Failed to find the column:PlAnT") stop(e)
  +   })
  +   
  +   m <- hashed.model.matrix(~ Plant:Type:Treatment, CO2, create.mapping = TRUE, signed.hash = TRUE)
  +   map <- hash.mapping(m)
  +   map <- map[grepl("\\w+:\\w+:\\w+", names(map))]
  +   checkTrue(all(hashed.interaction.value(names(map)) %% (2^18) + 1== map),
  +             "The hashed.interaction.value gives inconsistent result of hashed.model.matrix")
  + }
  Loading required package: RUnit
  Error in .hashed.model.matrix.dataframe(tf, data, hash.size, transpose,  : 
    c++ exception (unknown reason)
  Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/feature.Rcheck/00install.out’ for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/FieldSim.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘EML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fingerPro.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘quick_charts.Rmd’ using rmarkdown
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.

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 normalizePath(f2) :
  path[1]="webshot114e76fe61b6d.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot114e76fe61b6d.png': No such file or directory
Quitting from lines 125-134 (quick_charts.Rmd) 
Error: processing vignette 'quick_charts.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘quick_charts.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lifeExpectancy.Rmd’ using rmarkdown
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 76-77 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘lifeExpectancy.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.5Mb
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fit4NM.Rcheck/00install.out’ for details.
No protocol specified
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(R:12455): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
'library' or 'require' calls to packages already attached by Depends:
  ‘RGtk2’ ‘cairoDevice’ ‘gWidgets’ ‘gWidgetsRGtk2’ ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
No protocol specified
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(R:12463): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
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(R:12471): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
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(R:12479): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
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(R:12539): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
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(R:12547): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
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(R:12555): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
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(R:12563): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
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(R:12577): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
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.
Running examples in ‘fit4NM-Ex.R’ failed
The error most likely occurred in:

> ### Name: fit4NM
> ### Title: Platform for NONMEM
> ### Aliases: fit4NM
> ### Keywords: utilities
> 
> ### ** Examples
> 
> fit4NM()

(R:12602): GLib-GObject-WARNING **: invalid (NULL) pointer instance

(R:12602): GLib-GObject-CRITICAL **: g_signal_connect_data: assertion `G_TYPE_CHECK_INSTANCE (instance)' failed

(R:12602): Gtk-WARNING **: Screen for GtkWindow not set; you must always set
a screen for a GtkWindow before using the window

(R:12602): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:12602): Gdk-CRITICAL **: gdk_colormap_get_visual: assertion `GDK_IS_COLORMAP (colormap)' failed

(R:12602): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:12602): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:12602): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:12602): Gdk-CRITICAL **: gdk_window_new: assertion `GDK_IS_WINDOW (parent)' failed

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: .RGtkCall("S_gtk_widget_show", object, PACKAGE = "RGtk2")
 2: method(obj, ...)
 3: window$Show()
 4: .gwindow(toolkit, title, visible, width, height, parent, handler,     action, ...)
 5: .gwindow(toolkit, title, visible, width, height, parent, handler,     action, ...)
 6: gwindow("GUI for NONMEM", width = 850, height = 300)
 7: fit4NM()
An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Warning in engine$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 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

SUMMARY: processing the following file failed:
  ‘fitbitScraper-examples.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   2.9Mb
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/float.Rcheck/00install.out’ for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
installed size is 48.0Mb
  sub-directories of 1Mb or more:
    libs  46.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_fontHind.Rmd’ using rmarkdown
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 38-49 (Using_fontHind.Rmd) 
Error: processing vignette 'Using_fontHind.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Using_fontHind.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_fontMPlus.Rmd’ using rmarkdown
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 56-67 (Using_fontMPlus.Rmd) 
Error: processing vignette 'Using_fontMPlus.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Using_fontMPlus.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/foodweb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ForImp.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘formattable-data-frame.Rmd’ using rmarkdown
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 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘formattable-data-frame.Rmd’

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

SUMMARY: processing the following file failed:
  ‘formattable-data-frame.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-formulaic.Rmd’ using rmarkdown
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 127-132 (Introduction-to-formulaic.Rmd) 
Error: processing vignette 'Introduction-to-formulaic.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Introduction-to-formulaic.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction-to-formulaic.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘seasonal’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   4.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Found the following significant warnings:
  c_hd_mf.cpp:157:12: warning: explicitly assigning value of variable of type 'Eigen::VectorXd' (aka 'Matrix<double, Dynamic, 1>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/FRegSigCom.Rcheck/00install.out’ for details.
installed size is 61.7Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs  59.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   6.0Mb
Package unavailable to check Rd xrefs: ‘frm’
installed size is 40.5Mb
  sub-directories of 1Mb or more:
    libs  40.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/frontiles.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fsbrain.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [8s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 69 | SKIPPED: 15 | WARNINGS: 2553 | FAILED: 37 ]
  1. Error: A label can be extracted from a region of a loaded annotation (@test-atlas.R#3) 
  2. Error: A label can be extracted from a region of an annotation file (@test-atlas.R#31) 
  3. Error: Labels can be extracted from a region of an annotation file for a group of subjects (@test-atlas.R#43) 
  4. Error: Loading of native space whole brain morph data on group level works (@test-fsdir-abstraction-group.R#3) 
  5. Error: Loading of native space whole brain morph data restricted to the cortex on group level works (@test-fsdir-abstraction-group.R#29) 
  6. Error: Loading of standard space whole brain morph data on group level works (@test-fsdir-abstraction-group.R#57) 
  7. Error: Label data can be read on group level (@test-fsdir-abstraction-group.R#79) 
  8. Error: Annotation data can be read on group level (@test-fsdir-abstraction-group.R#97) 
  9. Error: Loading of native space whole brain morph data on subject level works (@test-fsdir-abstraction-subject.R#3) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fulltext.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘futureheatwaves.Rmd’ using rmarkdown
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 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘futureheatwaves.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘chart_themes.Rmd’ using rmarkdown
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.
g3viz: visualizing gene/genome/gentics data for fun.
Any questions, please send emails to <g3viz.group@gmail.com>
Please send questions to cbioportal@googlegroups.com
Quitting from lines 48-58 (chart_themes.Rmd) 
Error: processing vignette 'chart_themes.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘chart_themes.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
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.
g3viz: visualizing gene/genome/gentics data for fun.
Any questions, please send emails to <g3viz.group@gmail.com>
Quitting from lines 103-114 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘chart_themes.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ArrayBin’
Package which this enhances but not available for checking: ‘doMPI’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.9Mb
installed size is 79.9Mb
  sub-directories of 1Mb or more:
    libs  79.5Mb
installed size is 58.9Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     55.6Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  14.9Mb
Packages suggested but not available for checking:
  'classGraph', 'graph', 'Rgraphviz'
installed size is 170.2Mb
  sub-directories of 1Mb or more:
    L8NY18    2.2Mb
    libs    166.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/gdimap.Rcheck/00install.out’ for details.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Running ‘testthat.R’ [6s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("genBaRcode")
  ── 1. Error: (unknown) (@test_raw_data_functions.R#3)  ─────────────────────────
  package 'GenomeInfoDb' could not be loaded
  Backtrace:
   1. base::library(ShortRead)
   2. base::.getRequiredPackages2(pkgInfo, quietly = quietly)
   3. base::library(...)
   4. base::.getRequiredPackages2(pkgInfo, quietly = quietly)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 17 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 1 ]
  1. Error: (unknown) (@test_raw_data_functions.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘genBaRcode_GUI_Vignette.Rmd’ using rmarkdown
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.
--- finished re-building ‘genBaRcode_GUI_Vignette.Rmd’

--- re-building ‘genBaRcode_Vignette.Rmd’ using rmarkdown
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 155-176 (genBaRcode_Vignette.Rmd) 
Error: processing vignette 'genBaRcode_Vignette.Rmd' failed with diagnostics:
there is no package called 'GenomeInfoDbData'
--- failed re-building ‘genBaRcode_Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [9s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] "clustering genes from baseline samples normalized to mean..."
  [1] "clustering genes from all samples normalized to mean..."
  [1] "clustering genes from all samples normalized to baseline..."
  [1] "clustering genes from baseline samples normalized to mean..."
  [1] "clustering genes from baseline samples normalized to controls..."
  [1] "clustering genes from all samples normalized to mean..."
  [1] "clustering genes from all samples normalized to controls..."
  [1] "clustering genes from all samples normalized to baseline..."
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 134 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 2 ]
  1. Error: genModelResults outputs correctly for one comparison (@test_genModelResults.R#64) 
  2. Error: genModelResults outputs correctly for multiple comparisons (@test_genModelResults.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GENEAsphere.Rcheck/00install.out’ for details.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/geno2proteo.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'KEGG.db', 'reactome.db', 'AnnotationDbi'
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/gensphere.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/geoelectrics.Rcheck/00install.out’ for details.
Output for data("sinkhole", package = "geoelectrics"):
  Warning messages:
  1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
  2: 'rgl_init' failed, running with rgl.useNULL = TRUE
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   4.0Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R         8.8Mb
    extdata   1.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/geomorph.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   4.9Mb
Package required and available but unsuitable version: ‘parallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [33s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(getCRUCLdata)
  > 
  > test_check("getCRUCLdata")
  ── 1. Failure: cache directory is created if necessary (@test_caching.R#29)  ───
  dir.exists(manage_cache$cache_path_get()) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 23 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: cache directory is created if necessary (@test_caching.R#29) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘RGtk2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘IntroductionToGFD.Rmd’ using rmarkdown
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 106-107 (IntroductionToGFD.Rmd) 
Error: processing vignette 'IntroductionToGFD.Rmd' failed with diagnostics:
there is no package called 'RGtk2'
--- failed re-building ‘IntroductionToGFD.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GFORCE.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GGEBiplotGUI.Rcheck/00install.out’ for details.
Running examples in ‘GGEBiplotGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: GGEBiplot
> ### Title: GGEBiplotGUI: Interactive GGE Biplots in R
> ### Aliases: GGEBiplot
> 
> ### ** Examples
> 
> data(Ontario)
> GGEBiplot(Data = Ontario)
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: GGEBiplot ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Switching to 'nipals' method.
  Missing values detected: (3%)
  Missing values detected: (3%)
  Switching to 'nipals' method.
  Missing values detected: (3%)
  Switching to 'nipals' method.
  ── 1. Failure: rgl works (@test_gge.R#162)  ────────────────────────────────────
  `{ ... }` produced warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 14 SKIPPED: 0 FAILED: 1
  1. Failure: rgl works (@test_gge.R#162) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  18.7Mb
Error(s) in re-building vignettes:
--- re-building ‘ggPredict.Rmd’ using rmarkdown
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.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra

Attaching package: 'ggiraphExtra'

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

    addLabelDf, getMapping

Loading required package: plyr
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 45-49 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘ggPredict.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
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.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
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.
Warning in normalizePath(f2) :
  path[1]="webshot8a65240e95b5.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot8a65240e95b5.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘ggPredict.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘gglogo-alphabet.Rmd’ using rmarkdown
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.

Attaching package: 'gglogo'

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

    fortify

Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Quitting from lines 45-52 (gglogo-alphabet.Rmd) 
Error: processing vignette 'gglogo-alphabet.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building ‘gglogo-alphabet.Rmd’

SUMMARY: processing the following file failed:
  ‘gglogo-alphabet.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.2Mb
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
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.

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: Matrix
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 185-186 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 64.5Mb
  sub-directories of 1Mb or more:
    libs  63.4Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    libs  40.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rnw’ using knitr
--- finished re-building ‘intro.Rnw’

--- re-building ‘parallel.Rnw’ using knitr

Execution halted
SUMMARY: processing the following file failed:
  ‘parallel.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 43.8Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb
installed size is 63.7Mb
  sub-directories of 1Mb or more:
    doc         1.1Mb
    libs       60.3Mb
    test_data   1.2Mb
glmulti,character-character-ANY-ANY: no visible global function
  definition for ‘regsubsets’
Undefined global functions or variables:
  regsubsets
Running examples in ‘glue-Ex.R’ failed
The error most likely occurred in:

> ### Name: glue_sql
> ### Title: Interpolate strings with SQL escaping
> ### Aliases: glue_sql glue_data_sql
> 
> ### ** Examples
> 
> con <- DBI::dbConnect(RSQLite::SQLite(), ":memory:")
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘digest’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GMMAT.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/gMOIP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Evaluation.cpp:173:9: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/gnmf.Rcheck/00install.out’ for details.
File ‘gnmf/libs/gnmf.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GPareto.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GPGame.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GPoM.FDLyapu.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GPoM.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘gprofiler2.Rmd’ using rmarkdown
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 239-240 (gprofiler2.Rmd) 
Error: processing vignette 'gprofiler2.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘gprofiler2.Rmd’

SUMMARY: processing the following file failed:
  ‘gprofiler2.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 48.5Mb
  sub-directories of 1Mb or more:
    libs  46.0Mb
Running ‘testthat.R’ [68s/77s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 3096 | SKIPPED: 309 | WARNINGS: 0 | FAILED: 25 ]
  1. Error: gpuMatrix Double Precision Matrix-Vector multiplication (@test_gpuMatrix_algebra.R#840) 
  2. Error: gpuMatrix Integer Precision Sum (@test_gpuMatrix_row_col.R#41) 
  3. Error: gpuMatrix Double Precision Sum (@test_gpuMatrix_row_col.R#67) 
  4. Error: gpuMatrix Double Precision Block Sum (@test_gpuMatrix_row_col.R#400) 
  5. Error: gpuVector Double precision tcrossprod (@test_gpuVector_algebra.R#607) 
  6. Error: Switching GPUs vclMatrix Double Precision Matrix Multiplication (@test_switch_gpu_vclMatrix_algebra.R#480) 
  7. Error: Switching GPUs vclMatrix Double Precision Matrix Subtraction (@test_switch_gpu_vclMatrix_algebra.R#507) 
  8. Error: Switching GPUs vclMatrix Double Precision Scalar Matrix Subtraction (@test_switch_gpu_vclMatrix_algebra.R#535) 
  9. Error: Switching GPUs vclMatrix Double Precision Unary Scalar Matrix Subtraction (@test_switch_gpu_vclMatrix_algebra.R#567) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   2.4Mb
    libs   2.9Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/graphscan.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Found the following significant warnings:
  Warning: package ‘edgeR’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GSAgm.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘impute’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/gsl.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error: package or namespace load failed for 'testthat' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
   there is no package called 'rlang'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘profiling.Rmd’ using rmarkdown
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 22-34 (profiling.Rmd) 
Error: processing vignette 'profiling.Rmd' failed with diagnostics:
package or namespace load failed for 'ggplot2' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'rlang'
--- failed re-building ‘profiling.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘interval’
Error(s) in re-building vignettes:
--- re-building ‘gunsales.Rmd’ using rmarkdown
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.
sh: line 1: 13995 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/x13ashtml /tmp/RtmpZhJtlI/x1336a159a99349/iofile -n -s 2> /dev/null
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x1251da579
#1  0x1251d9945
#2  0x7fff9ae44529
Quitting from lines 33-34 (gunsales.Rmd) 
Error: processing vignette 'gunsales.Rmd' failed with diagnostics:
X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
--- failed re-building ‘gunsales.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘run-tests.R’ [1s/1s]
Running the tests in ‘tests/run-tests.R’ failed.
Last 13 lines of output:
  > f <- Filter(function(x) !grepl("html", x), f)
  > 
  > sapply(f, function(i) {
  +   message("testing ", i)
  +   source(i)
  + })
  testing /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/gWidgets2/tests/button.R
  Loading required package: gWidgets2RGtk2
  Loading required package: memoise
  Loading required package: RGtk2
  No protocol specified
  R session is headless; GTK+ not initialized.
  Error in guiToolkit() : Can't load RGtk2
  Calls: sapply ... withVisible -> eval -> eval -> gwindow -> guiToolkit
  Execution halted
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
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.

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 40-43 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [1s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("hail")
  ── 1. Error: hail_hydra works (@test.R#4)  ─────────────────────────────────────
  cannot open the connection to 'https://or.water.usgs.gov/precip/walmart_ecoroof.rain'
  1: hail_hydra("Walmart Eco Roof") at testthat/test.R:4
  2: hydra_base(station_data$urls, station_data$stations)
  3: readLines(url)
  4: file(con, "r")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: hail_hydra works (@test.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_use.Rmd’ using rmarkdown
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 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Basic_use.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hchinamap.Rmd’ using rmarkdown
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.
trying URL 'https://czxb.github.io/br/chinadf.rda'
Content type 'application/octet-stream' length 3992 bytes
==================================================
downloaded 3992 bytes

Quitting from lines 50-58 (hchinamap.Rmd) 
Error: processing vignette 'hchinamap.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘hchinamap.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    CWrappers_1.10.2   2.6Mb
    CWrappers_1.10.3   2.6Mb
    libs               6.5Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Error(s) in re-building vignettes:
--- re-building ‘heatmaply.Rmd’ using rmarkdown
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.
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 1.0.0

Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.

The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>
======================

No protocol specified
Quitting from lines 108-110 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘heatmaply.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'rgl', 'FRB'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HeritSeq.Rcheck/00install.out’ for details.
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs  15.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hetGP_vignette.Rnw’ using knitr
Quitting from lines 434-443 (hetGP_vignette.Rnw) 
Error: processing vignette 'hetGP_vignette.Rnw' failed with diagnostics:
invalid 'z' limits
--- failed re-building ‘hetGP_vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HiCfeat.Rcheck/00install.out’ for details.
Unexported objects imported by ':::' calls:
  ‘ggplot2:::build_guides’ ‘ggplot2:::guide_axis’
  ‘ggplot2:::scales_list’
  See the note in ?`:::` about the use of this operator.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HierO.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
    libs   1.3Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        8.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/hiPOD.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   5.2Mb
Package suggested but not available for checking: ‘trackr’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HiveR.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   3.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/hmgm.Rcheck/00install.out’ for details.
No protocol specified
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘methods’ ‘rgl’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/hoardeR.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'iheatmapr', 'ropls'
Error(s) in re-building vignettes:
  ...
--- re-building ‘simulating-data.Rmd’ using rmarkdown
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.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 25-31 (simulating-data.Rmd) 
Error: processing vignette 'simulating-data.Rmd' failed with diagnostics:
there is no package called 'ropls'
--- failed re-building ‘simulating-data.Rmd’

SUMMARY: processing the following file failed:
  ‘simulating-data.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/homals.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hpackedbubble.Rmd’ using rmarkdown
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 35-49 (hpackedbubble.Rmd) 
Error: processing vignette 'hpackedbubble.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘hpackedbubble.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
File ‘hpa/libs/hpa.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Objects: ‘hpaBinary.o’, ‘hpaML.o’, ‘hpaSelection.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified

(R:8058): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
installed size is 48.9Mb
  sub-directories of 1Mb or more:
    libs  48.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
Running ‘testthat.R’ [52s/52s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   18. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   20. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   22. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   23. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   24. base:::withOneRestart(expr, restarts[[1L]])
   25. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 102 | SKIPPED: 18 | WARNINGS: 3 | FAILED: 3 ]
  1. Error: DESeq2_l2fc runs with default params (@test-DESeq2_l2fc.R#2) 
  2. Error: DESeq2_l2fc runs with sparsity_apply=heavy (@test-DESeq2_l2fc.R#15) 
  3. Error: HRSIP runs with default (@test-HRSIP.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HUM.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
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.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 161-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hwordcloud.Rmd’ using rmarkdown
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 48-53 (hwordcloud.Rmd) 
Error: processing vignette 'hwordcloud.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘hwordcloud.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/hyper.fit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/hypervolume.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ibmsunburst.Rmd’ using rmarkdown
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 25-37 (ibmsunburst.Rmd) 
Error: processing vignette 'ibmsunburst.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘ibmsunburst.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ICAMS.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
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 84-88 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
argument of length 0
--- failed re-building ‘example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.4Mb
    libs   5.9Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Package suggested but not available for checking: ‘mixAK’
Running examples in ‘iClick-Ex.R’ failed
The error most likely occurred in:

> ### Name: iClick.ARIMA
> ### Title: iClick GUI for ARIMA
> ### Aliases: iClick.ARIMA
> 
> ### ** Examples
> 
> 
> ##External data
> data("world20")
> y=na.omit(diff(log(world20[,1])))
> 
> ## Simulation data
> #dat=rnorm(200,5,1)
> #y=ts(dat, start = c(1970, 1), frequency = 12)
> 
> iClick.ARIMA(y)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: iClick.ARIMA ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/icosa.Rcheck/00install.out’ for details.
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  27.7Mb
Error(s) in re-building vignettes:
--- re-building ‘model_details.Rmd’ using rmarkdown
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 25-32 (model_details.Rmd) 
Error: processing vignette 'model_details.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘model_details.Rmd’

--- re-building ‘parameter_details.Rmd’ using rmarkdown
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 24-31 (parameter_details.Rmd) 
Error: processing vignette 'parameter_details.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘parameter_details.Rmd’

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

SUMMARY: processing the following files failed:
  ‘model_details.Rmd’ ‘parameter_details.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.2Mb
    libs  14.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     18.7Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘getstarted.Rmd’ using rmarkdown
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 87-89 (getstarted.Rmd) 
Error: processing vignette 'getstarted.Rmd' failed with diagnostics:
cannot open the connection to 'https://dane.imgw.pl/data/dane_pomiarowo_obserwacyjne/dane_hydrologiczne/miesieczne/mies_info.txt'
--- failed re-building ‘getstarted.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  IM4ECpp.cpp:24:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:24:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:22:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:32:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Immigrate.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   4.3Mb
Packages suggested but not available for checking: 'rsprng', 'Rmpi'
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
sh: line 1: 70608 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/x13ashtml /tmp/Rtmp4Q0D0Y/x13113c81c3a262c/iofile -n -s 2> /dev/null
Warning in system(paste(x13.bin, file, flags), intern = TRUE, ignore.stderr = TRUE) :
  running command '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/x13ashtml /tmp/Rtmp4Q0D0Y/x13113c81c3a262c/iofile -n -s 2>/dev/null' had status 133
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x128048579
#1  0x128047945
#2  0x7fff9841b529
Error: X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Packages suggested but not available for checking:
  'MLP', 'org.Hs.eg.db', 'a4Base'
Error(s) in re-building vignettes:
--- re-building ‘IntGraphTutorial.Rmd’ using rmarkdown
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.
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: DiagrammeR
Loading required package: DiagrammeRsvg
Loading required package: rsvg
Loading required package: gtools
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.
Warning in normalizePath(f2) :
  path[1]="webshot15a63ac4ea79.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot15a63ac4ea79.png': No such file or directory
Quitting from lines 32-34 (IntGraphTutorial.Rmd) 
Error: processing vignette 'IntGraphTutorial.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘IntGraphTutorial.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    libs  26.7Mb
.nndsvd.internal: no visible global function definition for ‘runif’
nmf.mnnals: no visible global function definition for ‘runif’
nmf.opt.k: no visible global function definition for ‘flush.console’
nmf.opt.k: no visible global function definition for ‘points’
nmf.opt.k: no visible global function definition for ‘lines’
nmf.opt.k: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  flush.console lines mtext points runif
Consider adding
  importFrom("graphics", "lines", "mtext", "points")
  importFrom("stats", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ionflows.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘coda’ ‘lattice’
  All declared Imports should be used.
Running examples in ‘IRATER-Ex.R’ failed
The error most likely occurred in:

> ### Name: clean.admb
> ### Title: delete IRATE (ADMB) run files
> ### Aliases: clean.admb clean.IRATE
> 
> ### ** Examples
> 
> example.setup <- IRATE.examples()
> new.setup <- new.setup.path <- example.setup[1] # select old IRATE setup to reparameterize
> print(new.setup) # print setup name to be run
[1] "HoenigNonMixing"
> old.setup.path <- system.file(paste0("IRATE.examples/",new.setup,".dat"), package = "IRATER")
> 
> system(paste("mkdir -p ",new.setup.path)) # create run folder for new setup
> system(paste("cp",old.setup.path, new.setup.path)) # copy old setup in new run folder
> setwd(new.setup.path)
> 
> run.IRATE(new.setup) # compile and run setup
sh: admb: command not found
Error in R2admb::compile_admb(setup.file, safe = safe, re = re, verbose = verbose,  : 
  base admb command failed: run setup_admb(), or check ADMB installation
Calls: run.IRATE -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘getting-started-with-irg.Rmd’ using rmarkdown
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.
ndvi                    package:irg                    R Documentation

_R_a_w _N_D_V_I _T_i_m_e _S_e_r_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     A data.table containing NDVI samples for ten points over ten years
     (2002-2012).

_F_o_r_m_a_t:

     A data.table with 2530 rows and 5 variables:

        • id - individual identifier

        • yr - year of sample

        • DayOfYear - julian day/day of year of sample

        • NDVI - sampled value

        • SummaryQA - Summary quality assessment value

     SummaryQA details:

        • 0 - Good data, use with confidence

        • 1 - Marginal data, useful but look at detailed QA for more
          information

        • 2 - Pixel covered with snow/ice

        • 3 - Pixel is cloudy

_E_x_a_m_p_l_e_s:

     # Load data.table
     library(data.table)
     
     # Read example data
     ndvi <- fread(system.file("extdata", "ndvi.csv", package = "irg"))
     

Quitting from lines 99-153 (getting-started-with-irg.Rmd) 
Error: processing vignette 'getting-started-with-irg.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘getting-started-with-irg.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started-with-irg.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Packages suggested but not available for checking: 'pcalg', 'Rgraphviz'
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown
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.
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

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

    isFALSE

Loading required package: rngtools
Loading required package: cluster
# NOTE - CRAN check detected: limiting maximum number of cores [2/8]
NMF - BioConductor layer [NO: missing Biobase] | Shared memory capabilities [OK] | Cores 2/2 | CRAN check
  To enable the Bioconductor layer, try: install.extras('
NMF
') [with Bioconductor repository enabled]
Quitting from lines 94-99 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'pcalg'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          15.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/JFE.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.6Mb
Found the following significant warnings:
  jomo1clmmC.c:105:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo1clmmhrC.c:107:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmC.c:128:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmhrC.c:132:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomooprobitC.c:84:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/jomo.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.7Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
Missing or unexported object: ‘tidyr::unnest_legacy’
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  16.6Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/kernhaz.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘org.Hs.eg.db’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/KernSmoothIRT.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/kmcudaR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/kml3d.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/kml.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/kmlShape.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘copper_mining_2d.Rmd’ using rmarkdown
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.
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 120-123 (copper_mining_2d.Rmd) 
Error: processing vignette 'copper_mining_2d.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘copper_mining_2d.Rmd’

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

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

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

SUMMARY: processing the following file failed:
  ‘copper_mining_2d.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘kstIO.Rnw’ using Sweave
Loading required package: pks
Loading required package: sets
Loading required package: MASS
Loading required package: stringr

Attaching package: ‘stringr’

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

    %>%

Loading required package: relations

Error: processing vignette 'kstIO.Rnw' failed with diagnostics:
 chunk 1 
Error in library("kst") : there is no package called ‘kst’

--- failed re-building ‘kstIO.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Rgraphviz’
Error(s) in re-building vignettes:
--- re-building ‘kst.Rnw’ using Sweave
Loading required package: proxy

Attaching package: ‘proxy’

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

    as.dist, dist

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

    as.matrix

Loading required package: relations
Loading required package: sets
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Error: processing vignette 'kst.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'kst.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./kst-012.pdf): PDF inclusion: required page does
 not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘kst.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   8.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/LambertW.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/LANDD.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
installed size is 144.2Mb
  sub-directories of 1Mb or more:
    libs  142.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_to_lavaanPlot.Rmd’ using rmarkdown
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 41-42 (Intro_to_lavaanPlot.Rmd) 
Error: processing vignette 'Intro_to_lavaanPlot.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Intro_to_lavaanPlot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/lba.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./lda_svi.h:1:9: warning: '_lda_svi_guard' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/lda.svi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘BiocParallel’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/leapp.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      6.4Mb
Packages suggested but not available for checking: 'gWidgetsRGtk2', 'RGtk2'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Understanding_lime.Rmd’ using rmarkdown
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 262-263 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Understanding_lime.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘linkspotterVignette.Rmd’ using rmarkdown
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 109-112 (linkspotterVignette.Rmd) 
Error: processing vignette 'linkspotterVignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘linkspotterVignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   9.1Mb
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs      21.8Mb
    testdata   1.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/LMERConvenienceFunctions.Rcheck/00install.out’ for details.
Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error in ls.problem(model.text.lsp) : 
  has.localsolver(ls.path) is not TRUE
Calls: ls.problem -> stopifnot
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘localsolver.Rmd’ using knitr
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
--- failed re-building ‘localsolver.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/longitudinalData.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RDRToolbox’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/loon.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/LoopRig.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [12s/75s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Could not get external gene names from biomart.  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. 
  Please report this on the support site at http://support.bioconductor.org 
  ── 1. Failure: run.cache base.dir in folder that does not have access (@test-run
  `run.cache(sum, 1, 2, 3, 4, 5, show.message = FALSE, base.dir = "/")` did not produce any warnings.
  
  ── 2. Failure: run.cache base.dir in folder that does not have access (@test-run
  `run.cache(sum, 1, 2, 3, 4, 5, show.message = FALSE, base.dir = "/daca")` did not produce any warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 147 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: run.cache base.dir in folder that does not have access (@test-run.cache.R#29) 
  2. Failure: run.cache base.dir in folder that does not have access (@test-run.cache.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/LOST.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/LSAfun.Rcheck/00install.out’ for details.
installed size is 51.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  49.3Mb
Running examples in ‘LTRCtrees-Ex.R’ failed
The error most likely occurred in:

> ### Name: ICtree
> ### Title: Fit a survival tree for interval-censored survival data
> ### Aliases: ICtree
> 
> ### ** Examples
> 
> library(interval)
Error in library(interval) : there is no package called ‘interval’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LTRCtrees.Rmd’ using rmarkdown
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 min(diff(sort(ux))) :
  no non-missing arguments to min; returning Inf
Quitting from lines 199-207 (LTRCtrees.Rmd) 
Error: processing vignette 'LTRCtrees.Rmd' failed with diagnostics:
there is no package called 'interval'
--- failed re-building ‘LTRCtrees.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LUCIDus-vignette.Rmd’ using rmarkdown
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 63-64 (LUCIDus-vignette.Rmd) 
Error: processing vignette 'LUCIDus-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘LUCIDus-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.1Mb
    libs   1.7Mb
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Maeswrap.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 12 ]
  1. Error: interactive_blur (@test_interactive_blur.R#6) 
  2. Error: interactive_canny (@test_interactive_canny.R#5) 
  3. Error: interactive_charcoal (@test_interactive_charcoal.R#6) 
  4. Error: interactive_composite (@test_interactive_composite.R#5) 
  5. Error: interactive_despeckle (@test_interactive_despeckle.R#6) 
  6. Error: interactive_emboss (@test_interactive_emboss.R#6) 
  7. Error: interactive_implode (@test_interactive_implode.R#6) 
  8. Error: interactive_modulate (@test_interactive_modulate.R#6) 
  9. Error: interactive_oilpaint (@test_interactive_oilpaint.R#6) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is 80.1Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  72.8Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  19.2Mb
Error(s) in re-building vignettes:
--- re-building ‘manhattanly.Rmd’ using rmarkdown
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.
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

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.
Warning in normalizePath(f2) :
  path[1]="webshotd4a14dcd902a.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotd4a14dcd902a.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘manhattanly.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘manipulateWidgets.Rmd’ using rmarkdown
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 normalizePath(f2) :
  path[1]="webshot9723ea5db42.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot9723ea5db42.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘manipulateWidgets.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/maotai.Rcheck/00install.out’ for details.
prepare_Rd: RGL: unable to open X11 display
prepare_Rd: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.4Mb
    libs         16.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mapmisc.Rnw’ using knitr
Loading required package: sp
Loading required package: raster
map images will be cached in  /tmp/Rtmpvjscv5/mapmiscCache
--- finished re-building ‘mapmisc.Rnw’

--- re-building ‘north.Rmd’ using docco_linear
Quitting from lines 221-238 (north.Rmd) 
Error: processing vignette 'north.Rmd' failed with diagnostics:
unable to find an inherited method for function 'coordinates' for signature '"numeric"'
--- failed re-building ‘north.Rmd’

pandoc --self-contained --to=html5 --css=http://diseasemapping.r-forge.r-project.org/webpage.css --output=north.html north.md	
make: pandoc: No such file or directory
make: *** [north.html] Error 1
Error in tools:::buildVignettes(dir = "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mapmisc.Rcheck/vign_test/mapmisc",  : 
  running 'make' failed
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
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 95-100 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.0Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   8.6Mb
Package suggested but not available for checking: ‘ASGSCA’
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mcca.Rcheck/00install.out’ for details.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   8.8Mb
Errors in running code in vignettes:
when running code in ‘mcemGLM-vignette.Rnw’
  ...
         6      :  6   6      :  6   Max.   :1.000  
         (Other):324   (Other):324                  

> fitBernoulli <- mcemGLMM(fixed = Mate ~ 0 + Cross, 
+     random = list(~0 + Female, ~0 + Male), data = salamander, 
+     family = "bernoulli", vcD .... [TRUNCATED] 

Execution halted

... incomplete output.  Crash?
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MDSMap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mdsOpt.Rcheck/00install.out’ for details.
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
Packages suggested but not available for checking:
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'org.Hs.eg.db'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Mega2R.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.6Mb
installed size is 76.9Mb
  sub-directories of 1Mb or more:
    libs  76.5Mb
Package required but not available: ‘GO.db’

Packages suggested but not available for checking: 'clpAPI', 'ctc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
No protocol specified

(R:50774): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:50780): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:50786): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified

(R:50792): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:50816): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:50840): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:50846): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:50852): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:50858): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:50870): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘MetaIntegrator.Rmd’ using rmarkdown
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 29-30 (MetaIntegrator.Rmd) 
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building ‘MetaIntegrator.Rmd’

--- re-building ‘MetaIntegratorRealExample.Rmd’ using rmarkdown_notangle
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.
--- finished re-building ‘MetaIntegratorRealExample.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'org.Hs.eg.db', 'annaffy', 'hgu133plus2.db', 'hgu133a.db',
  'hgu95av2.db'
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MetaPath.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'GEOquery', 'affy', 'hgu133plus2.db', 'doSMP', 'impute'
Packages suggested but not available for checking:
  'HTSFilter', 'DESeq', 'DESeq2'
Errors in running code in vignettes:
when running code in ‘metaRNASeq.Rnw’
  ...

> options(width = 60)

> library(metaRNASeq)

> library(DESeq2)

  When sourcing ‘metaRNASeq.R’:
Error: there is no package called ‘DESeq2’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘metaRNASeq.Rnw’ using Sweave

Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
 chunk 2 (label = loadparameters) 
Error in library(DESeq2) : there is no package called ‘DESeq2’

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

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

Error: Vignette re-building failed.
Execution halted
installed size is 77.8Mb
  sub-directories of 1Mb or more:
    libs  77.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.1Mb
    libs  18.6Mb
    misc   1.1Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MFHD.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mgcViz.Rcheck/00install.out’ for details.
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  21.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mgwrsar-basic_examples.Rmd’ using rmarkdown
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 91-94 (mgwrsar-basic_examples.Rmd) 
Error: processing vignette 'mgwrsar-basic_examples.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘mgwrsar-basic_examples.Rmd’

SUMMARY: processing the following file failed:
  ‘mgwrsar-basic_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Package suggested but not available for checking: ‘biotools’
Package unavailable to check Rd xrefs: ‘biotools’
Running examples in ‘micompr-Ex.R’ failed
The error most likely occurred in:

> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
sROC 0.1-2 loaded
MANOVA assumptions require 'MVN' and 'biotools' packages.
Error in `*tmp*`[[i]] : subscript out of bounds
Calls: assumptions -> assumptions.cmpoutput
Execution halted
Running ‘testthat.R’ [20s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  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(s) in re-building vignettes:
--- re-building ‘paper.Rnw’ using knitr
Quitting from lines 341-342 (paper.Rnw) 
Error: processing vignette 'paper.Rnw' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘paper.Rnw’

--- re-building ‘tolatex-examples.Rnw’ using knitr
Warning in wilcox.test.default(x = c(-2.17390550005803e-11, -2.17097451127302e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(2.13309370167281e-11, 2.12594386539422e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(1.99236183107132e-11, 1.97388771994156e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(1.00897068477934e-12, 1.02406971791424e-12,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(8.95727936267576e-13, 8.4909856923332e-13,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(9.80548975348938e-13, 8.81072992342524e-13,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(5.90887339058099e-11, 6.09077233093558e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(9.97119053991469e-15, 9.92695509127728e-15,  :
  cannot compute exact p-value with ties
--- finished re-building ‘tolatex-examples.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘gWidgets2RGtk2’
Error(s) in re-building vignettes:
--- re-building ‘milr-intro.Rmd’ using rmarkdown
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.
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 2.8390.
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

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.
Warning: 'switch' is deprecated.
Use 'strip.position' instead.
See help("Deprecated")
The penalty term is selected automatically with 100 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 3.2909.
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.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.

Execution halted
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   5.9Mb
Packages suggested but not available for checking: 'mixAK', 'BRugs'
Package unavailable to check Rd xrefs: ‘mixAK’
Found the following significant warnings:
  simcensor.cpp:91:16: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/missDeaths.Rcheck/00install.out’ for details.
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
Running examples in ‘MixSIAR-Ex.R’ failed
The error most likely occurred in:

> ### Name: mixsiar_gui
> ### Title: Run the GUI version of MixSIAR
> ### Aliases: mixsiar_gui
> 
> ### ** Examples
> 
> mixsiar_gui()
Error in mixsiar_gui() : 
  *** gWidgetsRGtk2 package not able to be loaded. ***
        If 'library('gWidgetsRGtk2')' does not work, MixSIAR GUI will not run.
        On Windows/Linux, try 'install.packages('gWidgetsRGtk2')'.
        On Mac, close R, download and install GTK+ from:
        http://r.research.att.com/#other. Then install latest X11 application
        (xQuartz) from http://xquartz.macosforge.org/landing/.

        If installing GTK+ continues to be problematic, consider using the
        script version of MixSIAR. See manual for help and examples.
Execution halted
Package suggested but not available for checking: ‘IlluminaHumanMethylation450kmanifest’
Error(s) in re-building vignettes:
  ...
--- re-building ‘comparison_mlr3pipelines_mlr_sklearn.Rmd’ using rmarkdown
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.
--- finished re-building ‘comparison_mlr3pipelines_mlr_sklearn.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
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 png::readPNG(path, native = TRUE, info = TRUE) :
  libpng warning: iCCP: CRC error
Quitting from lines 172-173 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    help   1.5Mb
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MMDai.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ALL’
Running examples in ‘MMDvariance-Ex.R’ failed
The error most likely occurred in:

> ### Name: gsMMD.v
> ### Title: Gene selection based on variances by using a mixture of marginal
> ###   distributions
> ### Aliases: gsMMD.v
> ### Keywords: classif
> 
> ### ** Examples
> 
>       t1 = proc.time()
>       library(ALL)
Error in library(ALL) : there is no package called ‘ALL’
Execution halted
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
Error(s) in re-building vignettes:
--- re-building ‘mnlogit.Rnw’ using Sweave
Package: mnlogit
Version: 1.2.6
Multinomial Logit Choice Models.
Scientific Computing Group, Sentrana Inc.
Loading required package: Formula
Loading required package: zoo

Attaching package: 'zoo'

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

    index

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

    as.Date, as.Date.numeric

Loading required package: lmtest

Attaching package: 'mlogit'

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

    hmftest, scoretest
Package required but not available: ‘doMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/molaR.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   4.3Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/morphomap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Morpho.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   6.4Mb
Error(s) in re-building vignettes:
--- re-building ‘tutorial.Rmd’ using rmarkdown
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.

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 342-344 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
The model needs too many iterations to provide reliable parameter estimates !
--- failed re-building ‘tutorial.Rmd’

--- re-building ‘modelling.Snw’ using Sweave
--- finished re-building ‘modelling.Snw’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Heatplus’
installed size is 51.7Mb
  sub-directories of 1Mb or more:
    R             1.1Mb
    libs         47.8Mb
    mathematica   1.5Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  14.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package unavailable to check Rd xrefs: ‘Biostrings’
Error(s) in re-building vignettes:
  ...
--- re-building ‘msaR.Rmd’ using rmarkdown
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 30-37 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘msaR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 39.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs  37.0Mb
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    libs  45.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘msir.Rmd’ using rmarkdown
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 normalizePath(f2) :
  path[1]="webshot127825d88bea8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot127825d88bea8.png': No such file or directory
Quitting from lines 102-104 (msir.Rmd) 
Error: processing vignette 'msir.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘msir.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MSIseq.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MSQC.Rcheck/00install.out’ for details.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  16.2Mb
Running examples in ‘mssqlR-Ex.R’ failed
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mtk.Rcheck/00install.out’ for details.
Packages required but not available:
  'org.Hs.eg.db', 'org.Mm.eg.db', 'org.Ce.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 83.5Mb
  sub-directories of 1Mb or more:
    libs  83.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Running examples in ‘multistateutils-Ex.R’ failed
The error most likely occurred in:

> ### Name: cohort_simulation
> ### Title: Runs a cohort discrete event simulation
> ### Aliases: cohort_simulation
> 
> ### ** Examples
> 
> library(multistateutils)
> library(mstate)
Loading required package: survival
> library(flexsurv)
> 
> # Convert data to long
> data(ebmt3)
> tmat <- trans.illdeath()
> long <- msprep(time=c(NA, 'prtime', 'rfstime'),
+                status=c(NA, 'prstat', 'rfsstat'),
+                data=ebmt3,
+                trans=tmat,
+                keep=c('age', 'dissub'))
> 
> # Fit parametric models
> models <- lapply(1:3, function(i) {
+     flexsurvreg(Surv(time, status) ~ age + dissub, data=long, dist='weibull')
+ })
> 
> sim <- cohort_simulation(models, ebmt3, tmat)

 *** caught illegal operation ***
address 0x109e65262, cause 'illegal opcode'

Traceback:
 1: desCpp(transitions, trans_mat, newdata_mat, start_times, start_states -     1, tcovs)
 2: data.table::as.data.table(desCpp(transitions, trans_mat, newdata_mat,     start_times, start_states - 1, tcovs))
 3: run_sim(transition_list, attr_mat, trans_mat, tcovs, start_times,     start_states)
 4: state_occupancy(models, trans_mat, newdata, tcovs, start_time,     start_state, ci, M, agelimit, agecol, agescale)
 5: cohort_simulation(models, ebmt3, tmat)
An irrecoverable exception occurred. R is aborting now ...
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  32: withOneRestart(expr, restarts[[1L]])
  33: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  34: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,     {        reporter$start_file(basename(path))        lister$start_file(basename(path))        source_file(path, new.env(parent = env), chdir = TRUE,             wrap = wrap)        reporter$.end_context()        reporter$end_file()    })
  35: FUN(X[[i]], ...)
  36: lapply(paths, test_file, env = env, reporter = current_reporter,     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  37: force(code)
  38: doWithOneRestart(return(expr), restart)
  39: withOneRestart(expr, restarts[[1L]])
  40: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  41: with_reporter(reporter = current_reporter, results <- lapply(paths,     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
  42: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  43: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap)
  44: test_package_dir(package = package, test_path = test_path, filter = filter,     reporter = reporter, ..., stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  45: test_check("multistateutils")
  An irrecoverable exception occurred. R is aborting now ...
installed size is 42.1Mb
  sub-directories of 1Mb or more:
    libs  42.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mvmesh.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_mvord2.Rmd’ using rmarkdown
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.
--- finished re-building ‘vignette_mvord2.Rmd’

--- re-building ‘vignette_mvord.Rnw’ using Sweave
Loading required package: minqa
Loading required package: BB
Loading required package: ucminf
Loading required package: dfoptim
Error: processing vignette 'vignette_mvord.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'vignette_mvord.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'vignette_mvord.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nat.nblast.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nat.templatebrains.Rcheck/00install.out’ for details.
Package required but not available: ‘sSeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/NeatMap.Rcheck/00install.out’ for details.
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘ConsensusClusterPlus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘netgsa.Rmd’ using rmarkdown
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 86-89 (netgsa.Rmd) 
Error: processing vignette 'netgsa.Rmd' failed with diagnostics:
error creating directory: /Users/urbanek/Library/Caches/graphite-bioc/12
--- failed re-building ‘netgsa.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.4Mb
Packages suggested but not available for checking:
  'limma', 'DESeq2', 'edgeR', 'org.Hs.eg.db'
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/neuroim.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Error(s) in re-building vignettes:
--- re-building ‘NFP.Rmd’ using rmarkdown
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.
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect,
    is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: graphite
Quitting from lines 135-143 (NFP.Rmd) 
Error: processing vignette 'NFP.Rmd' failed with diagnostics:
error creating directory: /Users/urbanek/Library/Caches/graphite-bioc/12
--- failed re-building ‘NFP.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    CppCode        1.2Mb
    R              6.0Mb
    classic-bugs   1.5Mb
    include        5.5Mb
    libs          19.0Mb
    tests          1.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/NIPTeR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nlcv.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘geocode.Rmd’ using rmarkdown
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 127-133 (geocode.Rmd) 
Error: processing vignette 'geocode.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘geocode.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
Found the following significant warnings:
  clang-7: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
  DIRsubrout.c:505:10: warning: explicitly assigning value of variable of type 'integer' (aka 'int') to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nloptr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/NNS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nonlinearTseries.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/NPCirc.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Package suggested but not available for checking: ‘PMA’
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs  16.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.0Mb
File ‘obliclus/libs/obliclus.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/OceanView.Rcheck/00install.out’ for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    doc    2.3Mb
    help   2.8Mb
    libs   3.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/OCNet.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ── 2. Failure: OLC encoding throws an error with odd-numbered requested lengths 
  `x` threw an error with unexpected message.
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 1 FAILED: 2
  1. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#20) 
  2. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
comp.freq: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/onemap.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ontologyPlot’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/OpenCL.Rcheck/00install.out’ for details.
installed size is 74.7Mb
  sub-directories of 1Mb or more:
    libs   64.9Mb
    share   9.7Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   6.0Mb
installed size is 189.4Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    libs    179.3Mb
    models    4.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/OpenRepGrid.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   3.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      4.1Mb
Packages suggested but not available for checking: 'gurobi', 'Rsymphony'
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Packages suggested but not available for checking:
  'GO.db', 'org.At.tair.db'
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/optiSel.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.7Mb
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/optiSolve.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘optparse.Rrst’ using knitr
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'optparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
--- failed re-building ‘optparse.Rrst’

SUMMARY: processing the following file failed:
  ‘optparse.Rrst’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘graph’
Packages suggested but not available for checking: 'IsoGene', 'Biobase'
File ‘OriGen/libs/OriGen.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/orthoDr.Rcheck/00install.out’ for details.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   5.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.9Mb
Error(s) in re-building vignettes:
--- re-building ‘Rcpp_API.Rmd’ using rmarkdown
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.
--- finished re-building ‘Rcpp_API.Rmd’

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

--- re-building ‘introduction.Rmd’ using rmarkdown
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 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘graph_packing.Rmd’ using rmarkdown
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.
--- finished re-building ‘graph_packing.Rmd’

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

--- re-building ‘progressive_packing.Rmd’ using rmarkdown
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 196-217 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘progressive_packing.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PACVr.Rcheck/00install.out’ for details.
Package required but not available: ‘GO.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘evals.Rmd’ using rmarkdown
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 13-19 (evals.Rmd) 
Error: processing vignette 'evals.Rmd' failed with diagnostics:
package or namespace load failed for 'futile.logger' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'formatR'
--- failed re-building ‘evals.Rmd’

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

--- re-building ‘pander.Rmd’ using rmarkdown
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.
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

--- finished re-building ‘pander.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ParallelPC-Ex.R’ failed
The error most likely occurred in:

> ### 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
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-parcoords-.Rmd’ using rmarkdown
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 27-30 (introduction-to-parcoords-.Rmd) 
Error: processing vignette 'introduction-to-parcoords-.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction-to-parcoords-.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘parmigene/libs/parmigene.so’:
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/patternize.Rcheck/00install.out’ for details.
Packages required but not available: 'jetset', 'Mfuzz', 'WGCNA'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘pbdPROF’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pbdPROF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pbdZMQ.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pca3d.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      2.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pcaL1.Rcheck/00install.out’ for details.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   7.0Mb
installed size is 100.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  97.2Mb
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PCGSE.Rcheck/00install.out’ for details.
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PCRedux.Rcheck/00install.out’ for details.
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs    6.5Mb
    share  11.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Package suggested but not available for checking: ‘globaltest’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/permGPU.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data       2.3Mb
    examples   2.6Mb
Found the following significant warnings:
  phreeqcpp/transport.cpp:794:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/phreeqc.Rcheck/00install.out’ for details.
installed size is 37.1Mb
  sub-directories of 1Mb or more:
    libs  36.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘phybreak_intro.Rmd’ using rmarkdown
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.

Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Advanced_Usage.Rmd’ using rmarkdown
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 normalizePath(f2) :
  path[1]="webshotc4dc454c7107.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotc4dc454c7107.png': No such file or directory
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Advanced_Usage.Rmd’

--- re-building ‘Basic_Use.Rmd’ using rmarkdown
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 30-32 (Basic_Use.Rmd) 
Error: processing vignette 'Basic_Use.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Basic_Use.Rmd’

SUMMARY: processing the following files failed:
  ‘Advanced_Usage.Rmd’ ‘Basic_Use.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/phylocurve.Rcheck/00install.out’ for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   9.3Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
Package required but not available: ‘rggobi’

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.
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PlasmaMutationDetector.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘S4Vectors’
No protocol specified

(R:80202): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:80210): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:80218): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified

(R:80226): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:80252): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:80280): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:80288): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:80296): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:80304): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:80318): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
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.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   7.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/plot3Drgl.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_plotdap.Rmd’ using rmarkdown
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 138-146 (using_plotdap.Rmd) 
Error: processing vignette 'using_plotdap.Rmd' failed with diagnostics:
Failed to open file /Users/urbanek/Library/Caches/R/rerddap/d3691d4726dcf37b41ff22352dc3ac7e.nc.
--- failed re-building ‘using_plotdap.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.7Mb
Package suggested but not available for checking: ‘mixOmics’
Running examples in ‘PLSbiplot1-Ex.R’ failed
The error most likely occurred in:

> ### 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
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/plsVarSel.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘pmc_tutorial.Rmd’ using rmarkdown
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.
Loading required package: ape
Loading required package: subplex

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: 'gridExtra'

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

    combine

Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda

Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘OpenCPU.Rmd’ using rmarkdown
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.
--- finished re-building ‘OpenCPU.Rmd’

--- re-building ‘vignette.Rmd’ using rmarkdown
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.
... activating corpus: GERMAPARLMINI
... activating corpus: REUTERS
Quitting from lines 140-141 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    R      6.8Mb
    data   4.0Mb
No protocol specified
Namespace in Imports field not imported from: ‘combinat’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘polynomials.Rmd’ using rmarkdown
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.
Error: processing vignette 'polynomials.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘polynomials.Rmd’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PPQplan.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘PPQnote.Rmd’ using rmarkdown
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.
--- finished re-building ‘PPQnote.Rmd’

--- re-building ‘PPQplan-vignette.Rmd’ using rmarkdown
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.
No protocol specified
Warning in normalizePath(f2) :
  path[1]="webshot83bd39d2f15.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot83bd39d2f15.png': No such file or directory
Quitting from lines 135-136 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PPQplan-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Package suggested but not available for checking: ‘PerfMeas’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/predict3d.Rcheck/00install.out’ for details.
No protocol specified
Namespaces in Imports field not imported from:
  ‘TH.data’ ‘moonBook’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘predict3d.Rmd’ using rmarkdown
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.
Loading required package: predict3d
No protocol specified
Loading required package: rgl
Quitting from lines 55-58 (predict3d.Rmd) 
Error: processing vignette 'predict3d.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘predict3d.Rmd’

SUMMARY: processing the following file failed:
  ‘predict3d.Rmd’

Error: Vignette re-building failed.
Execution halted
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/prim.Rcheck/00install.out’ for details.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   8.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRISMA.Rmd’ using rmarkdown
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 39-52 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PRISMA.Rmd’

--- re-building ‘exclusionflowcharts.Rmd’ using rmarkdown
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 25-31 (exclusionflowcharts.Rmd) 
Error: processing vignette 'exclusionflowcharts.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘exclusionflowcharts.Rmd’

SUMMARY: processing the following files failed:
  ‘PRISMA.Rmd’ ‘exclusionflowcharts.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/processR.Rcheck/00install.out’ for details.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      6.9Mb
Package suggested but not available for checking: ‘EBImage’
Running examples in ‘proftools-Ex.R’ failed
The error most likely occurred in:

> ### Name: filterProfileData
> ### Title: Filter Profile Data
> ### Aliases: filterProfileData
> ### Keywords: programming utilities
> 
> ### ** Examples
> 
> pd <- readProfileData(system.file("samples", "glmEx.out", package="proftools"))
> plotProfileCallGraph(pd)
Error in loadNamespace(name) : there is no package called ‘graph’
Calls: plotProfileCallGraph ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘proftools.Rnw’ using knitr
Quitting from lines 221-222 (proftools.Rnw) 
Error: processing vignette 'proftools.Rnw' failed with diagnostics:
there is no package called 'graph'
--- failed re-building ‘proftools.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'qtbase', 'RGtk2', 'cairoDevice', 'gWidgetsRGtk2'
Running ‘testthat.R’ [145s/146s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  20 warnings generated.
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 294 | SKIPPED: 1 | WARNINGS: 1 | FAILED: 9 ]
  1. Error: cross_validation (@test_diagnostics.R#25) 
  2. Error: cross_validation_logistic (@test_diagnostics.R#51) 
  3. Error: cross_validation_extra_regressors (@test_diagnostics.R#71) 
  4. Error: cross_validation_default_value_check (@test_diagnostics.R#86) 
  5. Error: cross_validation_uncertainty_disabled (@test_diagnostics.R#97) 
  6. Error: performance_metrics (@test_diagnostics.R#110) 
  7. Error: fit_predict_no_changepoints (@test_prophet.R#33) 
  8. Error: fit_predict_changepoint_not_in_history (@test_prophet.R#52) 
  9. Error: auto_weekly_seasonality (@test_prophet.R#448) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘ALDEx2’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.2Mb
Packages suggested but not available for checking:
  'Biostrings', 'GOSemSim', 'org.Hs.eg.db'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Found the following significant warnings:
  pinpolyhedronA.cc:594:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  pinpolyhedronA.cc:1766:5: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ptinpoly.Rcheck/00install.out’ for details.
Package required but not available: ‘tweeDEseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 40.3Mb
  sub-directories of 1Mb or more:
    libs  39.9Mb
installed size is 36.0Mb
  sub-directories of 1Mb or more:
    libs  35.5Mb
Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pulseTD.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘Data_Model.Rmd’ using rmarkdown
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.
--- finished re-building ‘Data_Model.Rmd’

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

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

--- re-building ‘PWFSLSmoke.Rmd’ using rmarkdown
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 163-164 (PWFSLSmoke.Rmd) 
Error: processing vignette 'PWFSLSmoke.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PWFSLSmoke.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PythonInR.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘admisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 60.4Mb
  sub-directories of 1Mb or more:
    libs  60.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/qpcR.Rcheck/00install.out’ for details.
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Found the following executable file:
  src/LICENSES/LZ4_LICENSE.txt
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/qtbase.Rcheck/00install.out’ for details.
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/qtlc.Rcheck/00install.out’ for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       3.0Mb
    libs      1.3Mb
Package required but not available: ‘qtbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘wilcox1973.Rmd’ using rmarkdown
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 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘wilcox1973.Rmd’

SUMMARY: processing the following file failed:
  ‘wilcox1973.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘quanteda.textmodels’
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   7.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/QuantifQuantile.Rcheck/00install.out’ for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   3.9Mb
File ‘QUIC/libs/QUIC.so’:
  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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘qVarSel/libs/qVarSel.so’:
  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.
'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/R330.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘RAbHIT-vignette.Rmd’ using rmarkdown
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.
Loading required package: ggplot2
RAbHIT version: 0.1.4
Warning: Ignoring unknown aesthetics: text
Warning: Ignoring unknown aesthetics: text
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 299-301 (RAbHIT-vignette.Rmd) 
Error: processing vignette 'RAbHIT-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘RAbHIT-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
No protocol specified
No protocol specified
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘Matrix’ ‘PharmacoGx’ ‘cluster’
  All declared Imports should be used.
No protocol specified
  No protocol specified
  Note: found 26 marked UTF-8 strings
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RadOnc.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RAINBOWR.Rcheck/00install.out’ for details.
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    libs  30.5Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   7.0Mb
Package unavailable to check Rd xrefs: ‘Heatplus’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   4.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RAPIDR.Rcheck/00install.out’ for details.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   9.6Mb
Package suggested but not available for checking: ‘rpanel’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rase.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
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.
Loading required package: Rcpp

Attaching package: 'lubridate'

The following objects are masked from 'package:data.table':

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

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

    date

Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 130-141 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   6.5Mb
No protocol specified

(R:15712): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rayshader.Rcheck/00install.out’ for details.
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  31.0Mb
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rblpapi.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   5.2Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘RCAL-vig.Rnw’ using Sweave
Loading required package: trust

Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rchallenge)
  > 
  > test_check("rchallenge")
  ── 1. Failure: pandoc available (@test-pandoc.R#2)  ────────────────────────────
  rmarkdown::pandoc_available("1.12.3") isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: pandoc available (@test-pandoc.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following executable file:
  src/vendor/clickhouse-cpp/contrib/lz4/LICENSE
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcmdrPlugin.BiclustGUI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcmdrPlugin.RiskDemo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcmdrPlugin.TeachingDemos.Rcheck/00install.out’ for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    corpora   7.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rcplex.Rcheck/00install.out’ for details.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    include   5.9Mb
    libs      2.0Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcppClassic.Rcheck/00install.out’ for details.
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     24.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcppMeCab.Rcheck/00install.out’ for details.
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcppMLPACK.Rcheck/00install.out’ for details.
installed size is 37.3Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      25.5Mb
    libs      9.9Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    include   6.2Mb
    libs      4.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    jsonexamples   3.8Mb
    libs           1.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rcrypt.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘rdf_intro.Rmd’ using rmarkdown
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.

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 41-42 (rdf_intro.Rmd) 
Error: processing vignette 'rdf_intro.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rdf_intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Found the following significant warnings:
  dist.cpp:19:33: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  dist.cpp:65:33: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  dist.cpp:111:36: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rdist.Rcheck/00install.out’ for details.
Running examples in ‘Rdsm-Ex.R’ failed
The error most likely occurred in:

> ### Name: readsync
> ### Title: Syncing file-backed variables.
> ### Aliases: readsync writesync
> 
> ### ** Examples
> 
> library(parallel)
> c2 <- makeCluster(2)
> mgrinit(c2)
Warning in for (v in val) { :
  closing unused connection 6 (<-localhost:11715)
Warning in for (v in val) { :
  closing unused connection 5 (<-localhost:11715)
[[1]]
[1] 0

[[2]]
[1] 0

> mgrmakevar(c2,"x",1,1,fs=TRUE)
Error in bigmemory::filebacked.big.matrix(nrow = nr, ncol = nc, type = vartype,  : 
  Backing file already exists! Either remove or specify
           different backing file
Calls: mgrmakevar -> <Anonymous>
Execution halted
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   7.8Mb
Error(s) in re-building vignettes:
--- re-building ‘recexcavAAR-vignette-1.Rmd’ using rmarkdown
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 13-17 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-1.Rmd’

--- re-building ‘recexcavAAR-vignette-2.Rmd’ using rmarkdown
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 13-17 (recexcavAAR-vignette-2.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-2.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-2.Rmd’

--- re-building ‘recexcavAAR-vignette-3.Rmd’ using rmarkdown
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 13-17 (recexcavAAR-vignette-3.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-3.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-3.Rmd’

SUMMARY: processing the following files failed:
  ‘recexcavAAR-vignette-1.Rmd’ ‘recexcavAAR-vignette-2.Rmd’
  ‘recexcavAAR-vignette-3.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   4.1Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs  16.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/red.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.7Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   2.4Mb
Error(s) in re-building vignettes:
--- re-building ‘getting-started.Rmd’ using rmarkdown
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.

Attaching package: 'rENA'

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

    show

Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 107-117 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘getting-started.Rmd’

--- re-building ‘means-rotation.Rmd’ using rmarkdown
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.
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout


Attaching package: 'rENA'

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

    show

Quitting from lines 56-82 (means-rotation.Rmd) 
Error: processing vignette 'means-rotation.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘means-rotation.Rmd’

SUMMARY: processing the following files failed:
  ‘getting-started.Rmd’ ‘means-rotation.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [102s/94s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 252 | SKIPPED: 47 | WARNINGS: 0 | FAILED: 41 ]
  1. Error: we can query actions for a sample project (@test-actions.R#10) 
  2. Error: we can query actions when no lockfile has yet been generated (@test-actions.R#32) 
  3. Error: package installation does not fail with non-writable cache (@test-cache.R#74) 
  4. Failure: the cache is used even if RENV_PATHS_LIBRARY is non-canonical (@test-cache.R#96) 
  5. Error: Suggest dependencies are ignored by default (@test-dependencies.R#196) 
  6. Error: Suggest dependencies are used when requested (@test-dependencies.R#204) 
  7. Error: library/ is excluded from .gitignore as appropriate (@test-infrastructure.R#39) 
  8. Error: requested version in DESCRIPTION file is honored (@test-install.R#21) 
  9. Error: packages can be installed from local sources (@test-install.R#107) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.8Mb
Found the following significant warnings:
  regalg.cpp:215:10: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
  regalg.cpp:454:10: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/resemble.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Package suggested but not available for checking: ‘rsolr’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/restlos.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs      3.1Mb
    swagger   1.4Mb
Running ‘testthat.R’ [8s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 3. Error: Properties are automatically converted in inherited classes (@test-
  Typea new-style class can't have only classic bases
  Backtrace:
   1. reticulate::PyClass(...)
   2. bt$type(classname, inherit, do.call(reticulate::dict, defs))
   3. reticulate:::py_call_impl(callable, dots$args, dots$keywords)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 114 | SKIPPED: 42 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: Can inherit from a Python class (@test-python-class.R#57) 
  2. Error: Can inherit from multiple Python classes (@test-python-class.R#84) 
  3. Error: Properties are automatically converted in inherited classes (@test-python-class.R#166) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/retistruct.Rcheck/00install.out’ for details.
No protocol specified
Namespace in Imports field not imported from: ‘RTriangle’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘log_parsing.Rmd’ using rmarkdown
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.
Read 1000 items
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
--- finished re-building ‘log_parsing.Rmd’

--- re-building ‘url_parsing.Rmd’ using rmarkdown
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.
Error: processing vignette 'url_parsing.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘url_parsing.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  33.0Mb
Package suggested but not available for checking: ‘MKmisc’
Running examples in ‘RFLPtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: RFLPtools-package
> ### Title: Tools to analyse RFLP-data
> ### Aliases: RFLPtools-package RFLPtools
> ### Keywords: package multivariate cluster
> 
> ### ** Examples
> 
> data(RFLPdata)
> res <- RFLPdist(RFLPdata)
> plot(hclust(res[[1]]), main = "Euclidean distance")
> 
> par(mfrow = c(1,2))
> plot(hclust(RFLPdist(RFLPdata, nrBands = 3)), cex = 0.7)
> RFLPplot(RFLPdata, nrBands = 3, mar.bottom = 6, cex.axis = 0.8)
> 
> data(RFLPref)
> RFLPrefplot(RFLPdata, RFLPref, nrBands = 6, cex.axis = 0.8)
> 
> 
> library(MKmisc)
Error in library(MKmisc) : there is no package called ‘MKmisc’
Execution halted
Errors in running code in vignettes:
when running code in ‘RFLPtools.Rnw’
  ...
 - attr(*, "Diag")= logi FALSE
 - attr(*, "Upper")= logi FALSE
 - attr(*, "method")= chr "maximum"
 - attr(*, "call")= language dist(x = x, method = "maximum")

> library(MKmisc)

  When sourcing ‘RFLPtools.R’:
Error: there is no package called ‘MKmisc’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘RFLPtools.Rnw’ using Sweave
Loading required package: RColorBrewer

Error: processing vignette 'RFLPtools.Rnw' failed with diagnostics:
 chunk 5 (label = cor) 
Error in library(MKmisc) : there is no package called ‘MKmisc’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘rfm-customer-level-data.Rmd’ using rmarkdown
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.

Attaching package: 'dplyr'

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

    group_rows

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 230-274 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rfm-customer-level-data.Rmd’

--- re-building ‘rfm-transaction-level-data.Rmd’ using rmarkdown
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.

Attaching package: 'dplyr'

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

    group_rows

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 227-271 (rfm-transaction-level-data.Rmd) 
Error: processing vignette 'rfm-transaction-level-data.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rfm-transaction-level-data.Rmd’

SUMMARY: processing the following files failed:
  ‘rfm-customer-level-data.Rmd’ ‘rfm-transaction-level-data.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: package ‘mixOmics’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RGCxGC.Rcheck/00install.out’ for details.
installed size is 144.9Mb
  sub-directories of 1Mb or more:
    libs      142.0Mb
    pictures    1.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.6Mb
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(rgeolocate)
  > 
  > test_check("rgeolocate")
  ── 1. Failure: non-existent files are detected (@test_maxmind.R#3)  ────────────
  `x` threw an error with unexpected message.
  Expected match: "could not be opened"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 51 SKIPPED: 0 FAILED: 1
  1. Failure: non-existent files are detected (@test_maxmind.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rggobi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rgl.Rcheck/00install.out’ for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc     3.7Mb
    fonts   1.5Mb
    libs    4.2Mb
Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.

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.
Error(s) in re-building vignettes:
--- re-building ‘WebGL.Rmd’ using rmarkdown
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 17-19 (WebGL.Rmd) 
Error: processing vignette 'WebGL.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘WebGL.Rmd’

--- re-building ‘legacyWebGL.Rmd’ using rmarkdown
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 17-19 (legacyWebGL.Rmd) 
Error: processing vignette 'legacyWebGL.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘legacyWebGL.Rmd’

--- re-building ‘rgl.Rmd’ using rmarkdown
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 16-19 (rgl.Rmd) 
Error: processing vignette 'rgl.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘rgl.Rmd’

SUMMARY: processing the following files failed:
  ‘WebGL.Rmd’ ‘legacyWebGL.Rmd’ ‘rgl.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rglwidget.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'graph', 'gWidgetsRGtk2', 'hyperdraw', 'hypergraph', 'playwith',
  'pmg', 'rggobi', 'Rgraphviz', 'SVGAnnotation'
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  11.1Mb
    libs   9.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_rhandsontable.Rmd’ using rmarkdown
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 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘intro_rhandsontable.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rhpc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: loading Rplot failed
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RHRV.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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No protocol specified
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No protocol specified
No protocol specified
No protocol specified
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No protocol specified
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.
Namespaces in Imports field not imported from:
  ‘httr’ ‘remotes’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘installr’
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RInside.Rcheck/00install.out’ for details.
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

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.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Running examples in ‘RISmed-Ex.R’ failed
The error most likely occurred in:

> ### Name: Cited
> ### Title: Number of citations
> ### Aliases: Cited
> 
> ### ** Examples
> 
> res <- EUtilsSummary("myeloma[ti]", mindate = "2002/01/01", maxdate = "2002/02/01", retmax = 5)
> Cited(res)
Warning in readLines(the_url) :
  cannot open URL 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?retmode=xml&dbfrom=pubmed&id=11818668&cmd=neighbor': HTTP status was '429 Unknown Error'
Error in readLines(the_url) : 
  cannot open the connection to 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?retmode=xml&dbfrom=pubmed&id=11818668&cmd=neighbor'
Calls: Cited -> Cited -> sapply -> lapply -> FUN -> readLines
Execution halted
Running examples in ‘RiverLoad-Ex.R’ failed
The error most likely occurred in:

> ### Name: method4
> ### Title: Load estimation with time-weighted concentration method
> ### Aliases: method4
> ### Keywords: univ
> 
> ### ** Examples
> 
> data("flow.data1", "conc.data1")
> union<-db.union(flow.data1, conc.data1)
> met4<-method4(union, 2)
> met4.month<-method4(union, 2, "month")
Error in x[[jj]][iseq] <- vjj : replacement has length zero
Calls: method4 -> [<- -> [<-.data.frame
Execution halted
Note: information on .o files is not available
File ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  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 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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
Packages suggested but not available for checking:
  'Biobase', 'genefilter', 'golubEsets'
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rknots.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 44.4Mb
  sub-directories of 1Mb or more:
    libs  43.8Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rLiDAR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rLindo.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Missing or unexported object: ‘tidyr::one_of’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    rmd   8.2Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RMark.Rcheck/00install.out’ for details.
installed size is 52.2Mb
  sub-directories of 1Mb or more:
    libs  51.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RmecabKo.Rcheck/00install.out’ for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.7Mb
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    libs  40.5Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    libs  28.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rMouse.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rmpi.Rcheck/00install.out’ for details.
Package required but not available: ‘splineTimeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Packages suggested but not available for checking: 'topGO', 'DESeq'
Packages unavailable to check Rd xrefs: ‘DESeq’, ‘topGO’
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doxygen   1.5Mb
    libs      3.2Mb
installed size is 97.5Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     95.4Mb
Found the following executable files:
  inst/extra/CD_BBI_16P02/CD_BBI_16P02-R1/10/fid
  inst/extra/CD_BBI_16P02/CD_BBI_16P02-R2/10/fid
  inst/extra/CD_BBI_16P02/CD_BBI_16P02-R3/10/fid
  inst/extra/CD_BBI_16P02/CD_BBI_16P02-R8/10/fid
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
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 188-195 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Column `is_oa` is unknown
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  17.0Mb
Package required but not available: ‘gprege’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'beadarrayExampleData',
  'illuminaHumanv3.db'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RobLoxBioC.Rcheck/00install.out’ for details.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
installed size is 33.0Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RockFab.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ROCS.Rcheck/00install.out’ for details.
Package required but not available: ‘clpAPI’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
sh: cmake: command not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: cmake: command not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘RobLox’
Package unavailable to check Rd xrefs: ‘RobLox’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ROracle.Rcheck/00install.out’ for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    libs    2.1Mb
    tests   1.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rpanel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rpdb.Rcheck/00install.out’ for details.
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rpg.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘NEWS.Rmd’ using rmarkdown
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.
--- finished re-building ‘NEWS.Rmd’

--- re-building ‘rpivotTableIntroduction.Rmd’ using rmarkdown
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 51-53 (rpivotTableIntroduction.Rmd) 
Error: processing vignette 'rpivotTableIntroduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rpivotTableIntroduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rpolyhedra.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rpoppler.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rpredictit-vignette.Rmd’ using rmarkdown
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 54-56 (rpredictit-vignette.Rmd) 
Error: processing vignette 'rpredictit-vignette.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘rpredictit-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rquake.Rcheck/00install.out’ for details.
installed size is 90.3Mb
  sub-directories of 1Mb or more:
    libs  89.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rrd.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RRphylo.Rcheck/00install.out’ for details.
No protocol specified
Namespace in Imports field not imported from: ‘mvMORPH’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rsampletrees.Rcheck/00install.out’ for details.
No protocol specified

(R:70774): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:70780): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:70786): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified

(R:70792): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:70816): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:70840): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:70846): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:70852): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:70858): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:70870): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
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.
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    dependencies  20.2Mb
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(rsconnect)
  > 
  > test_check("rsconnect")
  ── 1. Failure: linter warns about absolute paths and relative paths (@test-lint.
  as.numeric(absPathLintedIndices) not identical to 15.
  Lengths differ: 0 is not 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 257 | SKIPPED: 25 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: linter warns about absolute paths and relative paths (@test-lint.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Note: information on .o files is not available
File ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rserve.Rcheck/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’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is 46.4Mb
  sub-directories of 1Mb or more:
    libs  45.8Mb
installed size is 149.1Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    doc     4.5Mb
    libs  142.5Mb
Running examples in ‘rstanarm-Ex.R’ failed
The error most likely occurred in:

> ### Name: example_jm
> ### Title: Example joint longitudinal and time-to-event model
> ### Aliases: example_jm
> 
> ### ** Examples
> 
>   set.seed(123)
>   example_jm <- 
+      stan_jm(formulaLong = logBili ~ year + (1 | id), 
+              dataLong = pbcLong[1:101,],
+              formulaEvent = survival::Surv(futimeYears, death) ~ sex + trt, 
+              dataEvent = pbcSurv[1:15,],
+              time_var = "year",
+              # this next line is only to keep the example small in size!
+              chains = 1, seed = 12345, iter = 100, refresh = 0)
Loading required namespace: data.table
Fitting a univariate joint model.

Please note the warmup may be much slower than later iterations!
[1] "Error in sampler$call_sampler(args_list[[i]]) : "             
[2] "  empty_nested() must be true before calling recover_memory()"
error occurred during calling the sampler; sampling not done
Error in check_stanfit(stanfit) : 
  Invalid stanfit object produced please report bug
Calls: stan_jm -> stan_jm.fit -> check_stanfit
Execution halted
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    libs  28.0Mb
installed size is 227.5Mb
  sub-directories of 1Mb or more:
    libs  224.8Mb
installed size is 69.5Mb
  sub-directories of 1Mb or more:
    libs  68.3Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  13.2Mb
installed size is 61.3Mb
  sub-directories of 1Mb or more:
    libs  61.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rsymphony.Rcheck/00install.out’ for details.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    Lib  11.6Mb
Running ‘run_test.R’ [7s/7s]
Running the tests in ‘tests/run_test.R’ failed.
Complete output:
  > all_files <- list.files("testthat",full.names=T,pattern="*.R$")
  > 
  > sapply(all_files,source)
  Loading required package: magick
  Linking to ImageMagick 6.9.9.39
  Enabled features: cairo, fontconfig, freetype, lcms, pango, rsvg, webp
  Disabled features: fftw, ghostscript, x11
  Loading required package: XML
  Error: Test failed: 'RTestCollection write HTML summary errors'
  * `writeExecSummary.html(...)` produced warnings.
  * `writeExecSummary.html(...)` produced warnings.
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.9Mb
    projects   2.7Mb
Found the following significant warnings:
  getFunctions.cpp:90:16: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RTransProb.Rcheck/00install.out’ for details.
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  20.9Mb
Running ‘testthat.R’ [8s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 581 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 30 ]
  1. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#264) 
  2. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#268) 
  3. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#264) 
  4. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#268) 
  5. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#264) 
  6. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#268) 
  7. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#264) 
  8. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#268) 
  9. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#264) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘mcMat.Rmd’ using rmarkdown
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 20-26 (mcMat.Rmd) 
Error: processing vignette 'mcMat.Rmd' failed with diagnostics:
unable to load shared object '/private/tmp/RtmpoVHOoq/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_165ed6512ebe1/sourceCpp_2.so':
  dlopen(/private/tmp/RtmpoVHOoq/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_165ed6512ebe1/sourceCpp_2.so, 6): Library not loaded: rTRNG.so
  Referenced from: /private/tmp/RtmpoVHOoq/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_165ed6512ebe1/sourceCpp_2.so
  Reason: image not found
--- failed re-building ‘mcMat.Rmd’

--- re-building ‘rTRNG.Rmd’ using rmarkdown
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.
Building shared library for Rcpp code chunk...
Quitting from lines 106-129 (rTRNG.Rmd) 
Error: processing vignette 'rTRNG.Rmd' failed with diagnostics:
unable to load shared object '/private/tmp/Rtmpwa9L3n/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_1660a3dfcef98/sourceCpp_2.so':
  dlopen(/private/tmp/Rtmpwa9L3n/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_1660a3dfcef98/sourceCpp_2.so, 6): Library not loaded: rTRNG.so
  Referenced from: /private/tmp/Rtmpwa9L3n/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_1660a3dfcef98/sourceCpp_2.so
  Reason: image not found
--- failed re-building ‘rTRNG.Rmd’

--- re-building ‘rTRNG.useR2017.pdf.asis’ using asis
--- finished re-building ‘rTRNG.useR2017.pdf.asis’

SUMMARY: processing the following files failed:
  ‘mcMat.Rmd’ ‘rTRNG.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.6Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.4Mb
Running examples in ‘rviewgraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: rViewGraph
> ### Title: This is a function to create and start the Java graph animation
> ###   GUI.
> ### Aliases: rViewGraph rViewGraph.default rViewGraph.Matrix
> ###   rViewGraph.igraph
> ### Keywords: graph
> 
> ### ** Examples
> 
> # 
> # Viewing an Erdos Renyui random graph specified by random edges.
> f = sample(100,size=200,replace=TRUE)
> t = sample(100,size=200,replace=TRUE)
> vft = rViewGraph(cbind(f,t))
Error in .jnew("rviewgraph/RViewGraph", v, f, t, x, y, directed, running) : 
  java.awt.HeadlessException
Calls: rViewGraph ... rViewGraph.default -> rViewGraphCore -> init -> .jnew
Execution halted
installed size is 62.9Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs     58.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RVowpalWabbit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  qwiener.c:60:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  qwiener.c:69:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RWiener.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs    8.3Mb
    yacas   1.3Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs    9.1Mb
    yacas   1.3Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
No protocol specified
Namespaces in Imports field not imported from:
  ‘R6’ ‘mgcv’
  All declared Imports should be used.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SafeBayes.Rcheck/00install.out’ for details.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   8.8Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.4Mb
Packages suggested but not available for checking:
  'GO.db', 'GOstats', 'mixer', 'org.Sc.sgd.db'
Running examples in ‘sara4r-Ex.R’ failed
The error most likely occurred in:

> ### Name: sara4r
> ### Title: An R-GUI for Spatial Analysis of Surface Runoff using the
> ###   NRCS-CN Method
> ### Aliases: sara4r
> 
> ### ** Examples
> 
> sara4r()

(R:7958): GLib-GObject-WARNING **: invalid (NULL) pointer instance

(R:7958): GLib-GObject-CRITICAL **: g_signal_connect_data: assertion `G_TYPE_CHECK_INSTANCE (instance)' failed

(R:7958): Gtk-WARNING **: Screen for GtkWindow not set; you must always set
a screen for a GtkWindow before using the window

(R:7958): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:7958): Gdk-CRITICAL **: gdk_colormap_get_visual: assertion `GDK_IS_COLORMAP (colormap)' failed

(R:7958): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:7958): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:7958): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:7958): Gdk-CRITICAL **: gdk_window_new: assertion `GDK_IS_WINDOW (parent)' failed

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: .RGtkCall("S_gtk_widget_show_all", object, PACKAGE = "RGtk2")
 2: method(obj, ...)
 3: INIRENA$showAll()
 4: sara4r()
An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘sass.Rmd’ using rmarkdown
Warning in engine$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 50-51 (sass.Rmd) 
Error: processing vignette 'sass.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sass.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Malformed Title field: should not end in a period.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
Error(s) in re-building vignettes:
  ...
--- re-building ‘gettingstarted.Rmd’ using rmarkdown
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.
--- finished re-building ‘gettingstarted.Rmd’

--- re-building ‘article.Rnw’ using knitr
Error: processing vignette 'article.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘article.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/scpm.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘oligoClasses’
Packages required but not available: 'ALL', 'ConsensusClusterPlus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.7Mb
Found the following executable file:
  inst/external/env/bio14.bil
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘seasonalview’
Package unavailable to check Rd xrefs: ‘seasonalview’
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  13.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SEERaBomb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Segmentor3IsBack.Rcheck/00install.out’ for details.
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.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
No protocol specified
No protocol specified
Namespaces in Imports field not imported from:
  ‘htmlTable’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.1Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SeqFeatR.Rcheck/00install.out’ for details.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   8.7Mb
Found the following executable files:
  inst/vcf/all.anno.filtered.extract.headerFixed.bcf.gz.scIdx
  inst/vcf/all.anno.filtered.extract.vcf.gz.scIdx
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/sequenza.Rcheck/00install.out’ for details.
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
Packages suggested but not available for checking:
  'loomR', 'SingleCellExperiment', 'MAST', 'monocle'
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   7.7Mb
Package unavailable to check Rd xrefs: ‘loomR’
installed size is 187.5Mb
  sub-directories of 1Mb or more:
    doc      12.0Mb
    libs    171.3Mb
    sqlite    1.5Mb
Error(s) in re-building vignettes:
--- re-building ‘sf1.Rmd’ using rmarkdown
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.
--- finished re-building ‘sf1.Rmd’

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

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

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

--- re-building ‘sf5.Rmd’ using rmarkdown
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 213-215 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sf5.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘sfsmisc-Ex.R’ failed
The error most likely occurred in:

> ### Name: pkgLibs
> ### Title: R Package Compiled Code Library Dependencies (on Unix-alikes)
> ### Aliases: pkgLibs
> ### Keywords: interface
> 
> ### ** Examples
> 
> # for the example only using standard R packages :
> myPkgs <- c("stats", "MASS", "rpart", "Matrix")
> pl <- pkgLibs(myPkgs)
sh: ldd: command not found
Error in system(paste(cmd, so), intern = TRUE) : error in running command
Calls: pkgLibs -> lapply -> FUN -> lapply -> FUN -> sub -> system
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Found the following significant warnings:
  Warning: package ‘mixOmics’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/sgPLS.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘SGP.Rmd’ using rmarkdown
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 13-29 (SGP.Rmd) 
Error: processing vignette 'SGP.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP.Rmd’

--- re-building ‘SGP_Data_Analysis.Rmd’ using rmarkdown
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 13-29 (SGP_Data_Analysis.Rmd) 
Error: processing vignette 'SGP_Data_Analysis.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Analysis.Rmd’

--- re-building ‘SGP_Data_Preparation.Rmd’ using rmarkdown
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 13-29 (SGP_Data_Preparation.Rmd) 
Error: processing vignette 'SGP_Data_Preparation.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Preparation.Rmd’

SUMMARY: processing the following files failed:
  ‘SGP.Rmd’ ‘SGP_Data_Analysis.Rmd’ ‘SGP_Data_Preparation.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/shapes.Rcheck/00install.out’ for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    www   8.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/shinyRGL.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘edgeR’
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
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 89-90 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘getting-started.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started.Rmd’

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

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SimEUCartelLaw.Rcheck/00install.out’ for details.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  11.9Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
Package suggested but not available for checking: ‘topologyGSA’
Error(s) in re-building vignettes:
  ...
--- re-building ‘simPATHy.Rmd’ using rmarkdown
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 252-258 (simPATHy.Rmd) 
Error: processing vignette 'simPATHy.Rmd' failed with diagnostics:
there is no package called 'topologyGSA'
--- failed re-building ‘simPATHy.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SimRAD.Rcheck/00install.out’ for details.
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  18.2Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   5.9Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.5Mb
installed size is 31.8Mb
  sub-directories of 1Mb or more:
    libs  30.2Mb
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("slickR")
  ── 1. Error: slick div method: widget (@test-div_method.R#44)  ─────────────────
  Saving a widget with selfcontained = TRUE requires pandoc. For details see:
  https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
  Backtrace:
   1. testthat::expect_equal(...)
   5. slickR:::slick_div.htmlwidget(readRDS("../assets/widget1.Rds"))
   6. htmlwidgets::saveWidget(x, file = tf)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 27 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: slick div method: widget (@test-div_method.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CustomTable.Rmd’ using rmarkdown
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.
--- finished re-building ‘CustomTable.Rmd’

--- re-building ‘SmartEDA.Rmd’ using rmarkdown
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 132-133 (SmartEDA.Rmd) 
Error: processing vignette 'SmartEDA.Rmd' failed with diagnostics:
unused argument (options = options)
--- failed re-building ‘SmartEDA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: package ‘BiocParallel’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SmartSVA.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘SMITIDstruct’
Error(s) in re-building vignettes:
  ...
--- re-building ‘smm.Rnw’ using Sweave
Error: processing vignette 'smm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'smm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘smm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/smoothAPC.Rcheck/00install.out’ for details.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   8.9Mb
Found the following significant warnings:
  ./Scythe_IDE.cpp:70:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:107:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:108:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:109:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:147:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:148:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:149:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:189:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:211:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:212:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:262:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:265:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:266:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/smoothSurv.Rcheck/00install.out’ for details.
Running examples in ‘sm-Ex.R’ failed
The error most likely occurred in:

> ### Name: sm.surface3d
> ### Title: Adding a regression surface to an rgl plot.
> ### Aliases: sm.surface3d
> ### Keywords: nonparametric regression smooth
> 
> ### ** Examples
> 
> with(trawl, {
+    Zone93    <- (Year == 1 & Zone == 1)
+    Position  <- cbind(Longitude - 143, Latitude)
+    model1 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.1, 0.1), display = "rgl", xlab="Longitude - 143")
+    model2 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.2, 0.2), display = "none")
+    sm.surface3d(model2$eval.points, model2$est, model1$scaling, col = "red")
+ })
Error in sm.surface3d(model2$eval.points, model2$est, model1$scaling,  : 
  a scaling must be specified.
Calls: with -> with.default -> eval -> eval -> sm.surface3d
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/snpReady.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   5.5Mb
Error(s) in re-building vignettes:
--- re-building ‘novel_solutions.Rmd’ using rmarkdown
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.
--- finished re-building ‘novel_solutions.Rmd’

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

--- re-building ‘understanding_sortable_js.Rmd’ using rmarkdown
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.
Warning in normalizePath(f2) :
  path[1]="webshot2dfb12c986ff.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot2dfb12c986ff.png': No such file or directory
Quitting from lines 71-72 (understanding_sortable_js.Rmd) 
Error: processing vignette 'understanding_sortable_js.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘understanding_sortable_js.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘SciencesPo’
Packages suggested but not available for checking:
  'r2cytoscape', 'BiocStyle', 'hgu95av2.db', 'ALL', 'org.Hs.eg.db'
Package unavailable to check Rd xrefs: ‘ALL’
Error(s) in re-building vignettes:
--- re-building ‘SourceSet.Rmd’ using rmarkdown
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.
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect,
    is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Identifing all possible orderings..
Total run time: 1.46 secs
Identifing all possible orderings..
Total run time: 0.79 secs
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.
Warning in normalizePath(f2) :
  path[1]="webshot1036025ae8906.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot1036025ae8906.png': No such file or directory
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘SourceSet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Missing or unexported objects:
  ‘pomp::covariate_table’ ‘pomp::gillespie_hl’
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs  32.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_sparkline.Rmd’ using rmarkdown
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.
Warning in normalizePath(f2) :
  path[1]="webshot4c28b900111.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot4c28b900111.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘intro_sparkline.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  29.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  10.0Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    R      5.3Mb
    doc    4.9Mb
    help   5.4Mb
    libs   1.8Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs   9.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   3.2Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/sphereplot.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SphericalCubature.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/sppmix.Rcheck/00install.out’ for details.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   7.3Mb
Running examples in ‘SRRS-Ex.R’ failed
The error most likely occurred in:

> ### Name: SRRS-package
> ### Title: The Stepwise Response Refinement Screener (SRRS)
> ### Aliases: SRRS-package
> 
> ### ** Examples
> 
> SRRS()
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: SRRS -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 57.7Mb
  sub-directories of 1Mb or more:
    libs  57.4Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    include   9.9Mb
    lib       1.9Mb
Package which this enhances but not available for checking: ‘mnlogit’
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
No protocol specified

(R:4520): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:4528): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:4536): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified

(R:4544): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:4570): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:4598): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:4606): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:4614): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:4622): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:4636): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StatDA.Rcheck/00install.out’ for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   4.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.4Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.2Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.1Mb
    datasets   2.6Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’

Package suggested but not available for checking: ‘BSgenome.Ptroglodytes.UCSC.panTro5’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Packages suggested but not available for checking: 'limma', 'samr'
Found the following significant warnings:
  BIRCH/CFTree.cpp:18:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/stream.Rcheck/00install.out’ for details.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  10.0Mb
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    libs  32.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/STRMPS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/stR.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘stRvignette.Rmd’ using rmarkdown
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 13-17 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
there is no package called 'seasonal'
--- failed re-building ‘stRvignette.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SubVis.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘suddengains-tutorial.Rmd’ using rmarkdown
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 472-479 (suddengains-tutorial.Rmd) 
Error: processing vignette 'suddengains-tutorial.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘suddengains-tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘suddengains-tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/supervisedPRIM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Surrogate.Rcheck/00install.out’ for details.
No protocol specified
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
Package suggested but not available for checking: ‘BiocParallel’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/survHE.Rcheck/00install.out’ for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.2Mb
    doc    3.3Mb
Package unavailable to check Rd xrefs: ‘survJamda’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs   5.3Mb
File ‘svmpath/libs/svmpath.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: 'cplexAPI', 'clpAPI'
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/symbolicDA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/symengine.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘HTML.Rmd’ using rmarkdown
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.
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

Quitting from lines 44-45 (HTML.Rmd) 
Error: processing vignette 'HTML.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘HTML.Rmd’

--- re-building ‘tables.Rnw’ using Sweave
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: ‘Hmisc’

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

    format.pval, units

--- finished re-building ‘tables.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.1Mb
Package suggested but not available for checking: ‘duckdb’
Packages suggested but not available for checking:
  'limma', 'edgeR', 'DESeq2', 'S4Vectors'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    tklibs   4.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    libs  35.9Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    apps   2.0Mb
    libs   8.7Mb
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  15.9Mb
Running examples in ‘TELP-Ex.R’ failed
The error most likely occurred in:

> ### Name: telp
> ### Title: The Base Function of This Package The Free Evocation of Words
> ###   Technique
> ### Aliases: telp
> ### Keywords: function
> 
> ### ** Examples
> 
> telp()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: telp ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/tensorsparse.Rcheck/00install.out’ for details.
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       7.4Mb
    tessdata  14.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘testcorr.Rnw’ using Sweave
Error: processing vignette 'testcorr.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'testcorr.tex' failed.
Messages:
/usr/local/bin/texi2dvi: biber failed
--- failed re-building ‘testcorr.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'Rsymphony', 'gurobi'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.9Mb
    libs   3.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
Found the following significant warnings:
  ref.cpp:24:14: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:35:14: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:50:16: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:61:16: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/tidyxl.Rcheck/00install.out’ for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
File ‘tidyxl/libs/tidyxl.so’:
  Found ‘_abort’, possibly from ‘abort’ (C)
    Object: ‘xlex.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(s) in re-building vignettes:
--- re-building ‘Tigger-Vignette.Rmd’ using rmarkdown
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.
Loading required package: ggplot2

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

sh: sysctl: command not found
Quitting from lines 107-109 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command
--- failed re-building ‘Tigger-Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Tigger-Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [3s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] 2015-01-01 23:56:02 - 2015-01-01 == 23.9 hours
  
  ── 3. Failure: updates on ydas works correctly with leap year (@test-update.R#17
  time_update(...) not equal to ymd("2016-01-10", tz = "America/New_York").
  1/1 mismatches
  [1] 2016-01-10 23:56:02 - 2016-01-10 == 23.9 hours
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 685 SKIPPED: 0 FAILED: 3
  1. Failure: updates on ydas works correctly with leap year (@test-update.R#173) 
  2. Failure: updates on ydas works correctly with leap year (@test-update.R#175) 
  3. Failure: updates on ydas works correctly with leap year (@test-update.R#177) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/tkrgl.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/tkRplotR.Rcheck/00install.out’ for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    2.9Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘tmod.rmd’ using rmarkdown
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 51-59 (tmod.rmd) 
Error: processing vignette 'tmod.rmd' failed with diagnostics:
there is no package called 'limma'
--- failed re-building ‘tmod.rmd’

SUMMARY: processing the following file failed:
  ‘tmod.rmd’

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: ‘Rpoppler’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/tolerance.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'RGtk2', 'gWidgetsRGtk2'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/topologyGSA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ToxicoGx.Rcheck/00install.out’ for details.
File ‘tpr/libs/tpr.so’:
  Found ‘__ZNSt3__14cerrE’, 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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘TourDetrackeR.Rmd’ using rmarkdown
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.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Source : http://tile.stamen.com/toner/13/4056/2748.png
Source : http://tile.stamen.com/toner/13/4057/2748.png
Source : http://tile.stamen.com/toner/13/4056/2749.png
Source : http://tile.stamen.com/toner/13/4057/2749.png
Quitting from lines 106-108 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘TourDetrackeR.Rmd’

--- re-building ‘trackeR.Rnw’ using Sweave
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Loading required package: splines
Loading required package: Matrix

Attaching package: 'fda'

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

    matplot

--- finished re-building 'trackeR.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/TreeLS.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    extdata   1.4Mb
    libs      9.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/treespace.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is 85.2Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs  80.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘choropleth_maps_with_tricolore.Rmd’ using rmarkdown
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 130-139 (choropleth_maps_with_tricolore.Rmd) 
Error: processing vignette 'choropleth_maps_with_tricolore.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘choropleth_maps_with_tricolore.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/trinROC.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/TSclust.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘TSodbc’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/TSCS.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘TSodbc’
Package unavailable to check Rd xrefs: ‘TSodbc’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
> z <- TSget("ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT", 
+     eurostat)
Apr 16, 2019 10:07:08 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/dataflow/ESTAT/ei_nama_q/latest/
Apr 16, 2019 10:07:08 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
SEVERE: Internal Server Error

  When sourcing ‘Guide.R’:
Error: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxResponseException: (500): Error on the provider side.
Execution halted
when running code in ‘GuideAppendix.Stex’
  ...

> options(continue = "  ")

> user <- Sys.getenv("MYSQL_USER")

> setup <- RMySQL::dbConnect(RMySQL::MySQL(), dbname = "test")

  When sourcing ‘GuideAppendix.R’:
Error: Failed to connect to database: Error: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   8.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/tsmp.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Plotting_Time_Series.Rmd’ using rmarkdown
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.
Warning in normalizePath(f2) :
  path[1]="webshot100af396368a2.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot100af396368a2.png': No such file or directory
Quitting from lines 39-44 (Plotting_Time_Series.Rmd) 
Error: processing vignette 'Plotting_Time_Series.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Plotting_Time_Series.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/TTAinterfaceTrendAnalysis.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘BiocParallel’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ttScreening.Rcheck/00install.out’ for details.
Package required but not available: ‘ChemmineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following executable files:
  inst/examples/ko.txt
  inst/examples/ru/koi8-r.txt
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs       23.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/uFTIR.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
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 66-94 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ungroup.Rcheck/00install.out’ for details.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.6Mb
    libs   6.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  21.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/VALERIE.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 144.7Mb
  sub-directories of 1Mb or more:
    extdata    1.0Mb
    libs     143.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Error(s) in re-building vignettes:
--- re-building ‘basic_usage.Rmd’ using rmarkdown
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.

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

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.
Warning in normalizePath(f2) :
  path[1]="webshotcf6e309706a3.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotcf6e309706a3.png': No such file or directory
Quitting from lines 54-55 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘basic_usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/VecStatGraphs3D.Rcheck/00install.out’ for details.
Running examples in ‘VecStatGraphs3D-Ex.R’ failed
The error most likely occurred in:

> ### Name: DrawModuleAndAngleDistribution3D
> ### Title: Graphic representation of Module and Angle Distribution.
> ### Aliases: DrawModuleAndAngleDistribution3D
> ### Keywords: graphics
> 
> ### ** Examples
> 
>    FileName<-system.file("data/XYZcoor.txt", package="VecStatGraphs3D")
>    dat<-LoadData3D(FileName, Type=1)
>    DrawModuleAndAngleDistribution3D(dat, plane="XY");
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: DrawModuleAndAngleDistribution3D ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/vegan3d.Rcheck/00install.out’ for details.
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/vennplot.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    doc    1.2Mb
    help   2.9Mb
Package required but not available: ‘coRdon’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
No protocol specified
No protocol specified
No protocol specified
Namespaces in Imports field not imported from:
  ‘sp’ ‘viridis’
  All declared Imports should be used.
installed size is 55.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  54.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/viromeBrowser.Rcheck/00install.out’ for details.
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
installed size is 36.9Mb
  sub-directories of 1Mb or more:
    libs  36.6Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/VSE.Rcheck/00install.out’ for details.
File ‘waffect/libs/waffect.so’:
  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.
installed size is 58.7Mb
  sub-directories of 1Mb or more:
    libs  57.5Mb
Running examples in ‘walker-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_predict
> ### Title: Prediction intervals for walker object
> ### Aliases: plot_predict
> 
> ### ** Examples
> 
> set.seed(1)
> n <- 60
> slope <- 0.0001 + cumsum(rnorm(n, 0, sd = 0.01))
> beta <- numeric(n)
> beta[1] <- 1
> for(i in 2:n) beta[i] <- beta[i-1] + slope[i-1]
> ts.plot(beta)                
> x <- rnorm(n, 1, 0.5)
> alpha <- 2
> ts.plot(beta * x)
> 
> signal <- alpha + beta * x
> y <- rnorm(n, signal, 0.25)
> ts.plot(cbind(signal, y), col = 1:2)
> data_old <- data.frame(y = y[1:(n-10)], x = x[1:(n-10)])
> rw2_fit <- walker(y ~ 1 + 
+                     rw2(~ -1 + x,
+                         beta_prior = c(0, 10), 
+                         sigma_prior = c(0, 10), 
+                         slope_prior = c(0, 10)), 
+                   sigma_y_prior = c(0, 10), 
+                   beta_prior = c(0, 10),
+                   iter = 400, chains = 1, data = data_old)

SAMPLING FOR MODEL 'walker_lm' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 0.000887 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 8.87 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:   1 / 400 [  0%]  (Warmup)
[1] "Error in sampler$call_sampler(args_list[[i]]) : "
[2] "  c++ exception (unknown reason)"                
error occurred during calling the sampler; sampling not done
> 
> pred <- predict(rw2_fit, newdata = data.frame(x=x[(n-9):n]))
Stan model 'walker_lm' does not contain samples.
Stan model 'walker_lm' does not contain samples.
Error in matrix(0, n_iter, 0) : non-numeric matrix extent
Calls: predict -> predict.walker_fit -> matrix
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘walker.Rmd’ using rmarkdown
Warning in engine$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 124-128 (walker.Rmd) 
Error: processing vignette 'walker.Rmd' failed with diagnostics:
argument of length 0
--- failed re-building ‘walker.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘bioacoustics’
Package unavailable to check Rd xrefs: ‘bioacoustics’
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
Package required but not available: ‘GO.db’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [79s/71s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   1. base::suppressWarnings(...)
   9. wiserow:::row_means.matrix(char_mat, output_mode = "complex")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1045 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 7 ]
  1. Failure: row_sums can handle errors and edge cases appropriately. 
  2. Failure: row_sums can handle errors and edge cases appropriately. 
  3. Failure: row_sums can handle errors and edge cases appropriately. 
  4. Failure: row_sums can handle errors and edge cases appropriately. 
  5. Failure: row_means can handle errors and edge cases appropriately. 
  6. Failure: row_means can handle errors and edge cases appropriately. 
  7. Failure: row_means can handle errors and edge cases appropriately. 
  
  Error: testthat unit tests failed
  Execution halted
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
Error(s) in re-building vignettes:
--- re-building ‘overview.Rmd’ using rmarkdown
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.
Loading required package: ggplot2
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Warning: Removed 10 rows containing non-finite values (stat_smooth).
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 5 rows containing missing values (geom_path).
Warning: Removed 10 rows containing missing values (geom_point).

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: 'plotly'

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

    last_plot

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

    filter

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

    layout

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.
Warning in normalizePath(f2) :
  path[1]="webshot13f204f5efc8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot13f204f5efc8.png': No such file or directory
Quitting from lines 214-234 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted